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diff --git a/.flake8 b/.flake8
index 2d44c0a5f..76f42ce8a 100644
--- a/.flake8
+++ b/.flake8
@@ -1,4 +1,5 @@
[flake8]
+exclude = build*,__pycache__,third-party
max-line-length = 99
per-file-ignores =
- py_engine.py:E201,E202,E203,E501
\ No newline at end of file
+ py_engine.py:E201,E202,E203,E501
diff --git a/CMakeLists.txt b/CMakeLists.txt
index e36180b8d..41770fc4f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,228 +1,202 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jun 14 2010
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Sat Mar 13 2021
#
# @brief main configuration file
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#-------------------------------------------------------------------------------
# _ _
# | | | |
# __ _| | ____ _ _ __ | |_ _ _
# / _` | |/ / _` | '_ \| __| | | |
# | (_| | < (_| | | | | |_| |_| |
# \__,_|_|\_\__,_|_| |_|\__|\__,_|
#
#===============================================================================
+
#===============================================================================
# CMake Project
#===============================================================================
cmake_minimum_required(VERSION 3.5.1)
# add this options before PROJECT keyword
set(CMAKE_DISABLE_SOURCE_CHANGES ON)
set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
if(CMAKE_VERSION VERSION_GREATER 3.12)
cmake_policy(SET CMP0074 NEW)
endif()
-set(AKANTU_MAJOR_VERSION 4)
-set(AKANTU_MINOR_VERSION 0)
-set(AKANTU_PATCH_VERSION 0)
set(AKANTU_COPYRIGHT "2010-2021, EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)")
set(AKANTU_MAINTAINER "Nicolas Richart")
set(AKANTU_HOMEPAGE_URL "https://akantu.ch")
if(CMAKE_VERSION VERSION_GREATER 3.12)
project(Akantu
HOMEPAGE_URL "https://akantu.ch")
else()
project(Akantu)
endif()
enable_language(CXX)
#===============================================================================
# Misc. config for cmake
#===============================================================================
set(AKANTU_CMAKE_DIR "${PROJECT_SOURCE_DIR}/cmake")
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake")
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/Modules")
set(BUILD_SHARED_LIBS ON CACHE BOOL "Build shared libraries.")
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL
"Enable/Disable output of compile commands during generation" FORCE)
mark_as_advanced(BUILD_SHARED_LIBS)
if(NOT AKANTU_TARGETS_EXPORT)
set(AKANTU_TARGETS_EXPORT AkantuTargets)
endif()
include(CMakeVersionGenerator)
include(CMakePackagesSystem)
include(CMakeFlagsHandling)
include(AkantuPackagesSystem)
include(AkantuMacros)
include(AkantuCleaning)
#cmake_activate_debug_message()
include(GNUInstallDirs)
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
# add the automatically determined parts of the RPATH
# which point to directories outside the build tree to the install RPATH
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
#===============================================================================
# Version Number
#===============================================================================
-# AKANTU version number. An even minor number corresponds to releases.
+# AKANTU version number.
define_project_version()
#===============================================================================
# Options
#===============================================================================
-# Debug
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG -DAKANTU_NDEBUG"
- CACHE STRING "Flags used by the compiler during release builds" FORCE)
-
-#add_flags(cxx "-Wall -Wextra -pedantic -Werror")
-if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
- add_flags(cxx "-Wall -Wextra -pedantic") # -Weffc++
- set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG_INIT} -ggdb3"
- CACHE STRING "Flags used by the compiler during debug builds" FORCE)
- set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT} -ggdb3"
- CACHE STRING "Flags used by the compiler during debug builds" FORCE)
-
- option (FORCE_COLORED_OUTPUT "Always produce ANSI-colored output (GNU/Clang only)." FALSE)
- mark_as_advanced(FORCE_COLORED_OUTPUT)
- if(FORCE_COLORED_OUTPUT)
- if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
- add_flags(cxx "-fcolor-diagnostics")
- else()
- add_flags(cxx "-fdiagnostics-color=always")
- endif()
- endif()
-else()
- add_flags(cxx "-Wall")
-endif()
-
option(AKANTU_EXAMPLES "Activate examples" OFF)
option(AKANTU_TESTS "Activate tests" OFF)
option(AKANTU_RUN_IN_DOCKER "Set the approriate flage tu run in docker" OFF)
-set(AKANTU_PREFERRED_PYTHON_VERSION 3 CACHE STRING "Preferred version for python related things")
+set(AKANTU_PREFERRED_PYTHON_VERSION 3
+ CACHE STRING "Preferred version for python related things")
mark_as_advanced(AKANTU_PREFERRED_PYTHON_VERSION AKANTU_RUN_IN_DOCKER)
include(AkantuExtraCompilationProfiles)
#===============================================================================
# Dependencies
#===============================================================================
declare_akantu_types()
package_list_packages(${PROJECT_SOURCE_DIR}/packages
EXTRA_PACKAGES_FOLDER ${PROJECT_SOURCE_DIR}/extra_packages
NO_AUTO_COMPILE_FLAGS)
## meta option \todo better way to do it when multiple package give enable the
## same feature
if(AKANTU_SCOTCH)
set(AKANTU_PARTITIONER ON)
else()
set(AKANTU_PARTITIONER OFF)
endif()
if(AKANTU_MUMPS)
set(AKANTU_SOLVER ON)
else()
set(AKANTU_SOLVER OFF)
endif()
#===============================================================================
# Akantu library
#===============================================================================
add_subdirectory(src)
#===============================================================================
# Documentation
#===============================================================================
if(AKANTU_DOCUMENTATION OR AKANTU_DOCUMENTATION_MANUAL)
add_subdirectory(doc)
else()
set(AKANTU_DOC_EXCLUDE_FILES "${PROJECT_SOURCE_DIR}/doc/manual" CACHE INTERNAL "")
endif()
#===============================================================================
# Python interface
#===============================================================================
package_is_activated(python_interface _python_act)
if(_python_act)
if(IS_ABSOLUTE "${CMAKE_INSTALL_PREFIX}")
set(AKANTU_PYTHON_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
else()
set(AKANTU_PYTHON_INSTALL_PREFIX "${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_PREFIX}")
endif()
add_subdirectory(python)
endif()
#===============================================================================
# Examples and tests
#===============================================================================
include(AkantuTestsMacros)
include(AkantuExampleMacros)
if(AKANTU_TESTS)
option(AKANTU_BUILD_ALL_TESTS "Build all tests" ON)
find_package(GMSH REQUIRED)
endif()
# tests
add_test_tree(test)
if(AKANTU_EXAMPLES)
if(AKANTU_TESTS)
option(AKANTU_TEST_EXAMPLES "Run the examples" ON)
endif()
find_package(GMSH REQUIRED)
add_subdirectory(examples)
endif()
#===============================================================================
# Install and Packaging
#===============================================================================
include(AkantuInstall)
option(AKANTU_DISABLE_CPACK
"This option commands the generation of extra info for the \"make package\" target" ON)
mark_as_advanced(AKANTU_DISABLE_CPACK)
if(NOT AKANTU_DISABLE_CPACK)
include(AkantuCPack)
endif()
diff --git a/CTestConfig.cmake b/CTestConfig.cmake
index 23185704b..df24d6b21 100644
--- a/CTestConfig.cmake
+++ b/CTestConfig.cmake
@@ -1,45 +1,46 @@
#===============================================================================
# @file CTestConfig.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Thu Jan 06 2011
-# @date last modification: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for ctest
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
## This file should be placed in the root directory of your project.
## Then modify the CMakeLists.txt file in the root directory of your
## project to incorporate the testing dashboard.
## # The following are required to uses Dart and the Cdash dashboard
## ENABLE_TESTING()
## INCLUDE(CTest)
set(CTEST_PROJECT_NAME "Akantu")
set(CTEST_NIGHTLY_START_TIME "06:10:00 EST")
set(CTEST_CMAKE_GENERATOR "Unix Makefiles")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "lsmssrv1.epfl.ch")
set(CTEST_DROP_LOCATION "/CDash/submit.php?project=Akantu")
set(CTEST_DROP_SITE_CDASH TRUE)
diff --git a/cmake/AkantuCPack.cmake b/cmake/AkantuCPack.cmake
index 220f915ec..3a8727174 100644
--- a/cmake/AkantuCPack.cmake
+++ b/cmake/AkantuCPack.cmake
@@ -1,129 +1,130 @@
#===============================================================================
# @file AkantuCPack.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Wed Oct 17 2012
# @date last modification: Fri Jan 22 2016
#
# @brief Configure the packaging system
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
set(PACKAGE_FILE_NAME "akantu" CACHE STRING "Name of package to be generated")
mark_as_advanced(PACKAGE_FILE_NAME)
set(CPACK_SOURCE_GENERATOR "TGZ;TBZ2")
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Windows")
set(CPACK_GENERATOR "TGZ;DEB")
else()
set(CPACK_GENERATOR "TGZ;NSIS")
package_get_all_external_informations(
_external_include_dirs
_external_libraries
)
set(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS ${_external_libraries})
include(InstallRequiredSystemLibraries)
endif()
if(CMAKE_SYSTEM_PROCESSOR MATCHES "i.86" OR
CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64" OR
CMAKE_SYSTEM_PROCESSOR MATCHES "[aA][mM][dD]64")
if(CMAKE_SIZEOF_VOID_P EQUAL 8)
set(_arch "amd64")
else()
set(_arch "i386")
endif()
elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc")
set(_arch "powerpc")
else()
set(_arch "unknown")
endif()
if(WIN32 AND MINGW)
set(_arch "mingw32")
endif()
# General configuration
set(CPACK_PACKAGE_VENDOR "LSMS")
set(CPACK_PACKAGE_FILE_NAME "${PACKAGE_FILE_NAME}-${AKANTU_VERSION}-${_arch}")
set(CPACK_PACKAGE_VERSION "${AKANTU_VERSION}")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A multipurpose finite element library, Akantu")
set(CPACK_PACKAGE_NAME "akantu")
#set(CMAKE_PACKAGE_ICON "${PROJECT_SOURCE_DIR}/cmake/akantu.ico")
# Debian config package
package_get_all_package_system_dependency(deb _deb_deps)
package_get_all_package_system_dependency(deb-src _deb_src_deps)
set(CPACK_DEBIAN_PACKAGE_MAINTAINER "nicolas.richart@epfl.ch, guillaume.anciaux@epfl.ch")
set(CPACK_DEBIAN_PACKAGE_SECTION "Science")
set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE "${_arch}" CACHE STRING "Architecture of akantu's package")
set(CPACK_DEBIAN_PACKAGE_DEPENDS "${_deb_deps}")
set(CPACK_DEBIAN_PACKAGE_BUILDS_DEPENDSS "${_deb_src_deps}")
mark_as_advanced(CPACK_DEBIAN_PACKAGE_ARCHITECTURE)
# RPM package configuration
#set(CPACK_RPM_PACKAGE_REQUIRES "${${_project}_PACKAGE_SYSTEM_DEBIAN_PACKAGE_DEPENDS}")
# NSIS Windows installer
#set(CPACK_NSIS_MUI_ICON "${PROJECT_SOURCE_DIR}/cmake/akantu.ico")
#set(CPACK_NSIS_CONTACT "akantu@akantu.ch")
#set(CPACK_NSIS_MODIFY_PATH ON)
# Components description
set(CPACK_COMPONENTS_ALL lib dev bin python)
set(CPACK_COMPONENT_LIB_DISPLAY_NAME "Libraries")
set(CPACK_COMPONENT_BIN_DISPLAY_NAME "Examples")
set(CPACK_COMPONENT_PYTHON_DISPLAY_NAME "Python interface")
set(CPACK_COMPONENT_DEV_DISPLAY_NAME "C++ Headers")
set(CPACK_COMPONENT_DEV_DEPENDS lib)
set(CPACK_COMPONENT_BIN_DEPENDS lib)
set(CPACK_COMPONENT_PYTHON_DEPENDS lib)
set(CPACK_COMPONENT_LIB_DESCRIPTION
"Akantu libraries")
set(CPACK_COMPONENT_DEV_DESCRIPTION
"Akantu C/C++ header files")
set(CPACK_COMPONENT_LIB_GROUP "Akantu Libraries and Executables")
set(CPACK_COMPONENT_BIN_GROUP "Akantu Libraries and Executables")
set(CPACK_COMPONENT_PYTHON_GROUP "Akantu Libraries and Executables")
set(CPACK_COMPONENT_DEV_GROUP "Development")
set(CPACK_SOURCE_PACKAGE_FILE_NAME "${PACKAGE_FILE_NAME}-${AKANTU_VERSION}-src")
set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/COPYING")
include(AkantuCPackMacros)
generate_cpack_ignore_list(CPACK_SOURCE_IGNORE_FILES)
# for debug
# foreach(_file ${CPACK_SOURCE_IGNORE_FILES})
# message("IGNORE ${_file}")
# endforeach()
list(APPEND CPACK_SOURCE_IGNORE_FILES
"/.*build.*/" "/CVS/" "/\\\\.svn/" "/\\\\.bzr/" "/\\\\.hg/"
"/\\\\.hgignore" "/\\\\.git/" "/\\\\.idea/" "\\\\.swp$"
"\\\\.#" "/#" "~")
include(CPack)
diff --git a/cmake/AkantuCPackMacros.cmake b/cmake/AkantuCPackMacros.cmake
index 3c7f3a7fc..2f3f1edaf 100644
--- a/cmake/AkantuCPackMacros.cmake
+++ b/cmake/AkantuCPackMacros.cmake
@@ -1,153 +1,155 @@
#===============================================================================
-# @file AkantuCPack.cmake
+# @file AkantuCPackMacros.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Wed Jan 18 2015
+# @date creation: Mon Jan 18 2016
+# @date last modification: Fri Jan 22 2016
#
# @brief macros to help for cpack
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
# ==============================================================================
# let start the ugly things to list what should not be in the package
# ==============================================================================
function(generate_cpack_ignore_list ignore_list)
message(STATUS "Generating CPack ignore list...")
# get a full list of all the files include in the source folder
file(GLOB _first_level "${PROJECT_SOURCE_DIR}/*")
set(_all_files "${PROJECT_SOURCE_DIR}" ${_first_level})
foreach(_path ${_first_level})
if(IS_DIRECTORY "${_path}" AND
NOT _path MATCHES "build.*" AND
NOT _path MATCHES "\\.git.*")
file(GLOB_RECURSE _second_level "${_path}/*")
file(GLOB _second_extra_level "${_path}/*")
list(APPEND _all_files ${_second_level} ${_second_extra_level})
endif()
endforeach()
set(_dirs)
foreach(_file ${_all_files})
get_filename_component(_dir ${_file} DIRECTORY)
list(APPEND _dirs ${_dir})
endforeach()
list(REMOVE_DUPLICATES _dirs)
list(APPEND _all_files ${_dirs})
# getting list of all the files that should be in the source package
package_get_files_for_package(_all_package_files)
package_get_all_activated_packages(_activated_packages)
foreach(_pkg ${_activated_packages})
_package_get_filename(${_pkg} _file_name)
_package_get_source_files(${_pkg} _srcs _pub_hdrs _priv_hdrs)
_package_get_variable(TESTS_FILES ${_pkg} _tests_files)
# adding the source directory
set(_need_source_folder)
foreach(_src ${_srcs} ${_pub_hdrs} ${_priv_hdrs} ${_tests_files})
list(APPEND _need_source_folder ${PROJECT_SOURCE_DIR}/${_src})
endforeach()
_package_get_documentation_files(${_pkg} _doc_files)
# adding the manual directory
set(_all_docs)
_package_get_manual_folder(${_pkg} _doc_folder)
foreach(_file ${_doc_files})
list(APPEND _all_docs ${_doc_folder}/${_file})
endforeach()
_package_get_variable(EXAMPLES_FILES ${_pkg} _examples_files)
_package_get_variable(EXTRA_FILES ${_pkg} _extra_files)
# split the set in 2 for debug reasons
set(_package_files
${_file_name} ${_need_source_folder}
${_examples_files} ${_extra_files} ${_all_docs}
)
list(APPEND _all_package_files ${_package_files})
endforeach()
# generate ignore list
set(_ignore_list)
set(_keep_dirs)
set(_ignore_dirs)
foreach(_file ${_all_files})
set(_found FALSE)
foreach(_pkg_file ${_all_package_files})
if(IS_DIRECTORY "${_file}" AND
_pkg_file MATCHES "${_file}/.*")
set(_found TRUE)
list(APPEND _keep_dirs "${_file}")
break()
elseif(_pkg_file MATCHES "${_file}")
set(_found TRUE)
break()
endif()
endforeach()
if(NOT _found)
list(APPEND _ignore_list "${_file}")
if(IS_DIRECTORY "${_file}")
list(APPEND _ignore_dirs "${_file}")
endif()
endif()
endforeach()
# Save CMakeLists.txt in folder that are kept
foreach(_dir ${_keep_dirs})
if(EXISTS "${_dir}/CMakeLists.txt")
list(REMOVE_ITEM _ignore_list "${_dir}/CMakeLists.txt")
endif()
endforeach()
set(_tmp_ignore_list ${_ignore_list})
set(_ignore_list)
# cleaning the ignore
foreach(_file ${_tmp_ignore_list})
set(_found FALSE)
foreach(_dir ${_ignore_dirs})
if(_file MATCHES "${_dir}/.*")
set(_found TRUE)
break()
endif()
endforeach()
if(NOT _found)
if(IS_DIRECTORY ${_file})
list(APPEND _ignore_list "${_file}/")
else()
list(APPEND _ignore_list "${_file}")
endif()
endif()
endforeach()
list(SORT _ignore_list)
list(REMOVE_DUPLICATES _ignore_list)
set(${ignore_list} ${_ignore_list} PARENT_SCOPE)
endfunction()
# ==============================================================================
# Let's hope that after all this the list is complete and not to heavy for cpack
# ==============================================================================
diff --git a/cmake/AkantuCleaning.cmake b/cmake/AkantuCleaning.cmake
index d852abf84..5355f2efb 100644
--- a/cmake/AkantuCleaning.cmake
+++ b/cmake/AkantuCleaning.cmake
@@ -1,103 +1,106 @@
#===============================================================================
# @file AkantuCleaning.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Thu Jun 1, 2017
+# @date creation: Fri Oct 22 2010
+# @date last modification: Tue Feb 02 2021
#
# @brief set of tools to clean the code
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#===============================================================================
+
# Adding clang-format target if executable is found
find_program(CLANG_FORMAT_EXECUTABLE "clang-format")
# Adding clang-tidy target if executable is found
find_program(CLANG_TIDY_EXECUTABLE "clang-tidy")
find_program(RUN_CLANG_TIDY_EXECUTABLE "run-clang-tidy")
mark_as_advanced(
CLANG_FORMAT_EXECUTABLE
CLANG_TIDY_EXECUTABLE
RUN_CLANG_TIDY_EXECUTABLE
)
function(register_code_to_format)
if(NOT CLANG_FORMAT_EXECUTABLE)
endif()
add_custom_target(
clang-format-all
COMMAND ${CLANG_FORMAT_EXECUTABLE}
-style=file
--output-replacements-xml
${ARGN} || /bin/true
)
endfunction()
function(register_tidy_all directory)
if(NOT RUN_CLANG_TIDY_EXECUTABLE)
return()
endif()
add_custom_target(
clang-tidy-all
COMMAND ${RUN_CLANG_TIDY_EXECUTABLE}
${ARGN}
)
endfunction()
function(register_target_to_tidy target)
if(NOT CLANG_TIDY_EXECUTABLE)
return()
endif()
option(AKANTU_CLANG_TIDY_AUTOFIX OFF)
mark_as_advanced(AKANTU_CLANG_TIDY_AUTOFIX)
set(_autofix_option)
if(AKANTU_CLANG_TIDY_AUTOFIX)
set(_autofix_option -fix)
endif()
get_target_property(_sources ${target} SOURCES)
file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/clang-tidy)
set(_depends)
foreach(_src ${_sources})
get_filename_component(_src_dir ${_src} DIRECTORY)
file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/clang-tidy/${_src_dir})
add_custom_command(
OUTPUT ${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml
COMMAND ${CLANG_TIDY_EXECUTABLE}
-p=${PROJECT_BINARY_DIR}
-export-fixes=${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml
${_autofix_option}
${_src}
COMMENT "Tidying ${_src}"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
)
list(APPEND _depends ${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml)
endforeach()
add_custom_target(clang-tidy DEPENDS ${_depends})
endfunction()
diff --git a/cmake/AkantuExampleMacros.cmake b/cmake/AkantuExampleMacros.cmake
index 63d4c908a..3cf6951e3 100644
--- a/cmake/AkantuExampleMacros.cmake
+++ b/cmake/AkantuExampleMacros.cmake
@@ -1,155 +1,156 @@
#===============================================================================
# @file AkantuExampleMacros.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Fabian Barras <fabian.barras@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jan 18 2016
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Wed Jan 15 2020
#
# @brief macros for examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
include(AkantuSimulationMacros)
set(AKANTU_DRIVER_SCRIPT ${AKANTU_CMAKE_DIR}/akantu_test_driver.sh)
# ==============================================================================
function(register_example example_name)
_add_akantu_simulation(${example_name} ${ARGN} LIST_FILES _example_files)
if(DEFINED _add_examples_pkg)
package_add_to_variable(EXAMPLES_FILES ${_add_examples_pkg} ${_example_files})
endif()
if(AKANTU_TEST_EXAMPLES)
cmake_parse_arguments(_example
"PYTHON;PARALLEL"
"FILES_TO_COPY;DEPENDS"
"SCRIPT"
${ARGN}
)
if(_example_FILES_TO_COPY)
foreach(_file ${_example_FILES_TO_COPY})
_add_file_to_copy(${example_name} "${_file}")
endforeach()
endif()
if(_example_PARALLEL)
set(_exe ${MPIEXEC})
if(NOT _exe)
- set(_exe ${MPIEXEC_EXECUTABLE})
+ set(_exe ${MPIEXEC_EXECUTABLE})
endif()
set(_parallel_runner -p "${_exe} ${MPIEXEC_PREFLAGS} ${MPIEXEC_NUMPROC_FLAG}" -N "2")
endif()
if(NOT _example_SCRIPT)
- add_test(NAME ${example_name}-test
- COMMAND ${AKANTU_DRIVER_SCRIPT}
+ add_test(NAME ${example_name}-test
+ COMMAND ${AKANTU_DRIVER_SCRIPT}
${_parallel_runner}
-n "${example_name}-test"
-w "${CMAKE_CURRENT_BINARY_DIR}"
-e $<TARGET_FILE:${example_name}>)
elseif(_example_SCRIPT)
_add_file_to_copy(${example_name} "${_example_SCRIPT}")
if(_example_PYTHON)
- add_test(NAME ${example_name}-test
- COMMAND ${AKANTU_DRIVER_SCRIPT}
+ add_test(NAME ${example_name}-test
+ COMMAND ${AKANTU_DRIVER_SCRIPT}
${_parallel_runner}
-n "${example_name}-test"
-E "${PROJECT_BINARY_DIR}/akantu_environement.sh"
-w "${CMAKE_CURRENT_BINARY_DIR}"
-e "${PYTHON_EXECUTABLE}" "${_example_SCRIPT}")
else()
- add_test(NAME ${example_name}-test
- COMMAND ${AKANTU_DRIVER_SCRIPT}
+ add_test(NAME ${example_name}-test
+ COMMAND ${AKANTU_DRIVER_SCRIPT}
${_parallel_runner}
-n "${example_name}-test"
-w "${CMAKE_CURRENT_BINARY_DIR}"
-e "${_example_SCRIPT}")
endif()
endif()
endif()
endfunction()
# ==============================================================================
function(add_example et_name desc)
string(TOUPPER ${et_name} upper_name)
if(NOT _build_all_ex)
option(AKANTU_BUILD_ALL_EXAMPLES "Activate all examples" OFF)
set( _build_all_ex TRUE)
endif()
option(AKANTU_BUILD_EXAMPLES_${upper_name} ${desc} OFF)
if(AKANTU_BUILD_ALL_EXAMPLES)
mark_as_advanced(FORCE AKANTU_BUILD_EXAMPLES_${upper_name})
else()
mark_as_advanced(CLEAR AKANTU_BUILD_EXAMPLES_${upper_name})
endif()
if(AKANTU_BUILD_EXAMPLES_${upper_name} OR AKANTU_BUILD_ALL_EXAMPLES)
if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${et_name})
message(FATAL_ERROR "The folder ${CMAKE_CURRENT_SOURCE_DIR}/${et_name} "
- "that you try to register as an example sub-folder, does not exists.")
+ "that you try to register as an example sub-folder, does not exists.")
endif()
cmake_parse_arguments(_manage_example
""
""
"PACKAGE"
${ARGN}
)
if(_manage_example_PACKAGE)
set(_act TRUE)
foreach(_pkg ${_manage_example_PACKAGE})
- package_is_activated(${_pkg} _activated)
- if(NOT _activated)
+ package_is_activated(${_pkg} _activated)
+ if(NOT _activated)
set(_act FALSE)
- endif()
+ endif()
endforeach()
else()
message(SEND_ERROR "Examples should be associated to a package")
endif()
if(_act)
if(DEFINED _add_examples_pkg)
- set(_save_add_examples_pkg ${_add_examples_pkg})
+ set(_save_add_examples_pkg ${_add_examples_pkg})
endif()
list(GET _manage_example_PACKAGE 0 _pkg)
set(_add_examples_pkg ${_pkg})
add_subdirectory(${et_name})
unset(_add_examples_pkg)
if(DEFINED _save_add_examples_pkg)
- set(_add_examples_pkg ${_save_add_examples_pkg})
- unset(_save_add_examples_pkg)
+ set(_add_examples_pkg ${_save_add_examples_pkg})
+ unset(_save_add_examples_pkg)
endif()
endif()
endif()
endfunction()
diff --git a/cmake/AkantuExtraCompilationProfiles.cmake b/cmake/AkantuExtraCompilationProfiles.cmake
index 1076b809e..c39ff7480 100644
--- a/cmake/AkantuExtraCompilationProfiles.cmake
+++ b/cmake/AkantuExtraCompilationProfiles.cmake
@@ -1,92 +1,143 @@
+#===============================================================================
+# @file AkantuExtraCompilationProfiles.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Dec 02 2016
+# @date last modification: Wed Feb 03 2021
+#
+# @brief Compilation profiles
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+option (FORCE_COLORED_OUTPUT "Always produce ANSI-colored output (GNU/Clang only)." FALSE)
+mark_as_advanced(FORCE_COLORED_OUTPUT)
+if(FORCE_COLORED_OUTPUT)
+ if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+ add_flags(cxx "-fcolor-diagnostics")
+ else()
+ add_flags(cxx "-fdiagnostics-color=always")
+ endif()
+endif()
+
+
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG -DAKANTU_NDEBUG"
+ CACHE STRING "Flags used by the compiler during release builds" FORCE)
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG_INIT} -ggdb3"
+ CACHE STRING "Flags used by the compiler during debug builds" FORCE)
+ set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT} -ggdb3"
+ CACHE STRING "Flags used by the compiler during debug builds" FORCE)
+endif()
+
#Profiling
set(_profiling "-g -ggdb3 -pg -DNDEBUG -DAKANTU_NDEBUG -O2")
set(CMAKE_CXX_FLAGS_PROFILING ${_profiling}
CACHE STRING "Flags used by the compiler during profiling builds")
set(CMAKE_C_FLAGS_PROFILING ${_profiling}
CACHE STRING "Flags used by the compiler during profiling builds")
set(CMAKE_Fortran_FLAGS_PROFILING ${_profiling}
CACHE STRING "Flags used by the compiler during profiling builds")
set(CMAKE_EXE_LINKER_FLAGS_PROFILING "-pg"
CACHE STRING "Flags used by the linker during profiling builds")
set(CMAKE_SHARED_LINKER_FLAGS_PROFILING "-pg"
CACHE STRING "Flags used by the linker during profiling builds")
mark_as_advanced(
CMAKE_CXX_FLAGS_PROFILING
CMAKE_C_FLAGS_PROFILING
CMAKE_Fortran_FLAGS_PROFILING
CMAKE_EXE_LINKER_FLAGS_PROFILING
CMAKE_SHARED_LINKER_FLAGS_PROFILING
)
set(_coverage "-g -ggdb3 -DNDEBUG -DAKANTU_NDEBUG -O2 --coverage")
set(CMAKE_CXX_FLAGS_COVERAGE ${_coverage}
CACHE STRING "Flags used by the compiler during profiling builds" FORCE)
set(CMAKE_C_FLAGS_COVERAGE ${_coverage}
CACHE STRING "Flags used by the compiler during profiling builds" FORCE)
set(CMAKE_Fortran_FLAGS_COVERAGE ${_coverage}
CACHE STRING "Flags used by the compiler during profiling builds" FORCE)
set(CMAKE_SHARED_LINKER_FLAGS_COVERAGE ${_coverage}
CACHE STRING "Flags used by the compiler during profiling builds" FORCE)
set(CMAKE_EXE_LINKER_FLAGS_COVERAGE ${_coverage}
CACHE STRING "Flags used by the linker during sanitizing builds" FORCE)
mark_as_advanced(
CMAKE_CXX_FLAGS_COVERAGE
CMAKE_C_FLAGS_COVERAGE
CMAKE_Fortran_FLAGS_COVERAGE
CMAKE_SHARED_LINKER_FLAGS_COVERAGE
CMAKE_EXE_LINKER_FLAGS_COVERAGE
)
# Sanitize the code
if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "5.2") OR
CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(_blacklist " -fsanitize-blacklist=${PROJECT_SOURCE_DIR}/cmake/sanitize-blacklist.txt")
endif()
set(_sanitize "-g -ggdb3 -O2 -fsanitize=address -fsanitize=leak -fsanitize=undefined -fno-omit-frame-pointer${_blacklist}")
set(CMAKE_CXX_FLAGS_SANITIZE ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_C_FLAGS_SANITIZE ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_Fortran_FLAGS_SANITIZE ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_EXE_LINKER_FLAGS_SANITIZE ${_sanitize}
CACHE STRING "Flags used by the linker during sanitizing builds")
set(CMAKE_SHARED_LINKER_FLAGS_SANITIZE ${_sanitize}
CACHE STRING "Flags used by the linker during sanitizing builds")
mark_as_advanced(
CMAKE_CXX_FLAGS_SANITIZE
CMAKE_C_FLAGS_SANITIZE
CMAKE_Fortran_FLAGS_SANITIZE
CMAKE_SHARED_LINKER_FLAGS_SANITIZE
CMAKE_EXE_LINKER_FLAGS_SANITIZE
)
endif()
if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(_sanitize "-g -ggdb3 -O2 -fPIE -fsanitize=memory -fsanitize-memory-track-origins -fsanitize-recover=all -fno-omit-frame-pointer -fsanitize-blacklist=${PROJECT_SOURCE_DIR}/cmake/sanitize-blacklist.txt")
set(CMAKE_CXX_FLAGS_SANITIZEMEMORY ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_C_FLAGS_SANITIZEMEMORY ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_Fortran_FLAGS_SANITIZEMEMORY ${_sanitize}
CACHE STRING "Flags used by the compiler during sanitizing builds")
set(CMAKE_EXE_LINKER_FLAGS_SANITIZEMEMORY ${_sanitize}
CACHE STRING "Flags used by the linker during sanitizing builds")
set(CMAKE_SHARED_LINKER_FLAGS_SANITIZEMEMORY ${_sanitize}
CACHE STRING "Flags used by the linker during sanitizing builds")
mark_as_advanced(
CMAKE_CXX_FLAGS_SANITIZEMEMORY
CMAKE_C_FLAGS_SANITIZEMEMORY
CMAKE_Fortran_FLAGS_SANITIZEMEMORY
CMAKE_SHARED_LINKER_FLAGS_SANITIZEMEMORY
CMAKE_EXE_LINKER_FLAGS_SANITIZEMEMORY
)
endif()
diff --git a/cmake/AkantuInstall.cmake b/cmake/AkantuInstall.cmake
index 93b932af6..afd8e5159 100644
--- a/cmake/AkantuInstall.cmake
+++ b/cmake/AkantuInstall.cmake
@@ -1,163 +1,164 @@
#===============================================================================
# @file AkantuInstall.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Wed Oct 17 2012
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Fri Jan 15 2021
#
# @brief Create the files that allows users to link with Akantu in an other
# cmake project
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
# Config gen for external packages
#===============================================================================
configure_file(cmake/AkantuBuildTreeSettings.cmake.in
"${PROJECT_BINARY_DIR}/AkantuBuildTreeSettings.cmake" @ONLY)
file(WRITE "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
#===============================================================================
# @file AkantuConfigInclude.cmake
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @date Fri Jun 11 09:46:59 2010
#
# @section LICENSE
#
# Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
")
package_get_all_packages(_package_list)
foreach(_pkg_name ${_package_list})
# package_pkg_name(${_option} _pkg_name)
_package_is_activated(${_pkg_name} _acctivated)
_package_get_real_name(${_pkg_name} _real_name)
string(TOUPPER ${_real_name} _real_pkg_name)
file(APPEND "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
set(AKANTU_HAS_${_real_pkg_name} ${_acctivated})")
_package_get_libraries(${_pkg_name} _libs)
if(_libs)
file(APPEND "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
set(AKANTU_${_real_pkg_name}_LIBRARIES ${_libs})")
endif()
_package_get_include_dir(${_pkg_name} _incs)
if(_incs)
file(APPEND "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
set(AKANTU_${_real_pkg_name}_INCLUDE_DIR ${_incs})
")
endif()
_package_get_compile_flags(${_pkg_name} CXX _compile_flags)
if(_compile_flags)
file(APPEND "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
set(AKANTU_${_real_pkg_name}_COMPILE_CXX_FLAGS ${_compile_flags})
")
endif()
endforeach()
file(APPEND "${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake" "
set(AKANTU_EXTRA_CXX_FLAGS \"${AKANTU_EXTRA_CXX_FLAGS}\")
")
# Create the AkantuConfig.cmake and AkantuConfigVersion files
get_filename_component(CONF_REL_INCLUDE_DIR "${CMAKE_INSTALL_PREFIX}" ABSOLUTE)
configure_file(cmake/AkantuConfig.cmake.in "${PROJECT_BINARY_DIR}/AkantuConfig.cmake" @ONLY)
configure_file(cmake/AkantuConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/AkantuConfigVersion.cmake" @ONLY)
configure_file(cmake/AkantuUse.cmake "${PROJECT_BINARY_DIR}/AkantuUse.cmake" COPYONLY)
package_is_activated(pybind11 _is_pybind11_activated)
package_is_activated(swig _is_swig_activated)
configure_file(cmake/akantu_environement.sh.in
${PROJECT_BINARY_DIR}/akantu_environement.sh @ONLY)
configure_file(cmake/akantu_environement.csh.in
${PROJECT_BINARY_DIR}/akantu_environement.csh @ONLY)
include(GNUInstallDirs)
package_is_activated(python_interface _is_acticated)
if(_is_acticated)
find_package(PythonInterp ${AKANTU_PREFERRED_PYTHON_VERSION})
configure_file(cmake/akantu_install_environement.sh.in
${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/akantu_environement.sh @ONLY)
configure_file(cmake/akantu_install_environement.csh.in
${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/akantu_environement.csh @ONLY)
install(FILES
${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/akantu_environement.sh
${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/akantu_environement.csh
DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/akantu${AKANTU_VERSION})
endif()
include(CMakePackageConfigHelpers)
configure_package_config_file(cmake/AkantuConfig.cmake.in
"${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
INSTALL_DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/${PROJECT_NAME}
)
write_basic_package_version_file(${PROJECT_BINARY_DIR}/AkantuConfigVersion.cmake
VERSION ${AKANTU_VERSION}
COMPATIBILITY SameMajorVersion)
# Install the export set for use with the install-tree
install(FILES
${PROJECT_SOURCE_DIR}/cmake/Modules/FindScaLAPACK.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindMETIS.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindParMETIS.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindPETSc.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindMumps.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindScotch.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindGMSH.cmake
${PROJECT_BINARY_DIR}/AkantuConfig.cmake
${PROJECT_BINARY_DIR}/AkantuConfigInclude.cmake
${PROJECT_BINARY_DIR}/AkantuConfigVersion.cmake
${PROJECT_SOURCE_DIR}/cmake/AkantuUse.cmake
${PROJECT_SOURCE_DIR}/cmake/AkantuSimulationMacros.cmake
${PROJECT_SOURCE_DIR}/cmake/Modules/FindGMSH.cmake
DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/cmake/${PROJECT_NAME}
COMPONENT dev)
diff --git a/cmake/AkantuMacros.cmake b/cmake/AkantuMacros.cmake
index 3e784c762..0615d7b41 100644
--- a/cmake/AkantuMacros.cmake
+++ b/cmake/AkantuMacros.cmake
@@ -1,273 +1,274 @@
#===============================================================================
# @file AkantuMacros.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Oct 22 2010
-# @date last modification: Tue Jan 19 2016
+# @date last modification: Tue Mar 24 2020
#
# @brief Set of macros used by akantu cmake files
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
function(set_third_party_shared_libirary_name _var _lib)
set(${_var}
${PROJECT_BINARY_DIR}/third-party/lib/${CMAKE_SHARED_LIBRARY_PREFIX}${_lib}${CMAKE_SHARED_LIBRARY_SUFFIX}
CACHE FILEPATH "" FORCE)
endfunction()
# ==============================================================================
function(_add_file_to_copy target file)
get_filename_component(_file_name_we ${file} NAME_WE)
get_filename_component(_file_name_ext ${file} EXT)
get_filename_component(_file_name ${file} NAME)
get_filename_component(_file_path ${file}
ABSOLUTE BASE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
configure_file(
${_file_path}
${CMAKE_CURRENT_BINARY_DIR}/${_file_name}
COPYONLY)
# set(copy_target copy_${_file_name_we}_${_file_name_ext}_${target})
# add_custom_target(${copy_target}
# DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/${_file_name})
# add_custom_command(
# OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${_file_name}
# COMMAND ${CMAKE_COMMAND} -E copy_if_different
# ${file}
# ${CMAKE_CURRENT_BINARY_DIR}
# WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
# DEPENDS ${_file_path}
# COMMENT "Copying file ${_file_name} for the target ${target}"
# )
# add_dependencies(${target} ${copy_target})
endfunction()
# ==============================================================================
function(get_target_list_of_associated_files tgt files)
if(TARGET ${tgt})
get_target_property(_type ${tgt} TYPE)
else()
set(_type ${tgt}-NOTFOUND)
endif()
if(_type STREQUAL "SHARED_LIBRARY"
OR _type STREQUAL "STATIC_LIBRARY"
OR _type STREQUAL "MODULE_LIBRARY"
OR _type STREQUAL "EXECUTABLE")
get_target_property(_srcs ${tgt} SOURCES)
set(_dep_ressources)
foreach(_file ${_srcs})
list(APPEND _dep_ressources ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
endforeach()
elseif(_type)
get_target_property(_dep_ressources ${tgt} RESSOURCES)
endif()
set(${files} ${_dep_ressources} PARENT_SCOPE)
endfunction()
#===============================================================================
# Generate the list of currently loaded materials
function(generate_material_list)
message(STATUS "Determining the list of recognized materials...")
package_get_all_include_directories(
AKANTU_LIBRARY_INCLUDE_DIRS
)
package_get_all_external_informations(
PRIVATE_INCLUDE AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR
INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
LIBRARIES AKANTU_EXTERNAL_LIBRARIES
)
set(_include_dirs
${AKANTU_INCLUDE_DIRS}
${AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR}
${AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR}
)
try_run(_material_list_run _material_list_compile
${CMAKE_BINARY_DIR}
${PROJECT_SOURCE_DIR}/cmake/material_lister.cc
CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${_include_dirs}" "-DCMAKE_CXX_STANDARD=14"
COMPILE_DEFINITIONS "-DAKANTU_CMAKE_LIST_MATERIALS"
COMPILE_OUTPUT_VARIABLE _compile_results
RUN_OUTPUT_VARIABLE _result_material_list)
if(_material_list_compile AND "${_material_list_run}" EQUAL 0)
message(STATUS "Materials included in Akantu:")
string(REPLACE "\n" ";" _material_list "${_result_material_list}")
foreach(_mat ${_material_list})
string(REPLACE ":" ";" _mat_key "${_mat}")
list(GET _mat_key 0 _key)
list(GET _mat_key 1 _class)
list(LENGTH _mat_key _l)
if("${_l}" GREATER 2)
list(REMOVE_AT _mat_key 0 1)
set(_opt " -- options: [")
foreach(_o ${_mat_key})
set(_opt "${_opt} ${_o}")
endforeach()
set(_opt "${_opt} ]")
else()
set(_opt "")
endif()
message(STATUS " ${_class} -- key: ${_key}${_opt}")
endforeach()
else()
message(STATUS "Could not determine the list of materials.")
message("${_compile_results}")
endif()
endfunction()
#===============================================================================
# Declare the options for the types and defines the approriate typedefs
function(declare_akantu_types)
set(AKANTU_TYPE_FLOAT "double (64bit)" CACHE STRING "Precision force floating point types")
mark_as_advanced(AKANTU_TYPE_FLOAT)
set_property(CACHE AKANTU_TYPE_FLOAT PROPERTY STRINGS
"quadruple (128bit)"
"double (64bit)"
"float (32bit)"
)
set(AKANTU_TYPE_INTEGER "int (32bit)" CACHE STRING "Size of the integer types")
mark_as_advanced(AKANTU_TYPE_INTEGER)
set_property(CACHE AKANTU_TYPE_INTEGER PROPERTY STRINGS
"int (32bit)"
"long int (64bit)"
)
include(CheckTypeSize)
# ----------------------------------------------------------------------------
# Floating point types
# ----------------------------------------------------------------------------
if(AKANTU_TYPE_FLOAT STREQUAL "float (32bit)")
set(AKANTU_FLOAT_TYPE "float" CACHE INTERNAL "")
set(AKANTU_FLOAT_SIZE 4 CACHE INTERNAL "")
elseif(AKANTU_TYPE_FLOAT STREQUAL "double (64bit)")
set(AKANTU_FLOAT_TYPE "double" CACHE INTERNAL "")
set(AKANTU_FLOAT_SIZE 8 CACHE INTERNAL "")
elseif(AKANTU_TYPE_FLOAT STREQUAL "quadruple (128bit)")
check_type_size("long double" LONG_DOUBLE)
if(HAVE_LONG_DOUBLE)
set(AKANTU_FLOAT_TYPE "long double" CACHE INTERNAL "")
set(AKANTU_FLOAT_SIZE 16 CACHE INTERNAL "")
message("This feature is not tested and will most probably not compile")
else()
message(FATAL_ERROR "The type long double is not defined on your system")
endif()
else()
message(FATAL_ERROR "The float type is not defined")
endif()
include(CheckIncludeFileCXX)
include(CheckCXXSourceCompiles)
# ----------------------------------------------------------------------------
# Integer types
# ----------------------------------------------------------------------------
check_include_file_cxx(cstdint HAVE_CSTDINT)
if(NOT HAVE_CSTDINT)
check_include_file_cxx(stdint.h HAVE_STDINT_H)
if(HAVE_STDINT_H)
list(APPEND _int_include stdint.h)
endif()
else()
list(APPEND _int_include cstdint)
endif()
check_include_file_cxx(cstddef HAVE_CSTDDEF)
if(NOT HAVE_CSTDINT)
check_include_file_cxx(stddef.h HAVE_STDDEF_H)
if(HAVE_STDINT_H)
list(APPEND _int_include stddef.h)
endif()
else()
list(APPEND _int_include cstddef)
endif()
if(AKANTU_TYPE_INTEGER STREQUAL "int (32bit)")
set(AKANTU_INTEGER_SIZE 4 CACHE INTERNAL "")
check_type_size("int" INT)
if(INT EQUAL 4)
set(AKANTU_SIGNED_INTEGER_TYPE "int" CACHE INTERNAL "")
set(AKANTU_UNSIGNED_INTEGER_TYPE "unsigned int" CACHE INTERNAL "")
else()
check_type_size("int32_t" INT32_T LANGUAGE CXX)
if(HAVE_INT32_T)
set(AKANTU_SIGNED_INTEGER_TYPE "int32_t" CACHE INTERNAL "")
set(AKANTU_UNSIGNED_INTEGER_TYPE "uint32_t" CACHE INTERNAL "")
list(APPEND _extra_includes ${_int_include})
endif()
endif()
elseif(AKANTU_TYPE_INTEGER STREQUAL "long int (64bit)")
set(AKANTU_INTEGER_SIZE 8 CACHE INTERNAL "")
check_type_size("long int" LONG_INT)
if(LONG_INT EQUAL 8)
set(AKANTU_SIGNED_INTEGER_TYPE "long int" CACHE INTERNAL "")
set(AKANTU_UNSIGNED_INTEGER_TYPE "unsigned long int" CACHE INTERNAL "")
else()
check_type_size("long long int" LONG_LONG_INT)
if(HAVE_LONG_LONG_INT AND LONG_LONG_INT EQUAL 8)
set(AKANTU_SIGNED_INTEGER_TYPE "long long int" CACHE INTERNAL "")
set(AKANTU_UNSIGNED_INTEGER_TYPE "unsigned long long int" CACHE INTERNAL "")
else()
check_type_size("int64_t" INT64_T)
if(HAVE_INT64_T)
set(AKANTU_SIGNED_INTEGER_TYPE "int64_t" CACHE INTERNAL "")
set(AKANTU_UNSIGNED_INTEGER_TYPE "uint64_t" CACHE INTERNAL "")
list(APPEND _extra_includes ${_int_include})
endif()
endif()
endif()
else()
message(FATAL_ERROR "The integer type is not defined")
endif()
# ----------------------------------------------------------------------------
# includes
# ----------------------------------------------------------------------------
foreach(_inc ${_extra_includes})
set(_incs "#include <${_inc}>\n${_incs}")
endforeach()
set(AKANTU_TYPES_EXTRA_INCLUDES ${_incs} CACHE INTERNAL "")
endfunction()
function(mask_package_options prefix)
get_property(_list DIRECTORY PROPERTY VARIABLES)
foreach(_var ${_list})
if("${_var}" MATCHES "^${prefix}.*")
mark_as_advanced(${_var})
endif()
endforeach()
endfunction()
diff --git a/cmake/AkantuPackagesSystem.cmake b/cmake/AkantuPackagesSystem.cmake
index f7d13d99f..146937dfc 100644
--- a/cmake/AkantuPackagesSystem.cmake
+++ b/cmake/AkantuPackagesSystem.cmake
@@ -1,353 +1,355 @@
#===============================================================================
# @file AkantuPackagesSystem.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sat Jul 18 2015
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri Mar 16 2018
#
# @brief Addition to the PackageSystem specific for Akantu
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
# Element Types
#===============================================================================
#-------------------------------------------------------------------------------
function(package_declare_elements pkg)
set(_options
KIND
ELEMENT_TYPES
GEOMETRICAL_TYPES
INTERPOLATION_TYPES
GEOMETRICAL_SHAPES
GAUSS_INTEGRATION_TYPES
INTERPOLATION_KIND
FE_ENGINE_LISTS
)
cmake_parse_arguments(_opt_pkg
""
""
"${_options}"
${ARGN})
foreach(_opt ${_options})
if(_opt_pkg_${_opt})
package_set_variable(ET_${_opt} ${pkg} ${_opt_pkg_${_opt}})
endif()
endforeach()
endfunction()
#-------------------------------------------------------------------------------
function(_transfer_list_to_enum types enum)
if(${enum})
set(_enum_tmp ${${enum}})
else()
unset(_enum_tmp)
endif()
foreach(_type ${${types}})
# defining the types for the enum
if(DEFINED _enum_tmp)
set(_enum_tmp "${_enum_tmp}
${_type},")
else()
set(_enum_tmp "${_type},")
endif()
endforeach()
set(${enum} ${_enum_tmp} PARENT_SCOPE)
endfunction()
#-------------------------------------------------------------------------------
function(_transfer_list_to_boost_seq types boost_seq)
if(${boost_seq})
set(_boost_seq_tmp ${${boost_seq}})
endif()
foreach(_type ${${types}})
if(DEFINED _boost_seq_tmp)
set(_boost_seq_tmp "${_boost_seq_tmp}${_tabs}\\
(${_type})")
else()
set(_boost_seq_tmp " (${_type})")
endif()
string(LENGTH "${_type}" _length)
if(_length LESS 13)
set(_tabs "\t\t\t\t")
elseif(_length LESS 28)
set(_tabs "\t\t\t")
else()
set(_tabs "\t\t")
endif()
endforeach()
set(${boost_seq} ${_boost_seq_tmp} PARENT_SCOPE)
endfunction()
#-------------------------------------------------------------------------------
function(package_get_element_lists)
package_get_all_activated_packages(_activated_list)
set(_lists
KIND
ELEMENT_TYPES
GEOMETRICAL_TYPES
INTERPOLATION_TYPES
GEOMETRICAL_SHAPES
GAUSS_INTEGRATION_TYPES
INTERPOLATION_TYPES
INTERPOLATION_KIND
FE_ENGINE_LISTS
)
set(_element_kind "#define AKANTU_ELEMENT_KIND")
set(_all_element_types "#define AKANTU_ALL_ELEMENT_TYPE\t")
set(_inter_types_boost_seq "#define AKANTU_INTERPOLATION_TYPES\t\t")
foreach(_pkg_name ${_activated_list})
foreach(_list ${_lists})
string(TOLOWER "${_list}" _l_list)
_package_get_variable(ET_${_list} ${_pkg_name} _${_l_list})
_transfer_list_to_enum(_${_l_list} _${_l_list}_enum)
endforeach()
if(_interpolation_types)
_transfer_list_to_boost_seq(_interpolation_types _inter_types_boost_seq)
endif()
if(_kind)
string(TOUPPER "${_kind}" _u_kind)
if(_element_types)
set(_boosted_element_types "${_boosted_element_types}
#define AKANTU_ek_${_kind}_ELEMENT_TYPE\t")
_transfer_list_to_boost_seq(_element_types _boosted_element_types)
set(_boosted_element_types "${_boosted_element_types}\n")
# defininf the kinds variables
set(_element_kinds "${_element_kinds}
#define AKANTU_${_u_kind}_KIND\t(_ek_${_kind})")
# defining the full list of element
set(_all_element_types "${_all_element_types}\t\\
AKANTU_ek_${_kind}_ELEMENT_TYPE")
endif()
# defining the full list of kinds
set(_element_kind "${_element_kind}${_kind_tabs}\t\t\\
AKANTU_${_u_kind}_KIND")
set(_kind_tabs "\t")
# defining the macros
set(_boost_macros "${_boost_macros}
#define AKANTU_BOOST_${_u_kind}_ELEMENT_SWITCH(macro) \\
AKANTU_BOOST_ELEMENT_SWITCH(macro, \\
AKANTU_ek_${_kind}_ELEMENT_TYPE)
#define AKANTU_BOOST_${_u_kind}_ELEMENT_LIST(macro) \\
AKANTU_BOOST_APPLY_ON_LIST(macro, \\
AKANTU_ek_${_kind}_ELEMENT_TYPE)
")
list(APPEND _aka_fe_lists ${_fe_engine_lists})
foreach(_fe_engine_list ${_fe_engine_lists})
if(NOT DEFINED _fe_engine_list_${_fe_engine_list})
string(TOUPPER "${_fe_engine_list}" _u_list)
string(LENGTH "#define AKANTU_FE_ENGINE_LIST_${_u_list}" _length)
math(EXPR _length "72 - ${_length}")
set(_space "")
while(_length GREATER 0)
if(CMAKE_VERSION VERSION_GREATER 3.0)
string(CONCAT _space "${_space}" " ")
else()
set(_space "${_space} ")
endif()
math(EXPR _length "${_length} - 1")
endwhile()
set(_fe_engine_list_${_fe_engine_list}
"#define AKANTU_FE_ENGINE_LIST_${_u_list}${_space}\\
AKANTU_GENERATE_KIND_LIST((_ek_${_kind})")
else()
set(_fe_engine_list_${_fe_engine_list}
"${_fe_engine_list_${_fe_engine_list}}\t\t\t\t\\
(_ek_${_kind})")
endif()
endforeach()
endif()
endforeach()
if(_aka_fe_lists)
list(REMOVE_DUPLICATES _aka_fe_lists)
foreach(_fe_list ${_aka_fe_lists})
set(_aka_fe_defines "${_fe_engine_list_${_fe_list}})\n${_aka_fe_defines}")
endforeach()
endif()
foreach(_list ${_lists})
string(TOLOWER "${_list}" _l_list)
set(AKANTU_${_list}_ENUM ${_${_l_list}_enum} PARENT_SCOPE)
endforeach()
set(AKANTU_INTERPOLATION_TYPES_BOOST_SEQ ${_inter_types_boost_seq} PARENT_SCOPE)
set(AKANTU_ELEMENT_TYPES_BOOST_SEQ ${_boosted_element_types} PARENT_SCOPE)
set(AKANTU_ELEMENT_KINDS_BOOST_SEQ ${_element_kinds} PARENT_SCOPE)
set(AKANTU_ELEMENT_KIND_BOOST_SEQ ${_element_kind} PARENT_SCOPE)
set(AKANTU_ALL_ELEMENT_BOOST_SEQ ${_all_element_types} PARENT_SCOPE)
set(AKANTU_ELEMENT_KINDS_BOOST_MACROS ${_boost_macros} PARENT_SCOPE)
set(AKANTU_FE_ENGINE_LISTS ${_aka_fe_defines} PARENT_SCOPE)
endfunction()
#-------------------------------------------------------------------------------
function(package_get_element_types pkg list)
package_get_name(${pkg} _pkg_name)
_package_get_variable(ET_ELEMENT_TYPES ${_pkg_name} _tmp_list)
set(${list} ${_tmp_list} PARENT_SCOPE)
endfunction()
#===============================================================================
# Material specific
#===============================================================================
#-------------------------------------------------------------------------------
function(package_declare_material_infos pkg)
cmake_parse_arguments(_opt_pkg
""
""
"LIST;INCLUDE"
${ARGN})
package_set_variable(MATERIAL_LIST ${pkg} ${_opt_pkg_LIST})
package_set_variable(MATERIAL_INCLUDE ${pkg} ${_opt_pkg_INCLUDE})
endfunction()
#-------------------------------------------------------------------------------
function(package_get_all_material_includes includes)
_package_get_variable_for_activated(MATERIAL_INCLUDE _includes)
foreach(_mat_inc ${_includes})
if(DEFINED _mat_includes)
set(_mat_includes "${_mat_includes}\n#include \"${_mat_inc}\"")
else()
set(_mat_includes "#include \"${_mat_inc}\"")
endif()
endforeach()
set(${includes} ${_mat_includes} PARENT_SCOPE)
endfunction()
#-------------------------------------------------------------------------------
function(package_get_all_material_lists lists)
_package_get_variable_for_activated(MATERIAL_LIST _lists)
foreach(_mat_list ${_lists})
if(DEFINED _mat_lists)
set(_mat_lists "${_mat_lists}\n ${_mat_list}\t\t\t\\")
else()
set(_mat_lists " ${_mat_list}\t\t\t\\")
endif()
endforeach()
set(${lists} ${_mat_lists} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Extra files to consider in source package generated by CPack
# ------------------------------------------------------------------------------
function(package_declare_extra_files_to_package pkg)
set(_types SOURCES MANUAL TESTS PROJECT)
cmake_parse_arguments(_extra_files
""
""
"${_types}"
${ARGN})
set(_files ${_extra_files_UNPARSED_ARGUMENTS})
package_get_sources_folder(${pkg} _folder_SOURCES)
package_get_manual_folder(${pkg} _folder_MANUAL)
package_get_tests_folder(${pkg} _folder_TESTS)
set(_folder_PROJECT ${PROJECT_SOURCE_DIR})
foreach(_type ${_types})
if(_extra_files_${_type})
foreach(_file ${_extra_files_${_type}})
list(APPEND _files ${_folder_${_type}}/${_file})
if(NOT EXISTS ${_folder_${_type}}/${_file})
message(SEND_ERROR "The package ${pkg} tries to register the file ${_file} (as a ${_type} file).
This file cannot be found.")
endif()
endforeach()
endif()
endforeach()
package_set_variable(EXTRA_FILES ${pkg} ${_files})
endfunction()
# ------------------------------------------------------------------------------
function(package_add_files_to_package)
set(_files)
foreach(_file ${ARGN})
list(APPEND _files ${PROJECT_SOURCE_DIR}/${_file})
endforeach()
package_add_to_project_variable(EXTRA_FILES ${_files})
endfunction()
function(package_get_files_for_package files)
package_get_project_variable(EXTRA_FILES _tmp)
set(${files} ${_tmp} PARENT_SCOPE)
endfunction()
package_add_files_to_package(
.clang-format
AUTHORS
README
VERSION
COPYING
COPYING.lesser
CTestConfig.cmake
cmake/akantu_environement.sh.in
cmake/akantu_environement.csh.in
cmake/akantu_install_environement.sh.in
cmake/akantu_install_environement.csh.in
cmake/Modules/CMakeFlagsHandling.cmake
cmake/Modules/CMakePackagesSystem.cmake
cmake/Modules/CMakePackagesSystemGlobalFunctions.cmake
cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
cmake/Modules/CMakeVersionGenerator.cmake
cmake/Modules/PCHgcc.cmake
cmake/AkantuBuildTreeSettings.cmake.in
cmake/AkantuConfig.cmake.in
cmake/AkantuConfigVersion.cmake.in
cmake/AkantuCPack.cmake
cmake/AkantuCPackMacros.cmake
cmake/AkantuInstall.cmake
cmake/AkantuMacros.cmake
cmake/AkantuPackagesSystem.cmake
cmake/AkantuUse.cmake
cmake/AkantuSimulationMacros.cmake
cmake/material_lister.cc
cmake/Modules/FindGMSH.cmake
)
diff --git a/cmake/AkantuSimulationMacros.cmake b/cmake/AkantuSimulationMacros.cmake
index 3881b1fdf..b827a99e9 100644
--- a/cmake/AkantuSimulationMacros.cmake
+++ b/cmake/AkantuSimulationMacros.cmake
@@ -1,186 +1,186 @@
#===============================================================================
# @file AkantuSimulationMacros.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jan 18 2016
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Wed Aug 14 2019
#
# @brief macros for examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if(__AKANTU_SIMULATION_MACROS)
return()
endif()
set(__AKANTU_SIMULATION_MACROS TRUE)
#===============================================================================
function(add_akantu_simulation simulation_name)
_add_akantu_simulation(${simulation_name} ${ARGN})
endfunction()
#===============================================================================
function(_add_akantu_simulation simulation_name)
set(multi_variables
SCRIPT
SOURCES
FILES_TO_COPY
DEPENDS
DIRECTORIES_TO_CREATE
COMPILE_OPTIONS
USE_PACKAGES
)
cmake_parse_arguments(_simulation
"PYTHON;PARALLEL"
"LIST_FILES"
"${multi_variables}"
${ARGN}
)
set(_deps_OK TRUE)
if(_simulation_PYTHON)
list(APPEND _simulation_USE_PACKAGES python_interface)
endif()
if(_simulation_USE_PACKAGES)
foreach(_pkg ${_simulation_USE_PACKAGES})
package_is_activated(${_pkg} _activated)
if(_activated)
package_get_include_dir(${_pkg} _inc_dir)
list(APPEND _simulation_INCLUDE_DIRS ${_inc_dir})
package_get_libraries(${_pkg} _libraries)
list(APPEND _simulation_LIBRARIES ${_libraries})
package_get_compile_flags(${_pkg} CXX _flags)
list(APPEND _simulation_COMPILE_FLAGS "${_flags}")
else()
message("${simulation_name} use ${_pkg} but Akantu "
" has been compiled without this package")
set(_deps_OK FALSE)
endif()
endforeach()
endif()
package_get_compile_flags(BOOST CXX _flags)
list(APPEND _simulation_COMPILE_FLAGS "${_flags}")
package_get_include_dir(BOOST _boost_include_dir)
string(REPLACE ";" " " _tmp_flags "${_simulation_COMPILE_FLAGS}")
string(REGEX REPLACE " +" " " _simulation_COMPILE_FLAGS "${_tmp_flags}")
if(_deps_OK)
if(_simulation_UNPARSED_ARGUMENTS OR _simulation_SOURCES)
add_executable(${simulation_name}
${_simulation_UNPARSED_ARGUMENTS} ${_simulation_SOURCES})
target_link_libraries(${simulation_name}
- PRIVATE akantu ${_simulation_LIBRARIES})
+ PRIVATE akantu ${_simulation_LIBRARIES})
target_include_directories(${simulation_name}
- PRIVATE
- ${AKANTU_INCLUDE_DIRS}
- ${_boost_include_dir}
- ${_simulation_INCLUDE_DIRS})
+ PRIVATE
+ ${AKANTU_INCLUDE_DIRS}
+ ${_boost_include_dir}
+ ${_simulation_INCLUDE_DIRS})
if(_simulation_DEPENDS)
foreach(_deps ${_simulation_DEPENDS})
get_target_property(_type ${_deps} TYPE)
if(_type STREQUAL "SHARED_LIBRARY"
OR _type STREQUAL "STATIC_LIBRARY")
target_link_libraries(${simulation_name} PRIVATE ${_deps})
else()
add_dependencies(${simulation_name} ${_deps})
endif()
endforeach()
endif()
if(_simulation_COMPILE_OPTIONS)
set_target_properties(${simulation_name}
PROPERTIES COMPILE_DEFINITIONS "${_simulation_COMPILE_OPTIONS}")
endif()
if(_simulation_COMPILE_FLAGS)
set_target_properties(${simulation_name}
PROPERTIES COMPILE_FLAGS "${_simulation_COMPILE_FLAGS}")
endif()
endif()
if(_simulation_SCRIPT)
add_custom_target(${simulation_name} ALL
- COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_simulation_SCRIPT} ${CMAKE_CURRENT_BINARY_DIR}
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- BYPRODUCTS ${CMAKE_CURRENT_BINARY_DIR}/${_simulation_SCRIPT}
- DEPENDS ${_simulation_SCRIPT}
- )
+ COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_simulation_SCRIPT} ${CMAKE_CURRENT_BINARY_DIR}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+ BYPRODUCTS ${CMAKE_CURRENT_BINARY_DIR}/${_simulation_SCRIPT}
+ DEPENDS ${_simulation_SCRIPT}
+ )
if(_simulation_DEPENDS)
foreach(_deps ${_simulation_DEPENDS})
add_dependencies(${simulation_name} ${_deps})
endforeach()
endif()
endif()
# copy the needed files to the build folder
if(_simulation_FILES_TO_COPY)
file(COPY ${_simulation_FILES_TO_COPY} DESTINATION .)
endif()
# create the needed folders in the build folder
if(_simulation_DIRECTORIES_TO_CREATE)
foreach(_dir ${_simulation_DIRECTORIES_TO_CREATE})
if(IS_ABSOLUTE ${dir})
file(MAKE_DIRECTORY ${_dir})
else()
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${_dir})
endif()
endforeach()
endif()
endif()
if(_simulation_LIST_FILES)
set(_simulation_files)
foreach(_file ${_simulation_SCRIPT} ${_simulation_SOURCES}
${_simulation_UNPARSED_ARGUMENTS} ${_simulation_FILES_TO_COPY})
list(APPEND _simulation_files ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
- endforeach()
+ endforeach()
foreach(_dep ${_simulation_DEPENDS})
get_target_list_of_associated_files(${_dep} _dep_ressources)
if(_dep_ressources)
list(APPEND _simulation_files "${_dep_ressources}")
endif()
endforeach()
set(${_simulation_LIST_FILES} ${_simulation_files} PARENT_SCOPE)
endif()
endfunction()
diff --git a/cmake/AkantuTestsMacros.cmake b/cmake/AkantuTestsMacros.cmake
index ce970bb5f..5103e28cb 100644
--- a/cmake/AkantuTestsMacros.cmake
+++ b/cmake/AkantuTestsMacros.cmake
@@ -1,652 +1,653 @@
#===============================================================================
# @file AkantuTestsMacros.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Tue Jun 30 2020
#
# @brief macros for tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#[=======================================================================[.rst:
AkantuTestsMacros
-----------------
This modules provides the functions to helper to declare tests and folders
containing tests in akantu
.. command:: add_test_tree
add_test_tree(<test_direcotry>)
``<test_directory>`` is the entry direcroty of the full structure of
subfolders containing tests
.. command:: add_akantu_test
add_akantu_test(<dir> <desc>)
This function add a subdirectory ``<dir>`` of tests that will be conditionnaly
activable and will be visible only if the parent folder as been activated An
option ``AKANTU_BUILD_TEST_<dir>`` will appear in ccmake with the description
``<desc>``. The compilation of all tests can be forced with the option
``AKANTU_BUILD_ALL_TESTS``
.. command:: register_test
register_test(<test_name>
SOURCES <sources>...
PACKAGE <akantu_packages>...
SCRIPT <scirpt>
[FILES_TO_COPY <filenames>...]
[DEPENDS <targets>...]
[DIRECTORIES_TO_CREATE <directories>...]
[COMPILE_OPTIONS <flags>...]
[EXTRA_FILES <filnames>...]
[LINK_LIBRARIES <libraries>...]
[INCLUDE_DIRECTORIES <include>...]
[UNSABLE]
[PARALLEL]
[PARALLEL_LEVEL <procs>...]
)
This function defines a test ``<test_name>_run`` this test could be of
different nature depending on the context. If Just sources are provided the
test consist of running the executable generated. If a file ``<test_name>.sh``
is present the test will execute the script. And if a ``<test_name>.verified``
exists the output of the test will be compared to this reference file
The options are:
``SOURCES <sources>...``
The list of source files to compile to generate the executable of the test
``PACKAGE <akantu_packages>...``
The list of package to which this test belongs. The test will be activable
only of all the packages listed are activated
``SCRIPT <script>``
The script to execute instead of the executable
``FILES_TO_COPY <filenames>...``
List of files to copy from the source directory to the build directory
``DEPENDS <targets>...``
List of targets the test depends on, for example if a mesh as to be generated
``DIRECTORIES_TO_CREATE <directories>...``
Obsolete. This specifies a list of directories that have to be created in
the build folder
``COMPILE_OPTIONS <flags>...``
List of extra compilations options to pass to the compiler
``EXTRA_FILES <filnames>...``
Files to consider when generating a package_source
``UNSABLE``
If this option is specified the test can be unacitivated by the glocal option
``AKANTU_BUILD_UNSTABLE_TESTS``, this is mainly intendeed to remove test
under developement from the continious integration
``PARALLEL``
This specifies that this test should be run in parallel. It will generate a
series of test for different number of processors. This automaticaly adds a
dependency to the package ``AKANTU_PARALLEL``
``PARALLEL_LEVEL``
This defines the different processor numbers to use, if not defined the
macro tries to determine it in a "clever" way
]=======================================================================]
set(AKANTU_DRIVER_SCRIPT ${AKANTU_CMAKE_DIR}/akantu_test_driver.sh)
# ==============================================================================
macro(add_test_tree dir)
if(AKANTU_TESTS)
enable_testing()
include(CTest)
mark_as_advanced(BUILD_TESTING)
set(_akantu_current_parent_test ${dir} CACHE INTERNAL "Current test folder" FORCE)
set(_akantu_${dir}_tests_count 0 CACHE INTERNAL "" FORCE)
string(TOUPPER ${dir} _u_dir)
set(AKANTU_BUILD_${_u_dir} ON CACHE INTERNAL "${desc}" FORCE)
package_get_all_test_folders(_test_dirs)
foreach(_dir ${_test_dirs})
add_subdirectory(${_dir})
endforeach()
endif()
endmacro()
set(_test_flags
UNSTABLE
PARALLEL
PYTHON
GTEST
HEADER_ONLY
)
set(_test_one_variables
POSTPROCESS
SCRIPT
)
set(_test_multi_variables
SOURCES
FILES_TO_COPY
DEPENDS
DIRECTORIES_TO_CREATE
COMPILE_OPTIONS
EXTRA_FILES
LINK_LIBRARIES
INCLUDE_DIRECTORIES
PACKAGE
PARALLEL_LEVEL
)
# ==============================================================================
function(add_akantu_test dir desc)
if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${dir})
return()
endif()
set(_my_parent_dir ${_akantu_current_parent_test})
# initialize variables
set(_akantu_current_parent_test ${dir} CACHE INTERNAL "Current test folder" FORCE)
set(_akantu_${dir}_tests_count 0 CACHE INTERNAL "" FORCE)
# set the option for this directory
string(TOUPPER ${dir} _u_dir)
option(AKANTU_BUILD_${_u_dir} "${desc}")
mark_as_advanced(AKANTU_BUILD_${_u_dir})
# add the sub-directory
add_subdirectory(${dir})
# if no test can be activated make the option disappear
set(_force_deactivate_count FALSE)
if(${_akantu_${dir}_tests_count} EQUAL 0)
set(_force_deactivate_count TRUE)
endif()
# if parent off make the option disappear
set(_force_deactivate_parent FALSE)
string(TOUPPER ${_my_parent_dir} _u_parent_dir)
if(NOT AKANTU_BUILD_${_u_parent_dir})
set(_force_deactivate_parent TRUE)
endif()
if(_force_deactivate_parent OR _force_deactivate_count OR AKANTU_BUILD_ALL_TESTS)
if(NOT DEFINED _AKANTU_BUILD_${_u_dir}_SAVE)
set(_AKANTU_BUILD_${_u_dir}_SAVE ${AKANTU_BUILD_${_u_dir}} CACHE INTERNAL "" FORCE)
endif()
unset(AKANTU_BUILD_${_u_dir} CACHE)
if(AKANTU_BUILD_ALL_TESTS AND NOT _force_deactivate_count)
set(AKANTU_BUILD_${_u_dir} ON CACHE INTERNAL "${desc}" FORCE)
else()
set(AKANTU_BUILD_${_u_dir} OFF CACHE INTERNAL "${desc}" FORCE)
endif()
else()
if(DEFINED _AKANTU_BUILD_${_u_dir}_SAVE)
unset(AKANTU_BUILD_${_u_dir} CACHE)
set(AKANTU_BUILD_${_u_dir} ${_AKANTU_BUILD_${_u_dir}_SAVE} CACHE BOOL "${desc}")
unset(_AKANTU_BUILD_${_u_dir}_SAVE CACHE)
endif()
endif()
# adding up to the parent count
math(EXPR _tmp_parent_count "${_akantu_${dir}_tests_count} + ${_akantu_${_my_parent_dir}_tests_count}")
set(_akantu_${_my_parent_dir}_tests_count ${_tmp_parent_count} CACHE INTERNAL "" FORCE)
# restoring the parent current dir
set(_akantu_current_parent_test ${_my_parent_dir} CACHE INTERNAL "Current test folder" FORCE)
endfunction()
function(is_test_active is_active)
cmake_parse_arguments(_register_test
"${_test_flags}"
"${_test_one_variables}"
"${_test_multi_variables}"
${ARGN}
)
if(NOT _register_test_PACKAGE)
message(FATAL_ERROR "No reference package was defined for the test"
" ${test_name} in folder ${CMAKE_CURRENT_SOURCE_DIR}")
endif()
if(_register_test_PYTHON)
list(APPEND _register_test_PACKAGE python_interface)
endif()
set(_test_act TRUE)
# Activate the test anly if all packages associated to the test are activated
foreach(_package ${_register_test_PACKAGE})
package_is_activated(${_package} _act)
if(NOT _act)
set(_test_act FALSE)
endif()
endforeach()
# check if the test is marked unstable and if the unstable test should be run
if(_register_test_UNSTABLE AND NOT AKANTU_BUILD_UNSTABLE_TESTS)
set(_test_act FALSE)
endif()
if(_test_act)
# todo this should be checked for the build package_sources since the file will not be listed.
math(EXPR _tmp_parent_count "${_akantu_${_akantu_current_parent_test}_tests_count} + 1")
set(_akantu_${_akantu_current_parent_test}_tests_count ${_tmp_parent_count} CACHE INTERNAL "" FORCE)
endif()
string(TOUPPER ${_akantu_current_parent_test} _u_parent)
if(NOT (AKANTU_BUILD_${_u_parent} OR AKANTU_BUILD_ALL_TESTS))
set(_test_act FALSE)
endif()
set(${is_active} ${_test_act} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
function(register_gtest_sources)
cmake_parse_arguments(_register_test
"${_test_flags}"
"${_test_one_variables}"
"${_test_multi_variables}"
${ARGN}
)
is_test_active(_is_active ${ARGN})
register_test_files_to_package(${ARGN})
if(NOT _is_active)
return()
endif()
if(_register_test_PACKAGE)
set(_list ${_gtest_PACKAGE})
list(APPEND _list ${_register_test_PACKAGE})
list(REMOVE_DUPLICATES _list)
set(_gtest_PACKAGE ${_list} PARENT_SCOPE)
endif()
foreach (_var ${_test_flags})
if(_var STREQUAL "HEADER_ONLY")
if(NOT DEFINED_register_test_${_var})
set(_gtest_${_var} OFF PARENT_SCOPE)
elseif(NOT DEFINED _gtest_${_var})
set(_gtest_${_var} ON PARENT_SCOPE)
endif()
continue()
endif()
if(_register_test_${_var})
set(_gtest_${_var} ON PARENT_SCOPE)
else()
if(_gtest_${_var})
message("Another gtest file required ${_var} to be ON it will be globally set for this folder...")
endif()
endif()
endforeach()
if(_register_test_UNPARSED_ARGUMENTS)
list(APPEND _register_test_SOURCES ${_register_test_UNPARSED_ARGUMENTS})
endif()
foreach (_var ${_test_multi_variables})
if(_register_test_${_var})
set(_list ${_gtest_${_var}})
list(APPEND _list ${_register_test_${_var}})
list(REMOVE_DUPLICATES _list)
set(_gtest_${_var} ${_list} PARENT_SCOPE)
endif()
endforeach()
endfunction()
# ==============================================================================
function(akantu_pybind11_add_module target)
package_is_activated(pybind11 _pybind11_act)
if(_pybind11_act)
package_get_all_external_informations(
INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
)
pybind11_add_module(${target} ${ARGN})
target_link_libraries(${target} PRIVATE akantu)
target_include_directories(${target} SYSTEM PRIVATE ${PYBIND11_INCLUDE_DIR} ${PROJECT_SOURCE_DIR}/python)
set_property(TARGET ${target} PROPERTY DEBUG_POSTFIX "")
endif()
endfunction()
# ==============================================================================
function(register_gtest_test test_name)
if(NOT _gtest_PACKAGE)
return()
endif()
set(_argn ${test_name}_gtest)
set(_link_libraries GTest::GTest GTest::Main)
list(FIND _gtest_PACKAGE python_interface _pos)
package_is_activated(python_interface _python_interface_act)
if(_python_interface_act AND (NOT _pos EQUAL -1))
list(APPEND _link_libraries pybind11::embed)
set(_compile_flags COMPILE_OPTIONS "AKANTU_TEST_USE_PYBIND11")
endif()
is_test_active(_is_active ${ARGN} PACKAGE ${_gtest_PACKAGE})
if(NOT _is_active)
return()
endif()
register_gtest_sources(${ARGN}
SOURCES ${PROJECT_SOURCE_DIR}/test/test_gtest_main.cc
LINK_LIBRARIES ${_link_libraries}
PACKAGE ${_gtest_PACKAGE}
${_compile_flags}
)
foreach (_var ${_test_flags})
if(_gtest_${_var})
list(APPEND _argn ${_var})
unset(_gtest_${_var})
endif()
endforeach()
foreach (_var ${_test_multi_variables})
if(_gtest_${_var})
list(APPEND _argn ${_var} ${_gtest_${_var}})
unset(_gtest_${_var})
endif()
endforeach()
register_test(${_argn} GTEST)
target_include_directories(${test_name}_gtest PRIVATE ${PROJECT_SOURCE_DIR}/test)
endfunction()
# ==============================================================================
function(register_test test_name)
cmake_parse_arguments(_register_test
"${_test_flags}"
"${_test_one_variables}"
"${_test_multi_variables}"
${ARGN}
)
register_test_files_to_package(${ARGN})
is_test_active(_test_act ${ARGN})
if(NOT _test_act)
return()
endif()
set(_extra_args)
# check that the sources are files that need to be compiled
if(_register_test_SOURCES} OR _register_test_UNPARSED_ARGUMENTS)
set(_need_to_compile TRUE)
else()
set(_need_to_compile FALSE)
endif()
set(_compile_source)
foreach(_file ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS})
if(_file MATCHES "\\.cc$" OR _file MATCHES "\\.hh$")
list(APPEND _compile_source ${_file})
endif()
endforeach()
if(_compile_source)
# get the include directories for sources in activated directories
package_get_all_include_directories(
AKANTU_LIBRARY_INCLUDE_DIRS
)
# get the external packages compilation and linking informations
package_get_all_external_informations(
INTERFACE_INCLUDE AKANTU_EXTERNAL_INCLUDE_DIR
)
foreach(_pkg ${_register_test_PACKAGE})
package_get_nature(${_pkg} _nature)
if(_nature MATCHES "^external.*")
package_get_include_dir(${_pkg} _incl)
package_get_libraries(${_pkg} _libs)
list(APPEND _register_test_INCLUDE_DIRECTORIES ${_incl})
list(APPEND _register_test_LINK_LIBRARIES ${_libs})
endif()
endforeach()
# Register the executable to compile
add_executable(${test_name} ${_compile_source})
# set the proper includes to build most of the tests
target_include_directories(${test_name}
PRIVATE ${AKANTU_LIBRARY_INCLUDE_DIRS}
${AKANTU_EXTERNAL_INCLUDE_DIR}
${PROJECT_BINARY_DIR}/src
${_register_test_INCLUDE_DIRECTORIES})
if(NOT _register_test_HEADER_ONLY)
target_link_libraries(${test_name} PRIVATE akantu ${_register_test_LINK_LIBRARIES})
else()
get_target_property(_features akantu INTERFACE_COMPILE_FEATURES)
target_link_libraries(${test_name} ${_register_test_LINK_LIBRARIES})
target_compile_features(${test_name} PRIVATE ${_features})
endif()
# add the extra compilation options
if(_register_test_COMPILE_OPTIONS)
set_target_properties(${test_name}
PROPERTIES COMPILE_DEFINITIONS "${_register_test_COMPILE_OPTIONS}")
endif()
if(AKANTU_EXTRA_CXX_FLAGS)
set_target_properties(${test_name}
PROPERTIES COMPILE_FLAGS "${AKANTU_EXTRA_CXX_FLAGS}")
endif()
else()
add_custom_target(${test_name} ALL)
if(_register_test_UNPARSED_ARGUMENTS AND NOT _register_test_SCRIPT)
set(_register_test_SCRIPT ${_register_test_UNPARSED_ARGUMENTS})
endif()
endif()
if(_register_test_DEPENDS)
add_dependencies(${test_name} ${_register_test_DEPENDS})
endif()
# copy the needed files to the build folder
if(_register_test_FILES_TO_COPY)
foreach(_file ${_register_test_FILES_TO_COPY})
_add_file_to_copy(${test_name} "${_file}")
endforeach()
endif()
# create the needed folders in the build folder
if(_register_test_DIRECTORIES_TO_CREATE)
foreach(_dir ${_register_test_DIRECTORIES_TO_CREATE})
if(IS_ABSOLUTE ${dir})
file(MAKE_DIRECTORY "${_dir}")
else()
file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/${_dir}")
endif()
endforeach()
endif()
# register the test for ctest
set(_arguments -n "${test_name}")
if(_register_test_SCRIPT)
_add_file_to_copy(${test_name} ${_register_test_SCRIPT})
if(_register_test_PYTHON)
if(NOT PYTHONINTERP_FOUND)
find_package(PythonInterp ${AKANTU_PREFERRED_PYTHON_VERSION} REQUIRED)
endif()
list(APPEND _arguments -e "${PYTHON_EXECUTABLE}")
list(APPEND _extra_args "${_register_test_SCRIPT}")
add_dependencies(${test_name} py11_akantu)
else()
list(APPEND _arguments -e "./${_register_test_SCRIPT}")
endif()
elseif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh")
_add_file_to_copy(${test_name} ${test_name}.sh)
list(APPEND _arguments -e "./${test_name}.sh")
else()
list(APPEND _arguments -e "./${test_name}")
endif()
if(_register_test_GTEST)
list(APPEND _extra_args "--" "--gtest_output=xml:${PROJECT_BINARY_DIR}/gtest_reports/${test_name}.xml")
endif()
list(APPEND _arguments -E "${PROJECT_BINARY_DIR}/akantu_environement.sh")
package_is_activated(parallel _is_parallel)
if(_is_parallel AND AKANTU_TESTS_ALWAYS_USE_MPI AND NOT _register_test_PARALLEL)
set(_register_test_PARALLEL TRUE)
set(_register_test_PARALLEL_LEVEL 1)
endif()
if(_register_test_PARALLEL AND _is_parallel)
set(_exe ${MPIEXEC})
if(NOT _exe)
set(_exe ${MPIEXEC_EXECUTABLE})
endif()
list(APPEND _arguments -p "${_exe} ${MPIEXEC_PREFLAGS} ${MPIEXEC_NUMPROC_FLAG}")
if(_register_test_PARALLEL_LEVEL)
set(_procs "${_register_test_PARALLEL_LEVEL}")
elseif(CMAKE_VERSION VERSION_GREATER "3.0")
set(_procs)
if(MPIEXEC_MAX_NUMPROCS)
set(N MPIEXEC_MAX_NUMPROCS)
else()
include(ProcessorCount)
ProcessorCount(N)
endif()
while(N GREATER 1)
list(APPEND _procs ${N})
math(EXPR N "${N} / 2")
endwhile()
list(APPEND _procs 1)
endif()
if(NOT _procs)
set(_procs 2)
endif()
endif()
if(_register_test_POSTPROCESS)
list(APPEND _arguments -s "${_register_test_POSTPROCESS}")
file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${_register_test_POSTPROCESS}
FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
endif()
list(APPEND _arguments -w "${CMAKE_CURRENT_BINARY_DIR}")
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
list(APPEND _arguments -r "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
endif()
string(REPLACE ";" " " _command "${_arguments}")
# register them test
if(_procs)
foreach(p ${_procs})
add_test(NAME ${test_name}_${p} COMMAND ${AKANTU_DRIVER_SCRIPT} ${_arguments} -N ${p} ${_extra_args})
set_property(TEST ${test_name}_${p} PROPERTY PROCESSORS ${p})
endforeach()
else()
add_test(NAME ${test_name} COMMAND ${AKANTU_DRIVER_SCRIPT} ${_arguments} ${_extra_args})
set_property(TEST ${test_name} PROPERTY PROCESSORS 1)
endif()
endfunction()
function(register_test_files_to_package)
cmake_parse_arguments(_register_test
"${_test_flags}"
"${_test_one_variables}"
"${_test_multi_variables}"
${ARGN}
)
if(_register_test_PYTHON)
list(APPEND _register_test_PACKAGE python_interface)
endif()
set(_test_all_files)
# add the source files in the list of all files
foreach(_file ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS}
${_register_test_EXTRA_FILES} ${_register_test_SOURCES} ${_register_test_SCRIPT}
${_register_test_POSTPROCESS} ${_register_test_FILES_TO_COPY})
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${_file} OR EXISTS ${_file})
list(APPEND _test_all_files "${_file}")
else()
message("The file \"${_file}\" registred by the test \"${test_name}\" does not exists")
endif()
endforeach()
# add the different dependencies files (meshes, local libraries, ...)
foreach(_dep ${_register_test_DEPENDS})
get_target_list_of_associated_files(${_dep} _dep_ressources)
if(_dep_ressources)
list(APPEND _test_all_files "${_dep_ressources}")
endif()
endforeach()
# add extra files to the list of files referenced by a given test
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh")
list(APPEND _test_all_files "${test_name}.sh")
endif()
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified")
list(APPEND _test_all_files "${test_name}.verified")
endif()
if(_register_test_SCRIPT)
list(APPEND _test_all_files "${_register_test_SCRIPT}")
endif()
# clean the list of all files for this test and add them in the total list
foreach(_file ${_test_all_files})
get_filename_component(_full ${_file} ABSOLUTE)
file(RELATIVE_PATH __file ${PROJECT_SOURCE_DIR} ${_full})
list(APPEND _tmp "${__file}")
endforeach()
foreach(_pkg ${_register_test_PACKAGE})
package_get_name(${_pkg} _pkg_name)
_package_add_to_variable(TESTS_FILES ${_pkg_name} ${_tmp})
endforeach()
endfunction()
diff --git a/cmake/AkantuUse.cmake b/cmake/AkantuUse.cmake
index 8973e1a4b..3ac853456 100644
--- a/cmake/AkantuUse.cmake
+++ b/cmake/AkantuUse.cmake
@@ -1,73 +1,75 @@
#===============================================================================
# @file AkantuUse.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Dec 07 2010
-# @date last modification: Mon Aug 17 2015
+# @date last modification: Mon Mar 08 2021
#
# @brief CMake file for the library
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
if (DEFINED CMAKE_PACKAGES_SYSTEM_LOADED)
return()
endif()
set(CMAKE_PACKAGES_SYSTEM_LOADED TRUE)
function(package_is_activated pkg activated)
string(TOUPPER ${pkg} _u_pkg)
set(${activated} ${AKANTU_HAS_${_u_pkg}} PARENT_SCOPE)
endfunction()
function(package_get_include_dir pkg include_dir)
string(TOUPPER ${pkg} _u_pkg)
set(${include_dir} ${AKANTU_${_u_pkg}_INCLUDE_DIR} PARENT_SCOPE)
endfunction()
function(package_get_libraries pkg libs)
string(TOUPPER ${pkg} _u_pkg)
set(${libs} ${AKANTU_${_u_pkg}_LIBRARIES} PARENT_SCOPE)
endfunction()
function(package_get_compile_flags pkg lang flags)
string(TOUPPER ${pkg} _u_pkg)
set(${flags} ${AKANTU_${_u_pkg}_COMPILE_${lang}_FLAGS} PARENT_SCOPE)
endfunction()
function(get_target_list_of_associated_files tgt files)
get_target_property(_type ${tgt} TYPE)
if(_type STREQUAL "SHARED_LIBRARY"
OR _type STREQUAL "STATIC_LIBRARY"
OR _type STREQUAL "MODULE_LIBRARY"
OR _type STREQUAL "EXECUTABLE")
get_target_property(_srcs ${tgt} SOURCES)
set(_dep_ressources)
foreach(_file ${_srcs})
list(APPEND _dep_ressources ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
endforeach()
else()
get_target_property(_dep_ressources ${tgt} RESSOURCES)
endif()
set(${files} ${_dep_ressources} PARENT_SCOPE)
endfunction()
diff --git a/cmake/Modules/CMakeDebugMessages.cmake b/cmake/Modules/CMakeDebugMessages.cmake
index 0a2ae2dff..0f149f353 100644
--- a/cmake/Modules/CMakeDebugMessages.cmake
+++ b/cmake/Modules/CMakeDebugMessages.cmake
@@ -1,70 +1,73 @@
#===============================================================================
# @file CMakeDebugMessages.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Mar 16 2018
#
# @brief Debug message helper
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if(__CMAKE_DEBUG_MESSAGES)
return()
endif()
set(__CMAKE_DEBUG_MESSAGES TRUE)
macro(cmake_register_debug_message_module module)
set(_CMAKE_DEBUG_MESSAGE_MODULES ${CMAKE_DEBUG_MESSAGE_MODULES})
list(APPEND _CMAKE_DEBUG_MESSAGE_MODULES ${module})
set(CMAKE_DEBUG_MESSAGE_MODULES "${_CMAKE_DEBUG_MESSAGE_MODULES}"
CACHE INTERNAL "List of modules handled by the debug messages system" FORCE)
endmacro()
macro(cmake_activate_debug_message)
set(_default FALSE)
if(ARGC EQUAL 0)
set(_default TRUE)
endif()
foreach(_module ${CMAKE_DEBUG_MESSAGE_MODULES})
set(CMAKE_DEBUG_MESSAGE_${_module} ${_default} CACHE INTERNAL "" FORCE)
endforeach()
foreach(_module ${ARGN})
set(CMAKE_DEBUG_MESSAGE_${_module} TRUE CACHE INTERNAL "" FORCE)
endforeach()
endmacro()
macro(cmake_deactivate_debug_message)
foreach(_module ${CMAKE_DEBUG_MESSAGE_MODULES})
if(CMAKE_DEBUG_MESSAGE_${_module})
set(CMAKE_DEBUG_MESSAGE_${_module} FALSE CACHE INTERNAL "" FORCE)
endif()
endforeach()
endmacro()
macro(cmake_debug_message module)
if(CMAKE_DEBUG_MESSAGE_${module})
message("${PROJECT_NAME} - ${module}: ${ARGN}")
endif()
endmacro()
\ No newline at end of file
diff --git a/cmake/Modules/CMakeDetermineCCompiler.cmake b/cmake/Modules/CMakeDetermineCCompiler.cmake
index 1def08a1e..b1a4edc11 100644
--- a/cmake/Modules/CMakeDetermineCCompiler.cmake
+++ b/cmake/Modules/CMakeDetermineCCompiler.cmake
@@ -1,66 +1,66 @@
#===============================================================================
# @file CMakeDetermineCCompiler.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Mar 16 2018
#
# @brief CMake file to determine the compiler
#
-# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
macro(determine_compiler_version COMPILER)
exec_program(${CMAKE_CXX_COMPILER}
ARGS --version
OUTPUT_VARIABLE _temp
)
set(${COMPILER}_COMPILER_VERSION "" CACHE STRING "Vesion of ${COMPILER} compiler.")
string(REGEX MATCH "([0-9\\.]+)"
${COMPILER}_COMPILER_VERSION
${_temp}
)
mark_as_advanced(${COMPILER}_COMPILER_VERSION)
endmacro()
# Code from James Bigler (http://www.cmake.org/pipermail/cmake/2007-June/014460.html)
set(MANTA_COMPILER_NAME_REGEXPR "icc.*$")
if(NOT CMAKE_COMPILER_IS_GNUCC)
# This regular expression also matches things like icc-9.1
if(CMAKE_C_COMPILER MATCHES ${MANTA_COMPILER_NAME_REGEXPR})
set(AKANTU_USING_ICC TRUE)
endif(CMAKE_C_COMPILER MATCHES ${MANTA_COMPILER_NAME_REGEXPR})
else(NOT CMAKE_COMPILER_IS_GNUCC)
set(AKANTU_USING_GNUCC TRUE)
endif(NOT CMAKE_COMPILER_IS_GNUCC)
set(MANTA_COMPILER_NAME_REGEXPR "icpc.*$")
if(NOT CMAKE_COMPILER_IS_GNUCXX)
if(CMAKE_CXX_COMPILER MATCHES ${MANTA_COMPILER_NAME_REGEXPR})
set(AKANTU_USING_ICPC TRUE)
determine_compiler_version(INTEL)
#else mvsc/clang/ibm/... ?
endif(CMAKE_CXX_COMPILER MATCHES ${MANTA_COMPILER_NAME_REGEXPR})
else(NOT CMAKE_COMPILER_IS_GNUCXX)
set(AKANTU_USING_GNUCXX TRUE)
determine_compiler_version(GCC)
endif(NOT CMAKE_COMPILER_IS_GNUCXX)
diff --git a/cmake/Modules/CMakeDetermineCompiler.cmake b/cmake/Modules/CMakeDetermineCompiler.cmake
index 511ebfa74..b1ef6f01d 100644
--- a/cmake/Modules/CMakeDetermineCompiler.cmake
+++ b/cmake/Modules/CMakeDetermineCompiler.cmake
@@ -1,103 +1,101 @@
#===============================================================================
# @file CMakeDetermineCompiler.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Mar 16 2018
#
-# @brief
#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
# (To distribute this file outside of CMake, substitute the full
# License text for the above reference.)
macro(_cmake_find_compiler lang)
# Use already-enabled languages for reference.
get_property(_languages GLOBAL PROPERTY ENABLED_LANGUAGES)
list(REMOVE_ITEM _languages "${lang}")
if(CMAKE_${lang}_COMPILER_INIT)
# Search only for the specified compiler.
set(CMAKE_${lang}_COMPILER_LIST "${CMAKE_${lang}_COMPILER_INIT}")
else()
# Re-order the compiler list with preferred vendors first.
set(_${lang}_COMPILER_LIST "${CMAKE_${lang}_COMPILER_LIST}")
set(CMAKE_${lang}_COMPILER_LIST "")
# Prefer vendors of compilers from reference languages.
foreach(l ${_languages})
list(APPEND CMAKE_${lang}_COMPILER_LIST
${_${lang}_COMPILER_NAMES_${CMAKE_${l}_COMPILER_ID}})
endforeach()
# Prefer vendors based on the platform.
list(APPEND CMAKE_${lang}_COMPILER_LIST ${CMAKE_${lang}_COMPILER_NAMES})
# Append the rest of the list and remove duplicates.
list(APPEND CMAKE_${lang}_COMPILER_LIST ${_${lang}_COMPILER_LIST})
unset(_${lang}_COMPILER_LIST)
list(REMOVE_DUPLICATES CMAKE_${lang}_COMPILER_LIST)
if(CMAKE_${lang}_COMPILER_EXCLUDE)
list(REMOVE_ITEM CMAKE_${lang}_COMPILER_LIST
${CMAKE_${lang}_COMPILER_EXCLUDE})
endif()
endif()
# Look for directories containing compilers of reference languages.
set(_${lang}_COMPILER_HINTS)
foreach(l ${_languages})
if(CMAKE_${l}_COMPILER AND IS_ABSOLUTE "${CMAKE_${l}_COMPILER}")
get_filename_component(_hint "${CMAKE_${l}_COMPILER}" PATH)
if(IS_DIRECTORY "${_hint}")
list(APPEND _${lang}_COMPILER_HINTS "${_hint}")
endif()
unset(_hint)
endif()
endforeach()
# Find the compiler.
if(_${lang}_COMPILER_HINTS)
# Prefer directories containing compilers of reference languages.
list(REMOVE_DUPLICATES _${lang}_COMPILER_HINTS)
find_program(CMAKE_${lang}_COMPILER
NAMES ${CMAKE_${lang}_COMPILER_LIST}
PATHS ${_${lang}_COMPILER_HINTS}
NO_DEFAULT_PATH
DOC "${lang} compiler")
endif()
find_program(CMAKE_${lang}_COMPILER NAMES ${CMAKE_${lang}_COMPILER_LIST} DOC "${lang} compiler")
if(CMAKE_${lang}_COMPILER_INIT AND NOT CMAKE_${lang}_COMPILER)
set(CMAKE_${lang}_COMPILER "${CMAKE_${lang}_COMPILER_INIT}" CACHE FILEPATH "${lang} compiler" FORCE)
endif()
unset(_${lang}_COMPILER_HINTS)
unset(_languages)
# Look for a make tool provided by Xcode
if(CMAKE_${lang}_COMPILER STREQUAL "CMAKE_${lang}_COMPILER-NOTFOUND" AND CMAKE_HOST_APPLE)
foreach(comp ${CMAKE_${lang}_COMPILER_LIST})
execute_process(COMMAND xcrun --find ${comp}
OUTPUT_VARIABLE _xcrun_out OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_VARIABLE _xcrun_err)
if(_xcrun_out)
set_property(CACHE CMAKE_${lang}_COMPILER PROPERTY VALUE "${_xcrun_out}")
break()
endif()
endforeach()
endif()
endmacro()
diff --git a/cmake/Modules/CMakeFlagsHandling.cmake b/cmake/Modules/CMakeFlagsHandling.cmake
index 5de3a0716..2efd26c1a 100644
--- a/cmake/Modules/CMakeFlagsHandling.cmake
+++ b/cmake/Modules/CMakeFlagsHandling.cmake
@@ -1,69 +1,71 @@
#===============================================================================
# @file CMakeFlagsHandling.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
-# @date last modification: Tue Jul 14 2015
+# @date last modification: Fri Jan 15 2016
#
# @brief Set of macros used by akantu to handle the package system
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if(_CMAKE_FLAGS_HANDLING)
return()
endif()
set(_CMAKE_FLAGS_HANDLING TRUE)
#===============================================================================
# Compilation options handling
#===============================================================================
macro(_get_flags_message type desc)
if(${type} MATCHES "C..")
set(${desc} "Flags used by the compiler during all build types.")
elseif(${type} MATCHES "EXE_LINKER")
set(${desc} "Flags used by the linker.")
elseif(${type} MATCHES "SHARED_LINKER")
set(${desc} "Flags used by the linker during the creation of dll's.")
endif()
endmacro()
#===============================================================================
macro(add_flags type flag)
string(TOUPPER ${type} _type)
set(_var CMAKE_${_type}_FLAGS)
_get_flags_message(${_type} _desc)
string(REPLACE "${flag}" "match" _temp_var "${${_var}}")
if(NOT _temp_var MATCHES "match")
set(${_var} "${flag} ${${_var}}" CACHE STRING ${_desc} FORCE)
endif()
endmacro()
#===============================================================================
macro(remove_flags type flag)
string(TOUPPER ${type} _type)
set(_var CMAKE_${_type}_FLAGS)
_get_flags_message(${_type} _desc)
string(REPLACE "${flag} " "" ${_var} "${${_var}}")
set(${_var} "${${_var}}" CACHE STRING ${_desc} FORCE)
endmacro()
#===============================================================================
diff --git a/cmake/Modules/CMakePackagesSystem.cmake b/cmake/Modules/CMakePackagesSystem.cmake
index a8d2eea0e..d8bfd34c0 100644
--- a/cmake/Modules/CMakePackagesSystem.cmake
+++ b/cmake/Modules/CMakePackagesSystem.cmake
@@ -1,1106 +1,1108 @@
#===============================================================================
# @file CMakePackagesSystem.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Wed Jan 20 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Mon Mar 08 2021
#
# @brief Set of macros used by akantu to handle the package system
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#[=======================================================================[.rst:
#CMakePackagesSystem
#-------------------
#
#This package defines multiple function to handle packages. This packages can
#be of two kinds regular ones and extra_packages (ex: in akantu the LGPL part
#is regular packages and extra packages are on Propetary license)
#
#Package are loaded with the help of the command:
#
#.. command:: package_list_packages
#
# package_list_packages(<regular_package_folder>
# [ EXTRA_PACKAGE_FOLDER <extra_package_folder> ]
# [ SOURCE_FOLDER <source_folder>]
# [ TEST_FOLDER <test_folder> ]
# [ MANUAL_FOLDER <manual_folder> ]
# )
#
# This command will look for packages name like ``<regular_package_folder>/<package>.cmake``
# OR ``<extra_package_folder>/<package>/package.cmake``
#
#A package is a cmake script that should contain at list the declaration of a
#package
#
#.. command:: package_declare
#
# package_declare(<package real name>
# [EXTERNAL] [META] [ADVANCED] [NOT_OPTIONAL]
# [DESCRIPTION <description>] [DEFAULT <default_value>]
# [DEPENDS <pkg> ...]
# [BOOST_COMPONENTS <pkg> ...]
# [EXTRA_PACKAGE_OPTIONS <opt> ...]
# [COMPILE_FLAGS <lang> <flags>]
# [SYSTEM <ON|OFF|AUTO> [ <script_to_compile> ]]
# [FEATURES_PUBLIC <feature> ...]
# [FEATURES_PRIVATE <feature> ...]
# [EXCLUDE_FROM_ALL]
# )
#
#.. command:: package_declare_sources
#
# It can also declare multiple informations:
# source files:
#
# package_declare_sources(<package real name>
# <src1> <src2> ... <srcn>)
#
#.. command:: package_declare_documentation
#
# a LaTeX documentation
# package_declare_documentation(<package real name>
# <line1> <line2> ...<linen>)
#
#.. command:: package_declare_documentation_files
#
# LaTeX documentation files
# package_declare_documentation_files(<package real name>
# <file1> <file2> ... <filen>)
#
#Different function can also be retrieved from the package system by using the
#different accessors
#
#.. command:: package_get_name
# package_get_name(<pkg> <retval>)
#
#.. command:: package_get_real_name
# package_get_real_name(<pkg> <retval>)
#
#.. command:: package_get_option_name
# package_get_option_name(<pkg> <retval>)
#
#.. command:: package_use_system
# package_use_system(<pkg> <retval>)
#
#.. command:: package_get_nature
# package_get_nature(<pkg> <retval>)
#
#.. command:: package_get_description
# package_get_description(<pkg> <retval>)
#
#.. command:: package_get_filename
# package_get_filename(<pkg> <retval>)
#
#.. command:: package_get_sources_folder
# package_get_sources_folder(<pkg> <retval>)
#.. command:: package_get_tests_folder
# package_get_tests_folder(<pkg> <retval>)
#.. command:: package_get_manual_folder
# package_get_manual_folder(<pkg> <retval>)
#
#.. command:: package_get_find_package_extra_options
# package_get_find_package_extra_options(<pkg> <retval>)
#
#.. command:: package_get_compile_flags
# package_get_compile_flags(<pkg> <lang> <retval>)
#.. command:: package_set_compile_flags
# package_set_compile_flags(<pkg> <lang> <flag1> <flag2> ... <flagn>)
#
#.. command:: package_get_include_dir
# package_get_include_dir(<pkg> <retval>)
#.. command:: package_set_include_dir
# package_set_include_dir(<pkg> <inc1> <inc2> ... <incn>)
#.. command:: package_add_include_dir
# package_add_include_dir(<pkg> <inc1> <inc2> ... <incn>)
#
#.. command:: package_get_libraries
# package_get_libraries(<pkg> <retval>)
#.. command:: package_set_libraries
# package_set_libraries(<pkg> <lib1> <lib2> ... <libn>)
#
#.. command:: package_add_extra_dependency
# package_add_extra_dependency(pkg <dep1> <dep2> ... <depn>)
#.. command:: package_rm_extra_dependency
# package_rm_extra_dependency(<pkg> <dep>)
#.. command:: package_get_extra_dependencies
# package_get_extra_dependencies(<pkg> <retval>)
#
#.. command:: package_is_activated
# package_is_activated(<pkg> <retval>)
#.. command:: package_is_deactivated
# package_is_deactivated(<pkg> <retval>)
#
#.. command:: package_get_dependencies
# package_get_dependencies(<pkg> <PRIVATE|INTERFACE> <retval>)
#.. command:: package_add_dependencies
# package_add_dependencies(<pkg> <PRIVATE|INTERFACE> <dep1> <dep2> ... <depn>)
# package_remove_dependencies(<pkg> <dep1> <dep2> ... <depn>)
# package_remove_dependency(<pkg> <dep>)
#
#.. command:: package_on_enabled_script
# package_on_enabled_script(<pkg> <script>)
#
#.. command:: package_get_all_source_files
# package_get_all_source_files(<srcs> <public_headers> <private_headers>)
#.. command:: package_get_all_include_directories
# package_get_all_include_directories(<inc_dirs>)
#.. command:: package_get_all_external_informations
# package_get_all_external_informations(<include_dir> <libraries>)
#.. command:: package_get_all_definitions
# package_get_all_definitions(<definitions>)
#.. command:: package_get_all_extra_dependencies
# package_get_all_extra_dependencies(<dependencies>)
#.. command:: package_get_all_test_folders
# package_get_all_test_folders(<test_dirs>)
#.. command:: package_get_all_documentation_files
# package_get_all_documentation_files(<doc_files>)
#.. command:: package_get_all_activated_packages
# package_get_all_activated_packages(<activated_list>)
#.. command:: package_get_all_deactivated_packages
# package_get_all_deactivated_packages(<deactivated_list>)
#.. command:: package_get_all_packages
# package_get_all_packages(<packages_list>)
#.. command:: package_get_all_features_public
# package_get_all_features_public(<features>)
#.. command:: package_get_all_features_private
# package_get_all_features_private(<features>)
#
#
# .. command:: package_set_package_system_dependency
#
# package_set_package_system_dependency(<pkg> <system> <dep1>
# <dep2> ... <depn>)
#
# .. command:: package_get_package_system_dependency
#
# package_get_package_system_dependency(<pkg> <var>)
#
#
#]=======================================================================]
if (DEFINED CMAKE_PACKAGES_SYSTEM_LOADED)
return()
endif()
set(CMAKE_PACKAGES_SYSTEM_LOADED TRUE)
include(CMakeParseArguments)
#===============================================================================
# Package Management
#===============================================================================
if(__CMAKE_PACKAGES_SYSTEM)
return()
endif()
set(__CMAKE_PACKAGES_SYSTEM TRUE)
if(CMAKE_VERSION VERSION_GREATER 3.1.2)
cmake_policy(SET CMP0054 NEW)
endif()
#===============================================================================
option(AUTO_MOVE_UNKNOWN_FILES
"Give to cmake the permission to move the unregistered files to the ${PROJECT_SOURCE_DIR}/tmp directory" FALSE)
mark_as_advanced(AUTO_MOVE_UNKNOWN_FILES)
include(CMakePackagesSystemGlobalFunctions)
include(CMakePackagesSystemPrivateFunctions)
# ==============================================================================
# "Public" Accessors
# ==============================================================================
# ------------------------------------------------------------------------------
# Package name
# ------------------------------------------------------------------------------
function(package_get_name pkg pkg_name)
string(TOUPPER ${PROJECT_NAME} _project)
string(REPLACE "-" "_" _str_pkg "${pkg}")
string(TOUPPER ${_str_pkg} _u_package)
set(${pkg_name} ${_project}_PKG_${_u_package} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Real name
# ------------------------------------------------------------------------------
function(package_get_real_name pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_real_name(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Option name
# ------------------------------------------------------------------------------
function(package_get_option_name pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_option_name(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Set if system package or compile external lib
# ------------------------------------------------------------------------------
function(package_use_system pkg ret)
package_get_name(${pkg} _pkg_name)
_package_use_system(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_add_third_party_script_variable pkg var)
package_get_name(${pkg} _pkg_name)
_package_add_third_party_script_variable(${_pkg_name} ${var} ${ARGN})
set(${var} ${ARGN} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Add package's targets to the export list
# ------------------------------------------------------------------------------
function(package_add_to_export_list pkg)
package_get_name(${pkg} _pkg_name)
_package_add_to_export_list(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Removes packages's targets from export list
# ------------------------------------------------------------------------------
function(package_remove_from_export_list pkg)
package_get_name(${pkg} _pkg_name)
_package_remove_from_export_list(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Nature
# ------------------------------------------------------------------------------
function(package_get_nature pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_nature(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Description
# ------------------------------------------------------------------------------
function(package_get_description pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_description(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Package file name
# ------------------------------------------------------------------------------
function(package_get_filename pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_filename(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Source files
# ------------------------------------------------------------------------------
function(package_get_source_files pkg ret_srcs ret_pub ret_priv)
package_get_name(${pkg} _pkg_name)
_package_get_source_files(${_pkg_name} _tmp_srcs _tmp_pub _tmp_priv)
set(${ret_srcs} ${_tmp_srcs} PARENT_SCOPE)
set(${ret_pub} ${_tmp_pub} PARENT_SCOPE)
set(${ret_priv} ${_tmp_pric} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Source folder
# ------------------------------------------------------------------------------
function(package_get_sources_folder pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_sources_folder(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Test folder
# ------------------------------------------------------------------------------
function(package_get_tests_folder pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_tests_folder(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Manual folder
# ------------------------------------------------------------------------------
function(package_get_manual_folder pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_manual_folder(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Extra option for the find_package
# ------------------------------------------------------------------------------
function(package_get_find_package_extra_options pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_find_package_extra_options(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_set_find_package_extra_options pkg)
package_get_name(${pkg} _pkg_name)
_package_set_find_package_extra_options(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Compilation flags
# ------------------------------------------------------------------------------
function(package_get_compile_flags pkg lang ret)
package_get_name(${pkg} _pkg_name)
_package_get_compile_flags(${_pkg_name} ${lang} _tmp)
set(${ret} "${_tmp}" PARENT_SCOPE)
endfunction()
function(package_set_compile_flags pkg lang)
package_get_name(${pkg} _pkg_name)
_package_set_compile_flags(${_pkg_name} ${lang} ${ARGN})
endfunction()
function(package_unset_compile_flags pkg lang)
package_get_name(${pkg} _pkg_name)
_package_unset_compile_flags(${_pkg_name} ${lang})
endfunction()
# ------------------------------------------------------------------------------
# Include dir
# ------------------------------------------------------------------------------
function(package_get_include_dir pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_include_dir(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_set_include_dir pkg)
package_get_name(${pkg} _pkg_name)
_package_set_include_dir(${_pkg_name} ${ARGN})
endfunction()
function(package_add_include_dir pkg)
package_get_name(${pkg} _pkg_name)
_package_add_include_dir(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Libraries
# ------------------------------------------------------------------------------
function(package_get_libraries pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_libraries(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_set_libraries pkg)
package_get_name(${pkg} _pkg_name)
_package_set_libraries(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Extra dependencies like custom commands of ExternalProject
# ------------------------------------------------------------------------------
function(package_add_extra_dependency pkg)
package_get_name(${pkg} _pkg_name)
_package_add_extra_dependency(${_pkg_name} ${ARGN})
endfunction()
function(package_rm_extra_dependency pkg dep)
package_get_name(${pkg} _pkg_name)
_package_rm_extra_dependency(${_pkg_name} ${dep})
endfunction()
function(package_get_extra_dependencies pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_extra_dependencies(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Activate/deactivate
# ------------------------------------------------------------------------------
function(package_is_activated pkg ret)
package_get_name(${pkg} _pkg_name)
_package_is_activated(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_is_deactivated pkg ret)
package_get_name(${pkg} _pkg_name)
_package_is_deactivated(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Direct dependencies
# ------------------------------------------------------------------------------
function(package_get_dependencies pkg type ret)
package_get_name(${pkg} _pkg_name)
_package_get_dependencies(${_pkg_name} ${type} _tmp_name)
_package_get_real_name(${_tmp_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_add_dependencies pkg type)
package_get_name(${pkg} _pkg_name)
foreach(_dep ${ARGN})
package_get_name(${_dep} _dep_pkg_name)
list(APPEND _tmp_deps ${_dep_pkg_name})
endforeach()
_package_add_dependencies(${_pkg_name} ${type} ${_tmp_deps})
endfunction()
function(package_remove_dependencies pkg type)
foreach(_dep ${ARGN})
package_remove_dependency(${pkg} _dep)
endforeach()
endfunction()
function(package_remove_dependency pkg dep)
package_get_name(${pkg} _pkg_name)
package_get_name(${dep} _dep_pkg_name)
_package_remove_dependency(${_pkg_name} PRIVATE ${_dep_pkg_name})
_package_remove_dependency(${_pkg_name} INTERFACE ${_dep_pkg_name})
endfunction()
# ------------------------------------------------------------------------------
# Documentation related functions
# ------------------------------------------------------------------------------
function(package_declare_documentation pkg)
package_get_name(${pkg} _pkg_name)
_package_set_documentation(${_pkg_name} ${ARGN})
endfunction()
function(package_declare_documentation_files pkg)
package_get_name(${pkg} _pkg_name)
_package_set_documentation_files(${_pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Set any user variables needed
# ------------------------------------------------------------------------------
function(package_set_variable variable pkg)
package_get_name(${pkg} _pkg_name)
_package_set_variable(${variable} ${_pkg_name} ${ARGN})
endfunction()
function(package_add_to_variable variable pkg)
package_get_name(${pkg} _pkg_name)
_package_add_to_variable(${variable} ${_pkg_name} ${ARGN})
endfunction()
function(package_get_variable variable pkg value)
package_get_name(${pkg} _pkg_name)
_package_get_variable(${variable} ${_pkg_name} _value_tmp)
if(_value_tmp)
set(${value} ${_value_tmp} PARENT_SCOPE)
else()
unset(${value} PARENT_SCOPE)
endif()
endfunction()
# ------------------------------------------------------------------------------
# Exteral package system as apt rpm dependencies
# ------------------------------------------------------------------------------
function(package_set_package_system_dependency pkg system)
package_get_name(${pkg} _pkg_name)
_package_set_package_system_dependency(${_pkg_name} ${system} ${ARGN})
endfunction()
function(package_get_package_system_dependency pkg system var)
package_get_name(${pkg} _pkg_name)
_package_set_package_system_dependency(${_pkg_name} ${sytem} _tmp)
set(${var} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# ==============================================================================
# Global accessors
# ==============================================================================
# ------------------------------------------------------------------------------
# get the list of source files
# ------------------------------------------------------------------------------
function(package_get_all_source_files SRCS PUBLIC_HEADERS PRIVATE_HEADERS)
string(TOUPPER ${PROJECT_NAME} _project)
unset(_tmp_srcs)
unset(_tmp_public_headers)
unset(_tmp_private_headers)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_source_files(${_pkg_name}
_pkg_srcs
_pkg_public_headers
_pkg_private_headers
)
list(APPEND _tmp_srcs ${_pkg_srcs})
list(APPEND _tmp_public_headers ${_pkg_public_headers})
list(APPEND _tmp_private_headers ${_pkg_private_headers})
endforeach()
set(${SRCS} ${_tmp_srcs} PARENT_SCOPE)
set(${PUBLIC_HEADERS} ${_tmp_public_headers} PARENT_SCOPE)
set(${PRIVATE_HEADERS} ${_tmp_private_headers} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get include directories
# ------------------------------------------------------------------------------
function(package_get_all_include_directories inc_dirs)
set(_tmp)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
foreach(_type SRCS PUBLIC_HEADERS PRIVATE_HEADERS)
foreach(_file ${${_pkg_name}_${_type}})
get_filename_component(_path "${_file}" PATH)
list(APPEND _tmp "${_path}")
endforeach()
endforeach()
endforeach()
if(_tmp)
list(REMOVE_DUPLICATES _tmp)
endif()
set(${inc_dirs} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get external libraries informations
# ------------------------------------------------------------------------------
function(package_get_all_external_informations)
cmake_parse_arguments(_opt "" "PRIVATE_INCLUDE;INTERFACE_INCLUDE;LIBRARIES" "" ${ARGN})
foreach(_type PRIVATE INTERFACE)
if(_opt_${_type}_INCLUDE)
_package_get_variable_for_external_dependencies(INCLUDE_DIR ${_type} tmp_INCLUDE_DIR)
foreach(_dir ${tmp_INCLUDE_DIR})
string(FIND "${_dir}" "${CMAKE_CURRENT_SOURCE_DIR}" _pos)
if(NOT _pos EQUAL -1)
list(REMOVE_ITEM tmp_INCLUDE_DIR ${_dir})
endif()
endforeach()
set(${_opt_${_type}_INCLUDE} ${tmp_INCLUDE_DIR} PARENT_SCOPE)
endif()
endforeach()
if(_opt_LIBRARIES)
_package_get_variable_for_external_dependencies(LIBRARIES PRIVATE tmp_LIBRARIES)
_package_get_variable_for_external_dependencies(LIBRARIES INTERFACE tmp_LIBRARIES_INTERFACE)
set(${_opt_LIBRARIES} ${tmp_LIBRARIES} ${tmp_LIBRARIES_INTERFACE} PARENT_SCOPE)
endif()
endfunction()
# ------------------------------------------------------------------------------
# Get export list for all activated packages
# ------------------------------------------------------------------------------
function(package_get_all_export_list export_list)
_package_get_variable_for_activated(EXPORT_LIST _tmp)
set(${export_list} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get definitions like external projects
# ------------------------------------------------------------------------------
function(package_get_all_definitions definitions)
_package_get_variable_for_activated(OPTION_NAME _tmp)
set(${definitions} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get extra dependencies like external projects
# ------------------------------------------------------------------------------
function(package_get_all_extra_dependencies deps)
_package_get_variable_for_activated(EXTRA_DEPENDENCY _tmp)
set(${deps} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get extra infos
# ------------------------------------------------------------------------------
function(package_get_all_test_folders TEST_DIRS)
_package_get_variable_for_activated(TEST_FOLDER _tmp)
set(${TEST_DIRS} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get compilation flags
# ------------------------------------------------------------------------------
function(package_get_all_compilation_flags LANG FLAGS)
_package_get_variable_for_activated(COMPILE_${LANG}_FLAGS _tmp_flags)
string(REPLACE ";" " " _flags "${_tmp_flags}")
set(${FLAGS} ${_flags} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Documentation informations
# ------------------------------------------------------------------------------
function(package_get_all_documentation_files doc_files)
set(_tmp_DOC_FILES)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_manual_folder(${_pkg_name} _doc_dir)
_package_get_documentation_files(${_pkg_name} _doc_files)
foreach(_doc_file ${_doc_files})
list(APPEND _tmp_DOC_FILES ${_doc_dir}/${_doc_file})
endforeach()
endforeach()
if(_tmp_DOC_FILES)
list(REMOVE_DUPLICATES _tmp_DOC_FILES)
endif()
set(${doc_files} ${_tmp_DOC_FILES} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get package systems dependencies
# ------------------------------------------------------------------------------
function(package_get_all_package_system_dependency system deps)
string(TOUPPER ${system} _u_system)
_package_get_variable_for_activated(PACKAGE_SYSTEM_${_u_system} _tmp)
set(${deps} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# List packages
# ------------------------------------------------------------------------------
function(package_get_all_activated_packages activated_list)
package_get_project_variable(ACTIVATED_PACKAGE_LIST _activated_list)
set(${activated_list} ${_activated_list} PARENT_SCOPE)
endfunction()
function(package_get_all_deactivated_packages deactivated_list)
package_get_project_variable(DEACTIVATED_PACKAGE_LIST _deactivated_list)
set(${deactivated_list} ${_deactivated_list} PARENT_SCOPE)
endfunction()
function(package_get_all_packages packages_list)
package_get_project_variable(ALL_PACKAGES_LIST _packages_list)
set(${packages_list} ${_packages_list} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# List all the needed features
# ------------------------------------------------------------------------------
function(package_get_all_features_public features)
_package_get_variable_for_activated(FEATURES_PUBLIC _tmp)
set(${features} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_get_all_features_private features)
_package_get_variable_for_activated(FEATURES_PRIVATE _tmp)
set(${features} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Callbacks
# ------------------------------------------------------------------------------
function(package_on_enabled_script pkg script)
package_get_name(${pkg} _pkg_name)
_package_on_enable_script(${_pkg_name} "${script}")
endfunction()
# ------------------------------------------------------------------------------
# list all the packages in the PACKAGE_FOLDER
# extra packages can be given with an EXTRA_PACKAGE_FOLDER
# <package_folder>/<package>.cmake
#
# Extra packages folder structure
# <extra_package_folder>/<package>/package.cmake
# /src
# /test
# /manual
#
# ------------------------------------------------------------------------------
function(package_list_packages PACKAGE_FOLDER)
cmake_parse_arguments(_opt_pkg
"NO_AUTO_COMPILE_FLAGS"
"SOURCE_FOLDER;EXTRA_PACKAGES_FOLDER;TEST_FOLDER;MANUAL_FOLDER"
""
${ARGN})
string(TOUPPER ${PROJECT_NAME} _project)
# Cleaning some states to start correctly
package_get_all_packages(_already_loaded_pkg)
foreach(_pkg_name ${_already_loaded_pkg})
_package_unset_extra_dependencies(${_pkg_name})
_package_unset_dependencies(${_pkg_name} PRIVATE)
_package_unset_dependencies(${_pkg_name} INTERFACE)
_package_unset_activated(${_pkg_name})
endforeach()
if(_opt_pkg_SOURCE_FOLDER)
set(_src_folder "${_opt_pkg_SOURCE_FOLDER}")
else()
set(_src_folder "src/")
endif()
get_filename_component(_abs_src_folder ${_src_folder} ABSOLUTE)
if(_opt_pkg_TEST_FOLDER)
set(_test_folder "${_opt_pkg_TEST_FOLDER}")
else()
set(_test_folder "test/")
endif()
if(_opt_pkg_MANUAL_FOLDER)
set(_manual_folder "${_opt_pkg_MANUAL_FOLDER}")
else()
set(_manual_folder "doc/manual")
endif()
if(_opt_pkg_NO_AUTO_COMPILE_FLAGS)
package_set_project_variable(NO_AUTO_COMPILE_FLAGS TRUE)
else()
package_set_project_variable(NO_AUTO_COMPILE_FLAGS FALSE)
endif()
get_filename_component(_abs_test_folder ${_test_folder} ABSOLUTE)
get_filename_component(_abs_manual_folder ${_manual_folder} ABSOLUTE)
# check all the packages in the <package_folder>
file(GLOB _package_list "${PACKAGE_FOLDER}/*.cmake")
set(_package_files)
foreach(_pkg ${_package_list})
get_filename_component(_basename ${_pkg} NAME)
if(NOT _basename MATCHES "^\\.#.*")
list(APPEND _package_files ${_basename})
endif()
endforeach()
if(_package_files)
list(SORT _package_files)
endif()
# check all packages
set(_packages_list_all)
foreach(_pkg_file ${_package_files})
string(REGEX REPLACE "[0-9]+_" "" _pkg_file_stripped ${_pkg_file})
string(REGEX REPLACE "\\.cmake" "" _pkg ${_pkg_file_stripped})
set(_current_src_folder "${_abs_src_folder}" CACHE INTERNAL "" FORCE)
set(_current_test_folder "${_abs_test_folder}" CACHE INTERNAL "" FORCE)
set(_current_manual_folder "${_abs_manual_folder}" CACHE INTERNAL "" FORCE)
include("${PACKAGE_FOLDER}/${_pkg_file}")
unset(_current_src_folder CACHE)
unset(_current_test_folder CACHE)
unset(_current_manual_folder CACHE)
endforeach()
# check the extra_packages if they exists
if(_opt_pkg_EXTRA_PACKAGES_FOLDER)
file(GLOB _extra_package_list RELATIVE
"${_opt_pkg_EXTRA_PACKAGES_FOLDER}" "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/*")
foreach(_pkg ${_extra_package_list})
if(EXISTS "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/package.cmake")
package_get_name(${_pkg} _pkg_name)
_package_set_filename(${_pkg_name}
"${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/package.cmake")
set(_current_src_folder "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/src" CACHE INTERNAL "" FORCE)
if(EXISTS "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/test")
set(_current_test_folder "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/test" CACHE INTERNAL "" FORCE)
endif()
if(EXISTS "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/manual")
set(_current_manual_folder "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/manual" CACHE INTERNAL "" FORCE)
endif()
list(APPEND _extra_pkg_src_folders "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/src")
include("${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/package.cmake")
unset(_current_src_folder CACHE)
unset(_current_test_folder CACHE)
unset(_current_manual_folder CACHE)
endif()
endforeach()
endif()
_package_build_rdependencies()
_package_load_packages()
_package_check_files_exists()
_package_check_files_registered(${_abs_src_folder} ${_extra_pkg_src_folders})
# Load boost components if boost was loaded
package_is_activated(Boost _ret)
if(_ret)
_package_load_boost_components()
endif()
endfunction()
# ------------------------------------------------------------------------------
# macro to include internal/external packages packages
# package_declare(<package real name>
# [EXTERNAL] [META] [ADVANCED] [NOT_OPTIONAL]
# [DESCRIPTION <description>] [DEFAULT <default_value>]
# [DEPENDS <pkg> ...]
# [BOOST_COMPONENTS <pkg> ...]
# [EXTRA_PACKAGE_OPTIONS <opt> ...]
# [COMPILE_FLAGS <lang> <flags>]
# [SYSTEM <bool> [ <script_to_compile> ]]
# [FEATURES_PUBLIC <feature> ...]
# [FEATURES_PRIVATE <feature> ...])
# ------------------------------------------------------------------------------
function(package_declare pkg)
package_get_name(${pkg} _pkg_name)
_package_set_real_name(${_pkg_name} ${pkg})
_package_set_filename(${_pkg_name} "${CMAKE_CURRENT_LIST_FILE}")
_package_set_sources_folder(${_pkg_name} "${_current_src_folder}")
_package_variable_unset(SRCS ${_pkg_name})
_package_variable_unset(PUBLIC_HEADERS ${_pkg_name})
_package_variable_unset(PRIVATE_HEADERS ${_pkg_name})
if(_current_test_folder)
_package_set_tests_folder(${_pkg_name} "${_current_test_folder}")
endif()
if(_current_manual_folder)
_package_set_manual_folder(${_pkg_name} "${_current_manual_folder}")
endif()
package_get_project_variable(ALL_PACKAGES_LIST _tmp_pkg_list)
list(APPEND _tmp_pkg_list ${_pkg_name})
list(REMOVE_DUPLICATES _tmp_pkg_list)
package_set_project_variable(ALL_PACKAGES_LIST ${_tmp_pkg_list})
set(_options
EXTERNAL
NOT_OPTIONAL
META
ADVANCED
EXCLUDE_FROM_ALL)
set(_one_valued_options
DEFAULT
DESCRIPTION)
set(_multi_valued_options
DEPENDS
EXTRA_PACKAGE_OPTIONS
COMPILE_FLAGS
BOOST_COMPONENTS
SYSTEM
FEATURES_PUBLIC
FEATURES_PRIVATE)
cmake_parse_arguments(_opt_pkg
"${_options}"
"${_one_valued_options}"
"${_multi_valued_options}"
${ARGN})
if(_opt_pkg_UNPARSED_ARGUMENTS)
message("You gave to many arguments while registering the package ${pkg} \"${_opt_pkg_UNPARSED_ARGUMENTS}\"")
endif()
# set the nature
if(_opt_pkg_EXTERNAL)
_package_set_nature(${_pkg_name} "external")
elseif(_opt_pkg_META)
_package_set_nature(${_pkg_name} "meta")
else()
_package_set_nature(${_pkg_name} "internal")
endif()
_package_declare_option(${_pkg_name})
# set description
if(_opt_pkg_DESCRIPTION)
_package_set_description(${_pkg_name} ${_opt_pkg_DESCRIPTION})
else()
_package_set_description(${_pkg_name} "")
endif()
_package_get_option_name(${_pkg_name} _option_name)
_package_get_description(${_pkg_name} _description)
# get the default value
if(DEFINED _opt_pkg_DEFAULT)
set(_default ${_opt_pkg_DEFAULT})
else()
if(_opt_pkg_NOT_OPTIONAL)
set(_default ON)
else()
set(_default OFF)
endif()
endif()
# set the option if needed
if(_opt_pkg_NOT_OPTIONAL)
_package_get_nature(${_pkg_name} _nature)
_package_set_nature(${_pkg_name} "${_nature}_not_optional")
set(${_option_name} ${_default} CACHE INTERNAL "${_description}" FORCE)
mark_as_advanced(${_option_name})
else()
option(${_option_name} "${_description}" ${_default})
if(_opt_pkg_ADVANCED OR _opt_pkg_EXTERNAL)
mark_as_advanced(${_option_name})
endif()
endif()
# Set the option for third-partie that can be compiled as an ExternalProject
if(DEFINED _opt_pkg_SYSTEM)
list(LENGTH _opt_pkg_SYSTEM _length)
list(GET _opt_pkg_SYSTEM 0 _bool)
_package_set_system_option(${_pkg_name} ${_bool})
if(_length GREATER 1)
list(GET _opt_pkg_SYSTEM 1 _script)
_package_set_system_script(${_pkg_name} ${_script})
endif()
endif()
# set the dependecies
if(_opt_pkg_DEPENDS)
set(_deps_types PRIVATE PUBLIC INTERFACE)
cmake_parse_arguments(_pkg_deps
""
""
"${_deps_types}"
${_opt_pkg_DEPENDS})
list(APPEND _pkg_deps_PRIVATE ${_pkg_deps_UNPARSED_ARGUMENTS})
foreach(_type ${_deps_types})
set(_depends)
foreach(_dep ${_pkg_deps_${_type}})
package_get_name(${_dep} _dep_pkg_name)
list(APPEND _depends ${_dep_pkg_name})
endforeach()
_package_add_dependencies(${_pkg_name} ${_type} ${_depends})
endforeach()
endif()
# keep the extra option for the future find package
if(_opt_pkg_EXTRA_PACKAGE_OPTIONS)
_package_set_find_package_extra_options(${_pkg_name} "${_opt_pkg_EXTRA_PACKAGE_OPTIONS}")
endif()
# register the compilation flags
if(_opt_pkg_COMPILE_FLAGS)
set(_languages C CXX Fortran)
cmake_parse_arguments(_compile_flags
"" "" "${_languages}"
${_opt_pkg_COMPILE_FLAGS}
)
# this is done to maintain backward compatibility
if(_compile_flags_UNPARSED_ARGUMENTS)
set(_compile_flags_CXX ${_compile_flags_UNPARSED_ARGUMENTS})
endif()
foreach(_lang ${_languages})
if(_compile_flags_${_lang})
_package_set_compile_flags(${_pkg_name} ${_lang} ${_compile_flags_${_lang}})
else()
_package_unset_compile_flags(${_pkg_name} ${_lang})
endif()
endforeach()
endif()
# set the boost dependencies
if(_opt_pkg_BOOST_COMPONENTS)
_package_set_boost_component_needed(${_pkg_name} "${_opt_pkg_BOOST_COMPONENTS}")
endif()
set(_variables FEATURES_PUBLIC FEATURES_PRIVATE EXCLUDE_FROM_ALL)
foreach(_variable ${_variables})
if(_opt_pkg_${_variable})
_package_set_variable(${_variable} ${_pkg_name} "${_opt_pkg_${_variable}}")
endif()
endforeach()
endfunction()
# ------------------------------------------------------------------------------
# declare the source files of a given package
#
# package_declare_sources(<package> <list of sources>
# SOURCES <source file> ...
# PUBLIC_HEADER <header file> ...
# PRIVATE_HEADER <header file> ...)
# ------------------------------------------------------------------------------
function(package_declare_sources pkg)
package_get_name(${pkg} _pkg_name)
# get 3 lists, if none of the options given try to distinguish the different lists
cmake_parse_arguments(_opt_pkg
""
""
"SOURCES;PUBLIC_HEADERS;PRIVATE_HEADERS"
${ARGN})
set(_tmp_srcs ${_opt_pkg_SOURCES})
set(_tmp_pub_hdrs ${_opt_pkg_PUBLIC_HEADER})
set(_tmp_pri_hdrs ${_opt_pkg_PRIVATE_HEADERS})
foreach(_file ${_opt_pkg_UNPARSED_ARGUMENTS})
if(${_file} MATCHES ".*inline.*\\.cc")
list(APPEND _tmp_pub_hdrs ${_file})
elseif(${_file} MATCHES ".*\\.h+")
list(APPEND _tmp_pub_hdrs ${_file})
else()
list(APPEND _tmp_srcs ${_file})
endif()
endforeach()
_package_get_sources_folder(${_pkg_name} _src_folder)
foreach(_type _srcs _pub_hdrs _pri_hdrs)
set(${_type})
foreach(_file ${_tmp${_type}})
# get the full name
set(_full_path "${_src_folder}/${_file}")
list(APPEND ${_type} "${_full_path}")
endforeach()
endforeach()
set(${_pkg_name}_SRCS "${_srcs}"
CACHE INTERNAL "List of sources files" FORCE)
set(${_pkg_name}_PUBLIC_HEADERS "${_pub_hdrs}"
CACHE INTERNAL "List of public header files" FORCE)
set(${_pkg_name}_PRIVATE_HEADERS "${_pri_hdrs}"
CACHE INTERNAL "List of private header files" FORCE)
endfunction()
# ------------------------------------------------------------------------------
diff --git a/cmake/Modules/CMakePackagesSystemGlobalFunctions.cmake b/cmake/Modules/CMakePackagesSystemGlobalFunctions.cmake
index 2d8c1a484..cd91211b8 100644
--- a/cmake/Modules/CMakePackagesSystemGlobalFunctions.cmake
+++ b/cmake/Modules/CMakePackagesSystemGlobalFunctions.cmake
@@ -1,132 +1,134 @@
#===============================================================================
# @file CMakePackagesSystemGlobalFunctions.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sat Jul 18 2015
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri Mar 16 2018
#
# @brief Set of macros used by the package system to set internal variables
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
# ==============================================================================
# Package system meta functions
# ==============================================================================
function(package_set_project_variable variable)
string(TOUPPER ${PROJECT_NAME} _u_project)
set(${_u_project}_${variable} "${ARGN}" CACHE INTERNAL "" FORCE)
endfunction()
function(package_get_project_variable variable value_out)
string(TOUPPER ${PROJECT_NAME} _u_project)
set(${value_out} ${${_u_project}_${variable}} PARENT_SCOPE)
endfunction()
function(package_add_to_project_variable variable)
package_get_project_variable(${variable} _tmp_list)
list(APPEND _tmp_list ${ARGN})
if(_tmp_list)
list(REMOVE_DUPLICATES _tmp_list)
endif()
package_set_project_variable(${variable} ${_tmp_list})
endfunction()
# ==============================================================================
function(_package_set_variable variable pkg_name)
set(${pkg_name}_${variable} ${ARGN} CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_variable variable pkg_name value)
#unset(${value} PARENT_SCOPE)
if(DEFINED ${pkg_name}_${variable})
set(${value} ${${pkg_name}_${variable}} PARENT_SCOPE)
elseif(DEFINED ARGN)
set(${value} ${ARGN} PARENT_SCOPE)
else()
set(${value} PARENT_SCOPE)
endif()
endfunction()
# ==============================================================================
function(_package_variable_unset variable pkg_name)
unset(${pkg_name}_${variable} CACHE)
endfunction()
# ==============================================================================
function(_package_add_to_variable variable pkg_name)
_package_get_variable(${variable} ${pkg_name} _tmp_list)
list(APPEND _tmp_list ${ARGN})
if(_tmp_list)
list(REMOVE_DUPLICATES _tmp_list)
endif()
_package_set_variable(${variable} ${pkg_name} ${_tmp_list})
endfunction()
function(_package_remove_from_variable variable pkg_name value)
_package_get_variable(${variable} ${pkg_name} _tmp_list)
list(LENGTH _tmp_list _length)
if(_length GREATER 0)
list(REMOVE_ITEM _tmp_list ${value})
_package_set_variable(${variable} ${pkg_name} ${_tmp_list})
endif()
endfunction()
# ==============================================================================
function(_package_get_variable_for_packages variable values)
set(_list_values)
foreach(_pkg_name ${ARGN})
_package_get_variable(${variable} ${_pkg_name} _value)
list(APPEND _list_values ${_value})
endforeach()
if (_list_values)
list(REMOVE_DUPLICATES _list_values)
endif()
set(${values} ${_list_values} PARENT_SCOPE)
endfunction()
# ==============================================================================
function(_package_get_variable_for_activated variable values)
package_get_all_activated_packages(_activated_list)
_package_get_variable_for_packages(${variable} _list_values ${_activated_list})
set(${values} ${_list_values} PARENT_SCOPE)
endfunction()
# ==============================================================================
function(_package_get_variable_for_external_dependencies variable type values)
set(_list_packages)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_nature(${_pkg_name} _nature)
if(_nature MATCHES "^external.*")
list(APPEND _list_packages ${_pkg_name})
endif()
endforeach()
if (_list_packages)
list(REMOVE_DUPLICATES _list_packages)
_package_get_variable_for_packages(${variable} _list_values_deps ${_list_packages})
set(${values} ${_list_values_deps} PARENT_SCOPE)
endif()
endfunction()
# ==============================================================================
diff --git a/cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake b/cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
index d1a58736a..42eca6811 100644
--- a/cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
+++ b/cmake/Modules/CMakePackagesSystemPrivateFunctions.cmake
@@ -1,981 +1,984 @@
#===============================================================================
# @file CMakePackagesSystemPrivateFunctions.cmake
#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sat Jul 18 2015
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Mon Mar 08 2021
#
# @brief Set of macros used by the package system, internal functions
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if (DEFINED CMAKE_PACKAGES_SYSTEM_PRIVATE_FUNCTIONS_LOADED)
return()
endif()
set(CMAKE_PACKAGES_SYSTEM_PRIVATE_FUNCTIONS_LOADED TRUE)
# ==============================================================================
# "Private" Accessors
# ==============================================================================
# ------------------------------------------------------------------------------
# Real name
# ------------------------------------------------------------------------------
function(_package_get_real_name pkg_name real_name)
set(${real_name} ${${pkg_name}} PARENT_SCOPE)
endfunction()
function(_package_set_real_name pkg_name real_name)
set(${pkg_name} ${real_name} CACHE INTERNAL "" FORCE)
endfunction()
# ------------------------------------------------------------------------------
# Option name
# ------------------------------------------------------------------------------
function(_package_declare_option pkg_name)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
_package_get_nature(${pkg_name} _nature)
if(${_nature} MATCHES "internal" OR ${_nature} MATCHES "meta")
set(_opt_name ${_project}_${_u_package})
elseif(${_nature} MATCHES "external")
set(_opt_name ${_project}_USE_${_u_package})
else()
set(_opt_name UNKNOWN_NATURE_${_project}_${_u_package})
endif()
_package_set_variable(OPTION_NAME ${pkg_name} ${_opt_name})
endfunction()
function(_package_get_option_name pkg_name opt_name)
_package_get_variable(OPTION_NAME ${pkg_name} _opt_name)
set(${opt_name} ${_opt_name} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Set if system package or compile external lib
# ------------------------------------------------------------------------------
function(_package_set_system_option pkg_name default)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
set(${_project}_USE_SYSTEM_${_u_package} ${default} CACHE STRING
"Should akantu compile the third-party: \"${_real_name}\"")
mark_as_advanced(${_project}_USE_SYSTEM_${_u_package})
set_property(CACHE ${_project}_USE_SYSTEM_${_u_package} PROPERTY STRINGS ON OFF AUTO)
endfunction()
function(_package_use_system pkg_name use)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
if(DEFINED ${_project}_USE_SYSTEM_${_u_package})
if(${${_project}_USE_SYSTEM_${_u_package}} MATCHES "(ON|AUTO)")
set(${use} TRUE PARENT_SCOPE)
else()
set(${use} FALSE PARENT_SCOPE)
endif()
else()
set(${use} TRUE PARENT_SCOPE)
endif()
endfunction()
function(_package_has_system_fallback pkg_name fallback)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
if(DEFINED ${_project}_USE_SYSTEM_${_u_package})
if(${${_project}_USE_SYSTEM_${_u_package}} MATCHES "AUTO")
set(${fallback} TRUE PARENT_SCOPE)
else()
set(${fallback} FALSE PARENT_SCOPE)
endif()
else()
set(${fallback} FALSE PARENT_SCOPE)
endif()
endfunction()
function(_package_set_system_script pkg_name script)
_package_set_variable(COMPILE_SCRIPT ${pkg_name} "${script}")
endfunction()
function(_package_add_third_party_script_variable pkg_name var)
_package_set_variable(VARIABLE_${var} ${pkg_name} "${ARGN}")
set(${var} ${ARGN} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
function(_package_load_third_party_script pkg_name)
if(${pkg_name}_COMPILE_SCRIPT)
# set the stored variable
get_cmake_property(_all_vars VARIABLES)
foreach(_var ${_all_vars})
if(_var MATCHES "^${pkg_name}_VARIABLE_.*")
string(REPLACE "${pkg_name}_VARIABLE_" "" _orig_var "${_var}")
set(${_orig_var} ${${_var}})
endif()
endforeach()
_package_get_real_name(${pkg_name} _name)
string(TOUPPER "${_name}" _u_name)
_package_get_option_name(${pkg_name} _opt_name)
if(${_opt_name}_VERSION)
set(_version "${${_opt_name}_VERSION}")
set(${_u_name}_VERSION "${_version}" CACHE INTERNAL "" FORCE)
elseif(${_u_name}_VERSION)
set(_version "${${_u_name}_VERSION}")
endif()
# load the script
include(ExternalProject)
include(${${pkg_name}_COMPILE_SCRIPT})
if(${_u_name}_LIBRARIES)
_package_set_libraries(${pkg_name} ${${_u_name}_LIBRARIES})
list(APPEND _required_vars ${_u_name}_LIBRARIES)
endif()
if(${_u_name}_INCLUDE_DIR)
_package_set_include_dir(${pkg_name} ${${_u_name}_INCLUDE_DIR})
list(APPEND _required_vars ${_u_name}_INCLUDE_DIR)
endif()
include(FindPackageHandleStandardArgs)
if (NOT _required_vars)
message(FATAL_ERROR "The package ${_name} does not define any of the variables ${_u_name}_INCLUDE_DIR nor ${_u_name}_LIBRARIES")
endif()
if(CMAKE_VERSION VERSION_GREATER 2.8.12)
find_package_handle_standard_args(${_name}
REQUIRED_VARS ${_required_vars}
VERSION_VAR _version
FAIL_MESSAGE "Something was not configured by a the third-party script for ${_name}"
)
else()
find_package_handle_standard_args(${_name}
"Something was not configured by a the third-party script for ${_name}"
${_required_vars}
)
endif()
endif()
set(${pkg_name}_USE_SYSTEM_PREVIOUS FALSE CACHE INTERNAL "" FORCE)
endfunction()
# ------------------------------------------------------------------------------
# Nature
# ------------------------------------------------------------------------------
function(_package_set_nature pkg_name nature)
_package_set_variable(NATURE ${pkg_name} ${nature})
endfunction()
function(_package_get_nature pkg_name nature)
_package_get_variable(NATURE ${pkg_name} _nature "unknown")
set(${nature} ${_nature} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Description
# ------------------------------------------------------------------------------
function(_package_set_description pkg_name desc)
_package_set_variable(DESC ${pkg_name} ${desc})
endfunction()
function(_package_get_description pkg_name desc)
_package_get_variable(DESC ${pkg_name} _desc "No description set for the package ${${pkg_name}} (${pkg_name})")
set(${desc} ${_desc} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Package file name
# ------------------------------------------------------------------------------
function(_package_set_filename pkg_name file)
_package_set_variable(FILE ${pkg_name} ${file})
endfunction()
function(_package_get_filename pkg_name file)
_package_get_variable(FILE ${pkg_name} _file "No filename set for the package ${${pkg_name}}")
set(${file} ${_file} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Source folder
# ------------------------------------------------------------------------------
function(_package_set_sources_folder pkg_name src_folder)
_package_set_variable(SRC_FOLDER ${pkg_name} ${src_folder})
endfunction()
function(_package_get_sources_folder pkg_name src_folder)
_package_get_variable(SRC_FOLDER ${pkg_name} _src_folder)
set(${src_folder} ${_src_folder} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Test folder
# ------------------------------------------------------------------------------
function(_package_set_tests_folder pkg_name test_folder)
_package_set_variable(TEST_FOLDER ${pkg_name} ${test_folder})
endfunction()
function(_package_get_tests_folder pkg_name test_folder)
_package_get_variable(TEST_FOLDER ${pkg_name} _test_folder)
set(${test_folder} ${_test_folder} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Manual folder
# ------------------------------------------------------------------------------
function(_package_set_manual_folder pkg_name manual_folder)
_package_set_variable(MANUAL_FOLDER ${pkg_name} ${manual_folder})
endfunction()
function(_package_get_manual_folder pkg_name manual_folder)
_package_get_variable(MANUAL_FOLDER ${pkg_name} _manual_folder)
set(${manual_folder} ${_manual_folder} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Extra option for the find_package
# ------------------------------------------------------------------------------
function(_package_set_find_package_extra_options pkg_name)
_package_set_variable(FIND_PKG_OPTIONS ${pkg_name} ${ARGN})
endfunction()
function(_package_get_find_package_extra_options pkg_name options)
_package_get_variable(FIND_PKG_OPTIONS ${pkg_name} _options)
set(${options} ${_options} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Compilation flags
# ------------------------------------------------------------------------------
function(_package_set_compile_flags pkg_name lang)
_package_set_variable(COMPILE_${lang}_FLAGS ${pkg_name} ${ARGN})
endfunction()
function(_package_unset_compile_flags pkg_name lang)
_package_variable_unset(COMPILE_${lang}_FLAGS ${pkg_name})
endfunction()
function(_package_get_compile_flags pkg_name lang flags)
_package_get_variable(COMPILE_${lang}_FLAGS ${pkg_name} _tmp_flags)
string(REPLACE ";" " " _flags "${_tmp_flags}")
set(${flags} "${_flags}" PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Include dir
# ------------------------------------------------------------------------------
function(_package_set_include_dir pkg_name)
_package_set_variable(INCLUDE_DIR ${pkg_name} ${ARGN})
endfunction()
function(_package_get_include_dir pkg_name include_dir)
_package_get_variable(INCLUDE_DIR ${pkg_name} _include_dir "")
set(${include_dir} ${_include_dir} PARENT_SCOPE)
endfunction()
function(_package_add_include_dir pkg_name)
_package_add_to_variable(INCLUDE_DIR ${pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Libraries
# ------------------------------------------------------------------------------
function(_package_set_libraries pkg_name)
_package_set_variable(LIBRARIES ${pkg_name} ${ARGN})
endfunction()
function(_package_get_libraries pkg_name libraries)
_package_get_variable(LIBRARIES ${pkg_name} _libraries "")
set(${libraries} ${_libraries} PARENT_SCOPE)
endfunction()
function(_package_add_libraries pkg_name)
_package_add_to_variable(LIBRARIES ${pkg_name} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Extra dependencies like custom commands of ExternalProject
# ------------------------------------------------------------------------------
function(_package_add_extra_dependency pkg_name)
_package_add_to_variable(EXTRA_DEPENDENCY ${pkg_name} ${ARGN})
endfunction()
function(_package_rm_extra_dependency pkg_name dep)
_package_remove_from_variable(EXTRA_DEPENDENCY ${pkg_name} ${dep})
endfunction()
function(_package_set_extra_dependencies pkg)
_package_set_variable(EXTRA_DEPENDENCY ${pkg_name} ${ARGN})
endfunction()
function(_package_get_extra_dependencies pkg deps)
_package_get_variable(EXTRA_DEPENDENCY ${pkg_name} _deps "")
set(${deps} ${_deps} PARENT_SCOPE)
endfunction()
function(_package_unset_extra_dependencies pkg_name)
_package_variable_unset(EXTRA_DEPENDENCY ${pkg_name})
endfunction()
# ------------------------------------------------------------------------------
# Activate/deactivate
# ------------------------------------------------------------------------------
function(_package_activate pkg_name)
_package_set_variable(STATE ${pkg_name} ON)
endfunction()
function(_package_deactivate pkg_name)
_package_set_variable(STATE ${pkg_name} OFF)
endfunction()
function(_package_is_activated pkg_name act)
_package_get_variable(STATE ${pkg_name} _state OFF)
if(_state)
set(${act} TRUE PARENT_SCOPE)
else()
set(${act} FALSE PARENT_SCOPE)
endif()
endfunction()
function(_package_is_deactivated pkg_name act)
_package_get_variable(STATE ${pkg_name} _state OFF)
if(NOT _state)
set(${act} TRUE PARENT_SCOPE)
else()
set(${act} FALSE PARENT_SCOPE)
endif()
endfunction()
function(_package_unset_activated pkg_name)
_package_variable_unset(STATE ${pkg_name})
endfunction()
# ------------------------------------------------------------------------------
# Callbacks
# ------------------------------------------------------------------------------
function(_package_on_enable_script pkg_name script)
string(TOLOWER "${pkg_name}" _l_pkg_name)
set(_output_file "${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${_l_pkg_name}.cmake")
file(WRITE "${_output_file}"
"${script}")
_package_set_variable(CALLBACK_SCRIPT ${pkg_name} "${_output_file}")
endfunction()
function(_package_get_callback_script pkg_name filename)
_package_get_variable(CALLBACK_SCRIPT ${pkg_name} _filename NOTFOUND)
set(${filename} ${_filename} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Export list
# ------------------------------------------------------------------------------
function(_package_add_to_export_list pkg_name)
_package_add_to_variable(EXPORT_LIST ${pkg_name} ${ARGN})
endfunction()
function(_package_remove_from_export_list pkg_name)
_package_remove_from_variable(EXPORT_LIST ${pkg_name} ${ARGN})
endfunction()
function(_package_get_export_list pkg_name export_list)
_package_get_variable(EXPORT_LIST ${pkg_name} _export_list)
set(${export_list} ${_export_list} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Direct dependencies
# ------------------------------------------------------------------------------
function(_package_add_dependencies pkg_name type)
_package_add_to_variable(DEPENDENCIES_${type} ${pkg_name} ${ARGN})
endfunction()
function(_package_get_dependencies pkg_name type dependencies)
_package_get_variable(DEPENDENCIES_${type} ${pkg_name} _dependencies)
set(${dependencies} ${_dependencies} PARENT_SCOPE)
endfunction()
function(_package_unset_dependencies pkg_name type)
_package_variable_unset(DEPENDENCIES_${type} ${pkg_name})
endfunction()
function(_package_remove_dependency pkg_name type dep)
set(_deps ${${pkg_name}_DEPENDENCIES_${type}})
_package_get_fdependencies(${dep} _fdeps)
# check if this is the last reverse dependency
list(LENGTH _fdeps len)
list(FIND _fdeps ${pkg_name} pos)
if((len EQUAL 1) AND (NOT pos EQUAL -1))
_package_get_description(${dep} _dep_desc)
_package_get_option_name(${dep} _dep_option_name)
set(${_dep_option_name} ${${dep}_OLD} CACHE BOOL "${_dep_desc}" FORCE)
unset(${dep}_OLD CACHE)
endif()
# remove the pkg_name form the reverse dependency
_package_remove_fdependency(${dep} ${pkg_name})
list(FIND _deps ${dep} pos)
if(NOT pos EQUAL -1)
list(REMOVE_AT _deps ${pos})
_package_set_variable(DEPENDENCIES_${type} ${pkg_name} ${_deps})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Functions to handle reverse dependencies
# ------------------------------------------------------------------------------
function(_package_set_rdependencies pkg_name)
_package_set_variable(RDEPENDENCIES ${pkg_name} ${ARGN})
endfunction()
function(_package_get_rdependencies pkg_name rdependencies)
_package_get_variable(RDEPENDENCIES ${pkg_name} _rdependencies)
set(${rdependencies} ${_rdependencies} PARENT_SCOPE)
endfunction()
function(_package_add_rdependency pkg_name rdep)
# store the reverse dependency
_package_add_to_variable(RDEPENDENCIES ${pkg_name} ${rdep})
endfunction()
function(_package_remove_rdependency pkg_name rdep)
_package_remove_from_variable(RDEPENDENCIES ${pkg_name} ${rdep})
endfunction()
# ------------------------------------------------------------------------------
# Function to handle forcing dependencies (Package turn ON that enforce their
# dependencies ON)
# ------------------------------------------------------------------------------
function(_package_set_fdependencies pkg_name)
_package_set_variable(FDEPENDENCIES ${pkg_name} ${ARGN})
endfunction()
function(_package_get_fdependencies pkg_name fdependencies)
_package_get_variable(FDEPENDENCIES ${pkg_name} _fdependencies)
set(${fdependencies} ${_fdependencies} PARENT_SCOPE)
endfunction()
function(_package_add_fdependency pkg_name fdep)
# store the reverse dependency
_package_add_to_variable(FDEPENDENCIES ${pkg_name} ${fdep})
endfunction()
function(_package_remove_fdependency pkg_name fdep)
_package_remove_from_variable(FDEPENDENCIES ${pkg_name} ${fdep})
endfunction()
# ------------------------------------------------------------------------------
# Exteral package system as apt rpm dependencies
# ------------------------------------------------------------------------------
function(_package_set_package_system_dependency pkg system)
string(TOUPPER "${_system}" _u_system)
_package_set_variable(PACKAGE_SYSTEM_${_u_system} ${_pkg_name} ${ARGN})
endfunction()
function(_package_get_package_system_dependency pkg system var)
string(TOUPPER "${_system}" _u_system)
_package_get_variable(PACKAGE_SYSTEM_${_u_system} ${_pkg_name} ${_deps})
set(${var} ${_deps} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Documentation related functions
# ------------------------------------------------------------------------------
function(_package_set_documentation_files pkg_name)
_package_set_variable(DOCUMENTATION_FILES ${pkg_name} ${ARGN})
endfunction()
function(_package_get_documentation_files pkg_name doc_files)
_package_get_variable(DOCUMENTATION_FILES ${pkg_name} _doc_files "")
set(${doc_files} ${_doc_files} PARENT_SCOPE)
endfunction()
function(_package_set_documentation pkg_name)
# \n replaced by && and \\ by ££ to avoid cache problems
set(_doc_str "")
foreach(_str ${ARGN})
set(_doc_str "${_doc_str}&&${_str}")
endforeach()
string(REPLACE "\\" "££" _doc_escaped "${_doc_str}")
_package_set_variable(DOCUMENTATION ${pkg_name} "${_doc_str}")
endfunction()
function(_package_get_documentation pkg_name _doc)
# \n replaced by && and \\ by ££ to avoid cache problems
_package_get_variable(DOCUMENTATION ${pkg_name} _doc_tmp "")
string(REPLACE "££" "\\" _doc_escaped "${_doc_tmp}")
string(REPLACE "&&" "\n" _doc_newlines "${_doc_escaped}")
set(${_doc} "${_doc_newlines}" PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Special boost thingy
# ------------------------------------------------------------------------------
function(_package_set_boost_component_needed pkg_name)
_package_add_to_variable(BOOST_COMPONENTS_NEEDED ${pkg_name} ${ARGN})
package_get_name(Boost _boost_pkg_name)
_package_add_dependencies(${pkg_name} PRIVATE ${_boost_pkg_name})
endfunction()
function(_package_get_boost_component_needed pkg_name needed)
_package_get_variable(BOOST_COMPONENTS_NEEDED ${pkg_name} _needed)
set(${needed} ${_needed} PARENT_SCOPE)
endfunction()
function(_package_load_boost_components)
string(TOUPPER ${PROJECT_NAME} _project)
_package_get_variable_for_activated(BOOST_COMPONENTS_NEEDED _boost_needed_components)
package_get_name(Boost _pkg_name)
if(_boost_needed_components)
message(STATUS "Looking for Boost liraries: ${_boost_needed_components}")
foreach(_comp ${_boost_needed_components})
find_package(Boost COMPONENTS ${_comp} QUIET)
string(TOUPPER ${_comp} _u_comp)
if(Boost_${_u_comp}_FOUND)
message(STATUS " ${_comp}: FOUND")
package_set_project_variable(BOOST_${_u_comp} TRUE)
# Generate the libraries for the package
_package_add_libraries(${_pkg_name} ${Boost_${_u_comp}_LIBRARY})
else()
message(STATUS " ${_comp}: NOT FOUND")
endif()
endforeach()
endif()
endfunction()
# ------------------------------------------------------------------------------
# get the list of source files for a given package
# ------------------------------------------------------------------------------
function(_package_get_source_files pkg_name SRCS PUBLIC_HEADERS PRIVATE_HEADERS)
string(TOUPPER ${PROJECT_NAME} _project)
set(tmp_SRCS)
set(tmp_PUBLIC_HEADERS)
set(tmp_PRIVATE_HEADERS)
foreach(_type SRCS PUBLIC_HEADERS PRIVATE_HEADERS)
foreach(_file ${${pkg_name}_${_type}})
string(REPLACE "${CMAKE_CURRENT_SOURCE_DIR}/" "" _rel_file "${_file}")
list(APPEND tmp_${_type} "${_rel_file}")
endforeach()
endforeach()
set(${SRCS} ${tmp_SRCS} PARENT_SCOPE)
set(${PUBLIC_HEADERS} ${tmp_PUBLIC_HEADERS} PARENT_SCOPE)
set(${PRIVATE_HEADERS} ${tmp_PRIVATE_HEADERS} PARENT_SCOPE)
endfunction()
# ==============================================================================
# Internal functions
# ==============================================================================
# ------------------------------------------------------------------------------
# Build the reverse dependencies from the dependencies
# ------------------------------------------------------------------------------
function(_package_build_rdependencies)
package_get_all_packages(_pkg_list)
# set empty lists
foreach(_pkg_name ${_pkg_list})
set(${_pkg_name}_rdeps)
endforeach()
# fill the dependencies list
foreach(_pkg_name ${_pkg_list})
_package_get_dependencies(${_pkg_name} PRIVATE _deps_priv)
_package_get_dependencies(${_pkg_name} INTERFACE _deps_interface)
foreach(_dep_name ${_deps_priv} ${_deps_interface})
list(APPEND ${_dep_name}_rdeps ${_pkg_name})
endforeach()
endforeach()
# clean and set the reverse dependencies
foreach(_pkg_name ${_pkg_list})
if(${_pkg_name}_rdeps)
list(REMOVE_DUPLICATES ${_pkg_name}_rdeps)
_package_set_rdependencies(${_pkg_name} ${${_pkg_name}_rdeps})
endif()
endforeach()
endfunction()
# ------------------------------------------------------------------------------
# This function resolve the dependance order run the needed find_packages
# ------------------------------------------------------------------------------
function(_package_load_packages)
package_get_all_packages(_pkg_list)
# Activate the dependencies of activated package and generate an ordered list
# of dependencies
set(ordered_loading_list)
foreach(_pkg_name ${_pkg_list})
_package_load_dependencies_package(${_pkg_name} ordered_loading_list)
endforeach()
# Load the packages in the propoer order
foreach(_pkg_name ${ordered_loading_list})
_package_get_option_name(${_pkg_name} _option_name)
if(${_option_name})
_package_load_package(${_pkg_name})
else()
# deactivate the packages than can already be deactivated
_package_deactivate(${_pkg_name})
endif()
endforeach()
# generates the activated and unactivated lists of packages
set(_packages_activated)
set(_packages_deactivated)
foreach(_pkg_name ${_pkg_list})
_package_is_activated(${_pkg_name} _active)
set(_exclude FALSE)
_package_get_variable(EXCLUDE_FROM_ALL ${_pkg_name} _exclude)
if(_active AND NOT _exclude)
list(APPEND _packages_activated ${_pkg_name})
else()
list(APPEND _packages_deactivated ${_pkg_name})
endif()
endforeach()
# generate the list usable by the calling code
package_set_project_variable(ACTIVATED_PACKAGE_LIST "${_packages_activated}")
package_set_project_variable(DEACTIVATED_PACKAGE_LIST "${_packages_deactivated}")
endfunction()
# ------------------------------------------------------------------------------
# This load an external package and recursively all its dependencies
# ------------------------------------------------------------------------------
function(_package_load_dependencies_package pkg_name loading_list)
# Get packages informations
_package_get_option_name(${pkg_name} _pkg_option_name)
_package_get_dependencies(${pkg_name} PRIVATE _deps_private)
_package_get_dependencies(${pkg_name} INTERFACE _deps_interface)
set(_dependencies ${_deps_private} ${_deps_interface})
# handle the dependencies
foreach(_dep_name ${_dependencies})
_package_get_description(${_dep_name} _dep_desc)
_package_get_option_name(${_dep_name} _dep_option_name)
_package_get_fdependencies(${_dep_name} _fdeps)
if(${_pkg_option_name})
if("${_fdeps}" STREQUAL "")
set(${_dep_name}_OLD ${${_dep_option_name}} CACHE INTERNAL "" FORCE)
endif()
# set the option to on
set(_type BOOL)
_package_get_nature(${_dep_name} _nature)
if(_nature MATCHES ".*not_optional$")
set(_type INTERNAL)
endif()
set(${_dep_option_name} ON CACHE BOOL "${_dep_desc}" FORCE)
# store the reverse dependency
_package_add_fdependency(${_dep_name} ${pkg_name})
else()
# check if this is the last reverse dependency
list(LENGTH _fdeps len)
list(FIND _fdeps ${pkg_name} pos)
if((len EQUAL 1) AND (NOT pos EQUAL -1))
set(${_dep_option_name} ${${_dep_name}_OLD} CACHE BOOL "${_dep_desc}" FORCE)
unset(${_dep_name}_OLD CACHE)
endif()
# remove the pkg_name form the reverse dependency
_package_remove_fdependency(${_dep_name} ${pkg_name})
endif()
# recusively load the dependencies
_package_load_dependencies_package(${_dep_name} ${loading_list})
endforeach()
# get the compile flags
_package_get_compile_flags(${pkg_name} CXX _pkg_compile_flags)
package_get_project_variable(NO_AUTO_COMPILE_FLAGS _no_auto_compile_flags)
# if package option is on add it in the list
if(${_pkg_option_name})
list(FIND ${loading_list} ${pkg_name} _pos)
if(_pos EQUAL -1)
set(_tmp_loading_list ${${loading_list}})
list(APPEND _tmp_loading_list ${pkg_name})
set(${loading_list} "${_tmp_loading_list}" PARENT_SCOPE)
endif()
#add the comilation flags if needed
if(_pkg_compile_flags AND NOT _no_auto_compile_flags)
add_flags(cxx ${_pkg_compile_flags})
endif()
else()
#remove the comilation flags if needed
if(_pkg_comile_flags AND NOT _no_auto_compile_flags)
remove_flags(cxx ${_pkg_compile_flags})
endif()
endif()
endfunction()
# ------------------------------------------------------------------------------
# Load the package if it is an external one
# ------------------------------------------------------------------------------
function(_package_load_package pkg_name)
# load the package if it is an external
_package_get_nature(${pkg_name} _nature)
if(${_nature} MATCHES "external")
_package_use_system(${pkg_name} _use_system)
set(_activated TRUE)
if(_use_system)
_package_load_external_package(${pkg_name} _activated)
endif()
_package_has_system_fallback(${pkg_name} _fallback)
if((NOT _use_system) OR (_fallback AND (NOT _activated)))
_package_load_third_party_script(${pkg_name})
set(_activated TRUE)
endif()
if(_activated)
_package_activate(${pkg_name})
elseif()
_package_deactivate(${pkg_name})
endif()
else()
_package_activate(${pkg_name})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Load external packages
# ------------------------------------------------------------------------------
function(_package_load_external_package pkg_name activate)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER ${_real_name} _u_package)
if(NOT ${pkg_name}_USE_SYSTEM_PREVIOUS)
#if system was off before clear the cache of preset variables
get_cmake_property(_all_vars VARIABLES)
foreach(_var ${_all_vars})
if(_var MATCHES "^${_u_package}_.*")
unset(${_var} CACHE)
endif()
endforeach()
set(${pkg_name}_USE_SYSTEM_PREVIOUS TRUE CACHE INTERNAL "" FORCE)
endif()
_package_get_find_package_extra_options(${pkg_name} _options)
if(_options)
cmake_parse_arguments(_opt_pkg "" "LANGUAGE" "LINK_LIBRARIES;PREFIX;FOUND;ARGS" ${_options})
if(_opt_pkg_UNPARSED_ARGUMENTS)
message("You passed too many options for the find_package related to ${${pkg_name}} \"${_opt_pkg_UNPARSED_ARGUMENTS}\"")
endif()
endif()
if(_opt_pkg_LANGUAGE)
foreach(_language ${_opt_pkg_LANGUAGE})
enable_language(${_language})
endforeach()
endif()
# find the package
set(_required REQUIRED)
_package_has_system_fallback(${pkg_name} _fallback)
if(_fallback)
set(_required QUIET)
endif()
find_package(${_real_name} ${_required} ${_opt_pkg_ARGS})
# check if the package is found
if(_opt_pkg_PREFIX)
set(_package_prefix ${_opt_pkg_PREFIX})
else()
set(_package_prefix ${_u_package})
endif()
set(_act FALSE)
set(_prefix_to_consider)
if(DEFINED _opt_pkg_FOUND)
if(${_opt_pkg_FOUND})
set(_act TRUE)
set(_prefix_to_consider ${_package_prefix})
endif()
else()
foreach(_prefix ${_package_prefix})
if(${_prefix}_FOUND)
set(_act TRUE)
list(APPEND _prefix_to_consider ${_prefix})
endif()
endforeach()
endif()
if(_act)
foreach(_prefix ${_prefix_to_consider})
# Generate the include dir for the package
if(DEFINED ${_prefix}_INCLUDE_DIRS)
_package_set_include_dir(${pkg_name} ${${_prefix}_INCLUDE_DIRS})
elseif(DEFINED ${_prefix}_INCLUDE_DIR)
_package_set_include_dir(${pkg_name} ${${_prefix}_INCLUDE_DIR})
elseif(DEFINED ${_prefix}_INCLUDE_PATH)
_package_set_include_dir(${pkg_name} ${${_prefix}_INCLUDE_PATH})
endif()
# Generate the libraries for the package
if(_opt_pkg_LINK_LIBRARIES)
_package_set_libraries(${pkg_name} ${_opt_pkg_LINK_LIBRARIES})
elseif(DEFINED ${_prefix}_LIBRARIES)
_package_set_libraries(${pkg_name} ${${_prefix}_LIBRARIES})
elseif(DEFINED ${_prefix}_LIBRARY)
_package_set_libraries(${pkg_name} ${${_prefix}_LIBRARY})
endif()
endforeach()
_package_get_callback_script(${pkg_name} _script_file)
if(_script_file)
include("${_script_file}")
endif()
endif()
set(${activate} ${_act} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Sanity check functions
# ------------------------------------------------------------------------------
function(_package_check_files_exists)
set(_message FALSE)
package_get_all_packages(_pkg_list)
foreach(_pkg_name ${_pkg_list})
set(_pkg_files
${${_pkg_name}_SRCS}
${${_pkg_name}_PUBLIC_HEADERS}
${${_pkg_name}_PRIVATE_HEADERS}
)
_package_get_real_name(${_pkg_name} _real_name)
foreach(_file ${_pkg_files})
if(NOT EXISTS "${_file}")
if(NOT _message)
set(_message TRUE)
message("This file(s) is(are) present in a package but are not present on disk.")
endif()
message(" PACKAGE ${_real_name} FILE ${_file}")
endif()
endforeach()
endforeach()
if(_message)
message(SEND_ERROR "Please check the content of your packages to correct this warnings")
endif()
endfunction()
# ------------------------------------------------------------------------------
function(_package_check_files_registered)
set(_pkg_files)
package_get_all_packages(_pkg_list)
# generates a file list of registered files
foreach(_pkg_name ${_pkg_list})
list(APPEND _pkg_files
${${_pkg_name}_SRCS}
${${_pkg_name}_PUBLIC_HEADERS}
${${_pkg_name}_PRIVATE_HEADERS}
)
endforeach()
# generates the list of files in the source folders
set(_all_src_files)
foreach(_src_folder ${ARGN})
foreach(_ext "cc" "hh" "c" "h" "hpp")
file(GLOB_RECURSE _src_files "${_src_folder}/*.${_ext}")
list(APPEND _all_src_files ${_src_files})
endforeach()
endforeach()
if(_all_src_files)
list(REMOVE_DUPLICATES _all_src_files)
endif()
set(_not_registerd_files)
# check only sources files in the source folders
foreach(_src_folder ${ARGN})
foreach(_file ${_all_src_files})
if("${_file}" MATCHES "${_src_folder}")
list(FIND _pkg_files "${_file}" _index)
if (_index EQUAL -1)
list(APPEND _not_registerd_files ${_file})
endif()
endif()
endforeach()
endforeach()
if(AUTO_MOVE_UNKNOWN_FILES)
file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/unknown_files)
endif()
# warn the user and move the files if needed
if(_not_registerd_files)
if(EXISTS ${PROJECT_BINARY_DIR}/missing_files_in_packages)
file(REMOVE ${PROJECT_BINARY_DIR}/missing_files_in_packages)
endif()
message("This files are present in the source folders but are not registered in any package")
foreach(_file ${_not_registerd_files})
message(" ${_file}")
if(AUTO_MOVE_UNKNOWN_FILES)
get_filename_component(_file_name ${_file} NAME)
file(RENAME ${_file} ${PROJECT_BINARY_DIR}/unknown_files/${_file_name})
endif()
file(APPEND ${PROJECT_BINARY_DIR}/missing_files_in_packages "${_file}
")
endforeach()
if(AUTO_MOVE_UNKNOWN_FILES)
message(SEND_ERROR "The files where moved in the followinf folder ${PROJECT_BINARY_DIR}/unknown_files\n
Please register them in the good package or clean the sources")
else()
message(SEND_ERROR "Please register them in the good package or clean the sources")
endif()
endif()
endfunction()
# ------------------------------------------------------------------------------
diff --git a/cmake/Modules/CMakeVersionGenerator.cmake b/cmake/Modules/CMakeVersionGenerator.cmake
index 222d3418b..74a30e938 100644
--- a/cmake/Modules/CMakeVersionGenerator.cmake
+++ b/cmake/Modules/CMakeVersionGenerator.cmake
@@ -1,85 +1,241 @@
#===============================================================================
# @file CMakeVersionGenerator.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
# @date last modification: Mon Jan 18 2016
#
# @brief Set of macros used by akantu to handle the package system
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if(__DEFINE_PROJECT_VERSION__)
return()
endif()
set(__DEFINE_PROJECT_VERSION__ TRUE)
-macro(define_project_version)
- string(TOUPPER ${PROJECT_NAME} _project)
+function(_match_semver _input_semver prefix)
+ set(_semver_regexp
+ "^([0-9]+(\\.[0-9]+)?(\\.[0-9]+)?)(-([a-zA-Z0-9-]*))?(\\+(.*))?")
- if(EXISTS ${PROJECT_SOURCE_DIR}/VERSION)
- file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION ${_project}_VERSION)
-
- if("${${_project}_VERSION}" MATCHES "^([0-9]+)")
- string(REGEX REPLACE "^([0-9]+).*" "\\1" _ver_major "${${_project}_VERSION}")
- set(${_project}_MAJOR_VERSION ${_ver_major})
-
- if("${${_project}_VERSION}" MATCHES "^${_ver_major}\\.([0-9]+)")
- string(REGEX REPLACE "^${_ver_major}\\.([0-9]+).*" "\\1" _ver_minor "${${_project}_VERSION}")
- set(${_project}_MINOR_VERSION ${_ver_minor})
- if("${${_project}_VERSION}" MATCHES "^${_ver_major}\\.${_ver_minor}\\.([0-9a-zA-Z\\-]+)")
- string(REGEX REPLACE "^${_ver_major}\\.${_ver_minor}\\.([0-9a-zA-Z\\-]+).*" "\\1" _ver_build "${${_project}_VERSION}")
- set(${_project}_BUILD_VERSION ${_ver_build})
+ if(_input_semver MATCHES "^([0-9]+(\\.[0-9]+)?(\\.[0-9]+)?)(-([a-zA-Z0-9-]*))?(\\+(.*))?")
+ set(${prefix}_version ${CMAKE_MATCH_1} PARENT_SCOPE)
+ if(CMAKE_MATCH_4)
+ set(${prefix}_version_prerelease "${CMAKE_MATCH_5}" PARENT_SCOPE)
+ endif()
+
+ if(CMAKE_MATCH_6)
+ set(${prefix}_version_metadata "${CMAKE_MATCH_7}" PARENT_SCOPE)
+ endif()
+
+ endif()
+endfunction()
+
+function(_get_version_from_git)
+ if(NOT CMAKE_VERSION_GENERATOR_TAG_PREFIX)
+ set(CMAKE_VERSION_GENERATOR_TAG_PREFIX "av")
+ endif()
+
+
+ find_package(Git)
+ if(Git_FOUND)
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} describe
+ --tags
+ --abbrev=0
+ --match ${CMAKE_VERSION_GENERATOR_TAG_PREFIX}*
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ RESULT_VARIABLE _res
+ OUTPUT_VARIABLE _out_tag
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+ ERROR_VARIABLE _err_tag)
+
+ if(NOT _res EQUAL 0)
+ return()
+ endif()
+
+ string(REGEX REPLACE "^${CMAKE_VERSION_GENERATOR_TAG_PREFIX}(.*)" "\\1" _tag "${_out_tag}")
+
+ _match_semver("${_tag}" _tag)
+
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} describe
+ --tags
+ --dirty
+ --always
+ --long
+ --match ${CMAKE_VERSION_GENERATOR_TAG_PREFIX}*
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ RESULT_VARIABLE _res
+ OUTPUT_VARIABLE _out
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+ set(_git_version ${_tag_version} PARENT_SCOPE)
+
+ if(_tag_version_prerealease)
+ set(_git_version_prerelease ${_tag_version_prerealease} PARENT_SCOPE)
+ endif()
+
+ # git describe to PEP404 version
+ set(_version_regex
+ "^${CMAKE_VERSION_GENERATOR_TAG_PREFIX}${_tag}(-([0-9]+)-g([0-9a-f]+)(-dirty)?)?$")
+
+ if(_out MATCHES ${_version_regex})
+ if(CMAKE_MATCH_1)
+ if(_tag_version_metadata)
+ set(_metadata "${_tag_version_metadata}.")
+ endif()
+ set(_metadata "${_metadata}${CMAKE_MATCH_2}.${CMAKE_MATCH_3}")
+ endif()
+ if(CMAKE_MATCH_4)
+ set(_metadata "${_metadata}.dirty")
+ endif()
+ else()
+ execute_process(
+ COMMAND ${GIT_EXECUTABLE} rev-list HEAD --count
+ WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+ RESULT_VARIABLE _res
+ OUTPUT_VARIABLE _out_count
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+ if(_out MATCHES "^([0-9a-f]+)(-dirty)?$")
+ set(_metadata "${CMAKE_MATCH_1}")
+ if(_res EQUAL 0)
+ set(_metadata "${_out_count}.${_metadata}")
+ endif()
+
+ if(CMAKE_MATCH_2)
+ set(_metadata "${_metadata}.dirty")
endif()
endif()
endif()
- # else()
- # find_package(Subversion)
-
- # if(SUBVERSION_FOUND)
- # subversion_wc_info(${PROJECT_SOURCE_DIR} ${_project} ERROR_QUIET)
- # if(${${_project}_WC_FOUND})
- # set(${_project}_BUILD_VERSION ${${_project}_WC_REVISION})
- # set(${_project}_VERSION
- # "${${_project}_MAJOR_VERSION}.${${_project}_MINOR_VERSION}.${${_project}_BUILD_VERSION}"
- # )
- # endif()
- # endif()
+
+ set(_git_version_metadata ${_metadata} PARENT_SCOPE)
endif()
+endfunction()
- if(NOT ${_project}_VERSION)
- set(${_project}_VERSION
- "${${_project}_MAJOR_VERSION}.${${_project}_MINOR_VERSION}"
- )
+function(_get_version_from_file)
+ if(EXISTS ${PROJECT_SOURCE_DIR}/VERSION)
+ file(STRINGS ${PROJECT_SOURCE_DIR}/VERSION _file_version)
+ _match_semver("${_file_version}" "_file")
+ set(_file_version ${_file_version} PARENT_SCOPE)
+ if(_file_version_metadata)
+ set(_file_version_metadata ${_file_version_metadata} PARENT_SCOPE)
+ endif()
+
+ if(_file_version_prerelease)
+ set(_file_version_prerelease ${_file_version_prerelease} PARENT_SCOPE)
+ endif()
endif()
+endfunction()
- # Append the library version information to the library target properties
- if(NOT ${_project}_NO_LIBRARY_VERSION)
- message(STATUS "${PROJECT_NAME} version: ${${_project}_VERSION}")
+function(_get_metadata_from_ci)
+ if(NOT DEFINED ENV{CI})
+ return()
+ endif()
+
+ if(DEFINED ENV{CI_MERGE_REQUEST_ID})
+ set(_ci_version_metadata "ci.mr$ENV{CI_MERGE_REQUEST_ID}" PARENT_SCOPE)
+ elseif(DEFINED ENV{CI_COMMIT_SHORT_SHA})
+ set(_ci_version_metadata "ci.$ENV{CI_COMMIT_SHORT_SHA}" PARENT_SCOPE)
+ endif()
+endfunction()
+
+function(define_project_version)
+ string(TOUPPER ${PROJECT_NAME} _project)
+
+ _get_version_from_git()
+
+ if(_git_version)
+ set(_git_version ${_file_version})
+ if(_version_metadata)
+ set(_version_metadata "${_git_version_metadata}")
+ endif()
+
+ if (_git_version_prerelease)
+ set(_version_prerelease "${_git_version_prerelease}")
+ endif()
+ else()
+ # we can get metadata if and no version if not tag is properly defined
+ if(_git_version_metadata)
+ set(git_version_metadata ".${_git_version_metadata}")
+ endif()
+
+ _get_version_from_file()
+
+ if(_file_version_metadata)
+ set(_version_metadata "${_version_metadata}${_git_version_metadata}")
+ endif()
+ if (_file_version)
+ set(_version "${_file_version}")
+ endif()
+
+ if (_file_version_prerelease)
+ set(_version_prerelease "${_file_version_prerelease}")
+ endif()
+ endif()
+
+ _get_metadata_from_ci()
+
+ if(_version)
+ set(${_project}_VERSION ${_version} PARENT_SCOPE)
+ if(_version_prerelease)
+ set(_version_prerelease "-${_version_prerelease}")
+ endif()
+ if(_version_metadata)
+ set(_version_metadata "+${_version_metadata}")
+ if(_ci_version_metadata)
+ set(_version_metadata "${_version_metadata}.${_ci_version_metadata}")
+ endif()
+ endif()
+
+ set(_semver "${_version}${_version_prerelease}${_version_metadata}")
+ set(${_project}_SEMVER "${_semver}" PARENT_SCOPE)
+ message(STATUS "${PROJECT_NAME} version: ${_semver}")
+
+ if(_version MATCHES "^([0-9]+)(\\.([0-9]+))?(\\.([0-9]+))?")
+ set(_major_version ${CMAKE_MATCH_1})
+ set(${_project}_MAJOR_VERSION ${_major_version} PARENT_SCOPE)
+ if(CMAKE_MATCH_2)
+ set(_minor_version ${CMAKE_MATCH_3})
+ set(${_project}_MINOR_VERSION ${_minor_version} PARENT_SCOPE)
+ endif()
+ if(CMAKE_MATCH_4)
+ set(_patch_version ${CMAKE_MATCH_5})
+ set(${_project}_PATCH_VERSION ${_patch_version} PARENT_SCOPE)
+ endif()
+ endif()
+ else()
+ message(FATAL_ERROR "Could not determine the VERSION for ${PROJECT_NAME}")
+ endif()
+
+ if(NOT ${_project}_NO_LIBRARY_VERSION)
set(${_project}_LIBRARY_PROPERTIES ${${_project}_LIBRARY_PROPERTIES}
- VERSION "${${_project}_VERSION}"
- SOVERSION "${${_project}_MAJOR_VERSION}.${${_project}_MINOR_VERSION}"
+ VERSION "${_version}"
+ SOVERSION "${_major_version}.${_minor_version}"
)
endif()
-endmacro()
+endfunction()
diff --git a/cmake/Modules/FindCppArray.cmake b/cmake/Modules/FindCppArray.cmake
index 260351a19..d8230583d 100644
--- a/cmake/Modules/FindCppArray.cmake
+++ b/cmake/Modules/FindCppArray.cmake
@@ -1,34 +1,37 @@
#===============================================================================
# @file FindCppArray.cmake
#
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
#
-# @date creation: Sun Oct 19 2014
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Mar 16 2018
#
# @brief The find_package file for cpp-array library
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
find_path (CPPARRAY_INCLUDE_DIR expr.hpp PATH_SUFFIXES array)
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(CppArray DEFAULT_MSG CPPARRAY_INCLUDE_DIR)
diff --git a/cmake/Modules/FindEPSN.cmake b/cmake/Modules/FindEPSN.cmake
deleted file mode 100644
index d32e9e87b..000000000
--- a/cmake/Modules/FindEPSN.cmake
+++ /dev/null
@@ -1,55 +0,0 @@
-#===============================================================================
-# @file FindEPSN.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief The find_package file for EPSN
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-#===============================================================================
-find_path(EPSN_DIR EPSNConfig.cmake
- PATHS $ENV{EPSN_TOP}
- )
-
-
-if(EPSN_DIR)
- include(${EPSN_DIR}/EPSNConfig.cmake)
- set(EPSN_LIB_PATH ${EPSN_DIR}/lib
- ${EPSN_LIBRARIES_DIR}
- )
- find_library(EPSN_COMMON_LIBRARY epsn_common
- PATHS ${EPSN_LIB_PATH}
- )
- find_library(EPSN_SIMULATION_LIBRARY epsn_simulation
- PATHS ${EPSN_LIB_PATH}
- )
- include(${EPSN_DIR}/EPSNLibraryDepends.cmake)
-
- set(EPSN_LIBRARIES ${EPSN_SIMULATION_LIBRARY} ${EPSN_COMMON_LIBRARY})
-endif(EPSN_DIR)
-
-#===============================================================================
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(EPSN DEFAULT_MSG
- EPSN_LIBRARIES EPSN_INCLUDE_DIR)
diff --git a/cmake/Modules/FindFFTW.cmake b/cmake/Modules/FindFFTW.cmake
deleted file mode 100644
index b1e2d7996..000000000
--- a/cmake/Modules/FindFFTW.cmake
+++ /dev/null
@@ -1,71 +0,0 @@
-#===============================================================================
-# @file FindFFTW.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find_package for fftw
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-set(FFTW_VERSION "3" CACHE INTEGER "Version of FFTW required")
-
-if (FFTW_FIND_VERSION)
- set(FFTW_VERSION ${FFTW_FIND_VERSION} CACHE INTEGER "Version of FFTW required")
-endif()
-
-if (FFTW_VERSION EQUAL "2")
- find_library(FFTW_LIBRARIES fftw
- PATHS ${FFTW_DIR}
- PATH_SUFFIXES fftw/.libs/ lib
- )
- find_path(FFTW_INCLUDE_PATH fftw.h
- PATHS ${FFTW_DIR} $ENV{INCLUDE_PATH}
- PATH_SUFFIXES include fftw
- )
-else()
-
- find_library(FFTW_LIBRARIES fftw3
- PATHS ENV LD_LIBRARY_PATH
- )
- find_library(FFTW_THREAD_LIBRARY fftw3_threads
- PATHS ENV LD_LIBRARY_PATH
- )
- find_library(FFTW_OPENMP_LIBRARY fftw3_omp
- PATHS ENV LD_LIBRARY_PATH
- )
- find_path(FFTW_INCLUDE_PATH fftw3.h
- PATHS ENV INCLUDE_PATH
- PATH_SUFFIXES include fftw
- )
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(FFTW DEFAULT_MSG
- FFTW_LIBRARIES FFTW_INCLUDE_PATH)
-
-
-if(NOT FFTW_FOUND)
- set(FFTW_DIR "" CACHE PATH "Location of FFTW library.")
-endif(NOT FFTW_FOUND)
-
-mark_as_advanced(FFTW_LIBRARIES FFTW_OPENMP_LIBRARY FFTW_THREAD_LIBRARY FFTW_INCLUDE_PATH FFTW_VERSION)
diff --git a/cmake/Modules/FindGMSH.cmake b/cmake/Modules/FindGMSH.cmake
index 4661bc8ac..212bae0e4 100644
--- a/cmake/Modules/FindGMSH.cmake
+++ b/cmake/Modules/FindGMSH.cmake
@@ -1,110 +1,113 @@
#===============================================================================
# @file FindGMSH.cmake
#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Mon Dec 08 2014
-# @date last modification: Tue Jan 19 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Aug 14 2019
#
# @brief Find gmsh and delacre the add_mesh macro
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
find_program(GMSH gmsh
DOC "The mesh generetor gmsh")
mark_as_advanced(GMSH)
if (GMSH)
execute_process(COMMAND ${GMSH} --version
ERROR_VARIABLE GMSH_VERSION
ERROR_STRIP_TRAILING_WHITESPACE)
endif()
find_package(PackageHandleStandardArgs)
find_package_handle_standard_args(GMSH
REQUIRED_VARS GMSH
VERSION_VAR GMSH_VERSION)
#===============================================================================
function(ADD_MESH MESH_TARGET GEO_FILE)
if(NOT GMSH_FOUND)
return()
endif()
set(arguments
${MESH_TARGET} ${GEO_FILE}
${ARGN}
)
cmake_parse_arguments(_add_mesh
""
"OUTPUT;DIM;ORDER"
""
${arguments}
)
if(NOT _add_mesh_DIM AND NOT _add_mesh_ORDER)
list(GET _add_mesh_UNPARSED_ARGUMENTS 2 _add_mesh_DIM)
list(GET _add_mesh_UNPARSED_ARGUMENTS 3 _add_mesh_ORDER)
endif()
if(NOT _add_mesh_DIM)
set(_add_mesh_DIM 3)
endif()
if(NOT _add_mesh_ORDER)
set(_add_mesh_ORDER 1)
endif()
set(_geo_file ${CMAKE_CURRENT_SOURCE_DIR}/${GEO_FILE})
set(_r_geo_file "${GEO_FILE}")
if(_add_mesh_OUTPUT)
set(_msh_file ${CMAKE_CURRENT_BINARY_DIR}/${_add_mesh_OUTPUT})
set(_r_msh_file "${_add_mesh_OUTPUT}")
else(_add_mesh_OUTPUT)
get_filename_component(_msh_file "${GEO_FILE}" NAME_WE)
set(_r_msh_file "${_msh_file}.msh")
set(_msh_file ${CMAKE_CURRENT_BINARY_DIR}/${_msh_file}.msh)
endif(_add_mesh_OUTPUT)
if(GMSH_VERSION VERSION_LESS 3.0.0)
set(OPTIMIZE -optimize)
endif()
if(EXISTS ${_geo_file})
add_custom_command(
OUTPUT ${_msh_file}
DEPENDS ${_geo_file}
COMMAND ${GMSH}
ARGS -${_add_mesh_DIM} -order ${_add_mesh_ORDER} ${OPTIMIZE} -o ${_msh_file} ${_geo_file} 2>&1 > /dev/null
COMMENT "Generating the ${_add_mesh_DIM}D mesh ${_r_msh_file} (order ${_add_mesh_ORDER}) form the geometry ${_r_geo_file}"
)
add_custom_target(${MESH_TARGET}
DEPENDS ${_msh_file})
set_target_properties(${MESH_TARGET} PROPERTIES RESSOURCES ${_geo_file})
else(EXISTS ${_geo_file})
message(WARNING
"File ${_geo_file} not found for target ${MESH_TARGET}")
endif(EXISTS ${_geo_file})
endfunction()
diff --git a/cmake/Modules/FindGSL.cmake b/cmake/Modules/FindGSL.cmake
deleted file mode 100644
index 76ffa0bcd..000000000
--- a/cmake/Modules/FindGSL.cmake
+++ /dev/null
@@ -1,54 +0,0 @@
-#===============================================================================
-# @file FindGSL.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find package for gsl
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_path(GSL_INCLUDE_PATH gsl_math.h
- PATHS ${GSL_DIR} ENV C_INCLUDE_PATH
- PATH_SUFFIXES gsl
- )
-
-find_library(GSL_MAIN_LIBRARY NAME gsl
- PATHS ${GSL_DIR} ENV LIBRARY_PATH
- PATH_SUFFIXES lib
- )
-
-find_library(GSL_BLAS_LIBRARY NAME gslcblas
- PATHS ${GSL_DIR} ENV LIBRARY_PATH
- PATH_SUFFIXES lib
-)
-
-mark_as_advanced(GSL_INCLUDE_PATH)
-mark_as_advanced(GSL_MAIN_LIBRARY NAME)
-mark_as_advanced(GSL_BLAS_LIBRARY NAME)
-
-set(GSL_LIBRARIES ${GSL_MAIN_LIBRARY} ${GSL_BLAS_LIBRARY})
-
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(GSL DEFAULT_MSG
- GSL_LIBRARIES GSL_INCLUDE_PATH)
diff --git a/cmake/Modules/FindIOHelper.cmake b/cmake/Modules/FindIOHelper.cmake
index 1b9698dd8..9d4676559 100644
--- a/cmake/Modules/FindIOHelper.cmake
+++ b/cmake/Modules/FindIOHelper.cmake
@@ -1,59 +1,62 @@
#===============================================================================
# @file FindIOHelper.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief The find_package file for IOHelper
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
#set(IOHELPER_LIBRARY "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
find_library(IOHELPER_LIBRARY iohelper
PATHS ${IOHELPER_DIR}
PATH_SUFFIXES lib
)
find_path(IOHELPER_INCLUDE_DIR io_helper.hh
PATHS ${IOHELPER_DIR}
PATH_SUFFIXES include include/iohelper
)
#===============================================================================
mark_as_advanced(IOHELPER_LIBRARY)
mark_as_advanced(IOHELPER_INCLUDE_DIR)
#===============================================================================
find_package(ZLIB REQUIRED)
set(IOHELPER_LIBRARIES_ALL ${IOHELPER_LIBRARY} ${ZLIB_LIBRARIES})
set(IOHELPER_LIBRARIES ${IOHELPER_LIBRARIES_ALL} CACHE INTERNAL "Libraries for IOHelper" FORCE)
#===============================================================================
if(NOT IOHELPER_FOUND)
set(IOHELPER_DIR "" CACHE PATH "Location of IOHelper source directory.")
endif()
#===============================================================================
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(IOHelper DEFAULT_MSG IOHELPER_LIBRARY IOHELPER_INCLUDE_DIR)
diff --git a/cmake/Modules/FindInkscape.cmake b/cmake/Modules/FindInkscape.cmake
deleted file mode 100644
index c35b302ae..000000000
--- a/cmake/Modules/FindInkscape.cmake
+++ /dev/null
@@ -1,93 +0,0 @@
-#===============================================================================
-# @file FindInkscape.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find_package for inkscape
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-# Module thaat checks for inkscape
-#
-# Sets the following variables
-#
-# INSCAPE: Path to inkscape to generate .png's form .svg's
-#
-# Provides the following functions:
-#
-# inkscape_generate_png_from_svg([OUTPUT_DIR <output_dir>] <pngfile1.png> [<pngfile2.png> ....])
-#
-# Generates pngfile1, ... from svg input files pngfile1.svg, ....
-# The output directory can be specified with the option OUTPUT_DIR. If it is omitted
-# the files will be generated in CMAKE_CURRENT_BINARY_DIR.
-
-find_program(INKSCAPE inkscape DOC "Path to inkscape to generate png files from svg files")
-find_program(CONVERT convert DOC "Path to convert program")
-if(INKSCAPE)
- set(INKSCAPE_FOUND True)
-endif(INKSCAPE)
-
-include(CMakeParseArguments)
-
-function(inkscape_generate_png_from_svg)
- if(NOT INKSCAPE)
- return()
- endif(NOT INKSCAPE)
- cmake_parse_arguments(INKSCAPE "" "DPI" "" ${ARGN})
- if(NOT INKSCAPE_DPI)
- set(INKSCAPE_DPI 90)
- endif(NOT INKSCAPE_DPI)
-
- foreach(pic ${INKSCAPE_UNPARSED_ARGUMENTS})
- string(REGEX REPLACE "\\.[a-zA-Z]+" ".png" output ${pic})
- add_custom_command(OUTPUT ${output}
- COMMAND ${INKSCAPE} --export-dpi=${INKSCAPE_DPI} -e ${output} -f ${pic}
- DEPENDS ${pic}
- COMMENT "Generating ${output} from ${pic}"
- )
- endforeach(pic)
-endfunction(inkscape_generate_png_from_svg)
-
-function(inkscape_generate_eps_from_svg)
- cmake_parse_arguments(INKSCAPE "" "INPUT_DIR;OUTPUT_DIR;DPI" "" ${ARGN})
- if(NOT INKSCAPE_INPUT_DIR)
- set(INKSCAPE_INPUT_DIR ${CMAKE_CURRENT_SOURCE_DIR})
- endif(NOT INKSCAPE_INPUT_DIR)
- if(NOT INKSCAPE_INPUT_DIR)
- set(INKSCAPE_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
- endif(NOT INKSCAPE_INPUT_DIR)
-
- foreach(_pic ${INKSCAPE_UNPARSED_ARGUMENTS})
- string(REGEX REPLACE "\\.[a-zA-Z]+" ".png" input "${_pic}")
- string(REGEX REPLACE "\\.[a-zA-Z]+" ".svg" svginput "${_pic}")
-
- add_custom_target(${input}
- COMMAND ${INKSCAPE} --export-dpi=${INKSCAPE_DPI} -e ${input} ${CMAKE_CURRENT_SOURCE_DIR}/${svginput}
- COMMENT "Generating ${INKSCAPE_OUTPUT_DIR}/${pic} from ${CMAKE_CURRENT_SOURCE_DIR}/${input}")
- add_custom_command(OUTPUT ${_pic}
- COMMAND ${CONVERT} ${INKSCAPE_INPUT_DIR}/${input} EPS:${_pic}
- DEPENDS ${input}
- COMMENT "Converting ${INKSCAPE_INPUT_DIR}/${input} to ${INKSCAPE_OUTPUT_DIR}/${_pic}"
- WORKING_DIRECTORY ${INKSCAPE_OUTPUT_DIR})
- endforeach(_pic ${INKSCAPE_UNPARSED_ARGUMENTS})
-endfunction(inkscape_generate_eps_from_svg)
\ No newline at end of file
diff --git a/cmake/Modules/FindLAMMPS.cmake b/cmake/Modules/FindLAMMPS.cmake
deleted file mode 100644
index 81f456ef3..000000000
--- a/cmake/Modules/FindLAMMPS.cmake
+++ /dev/null
@@ -1,68 +0,0 @@
-#===============================================================================
-# @file FindLAMMPS.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find package for lammps
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_path(LAMMPS_INCLUDE_PATH lammps.h
- PATHS ${LAMMPS_DIR} ENV C_INCLUDE_PATH
- PATH_SUFFIXES src
- )
-
-#if (not ${LAMMPS_ARCH})
- file(GLOB ARCHS "${LAMMPS_INCLUDE_PATH}/liblmp*")
- foreach(loop_var IN ITEMS ${ARCHS})
- get_filename_component(loop_var ${loop_var} NAME)
- string(REGEX REPLACE ".so" "" loop_var ${loop_var})
- string(REGEX REPLACE "liblmp_" "" loop_var ${loop_var})
-# MESSAGE ("possible archs compiled for lammps : ${loop_var}")
- SET(LAMMPS_ARCH ${loop_var} CACHE INTERNAL "internal built version of lammps detection" FORCE)
-# MESSAGE ("libname : lmp_${LAMMPS_ARCH}")
- endforeach(loop_var)
-#endif(not ${LAMMPS_ARCH})
-
-
-find_library(LAMMPS_MAIN_LIBRARY NAME lmp_${LAMMPS_ARCH}
- PATHS ${LAMMPS_DIR}
- PATH_SUFFIXES src
- )
-
-if (NOT LAMMPS_MAIN_LIBRARY)
-set(LAMMPS_DIR "" CACHE PATH "Location of LAMMPS library.")
-endif (NOT LAMMPS_MAIN_LIBRARY)
-
-find_library(LAMMPS_MEAM_LIBRARIES NAME meam
- PATHS ${LAMMPS_DIR}
- PATH_SUFFIXES lib/meam
-)
-
-set(LAMMPS_LIBRARIES ${LAMMPS_MAIN_LIBRARY} ${LAMMPS_MEAM_LIBRARIES})
-SEPARATE_ARGUMENTS(LAMMPS_LIBRARIES)
-
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(LAMMPS DEFAULT_MSG
- LAMMPS_LIBRARIES LAMMPS_INCLUDE_PATH)
\ No newline at end of file
diff --git a/cmake/Modules/FindMETIS.cmake b/cmake/Modules/FindMETIS.cmake
index 267cf264d..7cfe8c513 100644
--- a/cmake/Modules/FindMETIS.cmake
+++ b/cmake/Modules/FindMETIS.cmake
@@ -1,37 +1,69 @@
+#===============================================================================
+# @file FindMETIS.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Apr 22 2016
+# @date last modification: Fri Mar 16 2018
+#
+# @brief FindPackage for the metis library
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
find_path(METIS_INCLUDE_DIR metis.h
PATHS "${METIS_DIR}"
ENV METIS_DIR
PATH_SUFFIXES include
)
find_library(METIS_LIBRARY NAMES metis
PATHS "${METIS_DIR}"
ENV METIS_DIR
PATH_SUFFIXES lib
)
mark_as_advanced(METIS_LIBRARY METIS_INCLUDE_DIR)
#===============================================================================
include(FindPackageHandleStandardArgs)
if(CMAKE_VERSION VERSION_GREATER 2.8.12)
if(METIS_INCLUDE_DIR)
file(STRINGS ${METIS_INCLUDE_DIR}/metis.h _versions
REGEX "^#define\ +METIS_VER_(MAJOR|MINOR|SUBMINOR) .*")
foreach(_ver ${_versions})
string(REGEX MATCH "METIS_VER_(MAJOR|MINOR|SUBMINOR) *([0-9.]+)" _tmp "${_ver}")
set(_metis_${CMAKE_MATCH_1} ${CMAKE_MATCH_2})
endforeach()
set(METIS_VERSION "${_metis_MAJOR}.${_metis_MINOR}" CACHE INTERNAL "")
endif()
find_package_handle_standard_args(METIS
REQUIRED_VARS
METIS_LIBRARY
METIS_INCLUDE_DIR
VERSION_VAR
METIS_VERSION)
else()
find_package_handle_standard_args(METIS DEFAULT_MSG
METIS_LIBRARY METIS_INCLUDE_DIR)
endif()
diff --git a/cmake/Modules/FindMumps.cmake b/cmake/Modules/FindMumps.cmake
index 0db04fb96..30e60646c 100644
--- a/cmake/Modules/FindMumps.cmake
+++ b/cmake/Modules/FindMumps.cmake
@@ -1,315 +1,320 @@
#===============================================================================
# @file FindMumps.cmake
#
+# @author Mathias Lebihain <mathias.lebihain@enpc.fr>
+# @author Philip Mueller <philip.mueller@math.ethz.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Oct 24 2014
-# @date last modification: Wed Jan 13 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 22 2021
#
# @brief The find_package file for the Mumps solver
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
set(_MUMPS_COMPONENTS "sequential" "parallel" "double" "float" "complex_double" "complex_float")
if(NOT Mumps_FIND_COMPONENTS)
set(Mumps_FIND_COMPONENTS "parallel" "double" "float" "complex_double" "complex_float")
endif()
#===============================================================================
enable_language(Fortran)
set(MUMPS_PRECISIONS)
set(MUMPS_PLAT)
foreach(_comp ${Mumps_FIND_COMPONENTS})
if("${_comp}" STREQUAL "sequential")
set(MUMPS_PLAT _seq) #default plat on debian based distribution
endif()
if("${_comp}" STREQUAL "float")
list(APPEND MUMPS_PRECISIONS s)
endif()
if("${_comp}" STREQUAL "double")
list(APPEND MUMPS_PRECISIONS d)
endif()
if("${_comp}" STREQUAL "complex_float")
list(APPEND MUMPS_PRECISIONS c)
endif()
if("${_comp}" STREQUAL "complex_double")
list(APPEND MUMPS_PRECISIONS z)
endif()
endforeach()
if(NOT MUMPS_PRECISIONS)
set(MUMPS_PRECISIONS s d c z)
endif()
list(GET MUMPS_PRECISIONS 0 _first_precision)
string(TOUPPER "${_first_precision}" _u_first_precision)
find_path(MUMPS_INCLUDE_DIR ${_first_precision}mumps_c.h
PATHS "${MUMPS_DIR}"
ENV MUMPS_DIR
PATH_SUFFIXES include
)
mark_as_advanced(MUMPS_INCLUDE_DIR)
set(_mumps_required_vars)
foreach(_precision ${MUMPS_PRECISIONS})
string(TOUPPER "${_precision}" _u_precision)
find_library(MUMPS_LIBRARY_${_u_precision}MUMPS NAMES ${_precision}mumps${MUMPS_PREFIX}
PATHS "${MUMPS_DIR}"
ENV MUMPS_DIR
PATH_SUFFIXES lib
)
mark_as_advanced(MUMPS_LIBRARY_${_u_precision}MUMPS)
list(APPEND _mumps_required_vars MUMPS_LIBRARY_${_u_precision}MUMPS)
list(APPEND MUMPS_LIBRARIES_ALL ${MUMPS_LIBRARY_${_u_precision}MUMPS})
endforeach()
if(MUMPS_LIBRARY_${_u_first_precision}MUMPS MATCHES ".*${_first_precision}mumps.*${CMAKE_STATIC_LIBRARY_SUFFIX}")
# Assuming mumps was compiled as a static library
set(MUMPS_LIBRARY_TYPE STATIC CACHE INTERNAL "" FORCE)
if (CMAKE_Fortran_COMPILER MATCHES ".*gfortran")
set(_compiler_specific gfortran)
elseif (CMAKE_Fortran_COMPILER MATCHES ".*ifort")
set(_compiler_specific ifcore)
else()
message("Compiler ${CMAKE_Fortran_COMPILER} is not known, you will probably "
"have to add semething instead of this message to be able to test mumps "
"install")
endif()
else()
set(MUMPS_LIBRARY_TYPE SHARED CACHE INTERNAL "" FORCE)
endif()
function(mumps_add_dependency _pdep _libs)
string(TOUPPER ${_pdep} _u_pdep)
if(_pdep STREQUAL "mumps_common")
find_library(MUMPS_LIBRARY_COMMON mumps_common${MUMPS_PREFIX}
PATHS "${MUMPS_DIR}"
ENV MUMPS_DIR
PATH_SUFFIXES lib
)
set(${_libs} ${MUMPS_LIBRARY_COMMON} PARENT_SCOPE)
mark_as_advanced(MUMPS_LIBRARY_COMMON)
elseif(_pdep STREQUAL "pord")
find_library(MUMPS_LIBRARY_PORD pord${MUMPS_PREFIX}
PATHS "${MUMPS_DIR}"
ENV MUMPS_DIR
PATH_SUFFIXES lib
)
set(${_libs} ${MUMPS_LIBRARY_PORD} PARENT_SCOPE)
mark_as_advanced(MUMPS_LIBRARY_PORD)
elseif(_pdep MATCHES "Scotch")
find_package(Scotch REQUIRED ${ARGN} QUIET)
if(ARGN)
list(GET ARGN 1 _comp)
string(TOUPPER ${_comp} _u_comp)
set(${_libs} ${SCOTCH_LIBRARY_${_u_comp}} PARENT_SCOPE)
else()
set(${_libs} ${${_u_pdep}_LIBRARIES} PARENT_SCOPE)
endif()
elseif(_pdep MATCHES "MPI")
if(MUMPS_PLAT STREQUAL "_seq")
find_library(MUMPS_LIBRARY_MPISEQ mpiseq${MUMPS_PREFIX}
PATHS "${MUMPS_DIR}"
ENV MUMPS_DIR
PATH_SUFFIXES lib
)
if (NOT MUMPS_LIBRARY_MPISEQ)
message("Could not find libmpiseq for sequential version of MUMPS, was "
"MUMPS compiled in sequential ?")
endif()
set(${_libs} ${MUMPS_LIBRARY_MPISEQ} PARENT_SCOPE)
mark_as_advanced(MUMPS_LIBRARY_MPISEQ)
else()
find_package(MPI REQUIRED C Fortran QUIET)
set(${_libs} ${MPI_C_LIBRARIES} ${MPI_Fortran_LIBRARIES} PARENT_SCOPE)
endif()
elseif(_pdep MATCHES "Threads")
find_package(Threads REQUIRED)
set(${_libs} Threads::Threads PARENT_SCOPE)
elseif(_pdep MATCHES "OpenMP")
find_package(OpenMP REQUIRED)
set(${_libs} OpenMP::OpenMP_C PARENT_SCOPE)
elseif(_pdep MATCHES "Math")
set(${_libs} m PARENT_SCOPE)
else()
find_package(${_pdep} REQUIRED QUIET)
set(${_libs} ${${_u_pdep}_LIBRARIES} ${${_u_pdep}_LIBRARY} PARENT_SCOPE)
endif()
endfunction()
function(mumps_find_dependencies)
set(_libraries_all m ${MUMPS_LIBRARIES_ALL})
set(_include_dirs ${MUMPS_INCLUDE_DIR})
set(_mumps_test_dir "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}")
file(READ ${CMAKE_CURRENT_LIST_DIR}/CheckFindMumps.c _output)
file(WRITE "${_mumps_test_dir}/mumps_test_code.c"
"#include <${_first_precision}mumps_c.h>
${_u_first_precision}MUMPS_STRUC_C id;
#define mumps_c ${_first_precision}mumps_c
#define Real ${_u_first_precision}MUMPS_REAL
")
if(MUMPS_PLAT STREQUAL _seq)
file(APPEND "${_mumps_test_dir}/mumps_test_code.c"
"#define MUMPS_SEQ
")
else()
file(APPEND "${_mumps_test_dir}/mumps_test_code.c"
"// #undef MUMPS_SEQ
")
find_package(MPI REQUIRED)
list(APPEND _compiler_specific ${MPI_C_LIBRARIES})
list(APPEND _include_dirs ${MPI_C_INCLUDE_PATH} ${MPI_INCLUDE_DIR})
endif()
file(APPEND "${_mumps_test_dir}/mumps_test_code.c" "${_output}")
#===============================================================================
set(_mumps_dep_symbol_BLAS ${_first_precision}gemm)
set(_mumps_dep_symbol_ScaLAPACK numroc)
set(_mumps_dep_symbol_LAPACK ilaenv)
set(_mumps_dep_symbol_MPI mpi_send)
set(_mumps_dep_symbol_Scotch SCOTCH_graphInit)
set(_mumps_dep_symbol_Scotch_ptscotch scotchfdgraphexit)
set(_mumps_dep_symbol_Scotch_esmumps esmumps)
set(_mumps_dep_symbol_mumps_common mumps_abort)
set(_mumps_dep_symbol_pord SPACE_ordering)
set(_mumps_dep_symbol_METIS metis_nodend)
set(_mumps_dep_symbol_Threads pthread_create)
set(_mumps_dep_symbol_OpenMP GOMP_loop_end_nowait)
# TODO find missing symbols for IOMP
set(_mumps_dep_symbol_Math lround)
set(_mumps_dep_symbol_ParMETIS ParMETIS_V3_NodeND)
# added for fucking macosx that cannot fail at link
set(_mumps_run_dep_symbol_mumps_common mumps_fac_descband)
set(_mumps_run_dep_symbol_MPI mpi_bcast)
set(_mumps_run_dep_symbol_ScaLAPACK idamax)
set(_mumps_dep_comp_Scotch_ptscotch COMPONENTS ptscotch)
set(_mumps_dep_comp_Scotch_esmumps COMPONENTS esmumps)
set(_mumps_potential_dependencies
mumps_common pord
BLAS LAPACK ScaLAPACK
MPI
Scotch Scotch_ptscotch Scotch_esmumps
METIS ParMETIS
Threads OpenMP
Math)
#===============================================================================
set(_retry_try_run TRUE)
set(_retry_count 0)
# trying only as long as we add dependencies to avoid inifinte loop in case of an unkown dependency
while (_retry_try_run AND _retry_count LESS 100)
try_run(_mumps_run _mumps_compiles
"${_mumps_test_dir}"
"${_mumps_test_dir}/mumps_test_code.c"
CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${_include_dirs}"
LINK_LIBRARIES ${_libraries_all} ${_libraries_all} ${_compiler_specific}
RUN_OUTPUT_VARIABLE _run
COMPILE_OUTPUT_VARIABLE _out)
set(_retry_compile FALSE)
#message("COMPILATION outputs: \n${_out} \n RUN OUTPUT \n${_run}")
if(_mumps_compiles AND NOT (_mumps_run STREQUAL "FAILED_TO_RUN"))
break()
endif()
foreach(_pdep ${_mumps_potential_dependencies})
#message("CHECKING ${_pdep}")
set(_add_pdep FALSE)
if (NOT _mumps_compiles AND
_out MATCHES "undefined reference.*${_mumps_dep_symbol_${_pdep}}")
set(_add_pdep TRUE)
#message("NEED COMPILE ${_pdep}")
elseif(_mumps_run STREQUAL "FAILED_TO_RUN" AND
DEFINED _mumps_run_dep_symbol_${_pdep} AND
_run MATCHES "${_mumps_run_dep_symbol_${_pdep}}")
set(_add_pdep TRUE)
#message("NEED RUN ${_pdep}")
endif()
if(_add_pdep)
mumps_add_dependency(${_pdep} _libs ${_mumps_dep_comp_${_pdep}})
#message("ADDING ${_libs}")
if(NOT _libs)
message(FATAL_ERROR "MUMPS depends on ${_pdep} but no libraries where found")
endif()
list(APPEND _libraries_all ${_libs})
set(_retry_try_run TRUE)
endif()
endforeach()
math(EXPR _retry_count "${_retry_count} + 1")
endwhile()
if(_retry_count GREATER 10)
message(FATAL_ERROR "Do not know what to do to link with mumps on your system, I give up!")
message("Last compilation outputs: \n${_out} \n And last run output \n${_run}")
endif()
if(APPLE)
# in doubt add some stuff because mumps was perhaps badly compiled
mumps_add_dependency(pord _libs)
list(APPEND _libraries_all ${_libs})
endif()
set(MUMPS_LIBRARIES_ALL ${_libraries_all} PARENT_SCOPE)
endfunction()
mumps_find_dependencies()
set(MUMPS_LIBRARIES ${MUMPS_LIBRARIES_ALL} CACHE INTERNAL "" FORCE)
#===============================================================================
include(FindPackageHandleStandardArgs)
if(CMAKE_VERSION VERSION_GREATER 2.8.12)
if(MUMPS_INCLUDE_DIR)
file(STRINGS ${MUMPS_INCLUDE_DIR}/dmumps_c.h _versions
REGEX "^#define MUMPS_VERSION .*")
foreach(_ver ${_versions})
string(REGEX MATCH "MUMPS_VERSION *\"([0-9.]+)\"" _tmp "${_ver}")
set(_mumps_VERSION ${CMAKE_MATCH_1})
endforeach()
set(MUMPS_VERSION "${_mumps_VERSION}" CACHE INTERNAL "")
endif()
find_package_handle_standard_args(Mumps
REQUIRED_VARS ${_mumps_required_vars}
MUMPS_INCLUDE_DIR
VERSION_VAR MUMPS_VERSION
)
else()
find_package_handle_standard_args(Mumps DEFAULT_MSG
${_mumps_required_vars} MUMPS_INCLUDE_DIR)
endif()
diff --git a/cmake/Modules/FindNLopt.cmake b/cmake/Modules/FindNLopt.cmake
deleted file mode 100644
index 725dc04a9..000000000
--- a/cmake/Modules/FindNLopt.cmake
+++ /dev/null
@@ -1,53 +0,0 @@
-#===============================================================================
-# @file FindNLopt.cmake
-#
-# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief The find_package file for NLopt optimization library
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_library(NLOPT_LIBRARIES NAMES nlopt_cxx
- PATHS ${NLOPT_DIR} ${NLOPT_INTERNAL_DIR}
- PATH_SUFFIXES lib
- )
-
-find_path(NLOPT_INCLUDE_DIR nlopt.hpp
- PATHS ${NLOPT_DIR} ${NLOPT_INTERNAL_DIR}
- PATH_SUFFIXES include
- )
-
-
-
-#===============================================================================
-mark_as_advanced(NLOPT_LIBRARIES)
-mark_as_advanced(NLOPT_INCLUDE_DIR)
-#===============================================================================
-if(NOT NLOPT_FOUND)
- set(NLOPT_DIR "" CACHE PATH "Location of NLOPT source directory.")
-endif()
-
-#===============================================================================
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(NLopt DEFAULT_MSG NLOPT_LIBRARIES NLOPT_INCLUDE_DIR)
-
diff --git a/cmake/Modules/FindNumpy.cmake b/cmake/Modules/FindNumpy.cmake
index 2c21b0025..cf04c7bd6 100644
--- a/cmake/Modules/FindNumpy.cmake
+++ b/cmake/Modules/FindNumpy.cmake
@@ -1,71 +1,74 @@
#===============================================================================
# @file FindNumpy.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 16 2015
+# @date last modification: Fri Jan 15 2016
#
# @brief The find_package file for numpy
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
find_package(PythonInterp)
#numpy includes
if(PYTHONINTERP_FOUND)
set(_get_include "from __future__ import print_function; import numpy; print(numpy.get_include(), end='')")
set(_get_version "from __future__ import print_function; import numpy; print(numpy.version.full_version, end=''),")
execute_process(COMMAND
${PYTHON_EXECUTABLE} -c "${_get_include}"
OUTPUT_VARIABLE _numpy_include_dir
ERROR_QUIET
RESULT_VARIABLE _res)
if(_res EQUAL 0)
set(NUMPY_INCLUDE_DIR "${_numpy_include_dir}" CACHE PATH "Include directory for numpy" FORCE)
execute_process(COMMAND
${PYTHON_EXECUTABLE} -c "${_get_version}"
OUTPUT_VARIABLE _numpy_version
ERROR_QUIET
RESULT_VARIABLE _res)
if(_res EQUAL 0)
set(NUMPY_VERSION "${_numpy_version}" CACHE STRING "Version of numpy")
else()
set(NUMPY_VERSION "NUMPY_VERSION-NOTFOUND" CACHE STRING "Version of numpy")
endif()
mark_as_advanced(NUMPY_INCLUDE_DIR NUMPY_VERSION)
else()
set(NUMPY_INCLUDE_DIR "NUMPY_INCLUDE_DIR-NOTFOUND" CACHE PATH "")
endif()
endif()
#===============================================================================
include(FindPackageHandleStandardArgs)
if(CMAKE_VERSION VERSION_GREATER 2.8.12)
find_package_handle_standard_args(Numpy
REQUIRED_VARS NUMPY_INCLUDE_DIR
VERSION_VAR NUMPY_VERSION)
else()
find_package_handle_standard_args(Numpy DEFAULT_MSG
NUMPY_INCLUDE_DIR NUMPY_VERSION)
endif()
diff --git a/cmake/Modules/FindPETSc.cmake b/cmake/Modules/FindPETSc.cmake
index 4b38ed674..c2cd30aa4 100644
--- a/cmake/Modules/FindPETSc.cmake
+++ b/cmake/Modules/FindPETSc.cmake
@@ -1,51 +1,84 @@
+#===============================================================================
+# @file FindPETSc.cmake
+#
+# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Jun 10 2020
+#
+# @brief FindPackage for the PETSc library
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
# - Try to find PETSc
# PETSC_FOUND - system has PETSc
# PETSC_INCLUDE_DIRS - the PETSc include directories
# PETSC_LIBRARIES - Link these to use PETSc
# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
if(PETSc_FIND_REQUIRED)
find_package(PkgConfig REQUIRED)
else()
find_package(PkgConfig QUIET)
if(NOT PKG_CONFIG_FOUND)
return()
endif()
endif()
pkg_search_module(_petsc PETSc)
# Some debug code
#get_property(_vars DIRECTORY PROPERTY VARIABLES)
#foreach(_var ${_vars})
# if ("${_var}" MATCHES "^_petsc")
# message("${_var} -> ${${_var}}")
# endif()
#endforeach()
if(_petsc_FOUND AND _petsc_VERSION)
set(PETSC_VERSION ${_petsc_VERSION})
endif()
if(_petsc_FOUND AND (NOT PETSC_LIBRARIES))
set(_petsc_libs)
foreach(_lib ${_petsc_LIBRARIES})
string(TOUPPER "${_lib}" _u_lib)
find_library(PETSC_LIBRARY_${_u_lib} ${_lib} PATHS ${_petsc_LIBRARY_DIRS})
list(APPEND _petsc_libs ${PETSC_LIBRARY_${_u_lib}})
mark_as_advanced(PETSC_LIBRARY_${_u_lib})
endforeach()
set(PETSC_LIBRARIES ${_petsc_libs} CACHE INTERNAL "")
set(PETSC_INCLUDE_DIRS ${_petsc_INCLUDE_DIRS} CACHE INTERNAL "")
if(NOT TARGET petsc::petsc)
add_library(petsc::petsc INTERFACE IMPORTED)
set_property(TARGET petsc::petsc PROPERTY INTERFACE_LINK_LIBRARIES ${PETSC_LIBRARIES})
set_property(TARGET petsc::petsc PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PETSC_INCLUDE_DIRS})
endif()
endif()
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args(PETSc
REQUIRED_VARS PETSC_LIBRARIES PETSC_INCLUDE_DIRS
VERSION_VAR PETSC_VERSION)
diff --git a/cmake/Modules/FindPQXX.cmake b/cmake/Modules/FindPQXX.cmake
deleted file mode 100644
index 70b68fb08..000000000
--- a/cmake/Modules/FindPQXX.cmake
+++ /dev/null
@@ -1,60 +0,0 @@
-#===============================================================================
-# @file FindPQXX.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief The find_package file for PostgreSQL C++ library
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_package(PostgreSQL REQUIRED)
-if(POSTGRESQL_FOUND)
- find_library(PQXX_LIBRARY NAMES pqxx
- HINTS ${PQXX_DIR} ENV PQXX_DIR
- DOC "Location of libpqxx library"
- )
-
- find_path(PQXX_HEADER_DIR NAMES pqxx/pqxx
- HINTS ${PQXX_DIR} ENV PQXX_DIR
- DOC "Path to pqxx/pqxx header file. Do not include the 'pqxx' directory in this value."
- )
-
- set(PQXX_INCLUDE_DIR "${PQXX_HEADER_DIR};${POSTGRESQL_INCLUDE_DIR}" CACHE STRING "Include directories for PostgreSQL C++ library" FORCE)
- set(PQXX_LIBRARIES "${PQXX_LIBRARY};${POSTGRESQL_LIBRARIES}" CACHE STRING "Link libraries for PostgreSQL C++ interface" FORCE)
-
- mark_as_advanced(PQXX_HEADER_DIR)
- mark_as_advanced(PQXX_INCLUDE_DIR)
- mark_as_advanced(PQXX_LIBRARY)
- mark_as_advanced(PQXX_LIBRARIES)
-endif()
-
-#===============================================================================
-if(NOT PQXX_FOUND)
- set(PQXX_DIR "" CACHE PATH "Help to find the location of pqxx library.")
- mark_as_advanced(PQXX_FOUND)
-endif()
-
-#===============================================================================
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(PQXX DEFAULT_MSG PQXX_LIBRARY PQXX_HEADER_DIR)
-
diff --git a/cmake/Modules/FindPTScotch.cmake b/cmake/Modules/FindPTScotch.cmake
index 490803384..f7059f763 100644
--- a/cmake/Modules/FindPTScotch.cmake
+++ b/cmake/Modules/FindPTScotch.cmake
@@ -1,107 +1,110 @@
#===============================================================================
# @file FindPTScotch.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Oct 24 2014
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Mar 16 2018
#
# @brief The find_package file for PT-Scotch
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
#if(PTSCOTCH_DIR)
# set(PTSCOTCH_LIBRARY "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
#endif(PTSCOTCH_DIR)
find_library(PTSCOTCH_LIBRARY ptscotch
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES src/libscotch lib
)
find_library(PTSCOTCH_LIBRARY_ERR ptscotcherr
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES src/libscotch lib
)
find_library(PTSCOTCH_LIBRARY_ESMUMPS ptesmumps
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES src/libscotch lib
)
find_library(PTSCOTCH_LIBRARY_METIS ptscotchmetis
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES src/libscotch lib
)
find_library(PTSCOTCH_LIBRARY_PARMETIS ptscotchparmetis
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES src/libscotch lib
)
find_path(PTSCOTCH_INCLUDE_PATH ptscotch.h
PATHS ${PTSCOTCH_DIR}
PATH_SUFFIXES include scotch src/libscotch include/scotch
)
#===============================================================================
mark_as_advanced(
PTSCOTCH_LIBRARY
PTSCOTCH_LIBRARY_ERR
PTSCOTCH_LIBRARY_ESMUMPS
PTSCOTCH_LIBRARY_METIS
PTSCOTCH_LIBRARY_PARMETIS
PTSCOTCH_INCLUDE_PATH)
set(PTSCOTCH_LIBRARIES_ALL ${PTSCOTCH_LIBRARY} ${PTSCOTCH_LIBRARY_ERR})
if(PTSCOTCH_LIBRARY_ESMUMPS)
set(PTSCOTCH_LIBRARIES_ALL ${PTSCOTCH_LIBRARY_ESMUMPS} ${PTSCOTCH_LIBRARIES_ALL})
endif()
if(PTSCOTCH_LIBRARY_METIS)
set(PTSCOTCH_LIBRARIES_ALL ${PTSCOTCH_LIBRARY_METIS} ${PTSCOTCH_LIBRARIES_ALL})
endif()
if(PTSCOTCH_LIBRARY_PARMETIS)
set(PTSCOTCH_LIBRARIES_ALL ${PTSCOTCH_LIBRARY_PARMETIS} ${PTSCOTCH_LIBRARIES_ALL})
endif()
set(PTSCOTCH_LIBRARIES ${PTSCOTCH_LIBRARIES_ALL} CACHE INTERNAL "Libraries for PT-Scotch" FORCE)
#===============================================================================
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(PTSCOTCH DEFAULT_MSG
PTSCOTCH_LIBRARY PTSCOTCH_LIBRARY_ERR PTSCOTCH_INCLUDE_PATH)
if(PTSCOTCH_INCLUDE_PATH)
file(STRINGS ${PTSCOTCH_INCLUDE_PATH}/scotch.h PTSCOTCH_INCLUDE_CONTENT)
string(REGEX MATCH "_cplusplus" _match ${PTSCOTCH_INCLUDE_CONTENT})
if(_match)
add_definitions(-DAKANTU_PTSCOTCH_NO_EXTERN)
endif()
endif()
#===============================================================================
if(NOT PTSCOTCH_FOUND)
set(PTSCOTCH_DIR "" CACHE PATH "Location of PT-Scotch library.")
endif(NOT PTSCOTCH_FOUND)
diff --git a/cmake/Modules/FindParMETIS.cmake b/cmake/Modules/FindParMETIS.cmake
index a105cc9af..2d99415b7 100644
--- a/cmake/Modules/FindParMETIS.cmake
+++ b/cmake/Modules/FindParMETIS.cmake
@@ -1,37 +1,69 @@
+#===============================================================================
+# @file FindParMETIS.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Apr 22 2016
+# @date last modification: Fri Mar 16 2018
+#
+# @brief FindPackage for the parmetis library
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
find_path(PARMETIS_INCLUDE_DIR parmetis.h
PATHS "${PARMETIS_DIR}"
ENV PARMETIS_DIR
PATH_SUFFIXES include
)
find_library(PARMETIS_LIBRARY NAMES parmetis
PATHS "${PARMETIS_DIR}"
ENV PARMETIS_DIR
PATH_SUFFIXES lib
)
mark_as_advanced(PARMETIS_LIBRARY PARMETIS_INCLUDE_DIR)
#===============================================================================
include(FindPackageHandleStandardArgs)
if(CMAKE_VERSION VERSION_GREATER 2.8.12)
if(PARMETIS_INCLUDE_DIR)
file(STRINGS ${PARMETIS_INCLUDE_DIR}/parmetis.h _versions
REGEX "^#define\ +PARMETIS_(MAJOR|MINOR|SUBMINOR)_VERSION .*")
foreach(_ver ${_versions})
string(REGEX MATCH "PARMETIS_(MAJOR|MINOR|SUBMINOR)_VERSION *([0-9.]+)" _tmp "${_ver}")
set(_parmetis_${CMAKE_MATCH_1} ${CMAKE_MATCH_2})
endforeach()
set(PARMETIS_VERSION "${_parmetis_MAJOR}.${_parmetis_MINOR}" CACHE INTERNAL "")
endif()
find_package_handle_standard_args(ParMETIS
REQUIRED_VARS
PARMETIS_LIBRARY
PARMETIS_INCLUDE_DIR
VERSION_VAR
PARMETIS_VERSION)
else()
find_package_handle_standard_args(ParMETIS DEFAULT_MSG
PARMETIS_LIBRARY PARMETIS_INCLUDE_DIR)
endif()
diff --git a/cmake/Modules/FindParaDiS.cmake b/cmake/Modules/FindParaDiS.cmake
deleted file mode 100644
index d92a77fd8..000000000
--- a/cmake/Modules/FindParaDiS.cmake
+++ /dev/null
@@ -1,45 +0,0 @@
-#===============================================================================
-# @file FindParaDiS.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find_package for paradis
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_library(PARADIS_LIBRARIES paradis
- PATHS ${PARADIS_DIR}
- PATH_SUFFIXES bin)
-
-find_path(PARADIS_INCLUDE_PATH ParadisGen.h
- PATHS ${PARADIS_DIR}
- PATH_SUFFIXES include
-)
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(PARADIS DEFAULT_MSG
- PARADIS_LIBRARIES PARADIS_INCLUDE_PATH)
-
-if (NOT PARADIS_FOUND)
- set(PARADIS_DIR "" CACHE PATH "Location of PARADIS library")
-endif(NOT PARADIS_FOUND)
\ No newline at end of file
diff --git a/cmake/Modules/FindPostgreSQL.cmake b/cmake/Modules/FindPostgreSQL.cmake
deleted file mode 100644
index ae8d12f16..000000000
--- a/cmake/Modules/FindPostgreSQL.cmake
+++ /dev/null
@@ -1,45 +0,0 @@
-#===============================================================================
-# @file FindPostgreSQL.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief The find_package file for PostgreSQL C library
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_library(POSTGRESQL_LIBRARIES NAMES pq
- PATH_SUFFIXES pgsql postgresql
- PATH ENV POSTGRESQL_DIR
- )
-
-find_path(POSTGRESQL_INCLUDE_DIR NAMES libpq-fe.h
- PATH_SUFFIXES pgsql postgresql
- PATHS ENV POSTGRESQL_DIR
- )
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(POSTGRESQL DEFAULT_MSG
- POSTGRESQL_LIBRARIES POSTGRESQL_INCLUDE_DIR)
-
-mark_as_advanced(POSTGRESQL_INCLUDE_DIR)
-mark_as_advanced(POSTGRESQL_LIBRARIES)
diff --git a/cmake/Modules/FindQVIEW.cmake b/cmake/Modules/FindQVIEW.cmake
deleted file mode 100644
index 1d57be6c4..000000000
--- a/cmake/Modules/FindQVIEW.cmake
+++ /dev/null
@@ -1,49 +0,0 @@
-#===============================================================================
-# @file FindQVIEW.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief The find_package file for libQVIEW
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_library(QVIEW_LIBRARIES NAME qview
- PATHS ${QVIEW_DIR}
- PATH_SUFFIXES lib
- )
-#===============================================================================
-find_path(QVIEW_INCLUDE_DIR libqview.h
- PATHS ${QVIEW_DIR}
- PATH_SUFFIXES include src
- )
-#===============================================================================
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(QVIEW DEFAULT_MSG
- QVIEW_LIBRARIES QVIEW_INCLUDE_DIR)
-
-#===============================================================================
-if(NOT QVIEW_FOUND)
- set(QVIEW_DIR "" CACHE PATH "Location of QVIEW library.")
-endif(NOT QVIEW_FOUND)
-
diff --git a/cmake/Modules/FindSIMULPACK.cmake b/cmake/Modules/FindSIMULPACK.cmake
deleted file mode 100644
index 82c51f22c..000000000
--- a/cmake/Modules/FindSIMULPACK.cmake
+++ /dev/null
@@ -1,118 +0,0 @@
-#===============================================================================
-# @file FindSIMULPACK.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find_package for simulpack
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-find_path(SIMULPACK_INCLUDE_PATH adlib.h
- PATHS ${SIMULPACK_DIR} ENV C_INCLUDE_PATH
- PATH_SUFFIXES include src adlib adlib-cmake
- )
-
-SET(USING_SIMULPACK_TEMPERATURE OFF CACHE BOOL "Activation of temperature within SIMULPACK plugin" )
-
-SET(SIMULPACK_MATERIALS "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_MECHANICS "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_MESHER3D "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_UTILS "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_FEM "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_LIBMYUTILS "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_SUBDI_COLLAPSE3D "-NOTFOUND" CACHE LIBRARY "" FORCE)
-SET(SIMULPACK_MESH_IO "-NOTFOUND" CACHE LIBRARY "" FORCE)
-
-
-FIND_LIBRARY(SIMULPACK_PMECHANICS NAME pmechanics
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_MESHER3D NAME mesher3d
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_MATERIALS NAME materials
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_MECHANICS NAME mechanics
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_FEM NAME fem
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_MYUTILS NAME myutils
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_UTILS NAME utils
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_SUBDI_COLLAPSE3D NAME subdi_collapse3d
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-FIND_LIBRARY(SIMULPACK_MESH_IO NAME mesh_io
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-
-IF (USING_SIMULPACK_TEMPERATURE)
-ADD_DEFINITIONS(-DUSING_SIMULPACK_TEMPERATURE)
-
-FIND_LIBRARY(SIMULPACK_MULTIPHYSICS NAME multiphysics
- PATHS ${SIMULPACK_DIR}
- PATHS ${SIMULPACK_LIB_PATH}
- PATH_SUFFIXES lib
- )
-ENDIF (USING_SIMULPACK_TEMPERATURE)
-
-
-set(SIMULPACK_LIBRARIES ${SIMULPACK_MULTIPHYSICS} ${SIMULPACK_MECHANICS} ${SIMULPACK_MESHER3D} ${SIMULPACK_UTILS} ${SIMULPACK_FEM} ${SIMULPACK_MATERIALS} ${SIMULPACK_MYUTILS} ${SIMULPACK_SUBDI_COLLAPSE3D} ${SIMULPACK_PMECHANICS} ${SIMULPACK_MESH_IO})
-SEPARATE_ARGUMENTS(SIMULPACK_LIBRARIES)
-#SET(SIMULPACK_INCLUDE_DIR "${SIMULPACK_SRC} ${SIMULPACK_SRC}/utils/include" CACHE STRING "simulpack includes" FORCE)
-#SEPARATE_ARGUMENTS(SIMULPACK_INCLUDE_DIR)
-
-if (NOT SIMULPACK_MECHANICS)
- set(SIMULPACK_DIR "" CACHE PATH "Location of SIMULPACK main tree.")
- set(SIMULPACK_LIB_PATH "" CACHE PATH "Additional path to search SimulPack libraries" )
-endif(NOT SIMULPACK_MECHANICS)
-
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(SIMULPACK DEFAULT_MSG
- SIMULPACK_MECHANICS SIMULPACK_MESHER3D SIMULPACK_UTILS SIMULPACK_FEM SIMULPACK_MATERIALS SIMULPACK_MYUTILS SIMULPACK_SUBDI_COLLAPSE3D SIMULPACK_PMECHANICS SIMULPACK_MESH_IO SIMULPACK_INCLUDE_PATH)
-
diff --git a/cmake/Modules/FindSubversion.cmake b/cmake/Modules/FindSubversion.cmake
deleted file mode 100644
index b7ea48d7e..000000000
--- a/cmake/Modules/FindSubversion.cmake
+++ /dev/null
@@ -1,118 +0,0 @@
-#===============================================================================
-# @file FindSubversion.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief find_package for subversion
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-# (To distribute this file outside of CMake, substitute the full
-# License text for the above reference.)
-
-find_program(Subversion_SVN_EXECUTABLE svn
- DOC "subversion command line client")
-mark_as_advanced(Subversion_SVN_EXECUTABLE)
-
-if(Subversion_SVN_EXECUTABLE)
- # the subversion commands should be executed with the C locale, otherwise
- # the message (which are parsed) may be translated, Alex
- set(_Subversion_SAVED_LC_ALL "$ENV{LC_ALL}")
- set(ENV{LC_ALL} C)
-
- execute_process(COMMAND ${Subversion_SVN_EXECUTABLE} --version
- OUTPUT_VARIABLE Subversion_VERSION_SVN
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
- # restore the previous LC_ALL
- set(ENV{LC_ALL} ${_Subversion_SAVED_LC_ALL})
-
- string(REGEX REPLACE "^(.*\n)?svn, version ([.0-9]+).*"
- "\\2" Subversion_VERSION_SVN "${Subversion_VERSION_SVN}")
-
- macro(Subversion_WC_INFO dir prefix)
- # the subversion commands should be executed with the C locale, otherwise
- # the message (which are parsed) may be translated, Alex
- set(_Subversion_SAVED_LC_ALL "$ENV{LC_ALL}")
- set(ENV{LC_ALL} C)
-
- execute_process(COMMAND ${Subversion_SVN_EXECUTABLE} info ${dir}
- OUTPUT_VARIABLE ${prefix}_WC_INFO
- ERROR_VARIABLE Subversion_svn_info_error
- RESULT_VARIABLE Subversion_svn_info_result
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
- if(NOT ${Subversion_svn_info_result} EQUAL 0)
- set(${prefix}_WC_FOUND FALSE)
- if(NOT "${ARGV2}" STREQUAL "ERROR_QUIET")
- message(SEND_ERROR "Command \"${Subversion_SVN_EXECUTABLE} info ${dir}\" failed with output:\n${Subversion_svn_info_error}")
- endif(NOT "${ARGV2}" STREQUAL "ERROR_QUIET")
- else(NOT ${Subversion_svn_info_result} EQUAL 0)
- set(${prefix}_WC_FOUND TRUE)
-
- string(REGEX REPLACE "^(.*\n)?URL: ([^\n]+).*"
- "\\2" ${prefix}_WC_URL "${${prefix}_WC_INFO}")
- string(REGEX REPLACE "^(.*\n)?Repository Root: ([^\n]+).*"
- "\\2" ${prefix}_WC_ROOT "${${prefix}_WC_INFO}")
- string(REGEX REPLACE "^(.*\n)?Revision: ([^\n]+).*"
- "\\2" ${prefix}_WC_REVISION "${${prefix}_WC_INFO}")
- string(REGEX REPLACE "^(.*\n)?Last Changed Author: ([^\n]+).*"
- "\\2" ${prefix}_WC_LAST_CHANGED_AUTHOR "${${prefix}_WC_INFO}")
- string(REGEX REPLACE "^(.*\n)?Last Changed Rev: ([^\n]+).*"
- "\\2" ${prefix}_WC_LAST_CHANGED_REV "${${prefix}_WC_INFO}")
- string(REGEX REPLACE "^(.*\n)?Last Changed Date: ([^\n]+).*"
- "\\2" ${prefix}_WC_LAST_CHANGED_DATE "${${prefix}_WC_INFO}")
-
- endif()
-
- # restore the previous LC_ALL
- set(ENV{LC_ALL} ${_Subversion_SAVED_LC_ALL})
-
- endmacro()
-
- macro(Subversion_WC_LOG dir prefix)
- # This macro can block if the certificate is not signed:
- # svn ask you to accept the certificate and wait for your answer
- # This macro requires a svn server network access (Internet most of the time)
- # and can also be slow since it access the svn server
- execute_process(COMMAND
- ${Subversion_SVN_EXECUTABLE} --non-interactive log -r BASE ${dir}
- OUTPUT_VARIABLE ${prefix}_LAST_CHANGED_LOG
- ERROR_VARIABLE Subversion_svn_log_error
- RESULT_VARIABLE Subversion_svn_log_result
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-
- if(NOT ${Subversion_svn_log_result} EQUAL 0)
- message(SEND_ERROR "Command \"${Subversion_SVN_EXECUTABLE} log -r BASE ${dir}\" failed with output:\n${Subversion_svn_log_error}")
- endif()
- endmacro()
-
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Subversion REQUIRED_VARS Subversion_SVN_EXECUTABLE
- VERSION_VAR Subversion_VERSION_SVN )
-
-# for compatibility
-set(Subversion_FOUND ${SUBVERSION_FOUND})
-set(Subversion_SVN_FOUND ${SUBVERSION_FOUND})
diff --git a/cmake/Modules/PCHgcc.cmake b/cmake/Modules/PCHgcc.cmake
deleted file mode 100644
index 528ff6a86..000000000
--- a/cmake/Modules/PCHgcc.cmake
+++ /dev/null
@@ -1,83 +0,0 @@
-#===============================================================================
-# @file PCHgcc.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Sun Oct 19 2014
-#
-# @brief
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-# (ADD_PCH_RULE _header_filename _src_list)
-# Version 7/26/2010 4:55pm
-#
-# use this macro before "add_executable"
-#
-# _header_filename
-# header to make a .gch
-#
-# _src_list
-# the variable name (do not use ${..}) which contains a
-# a list of sources (a.cpp b.cpp c.cpp ...)
-# This macro will append a header file to it, then this src_list can be used in
-# "add_executable..."
-#
-#
-# Now a .gch file should be generated and gcc should use it.
-# (add -Winvalid-pch to the cpp flags to verify)
-#
-# make clean should delete the pch file
-#
-# example : ADD_PCH_RULE(headers.h myprog_SRCS)
-
-
-function(ADD_PCH_RULE _header_filename _src_list)
- set(_gch_filename "${CMAKE_CURRENT_BINARY_DIR}/${_header_filename}.gch")
-
- list(APPEND ${_src_list} ${_gch_filename})
-
- set(_args ${CMAKE_CXX_FLAGS} -D__aka_inline__=inline)
-
- get_filename_component(_gch_filename_path ${_gch_filename} PATH)
- file(MAKE_DIRECTORY ${_gch_filename_path})
-
- # list(APPEND _args -c ${CMAKE_CURRENT_SOURCE_DIR}/${_header_filename})
- list(APPEND _args -c ${CMAKE_CURRENT_SOURCE_DIR}/${_header_filename} -o ${_gch_filename} -Winvalid-pch)
-
- get_directory_property(DIRINC INCLUDE_DIRECTORIES)
- foreach (_inc ${DIRINC})
- list(APPEND _args "-I" ${_inc})
- endforeach(_inc ${DIRINC})
- separate_arguments(_args)
-
- set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/${_header_filename} PROPERTIES GENERATED 1)
- set_source_files_properties(${_gch_filename} PROPERTIES GENERATED 1)
- add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${_header_filename}
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/${_header_filename} ${CMAKE_CURRENT_BINARY_DIR}/${_header_filename} # ensure same directory! Required by gcc
- DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${_header_filename}
- )
-
- add_custom_command(OUTPUT ${_gch_filename}
- COMMAND ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1} ${_args}
- DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${_header_filename}
- )
-endfunction(ADD_PCH_RULE _header_filename _src_list)
diff --git a/cmake/libakantu/__init__.py b/cmake/libakantu/__init__.py
index e69de29bb..dd656c4b9 100644
--- a/cmake/libakantu/__init__.py
+++ b/cmake/libakantu/__init__.py
@@ -0,0 +1,10 @@
+""" __init__.py: module for gdb pretty printer"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
diff --git a/cmake/libakantu/v3/__init__.py b/cmake/libakantu/v3/__init__.py
index cc2c5a24e..b9a9b8fe4 100644
--- a/cmake/libakantu/v3/__init__.py
+++ b/cmake/libakantu/v3/__init__.py
@@ -1,5 +1,18 @@
+
+""" __init__.py: module for gdb pretty printer for akantu v3"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import gdb
# Load the pretty-printers.
from .printers import register_akantu_printers
register_akantu_printers(gdb.current_objfile())
diff --git a/cmake/libakantu/v3/printers.py b/cmake/libakantu/v3/printers.py
index 4ec724d58..eca4d1e2b 100755
--- a/cmake/libakantu/v3/printers.py
+++ b/cmake/libakantu/v3/printers.py
@@ -1,392 +1,405 @@
#!/usr/bin/env python3
# encoding: utf-8
+
+""" printers.py: gdb pretty printers"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
#
# Inspired from boost's pretty printers from
# Rüdiger Sonderfeld <ruediger@c-plusplus.de>
# and from Pretty-printers for libstc++ from Free Software Foundation, Inc.
#
import gdb
import re
import sys
import itertools
__use_gdb_pp__ = True
try:
import gdb.printing
except ImportError:
__use_gdb_pp__ = False
class AkantuPrinter(object):
regex = None
@classmethod
def supports(cls, typename):
# print('{0} ~= {1}'.format(typename, cls.regex), file=sys.stderr)
return cls.regex.search(typename)
@classmethod
def get_basic_type(cls, value):
""" Determines the type associated to a value"""
_type = value.type
# If it points to a reference, get the reference.
if _type.code == gdb.TYPE_CODE_REF:
_type = _type.target()
# Get the unqualified type, stripped of typedefs.
_type = _type.unqualified().strip_typedefs()
return _type.tag
if __use_gdb_pp__:
__akantu_pretty_printers__ = \
gdb.printing.RegexpCollectionPrettyPrinter("libakantu-v3")
else:
class AkantuPrettyPrinters(object):
def __init__(self, name):
super(AkantuPrettyPrinters, self).__init__()
self.name = name
self.printers = {}
@property
def enabled(self):
return True
def add_printer(self, name, regex, printer):
self.printers[name] = printer
def __call__(self, val):
typename = AkantuPrinter.get_basic_type(val)
if not typename:
return None
for name, printer in self.printers.items():
if(printer.supports(typename)):
return printer
return None
__akantu_pretty_printers__ = AkantuPrettyPrinters("libakantu-v3")
def register_pretty_printer(pretty_printer):
"Registers a Pretty Printer"
__akantu_pretty_printers__.add_printer(pretty_printer.name,
pretty_printer.regex,
pretty_printer)
return pretty_printer
@register_pretty_printer
class AkaArrayPrinter(AkantuPrinter):
"""Pretty printer for akantu::Array<T>"""
regex = re.compile('^akantu::Array<(.*?), (true|false)>$')
name = 'akantu::Array'
def __init__(self, value):
self.typename = self.get_basic_type(value)
self.value = value
self.ptr = self.value['values']
self.size = int(self.value['size_'])
self.nb_component = int(self.value['nb_component'])
def display_hint(self):
return 'array'
def to_string(self):
m = self.regex.search(self.typename)
return 'Array<{0}>({1}, {2}) stored at {3}'.format(
m.group(1), self.size, self.nb_component, self.ptr)
def children(self):
_ptr = self.ptr
for i in range(self.size):
_values = ["{0}".format((_ptr + j).dereference())
for j in range(self.nb_component)]
_ptr = _ptr + self.nb_component
yield ('[{0}]'.format(i),
('{0}' if self.nb_component == 1 else '[{0}]').format(
', '.join(_values)))
if sys.version_info[0] > 2:
# Python 3 stuff
Iterator = object
else:
# Python 2 stuff
class Iterator:
"""Compatibility mixin for iterators
Instead of writing next() methods for iterators, write
__next__() methods and use this mixin to make them work in
Python 2 as well as Python 3.
Idea stolen from the "six" documentation:
<http://pythonhosted.org/six/#six.Iterator>
"""
def next(self):
return self.__next__()
class RbtreeIterator(Iterator):
"""
Turn an RB-tree-based container (std::map, std::set etc.) into
a Python iterable object.
"""
def __init__(self, rbtree):
self.size = rbtree['_M_t']['_M_impl']['_M_node_count']
self.node = rbtree['_M_t']['_M_impl']['_M_header']['_M_left']
self.count = 0
def __iter__(self):
return self
def __len__(self):
return int(self.size)
def __next__(self):
if self.count == self.size:
raise StopIteration
result = self.node
self.count = self.count + 1
if self.count < self.size:
# Compute the next node.
node = self.node
if node.dereference()['_M_right']:
node = node.dereference()['_M_right']
while node.dereference()['_M_left']:
node = node.dereference()['_M_left']
else:
parent = node.dereference()['_M_parent']
while node == parent.dereference()['_M_right']:
node = parent
parent = parent.dereference()['_M_parent']
if node.dereference()['_M_right'] != parent:
node = parent
self.node = node
return result
def get_value_from_aligned_membuf(buf, valtype):
"""Returns the value held in a __gnu_cxx::__aligned_membuf."""
return buf['_M_storage'].address.cast(valtype.pointer()).dereference()
def get_value_from_Rb_tree_node(node):
"""Returns the value held in an _Rb_tree_node<_Val>"""
try:
member = node.type.fields()[1].name
if member == '_M_value_field':
# C++03 implementation, node contains the value as a member
return node['_M_value_field']
elif member == '_M_storage':
# C++11 implementation, node stores value in __aligned_membuf
valtype = node.type.template_argument(0)
return get_value_from_aligned_membuf(node['_M_storage'], valtype)
except: # noqa: E722
pass
raise ValueError("Unsupported implementation for %s" % str(node.type))
def find_type(orig, name):
typ = orig.strip_typedefs()
while True:
# Strip cv-qualifiers. PR 67440.
search = '%s::%s' % (typ.unqualified(), name)
try:
return gdb.lookup_type(search)
except RuntimeError:
pass
# The type was not found, so try the superclass. We only need
# to check the first superclass, so we don't bother with
# anything fancier here.
field = typ.fields()[0]
if not field.is_base_class:
raise ValueError("Cannot find type %s::%s" % (str(orig), name))
typ = field.type
@register_pretty_printer
class AkaElementTypeMapArrayPrinter(AkantuPrinter):
"""Pretty printer for akantu::ElementTypeMap<Array<T>>"""
regex = re.compile('^akantu::ElementTypeMap<akantu::Array<(.*?), (true|false)>\*, akantu::(.*?)>$') # noqa: E501,W605
name = 'akantu::ElementTypeMapArray'
# Turn an RbtreeIterator into a pretty-print iterator.
class _rb_iter(Iterator):
def __init__(self, rbiter, type, ghost_type):
self.rbiter = rbiter
self.count = 0
self.type = type
self.ghost_type = ghost_type
def __iter__(self):
return self
def __next__(self):
if self.count % 2 == 0:
n = next(self.rbiter)
n = n.cast(self.type).dereference()
n = get_value_from_Rb_tree_node(n)
self.pair = n
item = "{0}:{1}".format(n['first'], self.ghost_type)
else:
item = self.pair['second'].dereference()
result = ('[{0}]'.format(self.count), item)
self.count = self.count + 1
return result
def _iter(self, not_ghost, ghost, type):
iter_size = (len(not_ghost), len(ghost))
it = self._rb_iter(not_ghost, type, '_not_ghost')
for _ in range(iter_size[0] * 2):
yield next(it)
it = self._rb_iter(ghost, type, '_ghost')
for _ in range(iter_size[1] * 2):
yield next(it)
raise StopIteration
def __init__(self, value):
self.typename = self.get_basic_type(value)
self.value = value
self.data = self.value['data']
self.ghost_data = self.value['ghost_data']
def to_string(self):
m = self.regex.search(self.typename)
return 'ElementTypMapArray<{0}> with '\
'{1} _not_ghost and {2} _ghost'.format(
m.group(1), len(RbtreeIterator(self.data)),
len(RbtreeIterator(self.ghost_data)))
def children(self):
# m = self.regex.search(self.typename)
rep_type = find_type(self.data.type, '_Rep_type')
node = find_type(rep_type, '_Link_type')
node = node.strip_typedefs()
return itertools.chain(
self._rb_iter(RbtreeIterator(self.data), node, "_not_ghost"),
self._rb_iter(RbtreeIterator(self.ghost_data), node, "_ghost"))
def display_hint(self):
return 'map'
# @register_pretty_printer
class AkaTensorPrinter(AkantuPrinter):
"""Pretty printer for akantu::Tensor<T>"""
regex = re.compile('^akantu::Tensor<(.*), +(.*), +(.*)>$')
name = 'akantu::Tensor'
value = None
typename = ""
ptr = None
dims = []
ndims = 0
def pretty_print(self):
def ij2str(i, j, m):
return "{0}".format((self.ptr+m*j + i).dereference())
def line(i, m, n):
return "[{0}]".format(", ".join((ij2str(i, j, m) for j in
range(n))))
m = int(self.dims[0])
if (self.ndims == 1):
n = 1
else:
n = int(self.dims[1])
return "[{0}]".format(", ".join(line(i, m, n) for i in range(m)))
def __init__(self, value):
self.typename = self.get_basic_type(value)
self.value = value
self.ptr = self.value['values']
self.dims = self.value['n']
def children(self):
yield ('values', self.pretty_print())
yield ('wrapped', self.value['wrapped'])
@register_pretty_printer
class AkaVectorPrinter(AkaTensorPrinter):
"""Pretty printer for akantu::Vector<T>"""
regex = re.compile('^akantu::Vector<(.*)>$')
name = 'akantu::Vector'
n = 0
ptr = 0x0
def __init__(self, value):
super(AkaVectorPrinter, self).__init__(value)
self.ndims = 1
def to_string(self):
m = self.regex.search(self.typename)
return 'Vector<{0}>({1}) [{2}]'.format(m.group(1), int(self.dims[0]),
str(self.ptr))
@register_pretty_printer
class AkaMatrixPrinter(AkaTensorPrinter):
"""Pretty printer for akantu::Matrix<T>"""
regex = re.compile('^akantu::Matrix<(.*)>$')
name = 'akantu::Matrix'
def __init__(self, value):
super(AkaMatrixPrinter, self).__init__(value)
self.ndims = 2
def to_string(self):
m = self.regex.search(self.typename)
return 'Matrix<%s>(%d, %d) [%s]' % (m.group(1), int(self.dims[0]),
int(self.dims[1]),
str(self.ptr))
@register_pretty_printer
class AkaElementPrinter(AkantuPrinter):
"""Pretty printer for akantu::Element"""
regex = re.compile('^akantu::Element$')
name = 'akantu::Element'
def __init__(self, value):
self.typename = self.get_basic_type(value)
self.value = value
self.element = self.value['element']
self.eltype = self.value['type']
self.ghost_type = self.value['ghost_type']
self._ek_not_defined = gdb.parse_and_eval('akantu::_not_defined')
self._casper = gdb.parse_and_eval('akantu::_casper')
self._max_uint = gdb.parse_and_eval('(akantu::UInt) -1')
def to_string(self):
if (self.element == self._max_uint) and \
(self.eltype == self._ek_not_defined) and \
(self.ghost_type == self._casper):
return 'ElementNull'
return 'Element({0}, {1}, {2})'.format(self.element, self.eltype,
self.ghost_type)
def register_akantu_printers(obj):
"Register Akantu Pretty Printers."
if __use_gdb_pp__:
gdb.printing.register_pretty_printer(obj, __akantu_pretty_printers__)
else:
if obj is None:
obj = gdb
obj.pretty_printers.append(__akantu_pretty_printers__)
diff --git a/cmake/material_lister.cc b/cmake/material_lister.cc
index 7847c3ec5..a6657d6f6 100644
--- a/cmake/material_lister.cc
+++ b/cmake/material_lister.cc
@@ -1,51 +1,54 @@
/**
* @file material_lister.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Mar 21 2014
- * @date last modification: Fri Mar 21 2014
+ * @date creation: Mon Jun 14 2010
+ * @date last modification: Fri Mar 16 2018
*
- * @brief Small code that print out the list of materials
+ * @brief Small code to generate a list of activated materials
*
- * * Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_list.hh"
#include <boost/preprocessor.hpp>
#include <iostream>
int main(__attribute__((unused)) int argc,
__attribute__((unused)) char * argv[]) {
#define PRINT_OUT_OPTIONS(r, data, i, elem) \
<< ":" << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem))
#define PRINT_OUT(r, data, elem) \
std::cout << BOOST_PP_STRINGIZE(BOOST_PP_ARRAY_ELEM(0, elem)) << ":" \
<< BOOST_PP_STRINGIZE(BOOST_PP_ARRAY_ELEM(1, elem)) BOOST_PP_IF( \
BOOST_PP_EQUAL(3, BOOST_PP_ARRAY_SIZE(elem)), \
BOOST_PP_SEQ_FOR_EACH_I(PRINT_OUT_OPTIONS, _, \
BOOST_PP_ARRAY_ELEM(2, elem)), ) \
<< std::endl;
BOOST_PP_SEQ_FOR_EACH(PRINT_OUT, "toto", AKANTU_MATERIAL_LIST);
return 0;
}
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index 59700fa1e..1fd8760d3 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -1,93 +1,37 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jan 30 2015
+# @date last modification: Fri Jan 29 2021
#
# @brief Build the documentation
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
if(AKANTU_DOCUMENTATION)
add_subdirectory(dev-doc)
endif()
-
-file(GLOB_RECURSE __all_files "*.*")
-set(_all_files)
-foreach(_file ${__all_files})
- if("${_file}" MATCHES "${PROJECT_SOURCE_DIR}/doc/manual")
- file(RELATIVE_PATH __file ${PROJECT_SOURCE_DIR} ${_file})
- list(APPEND _all_files ${__file})
- endif()
-endforeach()
-
-set(AKANTU_MANUAL_FILES)
-set(_akantu_manual_not_found_files)
-foreach(_pkg ${${_project}_PACKAGE_SYSTEM_PACKAGES_ON})
- string(TOUPPER "${_pkg}" _pkg)
- foreach(_f ${AKANTU_${_pkg}_MANUAL_FILES})
- #check if some file are registered but not present
- list(FIND _all_files doc/manual/${_f} _ret)
- if(_ret EQUAL -1)
- list(APPEND _akantu_manual_not_found_files "${_pkg}: doc/manual/${_f} ")
- else()
- list(APPEND AKANTU_MANUAL_FILES doc/manual/${_f})
- endif()
- endforeach()
-endforeach()
-
-if(_akantu_manual_not_found_files)
- message("")
- message("******************************************************")
- message("There are files registered in packages but not present")
- message("******************************************************")
- foreach(_file ${_akantu_manual_not_found_files})
- message(${_file})
- endforeach()
- message("******************************************************")
- message(FATAL_ERROR "abort")
-endif()
-
-################################################################
-#construct the list of files to exclude because not registered
-################################################################
-
-set(_akantu_doc_exclude_files)
-foreach(_file ${_all_files})
- list(FIND AKANTU_MANUAL_FILES ${_file} _ret)
- if(_ret EQUAL -1)
- list(APPEND _akantu_doc_exclude_files /${_file})
- endif()
-endforeach()
-
-list(REMOVE_ITEM _akantu_doc_exclude_files /doc/manual/CMakeLists.txt)
-
-set(AKANTU_DOC_EXCLUDE_FILES ${_akantu_doc_exclude_files}
- CACHE INTERNAL "Documentation files to excluse from Akantu Package" FORCE)
-
-if (AKANTU_DOCUMENTATION_MANUAL)
- add_subdirectory(manual)
-endif()
diff --git a/doc/dev-doc/CMakeLists.txt b/doc/dev-doc/CMakeLists.txt
index 182240509..e1df890c0 100644
--- a/doc/dev-doc/CMakeLists.txt
+++ b/doc/dev-doc/CMakeLists.txt
@@ -1,187 +1,87 @@
-# set(DOXYGEN_INPUT_DOX ${CMAKE_CURRENT_BINARY_DIR}/akantu.dox)
-# set(DOXYGEN_XML_DIR ${CMAKE_CURRENT_BINARY_DIR}/xml)
-# set(DOXYGEN_OUTPUT ${DOXYGEN_XML_DIR}/index.xml)
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri May 08 2020
+# @date last modification: Sun Nov 22 2020
+#
+# @brief Main cmake file for the documentation
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
# configured documentation tools and intermediate build results
set(BINARY_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}/_build")
# Sphinx cache with pickled ReST documents
set(SPHINX_CACHE_DIR "${CMAKE_CURRENT_BINARY_DIR}/_doctrees")
# HTML output directory
set(SPHINX_HTML_DIR "${CMAKE_CURRENT_BINARY_DIR}/html")
set(SPHINX_OUTPUT "${SPHINX_HTML_DIR}/index.html")
set(SPHINX_INPUT "${CMAKE_CURRENT_BINARY_DIR}/conf.py")
-# # ---------------------------------------------------------------------------- #
-# # Doxygen #
-# # ---------------------------------------------------------------------------- #
-# find_package(Doxygen REQUIRED)
-
-# set(DOXYGEN_WARNINGS NO)
-# set(DOXYGEN_QUIET YES)
-# if(CMAKE_VERBOSE_MAKEFILE)
-# set(DOXYGEN_WARNINGS YES)
-# set(DOXYGEN_QUIET NO)
-# endif(CMAKE_VERBOSE_MAKEFILE)
-
-# package_get_all_source_files(
-# AKANTU_LIBRARY_SRCS
-# AKANTU_LIBRARY_PUBLIC_HDRS
-# AKANTU_LIBRARY_PRIVATE_HDRS
-# )
-
-# package_get_all_include_directories(
-# _akantu_include_dirs
-# )
-
-# package_get_all_external_informations(
-# PRIVATE_INCLUDE AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR
-# INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
-# LIBRARIES AKANTU_EXTERNAL_LIBRARIES
-# )
-
-# list(APPEND _akantu_include_dirs
-# ${AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR}
-# ${AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR}
-# ${PROJECT_BINARY_DIR}/src)
-
-
-# file(STRINGS ${PROJECT_SOURCE_DIR}/.clang-format AKANTU_TAB_SIZE
-# REGEX "^TabWidth: *([0-9]*)"
-# )
-# string(REGEX REPLACE ".*([0-9]+)" "\\1" AKANTU_TAB_SIZE "${AKANTU_TAB_SIZE}")
-
-# if (CMAKE_VERSION VERSION_GREATER 3.9.5)
-# #set(DOXYGEN_WARNINGS YES)
-# #set(DOXYGEN_QUIET NO)
-# set(DOXYGEN_STRIP_FROM_PATH ${PROJECT_SOURCE_DIR})
-# set(DOXYGEN_STRIP_FROM_INC_PATH ${PROJECT_SOURCE_DIR})
-# set(DOXYGEN_TAB_SIZE ${AKANTU_TAB_SIZE})
-# set(DOXYGEN_ALIASES
-# "rst=\\verbatim embed:rst"
-# "endrst=\\endverbatim"
-# )
-# set(DOXYGEN_WARN_IF_UNDOCUMENTED NO)
-# set(DOXYGEN_WARN_IF_DOC_ERROR NO)
-# set(DOXYGEN_WARN_AS_ERROR NO)
-# set(DOXYGEN_EXCLUDE "${PROJECT_SOURCE_DIR}/src/common/aka_fwd.hh")
-# set(DOXYGEN_RECURSIVE YES)
-# set(DOXYGEN_EXCLUDE
-# "aka_named_argument.hh"
-# )
-# set(DOXYGEN_EXAMPLE_PATH "${PROJECT_SOURCE_DIR}/examples")
-# set(DOXYGEN_EXAMPLE_RECURSIVE YES)
-# set(DOXYGEN_SOURCE_BROWSER NO)
-# set(DOXYGEN_CLANG_ASSISTED_PARSING NO)
-# #set(DOXYGEN_CLANG_OPTIONS )
-# set(DOXYGEN_CLANG_DATABASE_PATH ${CMAKE_BINARY_DIR})
-# set(DOXYGEN_USE_MATHJAX YES)
-# set(DOXYGEN_GENERATE_HTML NO)
-# set(DOXYGEN_GENERATE_HTMLHELP NO)
-# set(DOXYGEN_GENERATE_LATEX NO)
-# set(DOXYGEN_GENERATE_XML YES)
-# set(DOXYGEN_XML_OUTPUT xml)
-# set(DOXYGEN_ENABLE_PREPROCESSING YES)
-# set(DOXYGEN_MACRO_EXPANSION YES)
-# set(DOXYGEN_INCLUDE_PATH ${_akantu_include_dirs})
-# set(DOXYGEN_PREDEFINED
-# ${AKANTU_DEFINITIONS}
-# "DOXYGEN"
-# # "AKANTU_TO_IMPLEMENT()="
-# # "DECLARE_NAMED_ARGUMENT()="
-# # "OPTIONAL_NAMED_ARGUMENT(n, v)=v"
-# # "REQUIRED_NAMED_ARGUMENT(n)="
-# )
-# set(DOXYGEN_COLLABORATION_GRAPH NO)
-# set(DOXYGEN_UML_LOOK YES)
-# set(DOXYGEN_TEMPLATE_RELATIONS YES)
-# set(DOXYGEN_CALL_GRAPH YES)
-# set(DOXYGEN_CALLER_GRAPH YES)
-# set(DOXYGEN_DOT_GRAPH_MAX_NODES 500)
-# set(DOXYGEN_SHOW_FILES NO)
-# set(DOXYGEN_LOOKUP_CACHE_SIZE 9)
-
-# set(_SRCS
-# ${PROJECT_BINARY_DIR}/src/aka_config.hh
-# ${PROJECT_BINARY_DIR}/src/aka_element_classes_info.hh
-# ${AKANTU_LIBRARY_SRCS}
-# ${AKANTU_LIBRARY_PUBLIC_HDRS}
-# ${AKANTU_LIBRARY_PRIVATE_HDRS}
-# )
-
-# list(REMOVE_ITEM _SRCS
-# "${PROJECT_SOURCE_DIR}/src/common/aka_named_argument.hh")
-
-# doxygen_add_docs(doxygen-doc
-# ${_SRCS}
-# USE_STAMP_FILE
-# COMMENT "Building XML documentation with Doxygen in ${DOXYGEN_XML_DIR}"
-# )
-
-# else()
-# string(REGEX REPLACE ";" " " AKANTU_DOXYGEN_DEFINTIONS "${AKANTU_DEFINITIONS};DOXYGEN")
-# string(REGEX REPLACE ";" " " AKANTU_DOXYGEN_INCLUDE_DIRS "${_akantu_include_dirs}")
-
-# make_directory(${DOXYGEN_XML_DIR})
-
-# configure_file(${CMAKE_CURRENT_SOURCE_DIR}/akantu.dox.in
-# ${DOXYGEN_INPUT_DOX}
-# )
-
-# add_custom_command(
-# OUTPUT ${DOXYGEN_OUTPUT}
-# COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_INPUT_DOX}
-# DEPENDS ${DOXYGEN_INPUT_DOX}
-# COMMENT "Building XML documentation with Doxygen in ${DOXYGEN_XML_DIR}"
-# )
-
-# add_custom_target(doxygen-doc ALL
-# DEPENDS ${DOXYGEN_OUTPUT}
-# )
-# endif()
-
# ---------------------------------------------------------------------------- #
# Sphinx #
# ---------------------------------------------------------------------------- #
find_package(Sphinx REQUIRED)
set(SPHINX_VERBOSE_FLAG "-q")
if(CMAKE_VERBOSE_MAKEFILE)
set(SPHINX_VERBOSE_FLAG)
endif(CMAKE_VERBOSE_MAKEFILE)
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/conf.py"
"${SPHINX_INPUT}"
@ONLY)
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/manual/manual-bibliography.bib"
"${CMAKE_CURRENT_BINARY_DIR}/manual/manual-bibliography.bib"
COPYONLY)
set(SPHINX_PARALLEL_FLAG)
if (SPHINX_VERSION VERSION_GREATER_EQUAL 1.7.0)
set(SPHINX_PARALLEL_FLAG -j auto)
endif()
set(_sphinx_command ${SPHINX_BUILD_EXECUTABLE}
${SPHINX_PARALLEL_FLAG}
${SPHINX_VERBOSE_FLAG} -b html
-c "${CMAKE_CURRENT_BINARY_DIR}"
-d "${SPHINX_CACHE_DIR}"
"${CMAKE_CURRENT_SOURCE_DIR}"
"${SPHINX_HTML_DIR}"
)
file(GLOB_RECURSE _SPHINX_SRCS
"*.rst")
add_custom_command(
OUTPUT ${SPHINX_OUTPUT}
COMMAND ${_sphinx_command}
DEPENDS ${SPHINX_INPUT} ${_SPHINX_SRCS}
COMMENT "Building HTML documentation with Sphinx in ${SPHINX_HTML_DIR}"
)
add_custom_target(sphinx-doc ALL
DEPENDS ${SPHINX_OUTPUT})
diff --git a/doc/dev-doc/manual/conf.py b/doc/dev-doc/manual/conf.py
index eec436ac9..d2eb437c8 100644
--- a/doc/dev-doc/manual/conf.py
+++ b/doc/dev-doc/manual/conf.py
@@ -1,205 +1,203 @@
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
-import os
-import subprocess
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- Project information -----------------------------------------------------
project = 'Akantu'
copyright = '2019-20, Laboratoire de Simulation en Mécanique des Solides, EPFL'
author = 'Nicolas Richart'
# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '3.0.0'
# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Number figures
numfig = True
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
# 'breathe'
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None
# Default programming language
highlight_language = 'cpp'
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['.static']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'Akantudoc'
# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'Akantu.tex', 'Akantu Documentation',
'Nicolas Richart', 'manual'),
]
# -- Options for manual page output ------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'akantu', 'Akantu Documentation',
[author], 1)
]
# -- Options for Texinfo output ----------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'Akantu', 'Akantu Documentation',
author, 'Akantu', 'One line description of project.',
'Miscellaneous'),
]
# -- Options for Epub output -------------------------------------------------
# Bibliographic Dublin Core info.
epub_title = project
# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''
# A unique identification for the text.
#
# epub_uid = ''
# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']
# -- Extension configuration -------------------------------------------------
# If on RTD build, run doxygen
# on_read_the_docs = os.environ.get('READTHEDOCS') == 'True'
# if on_read_the_docs:
# subprocess.call('cd ../../; mkdir -p build/doxygen; '
# + 'doxygen doxygen/Doxyfile', shell=True)
# breathe_projects = {
# 'akantu': '../../../build/doc/doxygen/xml'
# }
# breathe_default_project = 'akantu'
intersphinx_mapping = {
'numpy': ('https://docs.scipy.org/doc/numpy/', None),
'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
}
diff --git a/doc/dev-doc/manual/getting_started.rst b/doc/dev-doc/manual/getting_started.rst
index 6f37daa3e..36c8b7516 100644
--- a/doc/dev-doc/manual/getting_started.rst
+++ b/doc/dev-doc/manual/getting_started.rst
@@ -1,437 +1,470 @@
Getting Started
===============
-Compiling ``Akantu``
+Building ``Akantu``
--------------------
+Dependencies
+````````````
+
+In order to compile ``Akantu`` any compiler supporting fully C++14 should work
+In addition some libraries are required:
+
+ - CMake (>= 3.5.1)
+ - Boost (preprocessor and Spirit)
+ - zlib
+ - blas/lapack
+
+For the python interface:
+
+ - Python (>=3 is recommended)
+ - pybind11 (if not present the build system will try to download it)
+
+To run parallel simulations:
+
+ - MPI
+ - Scotch
+
+To use the static or implicit dynamic solvers at least one of the following libraries is needed:
+
+ - MUMPS (since this is usually compiled in static you also need MUMPS dependencies)
+ - PETSc
+
+To compile the tests and examples:
+
+ - Gmsh
+ - google-test (if not present the build system will try to download it)
+
+Configuring and compilation
+```````````````````````````
+
``Akantu`` is a `CMake <https://cmake.org/>`_ project, so to configure it, you can either
follow the usual way::
> cd akantu
> mkdir build
> cd build
> ccmake ..
[ Set the options that you need ]
> make
> make install
-All the ``Akantu`` options are documented in Appendix app:package-dependencies.
Writing a ``main`` function
---------------------------
``Akantu`` first needs to be initialized. The memory management included in the
core library handles the correct allocation and de-allocation of vectors,
structures and/or objects. Moreover, in parallel computations, the
initialization procedure performs the communication setup. This is achieved by
the function :cpp:func:`initialize <akantu::initialize>` that is used as
follows::
#include "aka_common.hh"
#include "..."
using namespace akantu;
int main(int argc, char *argv[]) {
- initialize("input_file.dat", argc, argv);
+ initialize("input_file.dat", argc, argv);
- // your code ...
+ // your code ...
}
The :cpp:func:`initialize <akantu::initialize>` function takes the text inpute
-file and the program parameters which can be parsed by ``Akantu`` in due form (see
-sect:parser). Obviously it is necessary to include all files needed in main. In
-this manual all provided code implies the usage of ``akantu`` as
+file and the program parameters which can be parsed by ``Akantu`` in due form
+(see sect:parser). Obviously it is necessary to include all files needed in
+main. In this manual all provided code implies the usage of ``akantu`` as
namespace.
Compiling your simulation
-------------------------
The easiest way to compile your simulation is to create a ``cmake`` project by
putting all your code in some directory of your choosing. Then, make sure that
you have ``cmake`` installed and create a ``CMakeLists.txt`` file. An example of
a minimal ``CMakeLists.txt`` file would look like this:
.. code-block:: cmake
project(my_simu)
cmake_minimum_required(VERSION 3.0.0)
find_package(Akantu REQUIRED)
add_akantu_simulation(my_simu my_simu.cc)
Then create a directory called ``build`` and inside it execute ``cmake
-DAkantu_DIR=<path_to_akantu> -DCMAKE_BUILD_TYPE=RelWithDebInfo ..``. If you
installed ``Akantu`` in a standard directory such as ``/usr/local`` (using
``make install``), you can omit the ``-DAkantu_DIR=<path_to_akantu>`` option.
Other why ``path_to_akantu`` is either the folder where you built ``Akantu`` if
you did not do a ``make install``, or if you installed ``Akantu`` in
``CMAKE_INSTALL_PREFIX`` it is ``<CMAKE_INSTALL_PREFIX>/share/cmake/Akantu``.
Once ``cmake`` managed to configure and generate a ``makefile`` you can just do
``make``
.. _loading_mesh:
Creating and Loading a Mesh
---------------------------
In its current state, ``Akantu`` supports three types of meshes: Gmsh, Abaqus and
Diana. Once a :cpp:class:`akantu::Mesh` object is created with a given spatial
dimension, it can be filled by reading a mesh input file. The method
:cpp:func:`read <akantu::Mesh::read>` of the class :cpp:class:`Mesh
<akantu::Mesh>` infers the mesh type from the file extension. If a non-standard
file extension is used, the mesh type has to be specified. ::
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
// Reading Gmsh files
mesh.read("my_gmsh_mesh.msh");
mesh.read("my_gmsh_mesh", _miot_gmsh);
The Gmsh reader adds the geometrical and physical tags as mesh data. The
physical values are stored as a :cpp:type:`UInt <akantu::UInt>` data called
``tag_0``, if a string name is provided it is stored as a ``std::string`` data
named ``physical_names``. The geometrical tag is stored as a :cpp:type:`UInt
<akantu::UInt>` data named ``tag_1``.
Using Arrays
------------
Data in ``Akantu`` can be stored in data containers implemented by the
:cpp:class:`akantu::Array` class. In its most basic usage, the :cpp:class:`Array
<akantu::Array>` class implemented in \akantu is similar to the ``std::vector``
class of the Standard Template Library (STL) for C++. A simple :cpp:class:`Array
<akantu::Array>` containing a sequence of ``nb_element`` values (of a given
type) can be generated with::
Array<type> example_array(nb_element);
where ``type`` usually is :cpp:type:`Real <akantu::Real>`, :cpp:type:`Int
<akantu::Int>`, :cpp:type:`UInt <akantu::UInt>` or ``bool``. Each value is
associated to an index, so that data can be accessed by typing::
auto & val = example_array(index);
``Arrays`` can also contain tuples of values for each index. In that case, the
number of components per tuple must be specified at the :cpp:class:`Array
<akantu::Array>` creation. For example, if we want to create an
:cpp:class:`Array <akantu::Array>` to store the coordinates (sequences of three
values) of ten nodes, the appropriate code is the following::
UInt nb_nodes = 10;
UInt spatial_dimension = 3;
Array<Real> position(nb_nodes, spatial_dimension);
In this case the :math:`x` position of the eighth node number will be given
by ``position(7, 0)`` (in C++, numbering starts at 0 and not 1). If
the number of components for the sequences is not specified, the
default value of 1 is used. Here is a list of some basic operations
that can be performed on :cpp:class:`Array <akantu::Array>`:
- :cpp:func:`resize(size) <akantu::ArrayDataLayer::resize>` change the size of
the :cpp:class:`Array <akantu::Array>`.
- :cpp:func:`clear <akantu::Array::clear>` reset the size of the
:cpp:class:`Array <akantu::Array>` to zero. (*warning* this changed in >
v4.0)
- :cpp:func:`set(t) <akantu::Array::set>` set all entries of the
:cpp:class:`Array <akantu::Array>` to ``t``.
- :cpp:func:`copy(const Array & other) <akantu::Array::copy>` copy another
:cpp:class:`Array <akantu::Array>` into the current one. The two
:cpp:class:`Arrays <akantu::Array>` should have the same number of
components.
- :cpp:func:`push_back(tuple) <akantu::Array::push_back>` append a tuple with
the correct number of components at the end of the :cpp:class:`Array <akantu::Array>`.
- :cpp:func:`erase(i) <akantu::Array::erase>` erase the value at the i-th position.
- :cpp:func:`find(value) <akantu::Array::find>` search ``value`` in the
current :cpp:class:`Array <akantu::Array>`. Return position index of the
first occurence or -1 if not found.
- :cpp:func:`storage() <akantu::Array::storage>` Return the address of the
allocated memory of the :cpp:class:`Array <akantu::Array>`.
Array iterators
---------------
It is very common in ``Akantu`` to loop over arrays to perform a specific treatment.
This ranges from geometric calculation on nodal quantities to tensor algebra (in
constitutive laws for example). The :cpp:class:`Array <akantu::Array>` object
has the possibility to request iterators in order to make the writing of loops
easier and enhance readability. For instance, a loop over the nodal coordinates
can be performed like::
// accessing the nodal coordinates Array
// with spatial_dimension components
const auto & nodes = mesh.getNodes();
for (const auto & coords : make_view(nodes, spatial_dimension)) {
// do what you need ....
}
In that example, each ``coords`` is a :cpp:class:`Vector\<Real\> <akantu::Vector>`
containing geometrical array of size ``spatial_dimension`` and the iteration is
conveniently performed by the :cpp:class:`Array <akantu::Array>` iterator.
The :cpp:class:`Array <akantu::Array>` object is intensively used to store
second order tensor values. In that case, it should be specified that the
returned object type is a matrix when constructing the iterator. This is done
when calling the :cpp:func:`make_view <akantu::make_view>`. For instance,
assuming that we have a :cpp:class:`Array <akantu::Array>` storing stresses, we
can loop over the stored tensors by::
for (const auto & stress :
make_view(stresses, spatial_dimension, spatial_dimension)) {
// stress is of type `const Matrix<Real>&`
}
In that last example, the :cpp:class:`Matrix\<Real\> <akantu::Matrix>` objects are
``spatial_dimension`` :math:`\times` ``spatial_dimension`` matrices. The light
objects :cpp:class:`Matrix\<T\> <akantu::Matrix>` and
:cpp:class:`Vector\<T\> <akantu::Vector>` can be used and combined to do most
common linear algebra. If the number of component is 1, it is possible to use
:cpp:func:`make_view <akantu::make_view>` to this effect.
In general, a mesh consists of several kinds of elements. Consequently, the
amount of data to be stored can differ for each element type. The
straightforward example is the connectivity array, namely the sequences of nodes
belonging to each element (linear triangular elements have fewer nodes than,
say, rectangular quadratic elements etc.). A particular data structure called
:cpp:class:`ElementTypeMapArray\<T\> <akantu::ElementTypeMapArray>` is provided
to easily manage this kind of data. It consists of a group of ``Arrays``, each
associated to an element type. The following code can retrieve the
:cpp:class:`ElementTypeMapArray\<UInt\> <akantu::ElementTypeMapArray>` which
stores the connectivity arrays for a mesh::
const ElementTypeMapArray<UInt> & connectivities =
mesh.getConnectivities();
Then, the specific array associated to a given element type can be obtained by::
const Array<UInt> & connectivity_triangle =
connectivities(_triangle_3);
where the first order 3-node triangular element was used in the presented piece
of code.
Vector & Matrix
```````````````
The :cpp:class:`Array\<T\> <akantu::Array>` iterators as presented in the previous
section can be shaped as :cpp:class:`Vector\<T\> <akantu::Vector>` or
:cpp:class:`Matrix\<T\> <akantu::Matrix>`. This objects represent 1st and 2nd order
tensors. As such they come with some functionalities that we will present a bit
more into detail in this here.
``Vector<T>``
'''''''''''''
- Accessors:
- :cpp:func:`v(i) <akantu::Vector::operator()>` gives the ``i`` -th
component of the vector ``v``
- :cpp:func:`v[i] <akantu::Vector::operator[]>` gives the ``i`` -th
component of the vector ``v``
- :cpp:func:`v.size() <akantu::Vector::size>` gives the number of component
- Level 1: (results are scalars)
- :cpp:func:`v.norm() <akantu::Vector::norm>` returns the geometrical norm
(:math:`L_2`)
- :cpp:func:`v.norm\<N\>() <akantu::Vector::norm<>>` returns the :math:`L_N`
norm defined as :math:`\left(\sum_i |v(i)|^N\right)^{1/N}`. N can take any
positive integer value. There are also some particular values for the most
commonly used norms, ``L_1`` for the Manhattan norm, ``L_2`` for the
geometrical norm and ``L_inf`` for the norm infinity.
- :cpp:func:`v.dot(x) <akantu::Vector::dot>` return the dot product of
``v`` and ``x``
- :cpp:func:`v.distance(x) <akantu::Vector::distance>` return the
geometrical norm of :math:`v - x`
- Level 2: (results are vectors)
- :cpp:func:`v += s <akantu::Vector::operator+=>`,
:cpp:func:`v -= s <akantu::Vector::operator-=>`,
:cpp:func:`v *= s <akantu::Vector::operator*=>`,
:cpp:func:`v /= s <akantu::Vector::operator/=>` those are element-wise
operators that sum, substract, multiply or divide all the component of ``v``
by the scalar ``s``
- :cpp:func:`v += x <akantu::Vector::operator+=>`, :cpp:func:`v -= x
<akantu::Vector::operator-=>` sums or substracts the vector ``x`` to/from
``v``
- :cpp:func:`v.mul(A, x, alpha) <akantu::Vector::mul>` stores the result of
:math:`\alpha \boldsymbol{A} \vec{x}` in ``v``, :math:`\alpha` is equal to 1
by default
- :cpp:func:`v.solve(A, b) <akantu::Vector::solve>` stores the result of
the resolution of the system :math:`\boldsymbol{A} \vec{x} = \vec{b}` in ``v``
- :cpp:func:`v.crossProduct(v1, v2) <akantu::Vector::crossProduct>`
computes the cross product of ``v1`` and ``v2`` and stores the result in
``v``
``Matrix<T>``
'''''''''''''
- Accessors:
- :cpp:func:`A(i, j) <akantu::Matrix::operator()>` gives the component
:math:`A_{ij}` of the matrix ``A``
- :cpp:func:`A(i) <akantu::Matrix::operator()>` gives the :math:`i^{th}`
column of the matrix as a ``Vector``
- :cpp:func:`A[k] <akantu::Matrix::operator[]>` gives the :math:`k^{th}`
component of the matrix, matrices are stored in a column major way, which
means that to access :math:`A_{ij}`, :math:`k = i + j M`
- :cpp:func:`A.rows() <akantu::Matrix::rows>` gives the number of rows of
``A`` (:math:`M`)
- :cpp:func:`A.cols() <akantu::Matrix::cols>` gives the number of columns
of ``A`` (:math:`N`)
- :cpp:func:`A.size() <akantu::Matrix::size>` gives the number of component
in the matrix (:math:`M \times N`)
- Level 1: (results are scalars)
- :cpp:func:`A.norm() <akantu::Matrix::norm>` is equivalent to
``A.norm<L_2>()``
- :cpp:func:`A.norm\<N\>() <akantu::Matrix::norm<>>` returns the :math:`L_N`
norm defined as :math:`\left(\sum_i\sum_j |A(i,j)|^N\right)^{1/N}`. N can take
any positive integer value. There are also some particular values for the most
commonly used norms, ``L_1`` for the Manhattan norm, ``L_2`` for the
geometrical norm and ``L_inf`` for the norm infinity.
- :cpp:func:`A.trace() <akantu::Matrix::trace>` return the trace of ``A``
- :cpp:func:`A.det() <akantu::Matrix::det>` return the determinant of ``A``
- :cpp:func:`A.doubleDot(B) <akantu::Matrix::doubleDot>` return the double
dot product of ``A`` and ``B``, :math:`\mat{A}:\mat{B}`
- Level 3: (results are matrices)
- :cpp:func:`A.eye(s) <akantu::Matrix::eye>`, ``Matrix<T>::eye(s)``
fills/creates a matrix with the :math:`s\mat{I}` with :math:`\mat{I}` the
identity matrix
- :cpp:func:`A.inverse(B) <akantu::Matrix::inverse>` stores
:math:`\mat{B}^{-1}` in ``A``
- :cpp:func:`A.transpose() <akantu::Matrix::transpose>` returns
:math:`\mat{A}^{t}`
- :cpp:func:`A.outerProduct(v1, v2) <akantu::Matrix::outerProduct>` stores
:math:`\vec{v_1} \vec{v_2}^{t}` in ``A``
- :cpp:func:`C.mul\<t_A, t_B\>(A, B, alpha) <akantu::Matrix::mul>`: stores
the result of the product of ``A`` and code{B} time the scalar ``alpha`` in
``C``. ``t_A`` and ``t_B`` are boolean defining if ``A`` and ``B`` should be
transposed or not.
+----------+----------+--------------+
|``t_A`` |``t_B`` |result |
| | | |
+----------+----------+--------------+
|false |false |:math:`\mat{C}|
| | |= \alpha |
| | |\mat{A} |
| | |\mat{B}` |
| | | |
+----------+----------+--------------+
|false |true |:math:`\mat{C}|
| | |= \alpha |
| | |\mat{A} |
| | |\mat{B}^t` |
| | | |
+----------+----------+--------------+
|true |false |:math:`\mat{C}|
| | |= \alpha |
| | |\mat{A}^t |
| | |\mat{B}` |
| | | |
+----------+----------+--------------+
|true |true |:math:`\mat{C}|
| | |= \alpha |
| | |\mat{A}^t |
| | |\mat{B}^t` |
+----------+----------+--------------+
- :cpp:func:`A.eigs(d, V) <akantu::Matrix::eigs>` this method computes the
eigenvalues and eigenvectors of ``A`` and store the results in ``d`` and
``V`` such that :math:`d(i) = \lambda_i` and :math:`V(i) = \vec{v_i}` with
:math:`\mat{A}\vec{v_i} = \lambda_i\vec{v_i}` and :math:`\lambda_1 > ... >
\lambda_i > ... > \lambda_N`
.. _sect-common-groups:
Mesh
----
Manipulating group of nodes and/or elements
```````````````````````````````````````````
``Akantu`` provides the possibility to manipulate subgroups of elements and
nodes. Any :cpp:class:`ElementGroup <akantu::ElementGroup>` and/or
:cpp:class:`NodeGroup <akantu::NodeGroup>` must be managed by a
:cpp:class:`GroupManager <akantu::GroupManager>`. Such a manager has the role to
associate group objects to names. This is a useful feature, in particular for
the application of the boundary conditions, as will be demonstrated in section
:ref:`sect-smm-boundary`. To most general group manager is the :cpp:class:`Mesh
<akantu::Mesh>` class which inherits from :cpp:class:`GroupManager
<akantu::GroupManager>`.
For instance, the following code shows how to request an element group
to a mesh:
.. code-block:: c++
// request creation of a group of nodes
NodeGroup & my_node_group = mesh.createNodeGroup("my_node_group");
// request creation of a group of elements
ElementGroup & my_element_group = mesh.createElementGroup("my_element_group");
/* fill and use the groups */
The ``NodeGroup`` object
''''''''''''''''''''''''
A group of nodes is stored in :cpp:class:`NodeGroup <akantu::NodeGroup>`
objects. They are quite simple objects which store the indexes of the selected
nodes in a :cpp:class:`Array\<UInt\> <akantu::Array>`. Nodes are selected by
adding them when calling :cpp:func:`add <akantu::NodeGroup::add>`. For instance
you can select nodes having a positive :math:`X` coordinate with the following
code:
.. code-block:: c++
const auto & nodes = mesh.getNodes();
auto & group = mesh.createNodeGroup("XpositiveNode");
for (auto && data : enumerate(make_view(nodes, spatial_dimension))){
auto node = std::get<0>(data);
const auto & position = std::get<1>(data);
if (position(0) > 0) group.add(node);
}
The ``ElementGroup`` object
'''''''''''''''''''''''''''
A group of elements is stored in :cpp:class:`ElementGroup
<akantu::ElementGroup>` objects. Since a group can contain elements of various
types the :cpp:class:`ElementGroup <akantu::ElementGroup>` object stores indexes
in a :cpp:class:`ElementTypeMapArray\<UInt\> <akantu::ElementTypeMapArray>`
object. Then elements can be added to the group by calling :cpp:func:`add
<akantu::ElementGroup::add>`.
For instance, selecting the elements for which the barycenter of the
nodes has a positive :math:`X` coordinate can be made with:
.. code-block:: c++
auto & group = mesh.createElementGroup("XpositiveElement");
Vector<Real> barycenter(spatial_dimension);
for_each_element(mesh, [&](auto && element) {
mesh.getBarycenter(element, barycenter);
if (barycenter(_x) > 0.) { group.add(element); }
});
diff --git a/doc/dev-doc/requirements.txt b/doc/dev-doc/requirements.txt
index b5fab5270..928953b0e 100644
--- a/doc/dev-doc/requirements.txt
+++ b/doc/dev-doc/requirements.txt
@@ -1,5 +1,6 @@
sphinx==3.4.3
-jinja2==3.0.1
-gitpython==3.1.18
+sphinx-rtd-theme==0.5.2
sphinxcontrib-bibtex==2.3.0
breathe==4.30.0
+jinja2==3.0.1
+gitpython==3.1.18
diff --git a/doc/manual/CMakeLists.txt b/doc/manual/CMakeLists.txt
index e9677205f..23a6529ce 100644
--- a/doc/manual/CMakeLists.txt
+++ b/doc/manual/CMakeLists.txt
@@ -1,168 +1,169 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Tue Jan 19 2016
+# @date last modification: Wed Jan 22 2020
#
# @brief Build the documentation
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#------------------------------------------------------------------------------#
function(get_doc_label pkg_name label)
string(REPLACE "_" "-" _pkg_tex_label_dash ${pkg_name})
string(TOLOWER "${_pkg_tex_label_dash}" _pkg_tex_label)
set(TOLOWER "${_pkg_tex_label_dash}" _pkg_tex_label)
set(${label} "pkg:${_pkg_tex_label}" PARENT_SCOPE)
endfunction()
function(get_doc_package_name pkg_name pkg_tex)
_package_get_option_name(${pkg_name} _opt_name)
string(REPLACE "_" "\\_" _pkg_tex "${_opt_name}")
set(${pkg_tex} ${_pkg_tex} PARENT_SCOPE)
endfunction()
#------------------------------------------------------------------------------#
function(generate_package_dependency_tex_doc pkg_name FILENAME LEVEL)
_package_get_option_name(${pkg_name} _opt_name)
string(REPLACE "_" "\\_" _pkg_tex "${_opt_name}")
get_doc_label(${pkg_name} _pkg_tex_label)
file(APPEND ${FILENAME} "\\AkantuPackageNameWithLabel{${_pkg_tex}}{${_pkg_tex_label}}{${LEVEL}}\\allowbreak\\xspace")
math(EXPR _sub_level "${LEVEL}+1")
_package_get_dependencies(${pkg_name} PRIVATE _private_dependencies)
_package_get_dependencies(${pkg_name} INTERFACE _interface_dependencies)
foreach(_dep_pkg_name ${_private_dependencies} ${_interface_dependencies})
generate_package_dependency_tex_doc(${_dep_pkg_name} ${FILENAME} ${_sub_level})
endforeach()
endfunction()
#------------------------------------------------------------------------------#
function(generate_package_tex_doc pkg_name FILENAME)
get_doc_package_name(${pkg_name} _pkg_tex)
get_doc_label(${pkg_name} _pkg_tex_label)
file(APPEND ${FILENAME} "\n\\begin{AkantuPackage}{${_pkg_tex}}{${_pkg_tex_label}}")
_package_get_documentation(${pkg_name} _doc)
if (_doc)
file(APPEND ${FILENAME} "${_doc}")
else()
_package_get_filename(${pkg_name} _file_path)
_package_get_real_name(${pkg_name} _pkg)
get_filename_component(_file ${_file_path} NAME)
string(REPLACE "_" "\\_" _escaped_file "${_file}")
string(REPLACE "_" "\\_" _escaped_pkg "${_pkg}")
set(_missing_doc
"{\\color{red} TODO}: No Documentation in {\\color{blue} \\href{${_file_path}}{${_escaped_file}}}"
""
"looking for the sequence: "
"\\begin{cmake}"
"\\package_declare_documentation("
" ${_escaped_pkg}"
" \"documentation text\""
" )"
"\\end{cmake}")
set(_missing_doc_str "")
foreach(_str ${_missing_doc})
set(_missing_doc_str "${_missing_doc_str}\n${_str}")
endforeach()
file(APPEND ${FILENAME} "${_missing_doc_str}")
endif()
_package_get_dependencies(${pkg_name} PRIVATE _private_dependencies)
_package_get_dependencies(${pkg_name} INTERFACE _interface_dependencies)
if(_private_dependencies OR _interface_dependencies)
file(APPEND ${FILENAME} "\n\\begin{AkantuPackageDependencies}")
foreach(_dep_pkg_name ${_private_dependencies} ${_interface_dependencies})
generate_package_dependency_tex_doc(${_dep_pkg_name} ${FILENAME} 1)
endforeach()
file(APPEND ${FILENAME} "\n\\end{AkantuPackageDependencies}")
endif()
file(APPEND ${FILENAME} "\n\\end{AkantuPackage}
")
endfunction()
#------------------------------------------------------------------------------#
#------------------------------------------------------------------------------#
set(AKANTU_MANUAL_SOURCE_FOLDER ${CMAKE_CURRENT_BINARY_DIR}/latex)
set(DOC_DEPS_TEX_FILENAME "${AKANTU_MANUAL_SOURCE_FOLDER}/manual-packages-doc.tex")
file(WRITE ${DOC_DEPS_TEX_FILENAME} "")
find_program(RUBBER_EXECUTABLE rubber)
if (NOT RUBBER_EXECUTABLE)
message(ERROR "Manual cannot be built without rubber latex compiler")
endif()
mark_as_advanced(RUBBER_EXECUTABLE)
package_get_all_documentation_files(_manual_files)
set(AKANTU_MANUAL_FILES_DEPEND)
set(AKANTU_MANUAL_FILES_COPY_COMMAND)
file(MAKE_DIRECTORY ${AKANTU_MANUAL_SOURCE_FOLDER})
foreach(_f ${_manual_files})
file(RELATIVE_PATH _rel_f ${CMAKE_CURRENT_SOURCE_DIR} "${_f}")
list(APPEND AKANTU_MANUAL_FILES_DEPEND ${_f})
list(APPEND AKANTU_MANUAL_FILES_COPY_COMMAND
COMMAND ${CMAKE_COMMAND} -E copy_if_different "${CMAKE_CURRENT_SOURCE_DIR}/${_rel_f}" "${_rel_f}")
endforeach()
set(MANUAL_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/akantu_ug-v${AKANTU_VERSION}.pdf)
add_custom_command(
OUTPUT ${MANUAL_OUTPUT}
DEPENDS ${AKANTU_MANUAL_FILES_DEPEND} ${DOC_DEPS_TEX_FILENAME}
${AKANTU_MANUAL_FILES_COPY_COMMAND}
COMMAND ${RUBBER_EXECUTABLE} -dfq manual
COMMAND ${CMAKE_COMMAND} -E copy manual.pdf ${MANUAL_OUTPUT}
WORKING_DIRECTORY ${AKANTU_MANUAL_SOURCE_FOLDER}
COMMENT "Compiling the user's manual"
)
set_directory_properties(latex/$)
add_custom_target(manual ALL DEPENDS ${MANUAL_OUTPUT})
install(FILES ${MANUAL_OUTPUT}
DESTINATION ${CMAKE_INSTALL_DOCDIR})
package_get_all_activated_packages(_package_list)
foreach (_pkg_name ${_package_list})
generate_package_tex_doc(${_pkg_name} ${DOC_DEPS_TEX_FILENAME})
endforeach()
configure_file(version-definition.tex.in "${AKANTU_MANUAL_SOURCE_FOLDER}/version-definition.tex" @ONLY)
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index 5a44de139..f94b0104a 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -1,55 +1,54 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Oct 22 2010
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Tue Oct 23 2018
#
# @brief List of examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_example(new_material "Example on how to add a new material in Akantu" PACKAGE core)
add_example(boundary_conditions "Example on hoy to set boundary conditions" PACKAGE core)
add_example(explicit "Example on how to run an explicit simulation" PACKAGE core)
add_example(io "Example on how to perform Input/Output operations" PACKAGE core)
add_example(implicit "Example on how to run an implicit simulation" PACKAGE implicit)
add_example(static "Example on how to run a static simulation" PACKAGE implicit)
add_example(parallel "Example of how to write a parallel code with Akantu" PACKAGE parallel)
add_example(cohesive_element "Cohesive element examples" PACKAGE cohesive_element)
add_example(structural_mechanics "Structural mechanics model examples" PACKAGE structural_mechanics)
add_example(heat_transfer "Example on how to run heat transfer simulation" PACKAGE heat_transfer)
add_example(python "Example on how to use the python interface" PACKAGE python_interface)
add_example(embedded "Example on how to run embedded model simulation" PACKAGE embedded)
add_example(contact_mechanics "Example on how to run contact mechanics model simulation" PACKAGE contact_mechanics)
add_example(phase_field "Example on how to run phase field model simulation" PACKAGE phase_field)
package_add_files_to_package(
examples/README.rst
cmake/AkantuExampleMacros.cmake
)
diff --git a/examples/boundary_conditions/CMakeLists.txt b/examples/boundary_conditions/CMakeLists.txt
index 05bdc3d42..bc5089378 100644
--- a/examples/boundary_conditions/CMakeLists.txt
+++ b/examples/boundary_conditions/CMakeLists.txt
@@ -1,36 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Wed Dec 16 2015
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Tue Feb 18 2020
#
# @brief CMakeLists for the cohesive examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_example(predefined_bc
"Example of predefined boundary condition" PACKAGE core)
add_example(user_defined_bc
"Example of user defined boundary condition" PACKAGE core)
add_example(python_user_defined_bc
"Example of python user defined boundary condition" PACKAGE pybind11)
diff --git a/examples/boundary_conditions/predefined_bc/CMakeLists.txt b/examples/boundary_conditions/predefined_bc/CMakeLists.txt
index 8d7036691..ec8e1af08 100644
--- a/examples/boundary_conditions/predefined_bc/CMakeLists.txt
+++ b/examples/boundary_conditions/predefined_bc/CMakeLists.txt
@@ -1,37 +1,37 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
#
-# @date creation: Wed Dec 16 2015
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Jan 22 2016
#
# @brief boundary condition example configuration
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(predefined_bc_mesh square.geo 2 1)
register_example(predefined_bc SOURCES predefined_bc.cc
DEPENDS predefined_bc_mesh
FILES_TO_COPY material.dat)
diff --git a/examples/boundary_conditions/predefined_bc/predefined_bc.cc b/examples/boundary_conditions/predefined_bc/predefined_bc.cc
index 7727c1459..4294771ef 100644
--- a/examples/boundary_conditions/predefined_bc/predefined_bc.cc
+++ b/examples/boundary_conditions/predefined_bc/predefined_bc.cc
@@ -1,60 +1,64 @@
/**
* @file predefined_bc.cc
*
+ * @author Zineb Fouad <zineb.fouad@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Dec 16 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Wed Aug 04 2010
+ * @date last modification: Wed Feb 06 2019
*
- * @brief boundary condition example
+ * @brief Example showing how to set boundary conditions
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Mesh mesh(2);
mesh.read("square.msh");
// model initialization
SolidMechanicsModel model(mesh);
model.initFull();
// Dirichlet boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "Fixed_x");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "Fixed_y");
// output in a paraview file
model.setBaseName("plate");
model.addDumpFieldVector("displacement");
model.addDumpField("blocked_dofs");
model.addDumpField("external_force");
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/boundary_conditions/python_user_defined_bc/CMakeLists.txt b/examples/boundary_conditions/python_user_defined_bc/CMakeLists.txt
index 292903124..9dddc776d 100644
--- a/examples/boundary_conditions/python_user_defined_bc/CMakeLists.txt
+++ b/examples/boundary_conditions/python_user_defined_bc/CMakeLists.txt
@@ -1,14 +1,47 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Mathias Lebihain <mathias.lebihain@enpc.fr>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Tue Feb 18 2020
+# @date last modification: Wed Feb 26 2020
+#
+# @brief Python examples
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(python_user_defined_bc_mesh fine_mesh.geo 2 1)
register_example(python_user_defined_bc
SOURCES python_user_defined_bc.cc
DEPENDS python_user_defined_bc_mesh
PYTHON
FILES_TO_COPY boundary_condition.py material.dat
)
target_include_directories(python_user_defined_bc
PRIVATE ${PROJECT_SOURCE_DIR}/python)
target_link_libraries(python_user_defined_bc
PRIVATE pybind11::embed)
diff --git a/examples/boundary_conditions/python_user_defined_bc/boundary_condition.py b/examples/boundary_conditions/python_user_defined_bc/boundary_condition.py
index da316c990..58184d8f0 100644
--- a/examples/boundary_conditions/python_user_defined_bc/boundary_condition.py
+++ b/examples/boundary_conditions/python_user_defined_bc/boundary_condition.py
@@ -1,13 +1,26 @@
#!/usr/bin/env python3
+
+""" boundary_condition.py: User defined boundary condition example"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import math
class SinBoundary:
def __init__(self, amplitude, phase):
self.amplitude = amplitude
self.phase = phase
def compute(self, disp, coord, flags):
disp[1] = - self.amplitude * math.sin(self.phase * coord[1])
flags[1] = True
diff --git a/examples/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc b/examples/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
index 33b5107be..215ad901f 100644
--- a/examples/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
+++ b/examples/boundary_conditions/python_user_defined_bc/python_user_defined_bc.cc
@@ -1,90 +1,97 @@
/**
* @file python_user_defined_bc.cc
*
- * @brief python-user-defined boundary condition example
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
+ * @date creation: Wed Aug 04 2010
+ * @date last modification: Tue Sep 08 2020
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @brief user define boundary condition example
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <iostream>
#include <pybind11/embed.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
using namespace akantu;
class PYBIND11_EXPORT SineBoundary : public BC::Dirichlet::DirichletFunctor {
public:
SineBoundary(Real amplitude, Real phase) {
py_module = py::module::import("boundary_condition");
py_sin_boundary = py_module.attr("SinBoundary")(amplitude, phase);
}
public:
inline void operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
py_sin_boundary.attr("compute")(primal, coord, flags);
}
protected:
py::object py_sin_boundary;
py::module py_module;
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
py::scoped_interpreter guard{};
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("fine_mesh.msh");
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
/// boundary conditions
Vector<Real> traction(2, 0.2);
SineBoundary sin_boundary(.2, 10.);
model.applyBC(sin_boundary, "Fixed_x");
model.applyBC(BC::Dirichlet::FixedValue(0., _y), "Fixed_y");
model.applyBC(BC::Neumann::FromTraction(traction), "Traction");
// output a paraview file with the boundary conditions
model.setBaseName("plate");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("external_force");
model.addDumpField("blocked_dofs");
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/boundary_conditions/user_defined_bc/CMakeLists.txt b/examples/boundary_conditions/user_defined_bc/CMakeLists.txt
index 920781217..33a7491ae 100644
--- a/examples/boundary_conditions/user_defined_bc/CMakeLists.txt
+++ b/examples/boundary_conditions/user_defined_bc/CMakeLists.txt
@@ -1,39 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Wed Dec 16 2015
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Jan 22 2016
#
# @brief boundary condition example configuration
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(user_defined_bc_mesh fine_mesh.geo 2 1)
register_example(user_defined_bc
SOURCES user_defined_bc.cc
DEPENDS user_defined_bc_mesh
FILES_TO_COPY material.dat
)
diff --git a/examples/boundary_conditions/user_defined_bc/user_defined_bc.cc b/examples/boundary_conditions/user_defined_bc/user_defined_bc.cc
index 6bad0e280..e098d96f1 100644
--- a/examples/boundary_conditions/user_defined_bc/user_defined_bc.cc
+++ b/examples/boundary_conditions/user_defined_bc/user_defined_bc.cc
@@ -1,87 +1,90 @@
/**
* @file user_defined_bc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Dec 16 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Wed Aug 04 2010
+ * @date last modification: Wed Feb 06 2019
*
- * @brief user-defined boundary condition example
+ * @brief example of boundary conditions
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class SineBoundary : public BC::Dirichlet::DirichletFunctor {
public:
SineBoundary(Real amp, Real phase, BC::Axis ax = _x)
: DirichletFunctor(ax), amplitude(amp), phase(phase) {}
public:
inline void operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(axis) = true;
primal(axis) = -amplitude * std::sin(phase * coord(1));
}
protected:
Real amplitude;
Real phase;
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("fine_mesh.msh");
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
/// boundary conditions
Vector<Real> traction(2, 0.2);
model.applyBC(SineBoundary(.2, 10., _x), "Fixed_x");
model.applyBC(BC::Dirichlet::FixedValue(0., _y), "Fixed_y");
model.applyBC(BC::Neumann::FromTraction(traction), "Traction");
// output a paraview file with the boundary conditions
model.setBaseName("plate");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("external_force");
model.addDumpField("blocked_dofs");
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/cohesive_element/CMakeLists.txt b/examples/cohesive_element/CMakeLists.txt
index fff54c3b8..4d01b7745 100644
--- a/examples/cohesive_element/CMakeLists.txt
+++ b/examples/cohesive_element/CMakeLists.txt
@@ -1,38 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Tue Jan 12 2016
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Fri Mar 16 2018
+#
+# @brief Cohesive element examples compilation
#
-# @brief CMakeLists for the cohesive examples
#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_example(cohesive_extrinsic "Extrinsic cohesive element" PACKAGE cohesive_element)
-add_example(cohesive_intrinsic "Intrinsic cohesive element" PACKAGE cohesive_element )
+add_example(cohesive_intrinsic "Intrinsic cohesive element" PACKAGE cohesive_element)
add_example(cohesive_extrinsic_ig_tg
"Extrinsic cohesive element with intergranular and transgranular material properties"
PACKAGE cohesive_element)
-
-#add_example(cohesive_extrinsic_implicit "Extrinsic cohesive element in implicit" PACKAGE cohesive_element)
diff --git a/examples/cohesive_element/cohesive_extrinsic/CMakeLists.txt b/examples/cohesive_element/cohesive_extrinsic/CMakeLists.txt
index b3de41926..b49dc219d 100644
--- a/examples/cohesive_element/cohesive_extrinsic/CMakeLists.txt
+++ b/examples/cohesive_element/cohesive_extrinsic/CMakeLists.txt
@@ -1,39 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Mon Mar 15 2021
+#
+# @brief Cohesive element examples in extrinsic compilation
#
-# @brief configuration for extrinsic cohesive elements
#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#add_mesh(cohesive_extrinsic_mesh triangle.geo 2 2)
register_example(cohesive_extrinsic
SOURCES cohesive_extrinsic.cc
#DEPENDS cohesive_extrinsic_mesh
FILES_TO_COPY material.dat triangle.msh
)
diff --git a/examples/cohesive_element/cohesive_extrinsic/cohesive_extrinsic.cc b/examples/cohesive_element/cohesive_extrinsic/cohesive_extrinsic.cc
index c444d4ba8..7b347c4d5 100644
--- a/examples/cohesive_element/cohesive_extrinsic/cohesive_extrinsic.cc
+++ b/examples/cohesive_element/cohesive_extrinsic/cohesive_extrinsic.cc
@@ -1,124 +1,129 @@
/**
* @file cohesive_extrinsic.cc
*
+ * @author Zineb Fouad <zineb.fouad@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Tue May 08 2012
+ * @date last modification: Wed Feb 06 2019
*
- * @brief Test for cohesive elements
+ * @brief Cohesive element examples in extrinsic
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 1000;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = true);
Real time_step = model.getStableTimeStep() * 0.05;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
CohesiveElementInserter & inserter = model.getElementInserter();
inserter.setLimit(_y, 0.30, 0.20);
model.updateAutomaticInsertion();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.dump();
/// initial conditions
Real loading_rate = 0.5;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
displacement(n, 1) += disp_update * position(n, 1);
}
model.checkCohesiveStress();
model.solveStep();
if (s % 10 == 0) {
model.dump();
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 200 * std::sqrt(2);
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt b/examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt
index 44f6e456c..590a61177 100644
--- a/examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt
+++ b/examples/cohesive_element/cohesive_extrinsic_ig_tg/CMakeLists.txt
@@ -1,37 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Tue Feb 18 2020
+#
+# @brief compilation of Cohesive element examples in extrinsic with 2 different bulk
+# materials
#
-# @brief Configuration for cohesive_extrinsic_IG_TG
#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
add_mesh(cohesive_extrinsic_ig_tg_mesh triangle.geo DIM 2 ORDER 1 OUTPUT square.msh)
register_example(cohesive_extrinsic_ig_tg
SOURCES cohesive_extrinsic_ig_tg.cc
DEPENDS cohesive_extrinsic_ig_tg_mesh
FILES_TO_COPY material.dat
)
diff --git a/examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc b/examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
index 35a2d3bf1..5c548a019 100644
--- a/examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
+++ b/examples/cohesive_element/cohesive_extrinsic_ig_tg/cohesive_extrinsic_ig_tg.cc
@@ -1,152 +1,153 @@
/**
* @file cohesive_extrinsic_ig_tg.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Jan 19 2021
*
- * @brief Test for considering different cohesive properties for intergranular
- * (IG) and
- * transgranular (TG) fractures in extrinsic cohesive elements
+ * @brief Cohesive element examples in extrinsic with 2 different bulk materials
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
class Velocity : public BC::Dirichlet::DirichletFunctor {
public:
explicit Velocity(SolidMechanicsModel & model, Real vel, BC::Axis ax = _x)
: DirichletFunctor(ax), model(model), vel(vel) {
disp = vel * model.getTimeStep();
}
public:
inline void operator()(UInt node, Vector<bool> & /*flags*/,
Vector<Real> & disp,
const Vector<Real> & coord) const {
Real sign = std::signbit(coord(axis)) ? -1. : 1.;
disp(axis) += sign * this->disp;
model.getVelocity()(node, axis) = sign * vel;
}
private:
SolidMechanicsModel & model;
Real vel, disp;
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 1000;
Mesh mesh(spatial_dimension);
mesh.read("square.msh");
SolidMechanicsModelCohesive model(mesh);
MaterialCohesiveRules rules{{{"btop", "bbottom"}, "tg_cohesive"},
{{"btop", "btop"}, "ig_cohesive"},
{{"bbottom", "bbottom"}, "ig_cohesive"}};
/// model initialization
auto cohesive_material_selector =
std::make_shared<MaterialCohesiveRulesSelector>(model, rules);
auto bulk_material_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
auto && current_selector = model.getMaterialSelector();
cohesive_material_selector->setFallback(bulk_material_selector);
bulk_material_selector->setFallback(current_selector);
model.setMaterialSelector(cohesive_material_selector);
model.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = true);
Real time_step = model.getStableTimeStep() * 0.05;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
auto & position = mesh.getNodes();
auto & velocity = model.getVelocity();
model.applyBC(BC::Dirichlet::FlagOnly(_y), "top");
model.applyBC(BC::Dirichlet::FlagOnly(_y), "bottom");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "left");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "right");
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("material_index");
model.dump();
/// initial conditions
Real loading_rate = 0.1;
// bar_height = 2
Real VI = loading_rate * 2 * 0.5;
for (auto && data : zip(make_view(position, spatial_dimension),
make_view(velocity, spatial_dimension))) {
std::get<1>(data) = loading_rate * std::get<0>(data);
}
model.dump();
Velocity vely(model, VI, _y);
Velocity velx(model, VI, _x);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.applyBC(vely, "top");
model.applyBC(vely, "bottom");
model.applyBC(velx, "left");
model.applyBC(velx, "right");
model.checkCohesiveStress();
model.solveStep();
if (s % 10 == 0) {
model.dump();
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
return 0;
}
diff --git a/examples/cohesive_element/cohesive_extrinsic_implicit/CMakeLists.txt b/examples/cohesive_element/cohesive_extrinsic_implicit/CMakeLists.txt
deleted file mode 100644
index 9f1038539..000000000
--- a/examples/cohesive_element/cohesive_extrinsic_implicit/CMakeLists.txt
+++ /dev/null
@@ -1,39 +0,0 @@
-#===============================================================================
-# @file CMakeLists.txt
-#
-# @author Mauro Corrado <mauro.corrado@epfl.ch>
-#
-# @date creation: Tue Jan 12 2016
-# @date last modification: Mon Jan 18 2016
-#
-# @brief Example for extrinsic cohesive elements in implicit
-#
-# @section LICENSE
-#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
-#
-#===============================================================================
-
-add_mesh(cohesive_extrinsic_implicit_mesh dcb_2d.geo 2 2)
-
-register_example(cohesive_extrinsic_implicit
- SOURCES cohesive_extrinsic_implicit.cc
- DEPENDS cohesive_extrinsic_implicit_mesh
- FILES_TO_COPY material.dat)
-
diff --git a/examples/cohesive_element/cohesive_extrinsic_implicit/cohesive_extrinsic_implicit.cc b/examples/cohesive_element/cohesive_extrinsic_implicit/cohesive_extrinsic_implicit.cc
deleted file mode 100644
index f06bdab75..000000000
--- a/examples/cohesive_element/cohesive_extrinsic_implicit/cohesive_extrinsic_implicit.cc
+++ /dev/null
@@ -1,172 +0,0 @@
-/**
- * @file cohesive_extrinsic_implicit.cc
- *
- * @author Nicolas Richart <nicolas.richart@epfl.ch>
- *
- * @date creation: Tue Jan 12 2016
- * @date last modification: Mon Jan 18 2016
- *
- * @brief Example for extrinsic cohesive elements in implicit
- *
- *
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
- *
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-#include "solid_mechanics_model_cohesive.hh"
-/* -------------------------------------------------------------------------- */
-#include <iostream>
-/* -------------------------------------------------------------------------- */
-
-using namespace akantu;
-
-int main(int argc, char * argv[]) {
- initialize("material.dat", argc, argv);
-
- debug::setDebugLevel(dblError);
-
- const UInt spatial_dimension = 2;
- const UInt max_steps = 20;
- const Real final_opening = 1e-4;
-
- Mesh mesh(spatial_dimension);
- mesh.read("dcb_2d.msh");
-
- SolidMechanicsModelCohesive model(mesh);
-
- /// model initialization
- model.initFull(SolidMechanicsModelCohesiveOptions(_static, true));
-
- // CohesiveElementInserter inserter(mesh);
- model.limitInsertion(_y, -0.000001, 0.000001);
- model.updateAutomaticInsertion();
-
- Real eps = 1e-11;
- Array<bool> & boundary = model.getBlockedDOFs();
- Array<Real> & position = mesh.getNodes();
- Array<Real> & displacement = model.getDisplacement();
-
- /// boundary conditions
- const Vector<Real> & lower = mesh.getLowerBounds();
- const Vector<Real> & upper = mesh.getUpperBounds();
- const Real left = lower[0];
- const Real right = upper[0];
-
- for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
- if (std::abs(position(n, 0) - left) < eps) {
- boundary(n, 1) = true;
- boundary(n, 0) = true;
- }
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) < 0.0)
- boundary(n, 1) = true;
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) > 0.0)
- boundary(n, 1) = true;
- }
-
- model.setBaseName("extr_impl");
- model.addDumpFieldVector("displacement");
- model.addDumpField("external_force");
- model.addDumpField("internal_force");
- model.addDumpField("stress");
- model.addDumpField("partitions");
- model.dump();
-
- // Dumping cohesive elements
- model.setBaseNameToDumper("cohesive elements", "cohe_elem_extr_impl");
- model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
- model.addDumpFieldToDumper("cohesive elements", "damage");
- model.dump("cohesive elements");
-
- // model.updateResidual();
-
- Real increment = final_opening / max_steps;
- Real tolerance = 1e-13;
- Real error;
- bool load_reduction = false;
- Real tol_increase_factor = 1.0e8;
-
- /// Main loop
- for (UInt nstep = 0; nstep < max_steps; ++nstep) {
- std::cout << "step no. " << nstep << std::endl;
-
- for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) > 0.0)
- displacement(n, 1) += increment;
-
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) < 0.0)
- displacement(n, 1) -= increment;
- }
-
- model.solveStepCohesive<_scm_newton_raphson_tangent,
- SolveConvergenceCriteria::_increment>(
- tolerance, error, 25, load_reduction, tol_increase_factor);
-
- // If convergence has not been reached, the load is reduced and
- // the incremental step is solved again.
- while (!load_reduction && error > tolerance) {
- load_reduction = true;
-
- std::cout << "LOAD STEP REDUCTION" << std::endl;
- increment = increment / 2.0;
-
- for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) > 0.0)
- displacement(n, 1) -= increment;
-
- if (std::abs(position(n, 0) - right) < eps && position(n, 1) < 0.0)
- displacement(n, 1) += increment;
- }
-
- UInt nb_cohesive_elements =
- mesh.getNbElement(spatial_dimension, _not_ghost, _ek_cohesive);
-
- model.solveStepCohesive<_scm_newton_raphson_tangent,
- SolveConvergenceCriteria::_increment>(
- tolerance, error, 25, load_reduction, tol_increase_factor);
-
- UInt new_nb_cohesive_elements =
- mesh.getNbElement(spatial_dimension, _not_ghost, _ek_cohesive);
-
- UInt nb_cohe[2];
- nb_cohe[0] = nb_cohesive_elements;
- nb_cohe[1] = new_nb_cohesive_elements;
-
- // Every time a new cohesive element is introduced, the variable
- // load_reduction is set to false, so that it is possible to
- // further iterate in the loop of load reduction. If no new
- // cohesive elements are introduced, usually there is no gain in
- // further reducing the load, even if convergence is not reached
- if (nb_cohe[0] == nb_cohe[1])
- load_reduction = true;
- else
- load_reduction = false;
- }
-
- model.dump();
- model.dump("cohesive elements");
-
- UInt nb_cohe_elems[1];
- nb_cohe_elems[0] =
- mesh.getNbElement(spatial_dimension, _not_ghost, _ek_cohesive);
- std::cout << "No. of cohesive elements: " << nb_cohe_elems[0] << std::endl;
- }
-
- finalize();
-
- return EXIT_SUCCESS;
-}
diff --git a/examples/cohesive_element/cohesive_extrinsic_implicit/dcb_2d.geo b/examples/cohesive_element/cohesive_extrinsic_implicit/dcb_2d.geo
deleted file mode 100644
index 3e7c9b5e4..000000000
--- a/examples/cohesive_element/cohesive_extrinsic_implicit/dcb_2d.geo
+++ /dev/null
@@ -1,26 +0,0 @@
-dx = 0.005;
-
-Point(1) = {0,0,0,dx};
-Point(2) = {0,0.05,0,dx};
-Point(3) = {0,-0.05,0,dx};
-Point(4) = {0.3,0,0,dx};
-Point(5) = {0.3,0.05,0,dx};
-Point(6) = {0.3,-0.05,0,dx};
-Line(1) = {1, 2};
-Line(2) = {2, 5};
-Line(3) = {5, 4};
-Line(4) = {1, 4};
-Line(5) = {1, 3};
-Line(6) = {6, 4};
-Line(7) = {3, 6};
-Line Loop(8) = {2, 3, -4, 1};
-Plane Surface(9) = {-8};
-Line Loop(10) = {5, 7, 6, -4};
-Plane Surface(11) = {10};
-Physical Surface("bulk") = {9,11};
-Physical Line("coh") = {4};
-
-Transfinite Surface "*";
-Recombine Surface "*";
-
-Mesh.SecondOrderIncomplete = 1;
diff --git a/examples/cohesive_element/cohesive_extrinsic_implicit/material.dat b/examples/cohesive_element/cohesive_extrinsic_implicit/material.dat
deleted file mode 100644
index 51c416afc..000000000
--- a/examples/cohesive_element/cohesive_extrinsic_implicit/material.dat
+++ /dev/null
@@ -1,18 +0,0 @@
-material elastic [
- name = bulk
- rho = 2500 # density
- E = 70e9 # young's modulus
- nu = 0.29 # poisson's ratio
-
-]
-
-material cohesive_linear [
- name = interface
- beta = 1
- G_c = 4.5e2
- kappa = 1
- penalty = 1.0e7
- sigma_c = 1.5e6
- contact_after_breaking = true
-]
-
diff --git a/examples/cohesive_element/cohesive_intrinsic/CMakeLists.txt b/examples/cohesive_element/cohesive_intrinsic/CMakeLists.txt
index a149423a4..0219a8680 100644
--- a/examples/cohesive_element/cohesive_intrinsic/CMakeLists.txt
+++ b/examples/cohesive_element/cohesive_intrinsic/CMakeLists.txt
@@ -1,37 +1,38 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Mon Mar 15 2021
+#
+# @brief Compilation of cohesive element example in intrinsic
#
-# @brief Intrinsic cohesive element configuration
#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#add_mesh( cohesive_intrinsic_mesh triangle.geo 2 2)
register_example(cohesive_intrinsic
SOURCES cohesive_intrinsic.cc
#DEPENDS cohesive_intrinsic_mesh
FILES_TO_COPY material.dat triangle.msh)
diff --git a/examples/cohesive_element/cohesive_intrinsic/cohesive_intrinsic.cc b/examples/cohesive_element/cohesive_intrinsic/cohesive_intrinsic.cc
index 02f853f4d..0fc8340e7 100644
--- a/examples/cohesive_element/cohesive_intrinsic/cohesive_intrinsic.cc
+++ b/examples/cohesive_element/cohesive_intrinsic/cohesive_intrinsic.cc
@@ -1,135 +1,138 @@
/**
* @file cohesive_intrinsic.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Tue May 08 2012
+ * @date last modification: Fri Jul 19 2019
*
- * @brief Test for cohesive elements
+ * @brief Cohesive element example in intrinsic
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void updateDisplacement(SolidMechanicsModelCohesive &,
const ElementGroup &, Real);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 350;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.26, -0.24);
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = false);
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
Array<bool> & boundary = model.getBlockedDOFs();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
for (UInt n = 0; n < nb_nodes; ++n) {
boundary(n, dim) = true;
}
}
model.setBaseName("intrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.dump();
/// update displacement
auto && elements = mesh.createElementGroup("diplacement");
Vector<Real> barycenter(spatial_dimension);
for_each_element(mesh,
[&](auto && el) {
mesh.getBarycenter(el, barycenter);
if (barycenter(_x) > -0.25)
elements.add(el, true);
},
_element_kind = _ek_regular);
Real increment = 0.01;
updateDisplacement(model, elements, increment);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
updateDisplacement(model, elements, increment);
if (s % 1 == 0) {
model.dump();
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 2 * sqrt(2);
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
static void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementGroup & group, Real increment) {
Array<Real> & displacement = model.getDisplacement();
for (auto && node : group.getNodeGroup().getNodes()) {
displacement(node, 0) += increment;
}
}
diff --git a/examples/contact_mechanics/CMakeLists.txt b/examples/contact_mechanics/CMakeLists.txt
index ddcad7d0f..98a6bfdec 100644
--- a/examples/contact_mechanics/CMakeLists.txt
+++ b/examples/contact_mechanics/CMakeLists.txt
@@ -1,53 +1,56 @@
#===============================================================================
# @file CMakeLists.txt
#
-# @author Mohit Pundir <mohit.anciaux@epfl.ch>
+# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Sat Jun 19 2021
+#
+# @brief configuration for contact mechanics example
#
-# @brief configuration for heat transfer example
#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
+
add_mesh(hertz hertz.geo 2 1)
add_mesh(cohesive-contact cohesive-contact.geo 2 1)
register_example(contact_explicit_dynamic
SOURCES contact_explicit_dynamic.cc
DEPENDS hertz
FILES_TO_COPY material.dat
)
register_example(contact_explicit_static
SOURCES contact_explicit_static.cc
DEPENDS hertz
FILES_TO_COPY material.dat
)
register_example(cohesive_contact_explicit_dynamic
SOURCES cohesive_contact_explicit_dynamic.cc
DEPENDS cohesive-contact
FILES_TO_COPY material-cohesive.dat
)
diff --git a/examples/contact_mechanics/cohesive_contact_explicit_dynamic.cc b/examples/contact_mechanics/cohesive_contact_explicit_dynamic.cc
index 9a6a82843..d8027083a 100644
--- a/examples/contact_mechanics/cohesive_contact_explicit_dynamic.cc
+++ b/examples/contact_mechanics/cohesive_contact_explicit_dynamic.cc
@@ -1,128 +1,159 @@
+/**
+ * @file cohesive_contact_explicit_dynamic.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Sat Jun 19 2021
+ * @date last modification: Wed Jun 23 2021
+ *
+ * @brief Contact mechanics test with cohesive elements
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
#include "coupler_solid_cohesive_contact.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
const UInt spatial_dimension = 2;
initialize("material-cohesive.dat", argc, argv);
Real time_step{0.};
Real time_factor = 0.1;
UInt max_steps = 25000;
Real max_displacement = 1e-3;
Mesh mesh(spatial_dimension);
mesh.read("cohesive-contact.msh");
CouplerSolidCohesiveContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModelCohesive();
auto & contact = coupler.getContactMechanicsModel();
auto && material_selector =
std::make_shared<MeshDataMaterialCohesiveSelector>(solid);
material_selector->setFallback(solid.getMaterialSelector());
solid.setMaterialSelector(material_selector);
auto && surface_selector = std::make_shared<CohesiveSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
coupler.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = true);
coupler.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "sides");
time_step = solid.getStableTimeStep();
time_step *= time_factor;
std::cout << "Time Step = " << time_step << "s (" << time_step << "s)"
<< std::endl;
coupler.setTimeStep(time_step);
coupler.setBaseName("cohesive-contact-explicit-dynamic");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("velocity");
coupler.addDumpFieldVector("normals");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("grad_u");
coupler.addDumpField("stress");
coupler.addDumpField("gaps");
coupler.addDumpField("areas");
auto & velocity = solid.getVelocity();
auto & gaps = contact.getGaps();
Real damping_ratio = 0.99;
auto increment = max_displacement / max_steps;
for (auto i : arange(max_steps)) {
coupler.applyBC(BC::Dirichlet::IncrementValue(increment, _y), "loading");
coupler.applyBC(BC::Dirichlet::IncrementValue(-increment, _y), "fixed");
coupler.solveStep();
solid.checkCohesiveStress();
// damping velocities only along the contacting zone
for (auto && tuple : zip(gaps, make_view(velocity, spatial_dimension))) {
auto & gap = std::get<0>(tuple);
auto & vel = std::get<1>(tuple);
if (gap > 0) {
vel *= damping_ratio;
}
}
// dumping energies
if (i % 1000 == 0) {
Real epot = solid.getEnergy("potential");
Real ekin = solid.getEnergy("kinetic");
std::cerr << i << "," << i * increment << "," << epot << "," << ekin
<< "," << epot + ekin << "," << std::endl;
}
if (i % 1000 == 0) {
coupler.dump();
}
}
for (auto i : arange(max_steps)) {
solid.applyBC(BC::Dirichlet::IncrementValue(-increment, _y), "loading");
solid.applyBC(BC::Dirichlet::IncrementValue(increment, _y), "fixed");
coupler.solveStep();
coupler.checkCohesiveStress();
// damping velocities only along the contacting zone
for (auto && tuple : zip(gaps, make_view(velocity, spatial_dimension))) {
auto & gap = std::get<0>(tuple);
auto & vel = std::get<1>(tuple);
if (gap > 0) {
vel *= damping_ratio;
}
}
// dumping energies
if (i % 1000 == 0) {
Real epot = solid.getEnergy("potential");
Real ekin = solid.getEnergy("kinetic");
std::cerr << i << "," << i * increment << "," << epot << "," << ekin
<< "," << epot + ekin << "," << std::endl;
}
if (i % 1000 == 0) {
coupler.dump();
}
}
}
diff --git a/examples/contact_mechanics/contact_explicit_dynamic.cc b/examples/contact_mechanics/contact_explicit_dynamic.cc
index fd7956f4c..da9406eff 100644
--- a/examples/contact_mechanics/contact_explicit_dynamic.cc
+++ b/examples/contact_mechanics/contact_explicit_dynamic.cc
@@ -1,104 +1,135 @@
+/**
+ * @file contact_explicit_dynamic.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Sun Jun 06 2021
+ *
+ * @brief Contact mechanics example in dynamic
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "contact_mechanics_model.hh"
#include "coupler_solid_contact.hh"
#include "non_linear_solver.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
const UInt spatial_dimension = 2;
initialize("material.dat", argc, argv);
Real time_step;
Real time_factor = 0.1;
UInt max_steps = 20000;
Real max_displacement = 5e-3;
Mesh mesh(spatial_dimension);
mesh.read("hertz.msh");
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
auto && selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names",solid);
solid.setMaterialSelector(selector);
coupler.initFull( _analysis_method = _explicit_lumped_mass);
auto && surface_selector = std::make_shared<PhysicalSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "fixed");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "fixed");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "loading");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "symmetry");
time_step = solid.getStableTimeStep();
time_step *= time_factor;
std::cout << "Time Step = " << time_step << "s (" << time_step
<< "s)" << std::endl;
coupler.setTimeStep(time_step);
coupler.setBaseName("contact-explicit-dynamic");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("velocity");
coupler.addDumpFieldVector("normals");
coupler.addDumpFieldVector("contact_force");
coupler.addDumpFieldVector("external_force");
coupler.addDumpFieldVector("internal_force");
coupler.addDumpField("gaps");
coupler.addDumpField("areas");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("grad_u");
coupler.addDumpField("stress");
auto & velocity = solid.getVelocity();
auto & gaps = contact.getGaps();
Real damping_ratio = 0.99;
auto increment = max_displacement/max_steps;
for (auto i : arange(max_steps)) {
solid.applyBC(BC::Dirichlet::IncrementValue(-increment, _y), "loading");
coupler.solveStep();
// damping velocities only along the contacting zone
for(auto && tuple : zip(gaps,
make_view(velocity, spatial_dimension))){
auto & gap = std::get<0>(tuple);
auto & vel = std::get<1>(tuple);
if(gap > 0) {
vel *= damping_ratio;
}
}
// dumping energies
if (i % 1000 == 0) {
Real epot = solid.getEnergy("potential");
Real ekin = solid.getEnergy("kinetic");
std::cerr << i << "," << i * increment << "," << epot << "," << ekin << ","
<< epot + ekin << "," << std::endl;
}
if (i % 1000 == 0) {
coupler.dump();
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/contact_mechanics/contact_explicit_static.cc b/examples/contact_mechanics/contact_explicit_static.cc
index 2df0bff15..b72b5895f 100644
--- a/examples/contact_mechanics/contact_explicit_static.cc
+++ b/examples/contact_mechanics/contact_explicit_static.cc
@@ -1,96 +1,97 @@
/**
- * @file test_contact_mechanics_model.cc
+ * @file contact_explicit_static.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Apr 30 2019
- * @date last modification: Tue Apr 30 2019
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Jun 23 2021
+ *
+ * @brief Example of contact mechanics in static
*
- * @brief Test for contact mechanics model class
*
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "contact_mechanics_model.hh"
#include "coupler_solid_contact.hh"
#include "non_linear_solver.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
const UInt spatial_dimension = 2;
initialize("material.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("hertz.msh");
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
auto && selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names",solid);
solid.setMaterialSelector(selector);
coupler.initFull(_analysis_method = _static);
auto && surface_selector = std::make_shared<PhysicalSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
coupler.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "fixed");
coupler.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "fixed");
coupler.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "loading");
coupler.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "symmetry");
coupler.setBaseName("contact-explicit-static");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("normals");
coupler.addDumpFieldVector("contact_force");
coupler.addDumpFieldVector("external_force");
coupler.addDumpFieldVector("internal_force");
coupler.addDumpField("gaps");
coupler.addDumpField("areas");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("grad_u");
coupler.addDumpField("stress");
auto max_steps = 100u;
for (auto _ [[gnu::unused]] : arange(max_steps)) {
auto increment = 1e-4;
coupler.applyBC(BC::Dirichlet::IncrementValue(-increment, _y), "loading");
coupler.solveStep();
coupler.dump();
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/embedded/CMakeLists.txt b/examples/embedded/CMakeLists.txt
index f825ba574..f894986d3 100644
--- a/examples/embedded/CMakeLists.txt
+++ b/examples/embedded/CMakeLists.txt
@@ -1,40 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
#
-# @date creation: Tue Dec 01 2015
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Mar 16 2018
+#
+# @brief Compilation of embedded solid mechanis model example
#
-# @brief configuration for embedded example
#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(concrete_mesh concrete.geo 2 2)
add_mesh(reinforcement_mesh reinforcement.geo 1 1)
register_example(embedded embedded.cc
DEPENDS concrete_mesh reinforcement_mesh
USE_PACKAGES CGAL
FILES_TO_COPY material.dat)
diff --git a/examples/embedded/embedded.cc b/examples/embedded/embedded.cc
index 54b757dd9..4785076c5 100644
--- a/examples/embedded/embedded.cc
+++ b/examples/embedded/embedded.cc
@@ -1,97 +1,99 @@
/**
* @file embedded.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Dec 01 2015
- * @date last modification: Mon Jan 18 2016
+ * @date last modification: Wed Feb 06 2019
*
- * @brief This code gives an example of a simulation using the embedded model
+ * @brief Embedded solid mechanis model example
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_model.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt dim = 2;
// Loading the concrete mesh
Mesh mesh(dim);
mesh.read("concrete.msh");
// Loading the reinforcement mesh
Mesh reinforcement_mesh(dim, "reinforcement_mesh");
// Exception is raised because reinforcement
// mesh contains only segments, i.e. 1D elements
try {
reinforcement_mesh.read("reinforcement.msh");
} catch (debug::Exception & e) {
}
// Model creation
EmbeddedInterfaceModel model(mesh, reinforcement_mesh, dim);
model.initFull(EmbeddedInterfaceModelOptions(_static));
// Boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "XBlocked");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "YBlocked");
Vector<Real> force(dim);
force(0) = 0.0;
force(1) = -1.0;
model.applyBC(BC::Neumann::FromTraction(force), "Force");
// Dumping the concrete
model.setBaseName("concrete");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.addDumpFieldTensor("stress");
// Dumping the reinforcement
model.setBaseNameToDumper("reinforcement", "reinforcement");
model.addDumpFieldTensorToDumper(
"reinforcement", "stress_embedded"); // dumping stress in reinforcement
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 1);
solver.set("threshold", 1e-6);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
model.solveStep();
// Dumping model
model.dump();
model.dump("reinforcement");
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/explicit/CMakeLists.txt b/examples/explicit/CMakeLists.txt
index 847687700..d9057327d 100644
--- a/examples/explicit/CMakeLists.txt
+++ b/examples/explicit/CMakeLists.txt
@@ -1,39 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Cyprien Wolff <cyprien.wolff@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Mon Jan 18 2016
#
# @brief configuration for explicit example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(explicit_dynamic_mesh bar.geo 3 1)
register_example(explicit_dynamic
SOURCES explicit_dynamic.cc
DEPENDS explicit_dynamic_mesh
FILES_TO_COPY material.dat)
diff --git a/examples/explicit/explicit_dynamic.cc b/examples/explicit/explicit_dynamic.cc
index 39e61bb08..5b09505fc 100644
--- a/examples/explicit/explicit_dynamic.cc
+++ b/examples/explicit/explicit_dynamic.cc
@@ -1,107 +1,110 @@
/**
* @file explicit_dynamic.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
*
- * @date creation: Sun Jul 12 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Jan 28 2021
*
- * @brief This code refers to the explicit dynamic example from the user manual
+ * @brief Example of explicit dynamic simulation in solid mechanics
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 3;
const Real pulse_width = 2.;
const Real A = 0.01;
Real time_step;
Real time_factor = 0.8;
UInt max_steps = 1000;
Mesh mesh(spatial_dimension);
if (Communicator::getStaticCommunicator().whoAmI() == 0)
mesh.read("bar.msh");
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass);
time_step = model.getStableTimeStep();
std::cout << "Time Step = " << time_step * time_factor << "s (" << time_step
<< "s)" << std::endl;
time_step *= time_factor;
model.setTimeStep(time_step);
/// boundary and initial conditions
Array<Real> & displacement = model.getDisplacement();
const Array<Real> & nodes = mesh.getNodes();
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
Real x = nodes(n) - 2;
// Sinus * Gaussian
Real L = pulse_width;
Real k = 0.1 * 2 * M_PI * 3 / L;
displacement(n) = A * sin(k * x) * exp(-(k * x) * (k * x) / (L * L));
}
std::ofstream energy;
energy.open("energy.csv");
energy << "id,rtime,epot,ekin,tot" << std::endl;
model.setBaseName("explicit_dynamic");
model.addDumpField("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("stress");
model.dump();
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
Real epot = model.getEnergy("potential");
Real ekin = model.getEnergy("kinetic");
energy << s << "," << s * time_step << "," << epot << "," << ekin << ","
<< epot + ekin << "," << std::endl;
if (s % 10 == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
model.dump();
}
energy.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/heat_transfer/CMakeLists.txt b/examples/heat_transfer/CMakeLists.txt
index a06d69fbb..4533d95df 100644
--- a/examples/heat_transfer/CMakeLists.txt
+++ b/examples/heat_transfer/CMakeLists.txt
@@ -1,53 +1,53 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Mar 16 2018
#
# @brief configuration for heat transfer example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(heat_transfer_mesh_2d square.geo 2 2)
add_mesh(heat_transfer_mesh_3d cube.geo 3 2)
register_example(heat_transfer_dynamics_2d
SOURCES heat_transfer_dynamics_2d.cc
DEPENDS heat_transfer_mesh_2d
FILES_TO_COPY material.dat
)
register_example(heat_transfer_static_2d
SOURCES heat_transfer_static_2d.cc
DEPENDS heat_transfer_mesh_2d
FILES_TO_COPY material.dat
)
register_example(heat_transfer_dynamics_3d
SOURCES heat_transfer_dynamics_3d.cc
DEPENDS heat_transfer_mesh_3d
FILES_TO_COPY material.dat
)
diff --git a/examples/heat_transfer/heat_transfer_dynamics_2d.cc b/examples/heat_transfer/heat_transfer_dynamics_2d.cc
index 1c1cdf860..e674486c0 100644
--- a/examples/heat_transfer/heat_transfer_dynamics_2d.cc
+++ b/examples/heat_transfer/heat_transfer_dynamics_2d.cc
@@ -1,100 +1,104 @@
/**
- * @file explicit_heat_transfer.cc
+ * @file heat_transfer_dynamics_2d.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Sun May 01 2011
+ * @date last modification: Fri Mar 16 2018
*
- * @brief test of the class HeatTransferModel on the 3d cube
+ * @brief Example of heat transfer model
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
const UInt spatial_dimension = 2;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
// create mesh
Mesh mesh(spatial_dimension);
mesh.read("square.msh");
HeatTransferModel model(mesh);
// initialize everything
model.initFull();
// get stable time step
Real time_step = model.getStableTimeStep() * 0.8;
std::cout << "time step is:" << time_step << std::endl;
model.setTimeStep(time_step);
// boundary conditions
const Array<Real> & nodes = model.getFEEngine().getMesh().getNodes();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & temperature = model.getTemperature();
double length = 1.;
UInt nb_nodes = model.getFEEngine().getMesh().getNbNodes();
for (UInt i = 0; i < nb_nodes; ++i) {
temperature(i) = 100.;
Real dx = nodes(i, 0) - length / 4.;
Real dy = 0.0;
Real dz = 0.0;
if (spatial_dimension > 1)
dy = nodes(i, 1) - length / 4.;
if (spatial_dimension == 3)
dz = nodes(i, 2) - length / 4.;
Real d = sqrt(dx * dx + dy * dy + dz * dz);
if (d < 0.1) {
boundary(i) = true;
temperature(i) = 300.;
}
}
model.setBaseName("heat_transfer_square2d");
model.addDumpField("temperature");
model.addDumpField("temperature_rate");
model.addDumpField("internal_heat_rate");
// main loop
int max_steps = 15000;
for (int i = 0; i < max_steps; i++) {
model.solveStep();
if (i % 100 == 0)
model.dump();
if (i % 10 == 0)
std::cout << "Step " << i << "/" << max_steps << std::endl;
}
std::cout << "\n\n Stable Time Step is : " << time_step << "\n \n"
<< std::endl;
return 0;
}
diff --git a/examples/heat_transfer/heat_transfer_dynamics_3d.cc b/examples/heat_transfer/heat_transfer_dynamics_3d.cc
index 5e7c844c5..db061c6fc 100644
--- a/examples/heat_transfer/heat_transfer_dynamics_3d.cc
+++ b/examples/heat_transfer/heat_transfer_dynamics_3d.cc
@@ -1,108 +1,110 @@
/**
- * @file test_heat_transfer_model_cube3d.cc
+ * @file heat_transfer_dynamics_3d.cc
*
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Fri Mar 16 2018
*
- * @brief test of the class HeatTransferModel on the 3d cube
+ * @brief Heat transfer model example in 3D
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "heat_transfer_model.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
UInt spatial_dimension = 3;
ElementType type = _tetrahedron_4;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("cube.msh");
HeatTransferModel model(mesh);
// initialize everything
model.initFull();
// get and set stable time step
Real time_step = model.getStableTimeStep() * 0.8;
std::cout << "Stable Time Step is : " << time_step / .8 << std::endl;
std::cout << "time step is:" << time_step << std::endl;
model.setTimeStep(time_step);
/// boundary conditions
const Array<Real> & nodes = mesh.getNodes();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & temperature = model.getTemperature();
UInt nb_nodes = mesh.getNbNodes();
double length;
length = 1.;
for (UInt i = 0; i < nb_nodes; ++i) {
temperature(i) = 100.;
// to insert a heat source
Real dx = nodes(i, 0) - length / 2.;
Real dy = nodes(i, 1) - length / 2.;
Real dz = nodes(i, 2) - length / 2.;
Real d = sqrt(dx * dx + dy * dy + dz * dz);
if (d < 0.1) {
boundary(i) = true;
temperature(i) = 300.;
}
}
model.setBaseName("heat_transfer_cube3d");
model.addDumpField("temperature");
model.addDumpField("temperature_rate");
model.addDumpField("internal_heat_rate");
// //for testing
int max_steps = 1000;
for (int i = 0; i < max_steps; i++) {
model.solveStep();
if (i % 100 == 0)
model.dump();
if (i % 10 == 0) {
std::cout << "Step " << i << "/" << max_steps << std::endl;
}
}
return 0;
}
diff --git a/examples/heat_transfer/heat_transfer_static_2d.cc b/examples/heat_transfer/heat_transfer_static_2d.cc
index 43601ffb3..b26e9f3dd 100644
--- a/examples/heat_transfer/heat_transfer_static_2d.cc
+++ b/examples/heat_transfer/heat_transfer_static_2d.cc
@@ -1,93 +1,95 @@
/**
- * @file test_heat_transfer_model_square2d_implicit.cc
+ * @file heat_transfer_static_2d.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri Mar 16 2018
*
- * @brief test of the class HeatTransferModel on the 3d cube
+ * @brief Heat transfer model example in 2D
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <fstream>
#include <iostream>
#include <string>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
UInt spatial_dimension = 2;
std::string base_name;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
// create mesh
Mesh mesh(spatial_dimension);
mesh.read("square.msh");
HeatTransferModel model(mesh);
// initialize everything
model.initFull(_analysis_method = _static);
// boundary conditions
const Array<Real> & nodes = mesh.getNodes();
Array<bool> & blocked_dofs = model.getBlockedDOFs();
Array<Real> & temperature = model.getTemperature();
double length = 1.;
UInt nb_nodes = nodes.size();
for (UInt i = 0; i < nb_nodes; ++i) {
temperature(i) = 100.;
Real dx = nodes(i, 0);
Real dy = nodes(i, 1);
Vector<Real> dX = {dx, dy};
dX -= length / 4.;
Real d = dX.norm();
if (d < 0.1) {
blocked_dofs(i) = true;
temperature(i) = 300.;
}
if (std::abs(dx) < 1e-4 || std::abs(dy) < 1e-4)
blocked_dofs(i) = true;
if (std::abs(dx - length) < 1e-4 || std::abs(dy - length) < 1e-4)
blocked_dofs(i) = true;
}
model.setBaseName("heat_transfer_static_2d");
model.addDumpField("temperature");
model.addDumpField("internal_heat_rate");
model.addDumpField("conductivity");
model.addDumpField("blocked_dofs");
model.dump();
model.solveStep();
model.dump();
return 0;
}
diff --git a/examples/implicit/CMakeLists.txt b/examples/implicit/CMakeLists.txt
index 87a7a4fde..e57598bd1 100644
--- a/examples/implicit/CMakeLists.txt
+++ b/examples/implicit/CMakeLists.txt
@@ -1,40 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Mon Jan 18 2016
#
# @brief configuration implicit tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
add_mesh(implicit_dynamic_mesh beam.geo 3 2)
register_example(implicit_dynamic
SOURCES implicit_dynamic.cc
DEPENDS implicit_dynamic_mesh
FILES_TO_COPY material_dynamic.dat
)
diff --git a/examples/implicit/implicit_dynamic.cc b/examples/implicit/implicit_dynamic.cc
index a0f05a424..16ed54d00 100644
--- a/examples/implicit/implicit_dynamic.cc
+++ b/examples/implicit/implicit_dynamic.cc
@@ -1,148 +1,151 @@
/**
* @file implicit_dynamic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Feb 28 2020
*
- * @brief This code refers to the implicit dynamic example from the user manual
+ * @brief Example of solid mechanics in implicit dynamic
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
const Real bar_length = 10.;
const Real bar_height = 1.;
const Real bar_depth = 1.;
const Real F = 5e3;
const Real L = bar_length;
const Real I = bar_depth * bar_height * bar_height * bar_height / 12.;
const Real E = 12e7;
const Real rho = 1000;
const Real m = rho * bar_height * bar_depth;
static Real w(UInt n) {
return n * n * M_PI * M_PI / (L * L) * sqrt(E * I / m);
}
static Real analytical_solution(Real time) {
return 2 * F * L * L * L / (pow(M_PI, 4) * E * I) *
((1. - cos(w(1) * time)) + (1. - cos(w(3) * time)) / 81. +
(1. - cos(w(5) * time)) / 625.);
}
const UInt spatial_dimension = 2;
const Real time_step = 1e-4;
const Real max_time = 0.62;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_dynamic.dat", argc, argv);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
if (prank == 0)
mesh.read("beam.msh");
mesh.distribute();
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _implicit_dynamic);
Material & mat = model.getMaterial(0);
mat.setParam("E", E);
mat.setParam("rho", rho);
Array<Real> & force = model.getExternalForce();
Array<Real> & displacment = model.getDisplacement();
// boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "blocked");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "blocked");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "roller");
const Array<UInt> & trac_nodes =
mesh.getElementGroup("traction").getNodeGroup().getNodes();
bool dump_node = false;
if (trac_nodes.size() > 0 && mesh.isLocalOrMasterNode(trac_nodes(0))) {
force(trac_nodes(0), 1) = F;
dump_node = true;
}
// output setup
std::ofstream pos;
pos.open("position.csv");
if (!pos.good())
AKANTU_ERROR("Cannot open file \"position.csv\"");
pos << "id,time,position,solution" << std::endl;
model.setBaseName("dynamic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.dump();
model.setTimeStep(time_step);
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 100);
solver.set("threshold", 1e-12);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
/// time loop
Real time = 0.;
for (UInt s = 1; time < max_time; ++s, time += time_step) {
if (prank == 0)
std::cout << s << "\r" << std::flush;
model.solveStep();
if (dump_node)
pos << s << "," << time << "," << displacment(trac_nodes(0), 1) << ","
<< analytical_solution(s * time_step) << std::endl;
if (s % 100 == 0)
model.dump();
}
std::cout << std::endl;
pos.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/io/CMakeLists.txt b/examples/io/CMakeLists.txt
index 1128600c0..95d1c10c8 100644
--- a/examples/io/CMakeLists.txt
+++ b/examples/io/CMakeLists.txt
@@ -1,33 +1,34 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Mon Dec 14 2015
+# @date last modification: Fri Jan 22 2016
#
# @brief CMakeLists for Input/Output examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_example(dumper "Examples on how to use DumperIOHelper to output data" PACKAGE iohelper)
add_example(parser "Examples on how to input data from text file in Akantu" PACKAGE core)
diff --git a/examples/io/dumper/CMakeLists.txt b/examples/io/dumper/CMakeLists.txt
index b8c2a4e1c..b5fdf5ea0 100644
--- a/examples/io/dumper/CMakeLists.txt
+++ b/examples/io/dumper/CMakeLists.txt
@@ -1,63 +1,62 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Fri Jul 19 2019
#
# @brief CMakeLists for DumperIOHelper examples
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(swiss_train_mesh swiss_train.geo 2 1)
add_library(locomotive_tools
locomotive_tools.cc
locomotive_tools.hh
)
package_get_include_dir(BOOST _boost_include_dir)
target_link_libraries(locomotive_tools PRIVATE akantu)
target_include_directories(locomotive_tools PRIVATE ${AKANTU_INCLUDE_DIRS} ${_boost_include_dir})
if(AKANTU_EXTRA_CXX_FLAGS)
set_target_properties(locomotive_tools PROPERTIES COMPILE_FLAGS ${AKANTU_EXTRA_CXX_FLAGS})
endif()
register_example(dumper_low_level
SOURCES dumper_low_level.cc
USE_PACKAGES IOHelper
DEPENDS swiss_train_mesh locomotive_tools
DIRECTORIES_TO_CREATE paraview
)
register_example(dumpable_interface
SOURCES dumpable_interface.cc
USE_PACKAGES IOHelper
DEPENDS swiss_train_mesh locomotive_tools
DIRECTORIES_TO_CREATE paraview
)
diff --git a/examples/io/dumper/dumpable_interface.cc b/examples/io/dumper/dumpable_interface.cc
index f6a4b47a9..fa5b6d2ea 100644
--- a/examples/io/dumper/dumpable_interface.cc
+++ b/examples/io/dumper/dumpable_interface.cc
@@ -1,189 +1,191 @@
/**
* @file dumpable_interface.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 17 2015
- * @date last modification: Mon Aug 31 2015
+ * @date last modification: Tue Sep 29 2020
*
- * @brief Example of dumpers::Dumpable interface.
+ * @brief Example usnig the dumper interface directly
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include "locomotive_tools.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
/*
In this example, we present dumpers::Dumpable which is an interface
for other classes who want to dump themselves.
Several classes of Akantu inheritate from Dumpable (Model, Mesh, ...).
In this example we reproduce the same tasks as example_dumper_low_level.cc
using this time Dumpable interface inherted by Mesh, NodeGroup and
ElementGroup.
It is then advised to read first example_dumper_low_level.cc.
*/
initialize(argc, argv);
// To start let us load the swiss train mesh and its mesh data information.
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("swiss_train.msh");
/*
swiss_train.msh has the following physical groups that can be viewed with
GMSH:
"$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
6
2 1 "red"
2 2 "white"
2 3 "lwheel_1"
2 4 "lwheel_2"
2 5 "rwheel_2"
2 6 "rwheel_1"
$EndPhysicalNames
..."
*/
// Grouping nodes and elements belonging to train wheels (=four mesh data).
ElementGroup & wheels_elements =
mesh.createElementGroup("wheels", spatial_dimension);
wheels_elements.append(mesh.getElementGroup("lwheel_1"));
wheels_elements.append(mesh.getElementGroup("lwheel_2"));
wheels_elements.append(mesh.getElementGroup("rwheel_1"));
wheels_elements.append(mesh.getElementGroup("rwheel_2"));
const Array<UInt> & lnode_1 =
(mesh.getElementGroup("lwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & lnode_2 =
(mesh.getElementGroup("lwheel_2")).getNodeGroup().getNodes();
const Array<UInt> & rnode_1 =
(mesh.getElementGroup("rwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & rnode_2 =
(mesh.getElementGroup("rwheel_2")).getNodeGroup().getNodes();
Array<Real> & node = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
// This time a 2D Array is created and a padding size of 3 is passed to
// NodalField in order to warp train deformation on Paraview.
Array<Real> displacement(nb_nodes, spatial_dimension);
// Create an ElementTypeMapArray for the colour
ElementTypeMapArray<UInt> colour("colour");
colour.initialize(mesh, _with_nb_element = true);
/* ------------------------------------------------------------------------ */
/* Creating dumpers */
/* ------------------------------------------------------------------------ */
// Create dumper for the complete mesh and register it as default dumper.
auto && dumper = std::make_shared<DumperParaview>("train", "./paraview/dumpable", false);
mesh.registerExternalDumper(dumper, "train", true);
mesh.addDumpMesh(mesh);
// The dumper for the filtered mesh can be directly taken from the
// ElementGroup and then registered as "wheels_elements" dumper.
auto && wheels = mesh.getGroupDumper("paraview_wheels", "wheels");
mesh.registerExternalDumper(wheels.shared_from_this(), "wheels");
mesh.setDirectoryToDumper("wheels", "./paraview/dumpable");
// Arrays and ElementTypeMapArrays can be added as external fields directly
mesh.addDumpFieldExternal("displacement", displacement);
ElementTypeMapArrayFilter<UInt> filtered_colour(
colour, wheels_elements.getElements());
auto colour_field_wheel =
std::make_shared<dumpers::ElementalField<UInt, Vector, true>>(
filtered_colour);
mesh.addDumpFieldExternal("color", colour_field_wheel);
mesh.addDumpFieldExternalToDumper("wheels", "displacement", displacement);
mesh.addDumpFieldExternalToDumper("wheels", "colour", colour);
// For some specific cases the Fields should be created, as when you want to
// pad an array
auto displacement_vector_field =
mesh.createNodalField(&displacement, "all", 3);
mesh.addDumpFieldExternal("displacement_as_paraview_vector",
displacement_vector_field);
mesh.addDumpFieldExternalToDumper("wheels", "displacement_as_paraview_vector",
displacement_vector_field);
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
// Fill the ElementTypeMapArray colour.
fillColour(mesh, colour);
/// Apply displacement and wheels rotation.
Real tot_displacement = 50.;
Real radius = 1.;
UInt nb_steps = 100;
Real theta = tot_displacement / radius;
Vector<Real> l_center(spatial_dimension);
Vector<Real> r_center(spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
l_center(i) = node(14, i);
r_center(i) = node(2, i);
}
for (UInt i = 0; i < nb_steps; ++i) {
displacement.zero();
Real step_ratio = Real(i) / Real(nb_steps);
Real angle = step_ratio * theta;
applyRotation(l_center, angle, node, displacement, lnode_1);
applyRotation(l_center, angle, node, displacement, lnode_2);
applyRotation(r_center, angle, node, displacement, rnode_1);
applyRotation(r_center, angle, node, displacement, rnode_2);
for (UInt j = 0; j < nb_nodes; ++j) {
displacement(j, _x) += step_ratio * tot_displacement;
}
/// Dump call is finally made through Dumpable interface.
mesh.dump();
mesh.dump("wheels");
}
finalize();
return 0;
}
diff --git a/examples/io/dumper/dumper_low_level.cc b/examples/io/dumper/dumper_low_level.cc
index ff18d8d9a..820834668 100644
--- a/examples/io/dumper/dumper_low_level.cc
+++ b/examples/io/dumper/dumper_low_level.cc
@@ -1,197 +1,200 @@
/**
* @file dumper_low_level.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 17 2015
+ * @date last modification: Tue Sep 29 2020
*
- * @brief Example of dumpers::DumperIOHelper low-level methods.
+ * @brief Example using the low level dumper interface
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "group_manager.hh"
#include "mesh.hh"
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
#include "dumper_iohelper_paraview.hh"
#include "locomotive_tools.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
/* This example aims at illustrating how to manipulate low-level methods of
DumperIOHelper.
The aims is to visualize a colorized moving train with Paraview */
initialize(argc, argv);
// To start let us load the swiss train mesh and its mesh data information.
// We aknowledge here a weel-known swiss industry for mesh donation.
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("swiss_train.msh");
Array<Real> & nodes = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
/* swiss_train.msh has the following physical groups that can be viewed with
GMSH:
"$MeshFormat
2.2 0 8
$EndMeshFormat
$PhysicalNames
6
2 1 "red"
2 2 "white"
2 3 "lwheel_1"
2 4 "lwheel_2"
2 5 "rwheel_2"
2 6 "rwheel_1"
$EndPhysicalNames
..."
*/
// Grouping nodes and elements belonging to train wheels (=four mesh data)
ElementGroup & wheels_elements =
mesh.createElementGroup("wheels", spatial_dimension);
wheels_elements.append(mesh.getElementGroup("lwheel_1"));
wheels_elements.append(mesh.getElementGroup("lwheel_2"));
wheels_elements.append(mesh.getElementGroup("rwheel_1"));
wheels_elements.append(mesh.getElementGroup("rwheel_2"));
const Array<UInt> & lnode_1 =
(mesh.getElementGroup("lwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & lnode_2 =
(mesh.getElementGroup("lwheel_2")).getNodeGroup().getNodes();
const Array<UInt> & rnode_1 =
(mesh.getElementGroup("rwheel_1")).getNodeGroup().getNodes();
const Array<UInt> & rnode_2 =
(mesh.getElementGroup("rwheel_2")).getNodeGroup().getNodes();
/* Note this Array is constructed with three components in order to warp train
deformation on Paraview. A more appropriate way to do this is to set a
padding in the NodalField (See example_dumpable_interface.cc.) */
Array<Real> displacement(nb_nodes, 3);
// ElementalField are constructed with an ElementTypeMapArray.
ElementTypeMapArray<UInt> colour;
colour.initialize(mesh, _with_nb_element = true);
/* ------------------------------------------------------------------------ */
/* Dumper creation */
/* ------------------------------------------------------------------------ */
// Creation of two DumperParaview. One for full mesh, one for a filtered
// mesh.
DumperParaview dumper("train", "./paraview/dumper", false);
DumperParaview wheels("wheels", "./paraview/dumper", false);
// Register the full mesh
dumper.registerMesh(mesh);
// Register a filtered mesh limited to nodes and elements from wheels groups
wheels.registerFilteredMesh(mesh, wheels_elements.getElements(),
wheels_elements.getNodeGroup().getNodes());
// Generate an output file of the two mesh registered.
dumper.dump();
wheels.dump();
/* At this stage no fields are attached to the two dumpers. To do so, a
dumpers::Field object has to be created. Several types of dumpers::Field
exist. In this example we present two of them.
NodalField to describe nodal displacements of our train.
ElementalField handling the color of our different part.
*/
// NodalField are constructed with an Array.
auto displ_field = std::make_shared<dumpers::NodalField<Real>>(displacement);
auto colour_field = std::make_shared<dumpers::ElementalField<UInt>>(colour);
// Register the freshly created fields to our dumper.
dumper.registerField("displacement", displ_field);
dumper.registerField("colour", colour_field);
// For the dumper wheels, fields have to be filtered at registration.
// Filtered NodalField can be simply registered by adding an Array<UInt>
// listing the nodes.
auto displ_field_wheel = std::make_shared<dumpers::NodalField<Real, true>>(
displacement, 0, 0, &(wheels_elements.getNodeGroup().getNodes()));
wheels.registerField("displacement", displ_field_wheel);
// For the ElementalField, an ElementTypeMapArrayFilter has to be created.
ElementTypeMapArrayFilter<UInt> filtered_colour(
colour, wheels_elements.getElements());
auto colour_field_wheel =
std::make_shared<dumpers::ElementalField<UInt, Vector, true>>(
filtered_colour);
wheels.registerField("colour", colour_field_wheel);
/* ------------------------------------------------------------------------ */
// Now that the dumpers are created and the fields are associated, let's
// paint and move the train!
// Fill the ElementTypeMapArray colour according to mesh data information.
fillColour(mesh, colour);
// Apply displacement and wheels rotation.
Real tot_displacement = 50.;
Real radius = 1.;
UInt nb_steps = 100;
Real theta = tot_displacement / radius;
Vector<Real> l_center(3);
Vector<Real> r_center(3);
for (UInt i = 0; i < spatial_dimension; ++i) {
l_center(i) = nodes(14, i);
r_center(i) = nodes(2, i);
}
for (UInt i = 0; i < nb_steps; ++i) {
displacement.zero();
Real angle = (Real)i / (Real)nb_steps * theta;
applyRotation(l_center, angle, nodes, displacement, lnode_1);
applyRotation(l_center, angle, nodes, displacement, lnode_2);
applyRotation(r_center, angle, nodes, displacement, rnode_1);
applyRotation(r_center, angle, nodes, displacement, rnode_2);
for (UInt j = 0; j < nb_nodes; ++j) {
displacement(j, 0) += (Real)i / (Real)nb_steps * tot_displacement;
}
// Output results after each moving steps for main and wheel dumpers.
dumper.dump();
wheels.dump();
}
finalize();
return 0;
}
diff --git a/examples/io/dumper/locomotive_tools.cc b/examples/io/dumper/locomotive_tools.cc
index 50002927b..bc550fdfa 100644
--- a/examples/io/dumper/locomotive_tools.cc
+++ b/examples/io/dumper/locomotive_tools.cc
@@ -1,90 +1,92 @@
/**
* @file locomotive_tools.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Mon Aug 17 2015
- * @date last modification: Mon Jan 18 2016
+ * @date last modification: Fri Feb 28 2020
*
- * @brief Common functions for the dumper examples
+ * @brief Small helper code for the dumper examples
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "locomotive_tools.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
void applyRotation(const Vector<Real> & center, Real angle,
const Array<Real> & nodes, Array<Real> & displacement,
const Array<UInt> & node_group) {
auto nodes_it = nodes.begin(nodes.getNbComponent());
auto disp_it = displacement.begin(center.size());
Array<UInt>::const_scalar_iterator node_num_it = node_group.begin();
Array<UInt>::const_scalar_iterator node_num_end = node_group.end();
Vector<Real> pos_rel(center.size());
for (; node_num_it != node_num_end; ++node_num_it) {
const Vector<Real> pos = nodes_it[*node_num_it];
for (UInt i = 0; i < pos.size(); ++i)
pos_rel(i) = pos(i);
Vector<Real> dis = disp_it[*node_num_it];
pos_rel -= center;
Real radius = pos_rel.norm();
if (std::abs(radius) < Math::getTolerance())
continue;
Real phi_i = std::acos(pos_rel(_x) / radius);
if (pos_rel(_y) < 0)
phi_i *= -1;
dis(_x) = std::cos(phi_i - angle) * radius - pos_rel(_x);
dis(_y) = std::sin(phi_i - angle) * radius - pos_rel(_y);
}
}
/* -------------------------------------------------------------------------- */
void fillColour(const Mesh & mesh, ElementTypeMapArray<UInt> & colour) {
const ElementTypeMapArray<std::string> & phys_data =
mesh.getData<std::string>("physical_names");
const Array<std::string> & txt_colour = phys_data(_triangle_3);
Array<UInt> & id_colour = colour(_triangle_3);
for (UInt i = 0; i < txt_colour.size(); ++i) {
std::string phy_name = txt_colour(i);
if (phy_name == "red")
id_colour(i) = 3;
else if (phy_name == "white" || phy_name == "lwheel_1" ||
phy_name == "rwheel_1")
id_colour(i) = 2;
else
id_colour(i) = 1;
}
}
diff --git a/examples/io/dumper/locomotive_tools.hh b/examples/io/dumper/locomotive_tools.hh
index 1700899d8..e15f5d62b 100644
--- a/examples/io/dumper/locomotive_tools.hh
+++ b/examples/io/dumper/locomotive_tools.hh
@@ -1,39 +1,40 @@
/**
* @file locomotive_tools.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Mon Aug 17 2015
+ * @date last modification: Mon Aug 24 2015
*
- * @brief interface for the common tools
+ * @brief Header for the locomotive helper for the dumpers
*
*
- * Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
- * Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
- * Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
void applyRotation(const ::akantu::Vector<::akantu::Real> & center,
::akantu::Real angle,
const ::akantu::Array<::akantu::Real> & nodes,
::akantu::Array<::akantu::Real> & displacement,
const ::akantu::Array<::akantu::UInt> & node_group);
void fillColour(const ::akantu::Mesh & mesh,
::akantu::ElementTypeMapArray<::akantu::UInt> & colour);
diff --git a/examples/io/parser/CMakeLists.txt b/examples/io/parser/CMakeLists.txt
index 88655648e..71f3a3d4d 100644
--- a/examples/io/parser/CMakeLists.txt
+++ b/examples/io/parser/CMakeLists.txt
@@ -1,40 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri Jan 15 2016
#
# @brief Tests insertion of cohesive elements
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(swiss_cheese_mesh swiss_cheese.geo 2 2)
register_example(example_parser
example_parser.cc
DEPENDS swiss_cheese_mesh
FILES_TO_COPY input_file.dat
)
diff --git a/examples/io/parser/example_parser.cc b/examples/io/parser/example_parser.cc
index d161f7686..40fda7f77 100644
--- a/examples/io/parser/example_parser.cc
+++ b/examples/io/parser/example_parser.cc
@@ -1,86 +1,88 @@
/**
* @file example_parser.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Mon Dec 14 2015
- * @date last modification: Mon Jan 18 2016
+ * @date last modification: Wed Feb 06 2019
*
- * @brief Example on how to parse input text file
+ * @brief Example of using the user parameter parser
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
// Precise in initialize the name of the text input file to parse.
initialize("input_file.dat", argc, argv);
// Get the user ParserSection.
const ParserSection & usersect = getUserParser();
// getParameterValue() allows to extract data associated to a given parameter
// name
// and cast it in the desired type set as template paramter.
Mesh mesh(usersect.getParameterValue<UInt>("spatial_dimension"));
mesh.read(usersect.getParameterValue<std::string>("mesh_file"));
// getParameter() can be used with variable declaration (destination type is
// explicitly known).
Int max_iter = usersect.getParameter("max_nb_iterations");
Real precision = usersect.getParameter("precision");
// Following NumPy convention, data can be interpreted as Vector or Matrix
// structures.
Matrix<Real> eigen_stress = usersect.getParameter("stress");
SolidMechanicsModel model(mesh);
model.initFull(SolidMechanicsModelOptions(_static));
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x),
usersect.getParameterValue<std::string>("outter_crust"));
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y),
usersect.getParameterValue<std::string>("outter_crust"));
model.applyBC(BC::Neumann::FromStress(eigen_stress),
usersect.getParameterValue<std::string>("inner_holes"));
model.setDirectory("./paraview");
model.setBaseName("swiss_cheese");
model.addDumpFieldVector("displacement");
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", max_iter);
solver.set("threshold", precision);
model.solveStep();
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/new_material/CMakeLists.txt b/examples/new_material/CMakeLists.txt
index 98a76ef50..63489de1a 100644
--- a/examples/new_material/CMakeLists.txt
+++ b/examples/new_material/CMakeLists.txt
@@ -1,49 +1,49 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
-# @date last modification: Tue Jan 19 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Tue Nov 20 2018
#
# @brief CMakeFile for new material example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-# @section DESCRIPTION
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
add_mesh(new_local_material_barre_trou_mesh barre_trou.geo 2 2)
register_example(new_local_material
SOURCES
local_material_damage.cc
local_material_damage.hh
local_material_damage_inline_impl.hh
new_local_material.cc
DEPENDS
new_local_material_barre_trou_mesh
FILES_TO_COPY
material.dat
)
add_example(viscoelastic_maxwell "Example on how to instantiate and obtaine energies from the viscoelastic maxwell material" PACKAGE core)
diff --git a/examples/new_material/local_material_damage.cc b/examples/new_material/local_material_damage.cc
index 0d32b122b..e3fa26252 100644
--- a/examples/new_material/local_material_damage.cc
+++ b/examples/new_material/local_material_damage.cc
@@ -1,108 +1,111 @@
/**
* @file local_material_damage.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Fri Jul 24 2020
*
* @brief Specialization of the material class for the damage material
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
LocalMaterialDamage::LocalMaterialDamage(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), damage("damage", *this) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, 0., _pat_parsable, "Young's modulus");
this->registerParam("nu", nu, 0.5, _pat_parsable, "Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->registerParam("Yd", Yd, 50., _pat_parsmod);
this->registerParam("Sd", Sd, 5000., _pat_parsmod);
damage.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::computePotentialEnergy(ElementType el_type) {
AKANTU_DEBUG_IN();
Real * epot = potential_energy(el_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
epot++;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
static bool material_is_alocated_local_damage [[gnu::unused]] =
MaterialFactory::getInstance().registerAllocator(
"local_damage",
[](UInt, const ID &, SolidMechanicsModel & model,
const ID & id) -> std::unique_ptr<Material> {
return std::make_unique<LocalMaterialDamage>(model, id);
});
} // namespace akantu
diff --git a/examples/new_material/local_material_damage.hh b/examples/new_material/local_material_damage.hh
index 1161310de..923e17a00 100644
--- a/examples/new_material/local_material_damage.hh
+++ b/examples/new_material/local_material_damage.hh
@@ -1,117 +1,119 @@
/**
* @file local_material_damage.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Aug 10 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Sep 29 2020
*
* @brief Material isotropic elastic
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
#define AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
namespace akantu {
class LocalMaterialDamage : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~LocalMaterialDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the potential energy for all elements
void computePotentialEnergy(ElementType el_type) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & damage);
/// compute the potential energy for on element
inline void computePotentialEnergyOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute the celerity of the fastest wave in the material
inline Real getCelerity(const Element & element) const override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "local_material_damage_inline_impl.hh"
#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_HH_ */
diff --git a/examples/new_material/local_material_damage_inline_impl.hh b/examples/new_material/local_material_damage_inline_impl.hh
index 90f85a170..646c7a9b9 100644
--- a/examples/new_material/local_material_damage_inline_impl.hh
+++ b/examples/new_material/local_material_damage_inline_impl.hh
@@ -1,90 +1,92 @@
/**
* @file local_material_damage_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Aug 10 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Wed Aug 04 2010
+ * @date last modification: Tue Sep 29 2020
*
* @brief Implementation of the inline functions of the material damage
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_
#define AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real & dam) {
Real trace = grad_u.trace();
/// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
sigma(i, j) =
(i == j) * lambda * trace + mu * (grad_u(i, j) + grad_u(j, i));
}
}
Real Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * grad_u(i, j);
}
}
Y *= 0.5;
Real Fd = Y - Yd - Sd * dam;
if (Fd > 0)
dam = (Y - Yd) / Sd;
dam = std::min(dam, 1.);
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computePotentialEnergyOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & epot) {
epot = 0.;
for (UInt i = 0, t = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j, ++t)
epot += sigma(i, j) * (grad_u(i, j) - (i == j));
epot *= .5;
}
/* -------------------------------------------------------------------------- */
inline Real LocalMaterialDamage::getCelerity(__attribute__((unused))
const Element & element) const {
// Here the fastest celerity is the push wave speed
return (std::sqrt((2 * mu + lambda) / rho));
}
} // namespace akantu
#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_INLINE_IMPL_HH_ */
diff --git a/examples/new_material/new_local_material.cc b/examples/new_material/new_local_material.cc
index 57f0f35d2..e885e4e90 100644
--- a/examples/new_material/new_local_material.cc
+++ b/examples/new_material/new_local_material.cc
@@ -1,102 +1,104 @@
/**
* @file new_local_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Aug 06 2015
- * @date last modification: Mon Jan 18 2016
+ * @date creation: Wed Aug 04 2010
+ * @date last modification: Wed Jan 15 2020
*
* @brief test of the class SolidMechanicsModel
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
#define bar_length 10.
#define bar_height 4.
akantu::Real eps = 1e-10;
int main(int argc, char * argv[]) {
akantu::initialize("material.dat", argc, argv);
UInt max_steps = 10000;
Real epot, ekin;
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("barre_trou.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass);
std::cout << model.getMaterial(0) << std::endl;
Real time_step = model.getStableTimeStep();
model.setTimeStep(time_step / 10.);
/// Dirichlet boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "Fixed_x");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "Fixed_y");
// Neumann boundary condition
Matrix<Real> stress(2, 2);
stress.eye(3e2);
model.applyBC(BC::Neumann::FromStress(stress), "Traction");
model.setBaseName("local_material");
model.addDumpField("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.addDumpField("grad_u");
model.addDumpField("stress");
model.addDumpField("damage");
model.dump();
for (UInt s = 0; s < max_steps; ++s) {
model.solveStep();
epot = model.getEnergy("potential");
ekin = model.getEnergy("kinetic");
if (s % 100 == 0)
std::cout << s << " " << epot << " " << ekin << " " << epot + ekin
<< std::endl;
if (s % 1000 == 0)
model.dump();
}
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/new_material/viscoelastic_maxwell/CMakeLists.txt b/examples/new_material/viscoelastic_maxwell/CMakeLists.txt
index 5ac1bd788..9e99d2d20 100644
--- a/examples/new_material/viscoelastic_maxwell/CMakeLists.txt
+++ b/examples/new_material/viscoelastic_maxwell/CMakeLists.txt
@@ -1,46 +1,48 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Emil Gallyamov <emil.gallyamov@epfl.ch>
#
-# @date creation: Tue Nov 20 2018
+# @date creation: Fri Oct 22 2010
+# @date last modification: Tue Nov 20 2018
#
# @brief CMakeFile for viscoelastic material example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
add_mesh(material_viscoelastic_maxwell_mesh material_viscoelastic_maxwell_mesh.geo 2 1)
register_example(material_viscoelastic_maxwell_energies
SOURCES material_viscoelastic_maxwell_energies.cc
DEPENDS material_viscoelastic_maxwell_mesh
USE_PACKAGES iohelper
FILES_TO_COPY material_viscoelastic_maxwell.dat
DIRECTORIES_TO_CREATE paraview
)
diff --git a/examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc b/examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
index 0b8b3f2ad..c614045d2 100644
--- a/examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
+++ b/examples/new_material/viscoelastic_maxwell/material_viscoelastic_maxwell_energies.cc
@@ -1,177 +1,179 @@
/**
* @file material_viscoelastic_maxwell_energies.cc
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
* @date creation: Tue Nov 20 2018
- * @date last modification:
+ * @date last modification: Sun Dec 30 2018
*
* @brief Example of using viscoelastic material and computing energies
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
#include "material_viscoelastic_maxwell.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_viscoelastic_maxwell.dat", argc, argv);
// sim data
Real eps = 0.1;
const UInt dim = 2;
Real sim_time = 100.;
Real T = 10.;
Mesh mesh(dim);
mesh.read("material_viscoelastic_maxwell_mesh.msh");
SolidMechanicsModel model(mesh);
/* ------------------------------------------------------------------------ */
/* Initialization */
/* ------------------------------------------------------------------------ */
model.initFull(_analysis_method = _static);
std::cout << model.getMaterial(0) << std::endl;
std::stringstream filename_sstr;
filename_sstr << "material_viscoelastic_maxwell_output.out";
std::ofstream output_data;
output_data.open(filename_sstr.str().c_str());
Material & mat = model.getMaterial(0);
Real time_step = 0.1;
UInt nb_nodes = mesh.getNbNodes();
const Array<Real> & coordinate = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & blocked = model.getBlockedDOFs();
/// Setting time step
model.setTimeStep(time_step);
model.setBaseName("dynamic");
model.addDumpFieldVector("displacement");
model.addDumpField("blocked_dofs");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.addDumpField("grad_u");
model.addDumpField("stress");
model.addDumpField("strain");
UInt max_steps = sim_time / time_step + 1;
Real time = 0.;
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 10);
solver.set("threshold", 1e-7);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
for (UInt s = 0; s <= max_steps; ++s) {
std::cout << "Time Step = " << time_step << "s" << std::endl;
std::cout << "Time = " << time << std::endl;
// impose displacement
Real epsilon = 0;
if (time < T) {
epsilon = eps * time / T;
} else {
epsilon = eps;
}
for (UInt n = 0; n < nb_nodes; ++n) {
if (Math::are_float_equal(coordinate(n, 0), 0.0)) {
displacement(n, 0) = 0;
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 1), 0.0)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = 0;
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 0), 0.001)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 1), 0.001)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
}
}
try {
model.solveStep();
} catch (debug::Exception & e) {
}
// for debugging
// auto int_force = model.getInternalForce();
// auto &K = model.getDOFManager().getMatrix("K");
// K.saveMatrix("K.mtx");
Int nb_iter = solver.get("nb_iterations");
Real error = solver.get("error");
bool converged = solver.get("converged");
if (converged) {
std::cout << "Converged in " << nb_iter << " iterations" << std::endl;
} else {
std::cout << "Didn't converge after " << nb_iter
<< " iterations. Error is " << error << std::endl;
return EXIT_FAILURE;
}
model.dump();
Real epot = mat.getEnergy("potential");
Real edis = mat.getEnergy("dissipated");
Real work = mat.getEnergy("work");
// data output
output_data << s * time_step << " " << epsilon << " " << epot << " " << edis
<< " " << work << std::endl;
time += time_step;
}
output_data.close();
finalize();
}
diff --git a/examples/parallel/CMakeLists.txt b/examples/parallel/CMakeLists.txt
index dd5d27a29..b3266b704 100644
--- a/examples/parallel/CMakeLists.txt
+++ b/examples/parallel/CMakeLists.txt
@@ -1,40 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
+# @date creation: Fri Oct 22 2010
+# @date last modification: Fri Jul 19 2019
#
# @brief configuration for a parallel example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
add_mesh(parallel_2d_mesh square_2d.geo 2 1)
register_example(parallel_2d
SOURCES parallel_2d.cc
DEPENDS parallel_2d_mesh
FILES_TO_COPY material.dat
PARALLEL)
diff --git a/examples/parallel/parallel_2d.cc b/examples/parallel/parallel_2d.cc
index 4dbe9aa32..007fac130 100644
--- a/examples/parallel/parallel_2d.cc
+++ b/examples/parallel/parallel_2d.cc
@@ -1,105 +1,108 @@
/**
* @file parallel_2d.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Mon Aug 09 2010
+ * @date last modification: Thu Mar 22 2018
*
* @brief Parallel example
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
UInt spatial_dimension = 2;
UInt max_steps = 10000;
Real time_factor = 0.8;
Real max_disp = 1e-6;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
if (prank == 0) {
// Read the mesh
mesh.read("square_2d.msh");
}
mesh.distribute();
SolidMechanicsModel model(mesh);
model.initFull();
if (prank == 0)
std::cout << model.getMaterial(0) << std::endl;
model.setBaseName("multi");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("velocity");
model.addDumpFieldVector("acceleration");
model.addDumpFieldTensor("stress");
model.addDumpFieldTensor("grad_u");
/// boundary conditions
Real eps = 1e-16;
const Array<Real> & pos = mesh.getNodes();
Array<Real> & disp = model.getDisplacement();
Array<bool> & boun = model.getBlockedDOFs();
Real left_side = mesh.getLowerBounds()(0);
Real right_side = mesh.getUpperBounds()(0);
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (std::abs(pos(i, 0) - left_side) < eps) {
disp(i, 0) = max_disp;
boun(i, 0) = true;
}
if (std::abs(pos(i, 0) - right_side) < eps) {
disp(i, 0) = -max_disp;
boun(i, 0) = true;
}
}
Real time_step = model.getStableTimeStep() * time_factor;
std::cout << "Time Step = " << time_step << "s" << std::endl;
model.setTimeStep(time_step);
model.dump();
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
if (s % 200 == 0)
model.dump();
if (prank == 0 && s % 100 == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/phase_field/CMakeLists.txt b/examples/phase_field/CMakeLists.txt
index e12c9ba1d..5411f5626 100644
--- a/examples/phase_field/CMakeLists.txt
+++ b/examples/phase_field/CMakeLists.txt
@@ -1,40 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Tue Oct 2 2018
+# @date creation: Fri Oct 22 2010
+# @date last modification: Thu Oct 10 2019
#
# @brief configuration for phase field example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(square_notch square_notch.geo 2 1)
register_example(phase_field_notch
SOURCES phase_field_notch.cc
DEPENDS square_notch
FILES_TO_COPY material_notch.dat
)
diff --git a/examples/phase_field/phase_field_notch.cc b/examples/phase_field/phase_field_notch.cc
index a57212bd8..8f76a5ba5 100644
--- a/examples/phase_field/phase_field_notch.cc
+++ b/examples/phase_field/phase_field_notch.cc
@@ -1,92 +1,123 @@
+/**
+ * @file phase_field_notch.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Tue Oct 02 2018
+ * @date last modification: Wed Apr 07 2021
+ *
+ * @brief Example of phase field model
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "phase_field_model.hh"
#include "solid_mechanics_model.hh"
#include "coupler_solid_phasefield.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <fstream>
#include <chrono>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using clk = std::chrono::high_resolution_clock;
using second = std::chrono::duration<double>;
using millisecond = std::chrono::duration<double, std::milli>;
const UInt spatial_dimension = 2;
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]){
initialize("material_notch.dat", argc, argv);
// create mesh
Mesh mesh(spatial_dimension);
mesh.read("square_notch.msh");
CouplerSolidPhaseField coupler(mesh);
auto & model = coupler.getSolidMechanicsModel();
auto & phase = coupler.getPhaseFieldModel();
model.initFull(_analysis_method = _static);
auto && mat_selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names", model);
model.setMaterialSelector(mat_selector);
auto && selector = std::make_shared<MeshDataPhaseFieldSelector<std::string>>(
"physical_names", phase);
phase.setPhaseFieldSelector(selector);
phase.initFull(_analysis_method = _static);
model.applyBC(BC::Dirichlet::FixedValue(0., _y), "bottom");
model.applyBC(BC::Dirichlet::FixedValue(0., _x), "left");
model.setBaseName("phase_notch");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpFieldVector("displacement");
model.addDumpField("damage");
model.dump();
UInt nbSteps = 1500;
Real increment = 1e-5;
auto start_time = clk::now();
for (UInt s = 1; s < nbSteps; ++s) {
if (s >= 500) {
increment = 1.e-6;
}
if (s % 10 == 0 ) {
constexpr char wheel[] = "/-\\|";
auto elapsed = clk::now() - start_time;
auto time_per_step = elapsed / s;
std::cout << "\r[" << wheel[(s / 10) % 4] << "] " << std::setw(5) << s
<< "/" << nbSteps << " (" << std::setprecision(2)
<< std::fixed << std::setw(8)
<< millisecond(time_per_step).count()
<< "ms/step - elapsed: " << std::setw(8)
<< second(elapsed).count() << "s - ETA: " << std::setw(8)
<< second((nbSteps - s) * time_per_step).count() << "s)"
<< std::string(' ', 20) << std::flush;
}
model.applyBC(BC::Dirichlet::IncrementValue(increment, _y), "top");
coupler.solve();
if ( s % 100 == 0) {
model.dump();
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/python/CMakeLists.txt b/examples/python/CMakeLists.txt
index 161c19dae..4bfa5c75e 100644
--- a/examples/python/CMakeLists.txt
+++ b/examples/python/CMakeLists.txt
@@ -1,12 +1,52 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Jan 22 2016
+# @date last modification: Tue Mar 30 2021
+#
+# @brief Main CMakeLists for python examples
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_subdirectory(custom-material)
add_subdirectory(dynamics)
add_subdirectory(eigen_modes)
add_subdirectory(plate-hole)
add_subdirectory(stiffness_matrix)
-add_subdirectory(structural_mechanics)
-add_subdirectory(fragmentation)
-add_subdirectory(contact-mechanics)
+add_example(structural_mechanics "structural mechanics example in python"
+ PACKAGE structural_mechanics)
+add_example(fragmentation "example of fragmentation in python"
+ PACKAGE cohesive_element)
+add_example(phase-field "phase-field example in python"
+ PACKAGE phase_field)
+add_example(cohesive "cohesive element examples in python"
+ PACKAGE cohesive_element)
+add_example(contact-mechanics "contact mechanics example in python"
+ PACKAGE contact_mechanics)
package_add_files_to_package(
examples/python/README.rst
)
diff --git a/examples/python/cohesive/CMakeLists.txt b/examples/python/cohesive/CMakeLists.txt
index 7c77b3046..ba073ccc7 100644
--- a/examples/python/cohesive/CMakeLists.txt
+++ b/examples/python/cohesive/CMakeLists.txt
@@ -1,8 +1,40 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Jul 19 2019
+# @date last modification: Fri Jul 19 2019
+#
+# @brief CMakeList for cohesive in python
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(plate plate.geo DIM 2)
register_example(cohesive_python
- SCRIPT cohesive.py
+ SCRIPT plate.py
PYTHON
FILES_TO_COPY material.dat
DEPENDS plate
)
diff --git a/examples/python/cohesive/plate.py b/examples/python/cohesive/plate.py
index 214f08c52..fccde62da 100644
--- a/examples/python/cohesive/plate.py
+++ b/examples/python/cohesive/plate.py
@@ -1,84 +1,96 @@
#!/usr/bin/env python3
+"""plate.py: Python example: plate with a hole breaking with cohesive
+elements"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import akantu as aka
import numpy as np
def solve(material_file, mesh_file, traction):
aka.parseInput(material_file)
spatial_dimension = 2
# -------------------------------------------------------------------------
# Initialization
# -------------------------------------------------------------------------
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
model = aka.SolidMechanicsModelCohesive(mesh)
model.initFull(_analysis_method=aka._static,
_is_extrinsic=True)
model.initNewSolver(aka._explicit_lumped_mass)
model.setBaseName('plate')
model.addDumpFieldVector('displacement')
model.addDumpFieldVector('external_force')
model.addDumpField('strain')
model.addDumpField('stress')
model.addDumpField('blocked_dofs')
model.setBaseNameToDumper('cohesive elements', 'cohesive')
model.addDumpFieldVectorToDumper('cohesive elements', 'displacement')
model.addDumpFieldToDumper('cohesive elements', 'damage')
- model.addDumpFieldVectorToDumper('cohesive elements', 'traction')
+ model.addDumpFieldVectorToDumper('cohesive elements', 'tractions')
model.addDumpFieldVectorToDumper('cohesive elements', 'opening')
# -------------------------------------------------------------------------
# Boundary conditions
# -------------------------------------------------------------------------
model.applyBC(aka.FixedValue(0.0, aka._x), 'XBlocked')
model.applyBC(aka.FixedValue(0.0, aka._y), 'YBlocked')
trac = np.zeros(spatial_dimension)
trac[int(aka._y)] = traction
print('Solve for traction ', traction)
model.getExternalForce()[:] = 0
model.applyBC(aka.FromTraction(trac), 'Traction')
solver = model.getNonLinearSolver('static')
solver.set('max_iterations', 100)
solver.set('threshold', 1e-10)
solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
model.solveStep('static')
model.dump()
model.dump('cohesive elements')
model.setTimeStep(model.getStableTimeStep()*0.1)
maxsteps = 100
for i in range(0, maxsteps):
print('{0}/{1}'.format(i, maxsteps))
model.checkCohesiveStress()
model.solveStep('explicit_lumped')
if i % 10 == 0:
model.dump()
model.dump('cohesive elements')
# -----------------------------------------------------------------------------
# main
# -----------------------------------------------------------------------------
def main():
mesh_file = 'plate.msh'
material_file = 'material.dat'
traction = .095
solve(material_file, mesh_file, traction)
# -----------------------------------------------------------------------------
if __name__ == '__main__':
main()
diff --git a/examples/python/contact-mechanics/CMakeLists.txt b/examples/python/contact-mechanics/CMakeLists.txt
index 40d1c1390..d02677d1a 100644
--- a/examples/python/contact-mechanics/CMakeLists.txt
+++ b/examples/python/contact-mechanics/CMakeLists.txt
@@ -1,7 +1,46 @@
-add_mesh(compression_mesh ./mesh/compression.geo DIM 2 ORDER 1)
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Sat Jun 19 2021
+# @date last modification: Fri Aug 06 2021
+#
+# @brief CMake file to python examples
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
+add_mesh(compression_mesh compression.geo DIM 2 ORDER 1)
register_example(compression
SCRIPT compression.py
PYTHON
- FILES_TO_COPY ./materials/compression.dat
+ FILES_TO_COPY compression.dat
DEPENDS compression_mesh)
+
+register_example(detection_explicit.py
+ SCRIPT detection-explicit.py
+ PYTHON
+ FILES_TO_COPY detection-explicit.dat
+ detection-explicit.msh
+ )
diff --git a/examples/python/contact-mechanics/materials/compression.dat b/examples/python/contact-mechanics/compression.dat
similarity index 100%
rename from examples/python/contact-mechanics/materials/compression.dat
rename to examples/python/contact-mechanics/compression.dat
diff --git a/examples/python/contact-mechanics/mesh/compression.geo b/examples/python/contact-mechanics/compression.geo
similarity index 100%
rename from examples/python/contact-mechanics/mesh/compression.geo
rename to examples/python/contact-mechanics/compression.geo
diff --git a/examples/python/contact-mechanics/compression.py b/examples/python/contact-mechanics/compression.py
index 85b995411..f35cb57a1 100755
--- a/examples/python/contact-mechanics/compression.py
+++ b/examples/python/contact-mechanics/compression.py
@@ -1,69 +1,81 @@
#!/usr/bin/env python3
+""" compression.py: Python contact mechanics example"""
+
+__author__ = "Mohit Pundir"
+__credits__ = [
+ "Mohit Pundir <mohit.pundir@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
import akantu as aka
max_steps = 20000
max_displacement = 1e-2
damping_interval = 10
damping_ratio = 0.9
spatial_dimension = 2
+
+
aka.parseInput('compression.dat')
mesh = aka.Mesh(spatial_dimension)
mesh.read('compression.msh')
coupler = aka.CouplerSolidContact(mesh)
solid = coupler.getSolidMechanicsModel()
contact = coupler.getContactMechanicsModel()
material_selector = aka.MeshDataMaterialSelectorString("physical_names", solid)
solid.setMaterialSelector(material_selector)
coupler.initFull(_analysis_method=aka._explicit_lumped_mass)
surface_selector = aka.PhysicalSurfaceSelector(mesh)
detector = contact.getContactDetector()
detector.setSurfaceSelector(surface_selector)
solid.applyBC(aka.FixedValue(0.0, aka._x), "sides")
time_step = solid.getStableTimeStep()
time_step *= 0.1
coupler.setTimeStep(time_step)
coupler.setBaseName("compression")
coupler.addDumpFieldVector("displacement")
coupler.addDumpFieldVector("contact_force")
coupler.addDumpFieldVector("external_force")
coupler.addDumpFieldVector("internal_force")
coupler.addDumpField("gaps")
coupler.addDumpField("areas")
coupler.addDumpField("blocked_dofs")
coupler.addDumpField("grad_u")
coupler.addDumpField("stress")
coupler.dump()
velocity = solid.getVelocity()
increment = max_displacement / max_steps
for s in range(0, max_steps):
print("Step : ", s)
solid.applyBC(aka.IncrementValue(-increment, aka._y), "loading")
solid.applyBC(aka.IncrementValue(increment, aka._y), "fixed")
coupler.solveStep()
if s % damping_interval == 0:
velocity *= damping_ratio
if s % 100 == 0:
coupler.dump()
diff --git a/examples/python/contact-mechanics/materials/detection-explicit.dat b/examples/python/contact-mechanics/detection-explicit.dat
similarity index 100%
rename from examples/python/contact-mechanics/materials/detection-explicit.dat
rename to examples/python/contact-mechanics/detection-explicit.dat
diff --git a/examples/python/contact-mechanics/mesh/detection-explicit.msh b/examples/python/contact-mechanics/detection-explicit.msh
similarity index 100%
rename from examples/python/contact-mechanics/mesh/detection-explicit.msh
rename to examples/python/contact-mechanics/detection-explicit.msh
diff --git a/examples/python/contact-mechanics/detection-explicit.py b/examples/python/contact-mechanics/detection-explicit.py
index bd72d87af..35d293d80 100755
--- a/examples/python/contact-mechanics/detection-explicit.py
+++ b/examples/python/contact-mechanics/detection-explicit.py
@@ -1,34 +1,49 @@
#!/usr/bin/env python3
+""" detection-explicit.py: Python contact detection example"""
+
+__author__ = "Mohit Pundir"
+__credits__ = [
+ "Mohit Pundir <mohit.pundir@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
import akantu as aka
import time
-
spatial_dimension = 2
-aka.parseInput('./materials/detection-explicit.dat')
+aka.parseInput('detection-explicit.dat')
mesh = aka.Mesh(spatial_dimension)
-mesh.read('./mesh/detection-explicit.msh')
+mesh.read('detection-explicit.msh')
model = aka.ContactMechanicsModel(mesh)
model.initFull(_analysis_method=aka._explicit_lumped_mass)
surface_selector = aka.PhysicalSurfaceSelector(mesh)
model.getContactDetector().setSurfaceSelector(surface_selector)
-
model.setBaseName("detection-explicit")
model.addDumpFieldVector("normals")
model.addDumpField("gaps")
model.addDumpField("areas")
-
start_time = time.time()
model.search()
finish_time = time.time()
print('Search time = %s seconds', finish_time - start_time)
model.dump()
# by default the contact model creates a group named contact_surface
contact_surface = mesh.getElementGroup("contact_surface")
+
+normals = model.getNormals()
+gaps = model.getGaps()
+contact_elements = list(model.getContactElements())
+
+print(normals)
+print(gaps.ravel())
+print(contact_elements)
diff --git a/examples/python/custom-material/CMakeLists.txt b/examples/python/custom-material/CMakeLists.txt
index ddcc31d6c..aa52caed6 100644
--- a/examples/python/custom-material/CMakeLists.txt
+++ b/examples/python/custom-material/CMakeLists.txt
@@ -1,13 +1,46 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Jan 22 2016
+# @date last modification: Thu Feb 20 2020
+#
+# @brief CMakeLists for custom-material examples
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(square square.geo DIM 2)
register_example(bi-material
SCRIPT bi-material.py
PYTHON
FILES_TO_COPY material.dat
DEPENDS square)
add_mesh(bar bar.geo DIM 2)
register_example(custom-material
SCRIPT custom-material.py
PYTHON
FILES_TO_COPY material.dat
DEPENDS bar)
diff --git a/examples/python/custom-material/bi-material.py b/examples/python/custom-material/bi-material.py
index 823f7dee8..57c0d7b41 100644
--- a/examples/python/custom-material/bi-material.py
+++ b/examples/python/custom-material/bi-material.py
@@ -1,180 +1,194 @@
+
+""" bi-material.py: Bi-material example handled with a internal field"""
+
+__author__ = "Guillaume Anciaux and Nicolas Richart"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import akantu as aka
import numpy as np
# ------------------------------------------------------------------------------
class LocalElastic(aka.Material):
def __init__(self, model, _id):
super().__init__(model, _id)
super().registerParamReal('E',
aka._pat_readable | aka._pat_parsable,
'Youngs modulus')
super().registerParamReal('nu',
aka._pat_readable | aka._pat_parsable,
'Poisson ratio')
# change it to have the initialize wrapped
super().registerInternalReal('factor', 1)
super().registerInternalReal('quad_coordinates', 2)
def initMaterial(self):
nu = self.getReal('nu')
E = self.getReal('E')
self.mu = E / (2 * (1 + nu))
self.lame_lambda = nu * E / (
(1. + nu) * (1. - 2. * nu))
# Second Lame coefficient (shear modulus)
self.lame_mu = E / (2. * (1. + nu))
super().initMaterial()
quad_coords = self.getInternalReal("quad_coordinates")
factor = self.getInternalReal("factor")
model = self.getModel()
model.getFEEngine().computeIntegrationPointsCoordinates(
quad_coords, self.getElementFilter())
for elem_type in factor.elementTypes():
factor = factor(elem_type)
coords = quad_coords(elem_type)
factor[:] = 1.
factor[coords[:, 1] < 0.5] = .5
# declares all the parameters that are needed
def getPushWaveSpeed(self, params):
return np.sqrt((self.lame_lambda + 2 * self.lame_mu) / self.rho)
# compute small deformation tensor
@staticmethod
def computeEpsilon(grad_u):
return 0.5 * (grad_u + np.einsum('aij->aji', grad_u))
# constitutive law
def computeStress(self, el_type, ghost_type):
grad_u = self.getGradU(el_type, ghost_type)
sigma = self.getStress(el_type, ghost_type)
n_quads = grad_u.shape[0]
grad_u = grad_u.reshape((n_quads, 2, 2))
factor = self.getInternalReal('factor')(
el_type, ghost_type).reshape(n_quads)
epsilon = self.computeEpsilon(grad_u)
sigma = sigma.reshape((n_quads, 2, 2))
trace = np.einsum('aii->a', grad_u)
sigma[:, :, :] = (
np.einsum('a,ij->aij', trace,
self.lame_lambda * np.eye(2))
+ 2. * self.lame_mu * epsilon)
sigma[:, :, :] = np.einsum('aij, a->aij', sigma, factor)
# constitutive law tangent modulii
def computeTangentModuli(self, el_type, tangent_matrix, ghost_type):
n_quads = tangent_matrix.shape[0]
tangent = tangent_matrix.reshape(n_quads, 3, 3)
factor = self.getInternalReal('factor')(
el_type, ghost_type).reshape(n_quads)
Miiii = self.lame_lambda + 2 * self.lame_mu
Miijj = self.lame_lambda
Mijij = self.lame_mu
tangent[:, 0, 0] = Miiii
tangent[:, 1, 1] = Miiii
tangent[:, 0, 1] = Miijj
tangent[:, 1, 0] = Miijj
tangent[:, 2, 2] = Mijij
tangent[:, :, :] = np.einsum('aij, a->aij', tangent, factor)
# computes the energy density
def computePotentialEnergy(self, el_type):
sigma = self.getStress(el_type)
grad_u = self.getGradU(el_type)
nquads = sigma.shape[0]
stress = sigma.reshape(nquads, 2, 2)
grad_u = grad_u.reshape((nquads, 2, 2))
epsilon = self.computeEpsilon(grad_u)
energy_density = self.getPotentialEnergy(el_type)
energy_density[:, 0] = 0.5 * np.einsum('aij,aij->a', stress, epsilon)
# ------------------------------------------------------------------------------
# applies manually the boundary conditions
def applyBC(model):
nbNodes = model.getMesh().getNbNodes()
position = model.getMesh().getNodes()
displacement = model.getDisplacement()
blocked_dofs = model.getBlockedDOFs()
width = 1.
height = 1.
epsilon = 1e-8
for node in range(0, nbNodes):
if((np.abs(position[node, 0]) < epsilon) or # left side
(np.abs(position[node, 0] - width) < epsilon)): # right side
blocked_dofs[node, 0] = True
displacement[node, 0] = 0 * position[node, 0] + 0.
if(np.abs(position[node, 1]) < epsilon): # lower side
blocked_dofs[node, 1] = True
displacement[node, 1] = - 1.
if(np.abs(position[node, 1] - height) < epsilon): # upper side
blocked_dofs[node, 1] = True
displacement[node, 1] = 1.
# register the material to the material factory
def allocator(dim, option, model, id):
return LocalElastic(model, id)
mat_factory = aka.MaterialFactory.getInstance()
mat_factory.registerAllocator("local_elastic", allocator)
# main parameters
spatial_dimension = 2
mesh_file = 'square.msh'
# read mesh
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
# parse input file
aka.parseInput('material.dat')
# init the SolidMechanicsModel
model = aka.SolidMechanicsModel(mesh)
model.initFull(_analysis_method=aka._static)
# configure the solver
solver = model.getNonLinearSolver()
solver.set("max_iterations", 2)
solver.set("threshold", 1e-3)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
# prepare the dumper
model.setBaseName("bimaterial")
model.addDumpFieldVector("displacement")
model.addDumpFieldVector("internal_force")
model.addDumpFieldVector("external_force")
model.addDumpField("strain")
model.addDumpField("stress")
# model.addDumpField("factor")
model.addDumpField("blocked_dofs")
# Boundary conditions
applyBC(model)
# solve the problem
model.solveStep()
# dump paraview files
model.dump()
epot = model.getEnergy('potential')
print('Potential energy: ' + str(epot))
diff --git a/examples/python/custom-material/custom-material.py b/examples/python/custom-material/custom-material.py
index 8e25b2d5b..a10a120e0 100644
--- a/examples/python/custom-material/custom-material.py
+++ b/examples/python/custom-material/custom-material.py
@@ -1,177 +1,189 @@
#!/usr/bin/env python3
+
+""" custom-material.py: Custom material example"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import numpy as np
import akantu as aka
# ------------------------------------------------------------------------------
class LocalElastic(aka.Material):
def __init__(self, model, _id):
super().__init__(model, _id)
super().registerParamReal('E',
aka._pat_readable | aka._pat_parsable,
'Youngs modulus')
super().registerParamReal('nu',
aka._pat_readable | aka._pat_parsable,
'Poisson ratio')
def initMaterial(self):
nu = self.getReal('nu')
E = self.getReal('E')
self.mu = E / (2 * (1 + nu))
self.lame_lambda = nu * E / (
(1. + nu) * (1. - 2. * nu))
# Second Lame coefficient (shear modulus)
self.lame_mu = E / (2. * (1. + nu))
super().initMaterial()
# declares all the parameters that are needed
def getPushWaveSpeed(self, element):
rho = self.getReal('rho')
return np.sqrt((self.lame_lambda + 2 * self.lame_mu) / rho)
# compute small deformation tensor
@staticmethod
def computeEpsilon(grad_u):
return 0.5 * (grad_u + np.einsum('aij->aji', grad_u))
# constitutive law
def computeStress(self, el_type, ghost_type):
grad_u = self.getGradU(el_type, ghost_type)
sigma = self.getStress(el_type, ghost_type)
n_quads = grad_u.shape[0]
grad_u = grad_u.reshape((n_quads, 2, 2))
epsilon = self.computeEpsilon(grad_u)
sigma = sigma.reshape((n_quads, 2, 2))
trace = np.einsum('aii->a', grad_u)
sigma[:, :, :] = (
np.einsum('a,ij->aij', trace,
self.lame_lambda * np.eye(2))
+ 2. * self.lame_mu * epsilon)
# constitutive law tangent modulii
def computeTangentModuli(self, el_type, tangent_matrix, ghost_type):
n_quads = tangent_matrix.shape[0]
tangent = tangent_matrix.reshape(n_quads, 3, 3)
Miiii = self.lame_lambda + 2 * self.lame_mu
Miijj = self.lame_lambda
Mijij = self.lame_mu
tangent[:, 0, 0] = Miiii
tangent[:, 1, 1] = Miiii
tangent[:, 0, 1] = Miijj
tangent[:, 1, 0] = Miijj
tangent[:, 2, 2] = Mijij
# computes the energy density
def computePotentialEnergy(self, el_type):
sigma = self.getStress(el_type)
grad_u = self.getGradU(el_type)
nquads = sigma.shape[0]
stress = sigma.reshape(nquads, 2, 2)
grad_u = grad_u.reshape((nquads, 2, 2))
epsilon = self.computeEpsilon(grad_u)
energy_density = self.getPotentialEnergy(el_type)
energy_density[:, 0] = 0.5 * np.einsum('aij,aij->a', stress, epsilon)
# register material to the MaterialFactory
def allocator(_dim, unused, model, _id):
return LocalElastic(model, _id)
mat_factory = aka.MaterialFactory.getInstance()
mat_factory.registerAllocator("local_elastic", allocator)
# ------------------------------------------------------------------------------
# main
# ------------------------------------------------------------------------------
spatial_dimension = 2
aka.parseInput('material.dat')
mesh_file = 'bar.msh'
max_steps = 250
time_step = 1e-3
# ------------------------------------------------------------------------------
# Initialization
# ------------------------------------------------------------------------------
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
# parse input file
aka.parseInput('material.dat')
model = aka.SolidMechanicsModel(mesh)
model.initFull(_analysis_method=aka._explicit_lumped_mass)
model.setBaseName("waves")
model.addDumpFieldVector("displacement")
model.addDumpFieldVector("acceleration")
model.addDumpFieldVector("velocity")
model.addDumpFieldVector("internal_force")
model.addDumpFieldVector("external_force")
model.addDumpField("strain")
model.addDumpField("stress")
model.addDumpField("blocked_dofs")
# ------------------------------------------------------------------------------
# boundary conditions
# ------------------------------------------------------------------------------
model.applyBC(aka.FixedValue(0, aka._x), "XBlocked")
model.applyBC(aka.FixedValue(0, aka._y), "YBlocked")
# ------------------------------------------------------------------------------
# initial conditions
# ------------------------------------------------------------------------------
displacement = model.getDisplacement()
nb_nodes = mesh.getNbNodes()
position = mesh.getNodes()
pulse_width = 1
A = 0.01
for i in range(0, nb_nodes):
# Sinus * Gaussian
x = position[i, 0] - 5.
L = pulse_width
k = 0.1 * 2 * np.pi * 3 / L
displacement[i, 0] = A * \
np.sin(k * x) * np.exp(-(k * x) * (k * x) / (L * L))
# ------------------------------------------------------------------------------
# timestep value computation
# ------------------------------------------------------------------------------
time_factor = 0.8
stable_time_step = model.getStableTimeStep() * time_factor
print("Stable Time Step = {0}".format(stable_time_step))
print("Required Time Step = {0}".format(time_step))
time_step = stable_time_step * time_factor
model.setTimeStep(time_step)
# ------------------------------------------------------------------------------
# loop for evolution of motion dynamics
# ------------------------------------------------------------------------------
print("step,step * time_step,epot,ekin,epot + ekin")
for step in range(0, max_steps + 1):
model.solveStep()
if step % 10 == 0:
model.dump()
epot = model.getEnergy('potential')
ekin = model.getEnergy('kinetic')
# output energy calculation to screen
print("{0},{1},{2},{3},{4}".format(step, step * time_step,
epot, ekin,
(epot + ekin)))
diff --git a/examples/python/dynamics/CMakeLists.txt b/examples/python/dynamics/CMakeLists.txt
index ebad09645..c8c35f241 100644
--- a/examples/python/dynamics/CMakeLists.txt
+++ b/examples/python/dynamics/CMakeLists.txt
@@ -1,6 +1,35 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @brief CMakeLists for solid mechanics dynamics example
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(bar_dynamics_mesh bar.geo DIM 2)
register_example(dynamics-python
SCRIPT dynamics.py
PYTHON
FILES_TO_COPY material.dat
DEPENDS bar_dynamics_mesh)
diff --git a/examples/python/dynamics/dynamics.py b/examples/python/dynamics/dynamics.py
index d1c2f7690..e4b1338dd 100644
--- a/examples/python/dynamics/dynamics.py
+++ b/examples/python/dynamics/dynamics.py
@@ -1,111 +1,123 @@
#!/usr/bin/env python3
+""" dynamics.py: solid mechanics dynamics example"""
+
+__author__ = "Guillaume Anciaux and Nicolas Richart"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import numpy as np
import akantu as aka
# -----------------------------------------------------------------------------
class MyFixedValue(aka.FixedValue):
def __init__(self, value, axis):
super().__init__(value, axis)
self.value = value
self.axis = int(axis)
def __call__(self, node, flags, disp, coord):
# sets the displacement to the desired value in the desired axis
disp[self.axis] = self.value
# sets the blocked dofs vector to true in the desired axis
flags[self.axis] = True
# -----------------------------------------------------------------------------
def main():
spatial_dimension = 2
mesh_file = 'bar.msh'
max_steps = 250
time_step = 1e-3
aka.parseInput('material.dat')
# -------------------------------------------------------------------------
# Initialization
# -------------------------------------------------------------------------
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
model = aka.SolidMechanicsModel(mesh)
model.initFull(_analysis_method=aka._explicit_lumped_mass)
# model.initFull(_analysis_method=aka._implicit_dynamic)
model.setBaseName("waves")
model.addDumpFieldVector("displacement")
model.addDumpFieldVector("acceleration")
model.addDumpFieldVector("velocity")
model.addDumpFieldVector("internal_force")
model.addDumpFieldVector("external_force")
model.addDumpField("strain")
model.addDumpField("stress")
model.addDumpField("blocked_dofs")
# -------------------------------------------------------------------------
# boundary conditions
# -------------------------------------------------------------------------
model.applyBC(MyFixedValue(0, aka._x), "XBlocked")
model.applyBC(MyFixedValue(0, aka._y), "YBlocked")
# -------------------------------------------------------------------------
# initial conditions
# -------------------------------------------------------------------------
displacement = model.getDisplacement()
nb_nodes = mesh.getNbNodes()
position = mesh.getNodes()
pulse_width = 1
A = 0.01
for i in range(0, nb_nodes):
# Sinus * Gaussian
x = position[i, 0] - 5.
L = pulse_width
k = 0.1 * 2 * np.pi * 3 / L
displacement[i, 0] = A * \
np.sin(k * x) * np.exp(-(k * x) * (k * x) / (L * L))
displacement[i, 1] = 0
# -------------------------------------------------------------------------
# timestep value computation
# -------------------------------------------------------------------------
time_factor = 0.8
stable_time_step = model.getStableTimeStep() * time_factor
print("Stable Time Step = {0}".format(stable_time_step))
print("Required Time Step = {0}".format(time_step))
time_step = stable_time_step * time_factor
model.setTimeStep(time_step)
# -------------------------------------------------------------------------
# loop for evolution of motion dynamics
# -------------------------------------------------------------------------
print("step,step * time_step,epot,ekin,epot + ekin")
for step in range(0, max_steps + 1):
model.solveStep()
if step % 10 == 0:
model.dump()
epot = model.getEnergy('potential')
ekin = model.getEnergy('kinetic')
# output energy calculation to screen
print("{0},{1},{2},{3},{4}".format(step, step * time_step,
epot, ekin,
(epot + ekin)))
return
# -----------------------------------------------------------------------------
if __name__ == "__main__":
main()
diff --git a/examples/python/eigen_modes/CMakeLists.txt b/examples/python/eigen_modes/CMakeLists.txt
index 8ee96d530..94975269f 100644
--- a/examples/python/eigen_modes/CMakeLists.txt
+++ b/examples/python/eigen_modes/CMakeLists.txt
@@ -1,5 +1,37 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+#
+# @date creation: Fri Jul 19 2019
+# @date last modification: Wed Aug 21 2019
+#
+# @brief Examples of computing eigen modes
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
register_example(eigen-modes
SCRIPT eigen_modes.py
FILES_TO_COPY material.dat image_saver.py
PYTHON
)
diff --git a/examples/python/eigen_modes/eigen_modes.py b/examples/python/eigen_modes/eigen_modes.py
index 5f7b72047..59cc6d77c 100644
--- a/examples/python/eigen_modes/eigen_modes.py
+++ b/examples/python/eigen_modes/eigen_modes.py
@@ -1,264 +1,275 @@
#!/usr/bin/env python
+""" eigen_modes.py: Examples computing Eigen modes"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import subprocess
import argparse
import akantu as aka
import numpy as np
from scipy.sparse.linalg import eigsh
from scipy.sparse import csr_matrix
try:
import matplotlib.pyplot as plt
from image_saver import ImageSaver
has_matplotlib = True
except ImportError:
has_matplotlib = False
# -----------------------------------------------------------------------------
# parser
# -----------------------------------------------------------------------------
parser = argparse.ArgumentParser(description='Eigen mode exo')
parser.add_argument('-m', '--mode_number', type=int,
help='precise the mode to study', default=2)
parser.add_argument('-wL', '--wave_width', type=float,
help='precise the width of the wave for '
'the initial displacement', default=5)
parser.add_argument('-L', '--Lbar', type=float,
help='precise the length of the bar', default=10)
parser.add_argument('-t', '--time_step', type=float,
help='precise the timestep',
default=None)
parser.add_argument('-n', '--max_steps', type=int,
help='precise the number of timesteps',
default=500)
parser.add_argument('-mh', '--mesh_h', type=float,
help='characteristic mesh size',
default=.2)
parser.add_argument('-p', '--plot', action='store_true',
help='plot the results')
args = parser.parse_args()
mode = args.mode_number
wave_width = args.wave_width
time_step = args.time_step
max_steps = args.max_steps
mesh_h = args.mesh_h
Lbar = args.Lbar
plot = args.plot
# -----------------------------------------------------------------------------
# Mesh Generation
# -----------------------------------------------------------------------------
geo_content = """
// Mesh size
h = {0};
""".format(mesh_h)
geo_content += """
h1 = h;
h2 = h;
// Dimensions of the bar
Lx = 10;
Ly = 1;
// ------------------------------------------
// Geometry
// ------------------------------------------
Point(101) = { 0.0, -Ly/2, 0.0, h1};
Point(102) = { Lx, -Ly/2, 0.0, h2};
Point(103) = { Lx, 0., 0.0, h2};
Point(104) = { Lx, Ly/2., 0.0, h2};
Point(105) = { 0.0, Ly/2., 0.0, h1};
Point(106) = { 0.0, 0., 0.0, h1};
Line(101) = {101,102};
Line(102) = {102,103};
Line(103) = {103,104};
Line(104) = {104,105};
Line(105) = {105,106};
Line(106) = {106,101};
Line(107) = {106,103};
Line Loop(108) = {101, 102, -107, 106};
Plane Surface(109) = {108};
Line Loop(110) = {103, 104, 105, 107};
Plane Surface(111) = {110};
Physical Surface(112) = {109, 111};
Transfinite Surface "*";
Recombine Surface "*";
Physical Surface(113) = {111, 109};
Physical Line("XBlocked") = {103, 102};
Physical Line("ImposedVelocity") = {105, 106};
Physical Line("YBlocked") = {104, 101};
"""
mesh_file = 'bar'
with open(mesh_file + '.geo', 'w') as f:
f.write(geo_content)
subprocess.call(['gmsh', '-2', mesh_file + '.geo'])
mesh_file = mesh_file + '.msh'
# -----------------------------------------------------------------------------
# Initialization
# -----------------------------------------------------------------------------
spatial_dimension = 2
aka.parseInput('material.dat')
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
model = aka.SolidMechanicsModel(mesh)
model.initFull(aka._implicit_dynamic)
model.setBaseName("waves-{0}".format(mode))
model.addDumpFieldVector("displacement")
model.addDumpFieldVector("acceleration")
model.addDumpFieldVector("velocity")
model.addDumpField("blocked_dofs")
# -----------------------------------------------------------------------------
# Boundary conditions
# -----------------------------------------------------------------------------
internal_force = model.getInternalForce()
displacement = model.getDisplacement()
acceleration = model.getAcceleration()
velocity = model.getVelocity()
blocked_dofs = model.getBlockedDOFs()
nbNodes = mesh.getNbNodes()
position = mesh.getNodes()
model.applyBC(aka.FixedValue(0.0, aka._x), "XBlocked")
model.applyBC(aka.FixedValue(0.0, aka._y), "YBlocked")
# ------------------------------------------------------------------------
# timestep value computation
# ------------------------------------------------------------------------
time_factor = 0.8
stable_time_step = model.getStableTimeStep() * time_factor
if time_step:
print("Required Time Step = {0}".format(time_step))
if stable_time_step * time_factor < time_step:
print("Stable Time Step = {0}".format(stable_time_step))
raise RuntimeError("required time_step too large")
print("Required Time Step = {0}".format(time_step))
else:
print("Stable Time Step = {0}".format(stable_time_step))
time_step = stable_time_step * time_factor
model.setTimeStep(time_step)
# ------------------------------------------------------------------------
# compute the eigen modes
# ------------------------------------------------------------------------
model.assembleStiffnessMatrix()
model.assembleMass()
stiff = model.getDOFManager().getMatrix('K')
stiff = aka.AkantuSparseMatrix(stiff).toarray()
mass = model.getDOFManager().getMatrix('M')
mass = aka.AkantuSparseMatrix(mass).toarray()
# select the non blocked DOFs by index in the mask
mask = np.equal(blocked_dofs.flatten(), False)
Mass_star = mass[mask, :]
Mass_star = csr_matrix(Mass_star[:, mask].copy())
K_star = stiff[mask, :]
K_star = csr_matrix(K_star[:, mask].copy())
print('getting the eigen values')
vals, vects = eigsh(K_star, M=Mass_star, which='SM', k=20)
# -----------------------------------------------------------------------------
# import the initial conditions in displacement
# -----------------------------------------------------------------------------
displacement.reshape(nbNodes*2)[mask] = vects[:, mode]
with open('modes.txt', 'a') as f:
f.write('{0} {1}\n'.format(mode, vals[mode]))
model.dump()
# -----------------------------------------------------------------------------
# prepare the storage of the dynamical evolution
# -----------------------------------------------------------------------------
e_p = np.zeros(max_steps + 1)
e_k = np.zeros(max_steps + 1)
e_t = np.zeros(max_steps + 1)
time = np.zeros(max_steps + 1)
norm = np.zeros(max_steps + 1)
epot = model.getEnergy('potential')
ekin = model.getEnergy('kinetic')
e_p[0] = epot
e_k[0] = ekin
e_t[0] = epot + ekin
time[0] = 0
if has_matplotlib:
disp_sav = ImageSaver(mesh, displacement, 0, Lbar)
velo_sav = ImageSaver(mesh, velocity, 0, Lbar)
# -----------------------------------------------------------------------------
# loop for evolution of motion dynamics
# -----------------------------------------------------------------------------
for step in range(1, max_steps + 1):
model.solveStep()
# outputs
epot = model.getEnergy('potential')
ekin = model.getEnergy('kinetic')
print(step, '/', max_steps, epot, ekin, epot + ekin)
e_p[step] = epot
e_k[step] = ekin
e_t[step] = epot + ekin
time[step] = (step + 1) * time_step
if has_matplotlib:
disp_sav.storeStep()
velo_sav.storeStep()
if step % 10 == 0:
model.dump()
if plot and has_matplotlib:
# --------------------------------------------------------------------------
# plot figures for global evolution
# --------------------------------------------------------------------------
# energy norms
plt.figure(1)
plt.plot(time, e_t, 'r', time, e_p, 'b', time, e_k, 'g')
# space-time diagram for diplacements
plt.figure(2)
plt.imshow(disp_sav.getImage(), extent=(0, Lbar, max_steps * time_step, 0))
plt.xlabel("Space ")
plt.ylabel("Time ")
# space-time diagram for velocities
plt.figure(3)
plt.imshow(velo_sav.getImage(), extent=(0, Lbar, max_steps * time_step, 0))
plt.xlabel("Velocity")
plt.ylabel("Time")
plt.show()
diff --git a/examples/python/eigen_modes/image_saver.py b/examples/python/eigen_modes/image_saver.py
index 41401ee1c..8db68619b 100644
--- a/examples/python/eigen_modes/image_saver.py
+++ b/examples/python/eigen_modes/image_saver.py
@@ -1,68 +1,79 @@
#!/usr/bin/env python3
+""" image_saver.py: Helper to save images"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import numpy as np
import matplotlib.pyplot as plt
# -----------------------------------------------------------------------------
class ImageSaver:
# -------------------------------------------------------------------------
# Constructors/Destructors
# -------------------------------------------------------------------------
def __init__(self, mesh, field, component, Lbar):
self.mesh = mesh
self.field_copy = None
self.field = field
self.component = component
self.max_value = 0
self.Lbar = Lbar
# compute the number of nodes in one direction
self.nb_nodes = 0
epsilon = 1e-8
nodes = mesh.getNodes()
for n in range(0, mesh.getNbNodes()):
if np.abs(nodes[n, 1]) < epsilon:
self.nb_nodes += 1
# -------------------------------------------------------------------------
# Methods
# -------------------------------------------------------------------------
def storeStep(self):
if self.field_copy is None:
current_size = 0
self.field_copy = np.zeros(self.nb_nodes)
else:
current_size = self.field_copy.shape[0]
self.field_copy.resize(current_size + self.nb_nodes)
epsilon = 1e-8
h = self.Lbar / (self.nb_nodes-1)
nodes = self.mesh.getNodes()
for n in range(0, self.mesh.getNbNodes()):
if np.abs(nodes[n, 1]) < epsilon:
normed_x = nodes[n, 0]/h + h/10.
index = int(normed_x)
self.field_copy[current_size +
index] = self.field[n, self.component]
if self.max_value < self.field[n, self.component]:
self.max_value = self.field[n, self.component]
def getImage(self):
width = int(self.nb_nodes)
height = int(self.field_copy.shape[0] / self.nb_nodes)
if np.abs(self.max_value) > 1e-8:
for n in range(0, self.field_copy.shape[0]):
self.field_copy[n] = 1 - self.field_copy[n] / self.max_value
img = self.field_copy.reshape((height, width))
return img
def saveImage(self, filename):
img = self.getImage()
plt.imshow(img)
plt.savefig(filename)
diff --git a/examples/python/fragmentation/CMakeLists.txt b/examples/python/fragmentation/CMakeLists.txt
index 6c63393a0..c034947cb 100644
--- a/examples/python/fragmentation/CMakeLists.txt
+++ b/examples/python/fragmentation/CMakeLists.txt
@@ -1,8 +1,40 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+#
+# @date creation: Tue Mar 30 2021
+# @date last modification: Tue Mar 30 2021
+#
+# @brief CMakeLists for fragmentation example
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(fragmentation_mesh fragmentation_mesh.geo DIM 2 ORDER 1)
register_example(fragmentation
SCRIPT fragmentation.py
FILES_TO_COPY material.dat
DEPENDS fragmentation_mesh
PYTHON
)
diff --git a/examples/python/fragmentation/fragmentation.py b/examples/python/fragmentation/fragmentation.py
index 021551a0e..5fd453dda 100644
--- a/examples/python/fragmentation/fragmentation.py
+++ b/examples/python/fragmentation/fragmentation.py
@@ -1,180 +1,191 @@
#!/usr/bin/env python
# coding: utf-8
+""" fragmentation.py: Fragmentation example"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
# import akantu
import akantu as aka
# import numpy for vector manipulation
import numpy as np
# ### Setting up the *SolidMechanicsModelCohesive*
# We need to read again the material file and the mesh
# Create the Solid Mechanics Cohesive Model in Akantu
# reading material file
aka.parseInput('material.dat')
# creating mesh
spatial_dimension = 2
mesh = aka.Mesh(spatial_dimension)
# geometry (as defined in geo file)
L = 10
length = L/100
mesh.read('fragmentation_mesh.msh')
# creates the model
model = aka.SolidMechanicsModelCohesive(mesh)
model.initFull(_analysis_method=aka._static, _is_extrinsic=True)
# Initialize the solver
# configures the static solver
solver = model.getNonLinearSolver('static')
solver.set('max_iterations', 100)
solver.set('threshold', 1e-10)
solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
# Initilize a new solver (explicit Newmark with lumped mass)
model.initNewSolver(aka._explicit_lumped_mass)
# Dynamic insertion of cohesive elements
model.updateAutomaticInsertion()
# Implement Boundary and initial conditions
# Dirichlet Boundary condition
# model.applyBC(aka.FixedValue(0., aka._x), 'left')
model.applyBC(aka.FixedValue(0., aka._y), 'bottom')
model.getExternalForce()[:] = 0
# ### Generate paraview files
# Initialization for bulk vizualisation
model.setBaseName('plate')
model.addDumpFieldVector('displacement')
model.addDumpFieldVector('velocity')
model.addDumpFieldVector('external_force')
model.addDumpField('strain')
model.addDumpField('stress')
model.addDumpField('blocked_dofs')
# Initialization of vizualisation for Cohesive model
model.setBaseNameToDumper('cohesive elements', 'cohesive')
model.addDumpFieldVectorToDumper('cohesive elements', 'displacement')
model.addDumpFieldToDumper('cohesive elements', 'damage')
model.addDumpFieldVectorToDumper('cohesive elements', 'tractions')
model.addDumpFieldVectorToDumper('cohesive elements', 'opening')
# Custom Dirichlet Boundary Condition to impose constant velocity
# Boundary functor fixing the displacement as it is
class FixedDisplacement (aka.DirichletFunctor):
'''
Fix the displacement at its current value
'''
def __init__(self, axis, vel):
super().__init__(axis)
self.axis = axis
self.time = 0
self.vel = vel
def set_time(self, t):
self.time = t
def __call__(self, node, flags, disp, coord):
# sets the blocked dofs vector to true in the desired axis
flags[int(self.axis)] = True
disp[int(self.axis)] = self.vel*self.time
functor_r = FixedDisplacement(aka._x, 1e-1)
model.applyBC(functor_r, 'right')
functor_l = FixedDisplacement(aka._x, -1e-1)
model.applyBC(functor_l, 'left')
# Initial condition : velocity gradient:
# in x = 0 we have -v and in x = L we have +v
nodes = model.getMesh().getNodes()
vel_field = np.zeros(nodes.shape)
vel_field[:, 0] = (2*nodes[:, 0]-L)/L*1e-1
model.getVelocity()[:] = vel_field
# ### Run the dynamical simulation
# Initialize data arrays
# Energies :
E_pot = []
E_kin = []
E_dis = []
E_rev = []
E_con = []
# Stress :
Stress = []
dt = model.getStableTimeStep()*0.1
# choose the timestep
model.setTimeStep(dt)
# set maximum number of iteration
maxsteps = 5000
# solve
for i in range(0, maxsteps):
time = dt*i
functor_r.set_time(time)
# fix displacements of the right boundary
model.applyBC(functor_r, 'right')
functor_l.set_time(time)
# fix displacements of the left boundary
model.applyBC(functor_l, 'left')
if i % 10 == 0:
model.dump()
model.dump('cohesive elements')
pass
if i % 50 == 0:
print('step {0}/{1}'.format(i, maxsteps))
model.checkCohesiveStress()
model.solveStep('explicit_lumped')
Ep = model.getEnergy("potential")
Ek = model.getEnergy("kinetic")
Ed = model.getEnergy("dissipated")
Er = model.getEnergy("reversible")
Ec = model.getEnergy("contact")
E_pot.append(Ep)
E_kin.append(Ek)
E_dis.append(Ed)
E_rev.append(Er)
E_con.append(Ec)
Stress_field = model.getMaterial(0).getStress(aka._triangle_3)
Stress_mean = np.mean(Stress_field)
Stress.append(Stress_mean)
# Use the fragment Manager
fragment_manager = aka.FragmentManager(model)
fragment_manager.computeAllData()
Nb_elem_per_frag = fragment_manager.getNbElementsPerFragment()
Nb_frag = fragment_manager.getNbFragment()
print('Nb_frag:', Nb_frag)
# Average number of elements per fragment
Nb_elem_mean = np.mean(Nb_elem_per_frag)
print('average Nb elem / fragment:', Nb_elem_mean)
# knowing the element size we can get the average fragment size
s_mean = Nb_elem_mean*length
print('average fragment size:', s_mean)
# ## Plots
# Plot stress as a function of time
Time = [i*dt for i in range(0, maxsteps)]
Stress_MPa = [x/10**6 for x in Stress]
diff --git a/test/test_python_interface/CMakeLists.txt b/examples/python/phase-field/CMakeLists.txt
similarity index 55%
copy from test/test_python_interface/CMakeLists.txt
copy to examples/python/phase-field/CMakeLists.txt
index 0e3c16319..27e7a0614 100644
--- a/test/test_python_interface/CMakeLists.txt
+++ b/examples/python/phase-field/CMakeLists.txt
@@ -1,41 +1,48 @@
#===============================================================================
# @file CMakeLists.txt
#
-# @author Fabian Barras <fabian.barras@epfl.ch>
-# @author Lucas Frerot <lucas.frerot@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Mon Feb 05 2018
+# @date creation: Tue Aug 03 2021
+# @date last modification: Tue Aug 03 2021
+#
+# @brief CMake file for phase-field python example
#
-# @brief Python Interface tests
#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
-akantu_pybind11_add_module(py11_akantu_test_common MODULE test_common.cc)
-add_mesh(mesh_dcb_2d mesh_dcb_2d.geo 2 2)
-register_test(test_python_interface
- SCRIPT test_pybind.py
+add_mesh(mesh_phasefield plate.geo DIM 2)
+add_mesh(mesh_phasefield_static plate_static.geo DIM 2)
+
+register_example(phasefield_dynamic
+ SCRIPT phasefield-dynamic.py
+ PYTHON
+ FILES_TO_COPY material.dat
+ DEPENDS mesh_phasefield
+ )
+
+register_example(phasefield_static
+ SCRIPT phasefield-static.py
PYTHON
- FILES_TO_COPY elastic.dat
- DEPENDS mesh_dcb_2d py11_akantu_test_common
- PACKAGE python_interface
+ FILES_TO_COPY material_static.dat
+ DEPENDS mesh_phasefield_static
)
diff --git a/examples/python/phase-field/material.dat b/examples/python/phase-field/material.dat
new file mode 100644
index 000000000..47514a0f0
--- /dev/null
+++ b/examples/python/phase-field/material.dat
@@ -0,0 +1,16 @@
+material phasefield [
+ name = virtual
+ rho = 1180. # density
+ E = 3.09e9 # young's modulus
+ nu = 0.35 # poisson's ratio
+ eta = 0.0
+ finite_deformation = false
+]
+
+phasefield exponential [
+ name = virtual
+ E = 3.09e9
+ nu = 0.35
+ gc = 300.
+ l0 = 0.1e-3
+]
diff --git a/examples/python/phase-field/material_static.dat b/examples/python/phase-field/material_static.dat
new file mode 100644
index 000000000..3ae8da692
--- /dev/null
+++ b/examples/python/phase-field/material_static.dat
@@ -0,0 +1,16 @@
+material phasefield [
+name = plate
+ rho = 1.
+ E = 210.0
+ nu = 0.3
+ eta = 0.0
+ Plane_Stress = false
+]
+
+phasefield exponential [
+ name = plate
+ l0 = 0.0075
+ gc = 2.7e-3
+ E = 210.0
+ nu = 0.3
+]
diff --git a/examples/python/phase-field/phasefield-dynamic.py b/examples/python/phase-field/phasefield-dynamic.py
index 9b7b822d9..390adc94f 100644
--- a/examples/python/phase-field/phasefield-dynamic.py
+++ b/examples/python/phase-field/phasefield-dynamic.py
@@ -1,172 +1,108 @@
#!/usr/bin/env python
# coding: utf-8
-import py11_akantu as aka
-import subprocess
-
-geometry_file = """
-h1 = 1e-4;
-h2 = 1e-3;
-L = 32e-3;
-H = 16e-3;
-l = 4e-3;
-Point(1) = {0, 0, 0, h1};
-Point(2) = {L, 0, 0, h1};
-Point(3) = {L, H/2, 0, h2};
-Point(4) = {0, H/2, 0, h2};
-Point(5) = {l, 0, 0, h1};
-
-Point(6) = {0, 0, 0, h1};
-Point(7) = {L, -H/2, 0, h2};
-Point(8) = {0, -H/2, 0, h2};
-
-
-Line(1) = {1, 5};
-Line(2) = {4, 1};
-Line(3) = {3, 4};
-Line(4) = {2, 3};
-Line(5) = {5, 2};
-
-Line Loop(1) = {2, 3, 4, 5, 1};
-Plane Surface(1) = {1};
-
-Line(6) = {5, 6};
-Line(7) = {6, 8};
-Line(8) = {8, 7};
-Line(9) = {7, 2};
-Line Loop(2) = {6, 7, 8, 9, -5};
-Plane Surface(2) = {2};
-
-
-Physical Surface(8) = {1,2};
-Physical Line("left") = {2,7};
-Physical Line("bottom") = {8};
-Physical Line("top") = {3};
-Physical Line("right") = {4,9};
-
-"""
-
-with open('plate.geo', 'w') as f:
- f.write(geometry_file)
-
-ret = subprocess.run("gmsh -2 -order 1 -o plate.msh plate.geo", shell=True)
-if ret.returncode:
- print("Beware, gmsh could not run: mesh is not regenerated")
-else:
- print("Mesh generated")
-
-material_file = """
-material phasefield [
- name = virtual
- rho = 1180. # density
- E = 3.09e9 # young's modulus
- nu = 0.35 # poisson's ratio
- eta = 0.0
- finite_deformation = false
-]
+""" phasefield-dynamic.py: Dynamic phasefield example in python"""
-phasefield exponential [
- name = virtual
- E = 3.09e9
- nu = 0.35
- gc = 300.
- l0 = 0.1e-3
+__author__ = "Mohit Pundir"
+__credits__ = [
+ "Mohit Pundir <mohit.pundir@epfl.ch>",
]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
-"""
-
-with open('material.dat', 'w') as f:
- f.write(material_file)
-
+import akantu as aka
# reading material file
aka.parseInput('material.dat')
# creating mesh
spatial_dimension = 2
mesh = aka.Mesh(spatial_dimension)
mesh.read('plate.msh')
model = aka.CouplerSolidPhaseField(mesh)
solid = model.getSolidMechanicsModel()
phase = model.getPhaseFieldModel()
# initializing the Solid Mechanics Model with implicit solver for static resolution
solid.initFull(_analysis_method=aka._static)
solver = solid.getNonLinearSolver('static')
solver.set('max_iterations', 100)
solver.set('threshold', 1e-10)
solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
-# adding another solver dynamic/quasi-static resolution (explicit Newmark with lumped mass)
+# adding another solver dynamic/quasi-static resolution (explicit Newmark with
+# lumped mass)
solid.initNewSolver(aka._explicit_lumped_mass)
# initializing the PhaseField Model with linear implicit solver for static resolution
phase.initFull(_analysis_method=aka._static)
# initializing the PhaseField Model with Newton Raphson implicit solver for static resolution
phase.getNewSolver("nonlinear_static", aka.TimeStepSolverType.static,
aka.NonLinearSolverType.newton_raphson)
phase.setIntegrationScheme("nonlinear_static", "damage",
aka.IntegrationSchemeType.pseudo_time)
solver = phase.getNonLinearSolver('nonlinear_static')
solver.set('max_iterations', 100)
solver.set('threshold', 1e-3)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
# Initialization for bulk vizualisation
solid.setBaseName('plate')
solid.addDumpFieldVector('displacement')
solid.addDumpFieldVector('external_force')
solid.addDumpFieldVector('velocity')
solid.addDumpField('strain')
solid.addDumpField('stress')
solid.addDumpField('damage')
solid.addDumpField('blocked_dofs')
class FixedDamage (aka.DirichletFunctor):
'''
- Fix the damage to 0
+ Fix the damage to 0
'''
def __init__(self, axis):
super().__init__(axis)
self.axis = axis
def __call__(self, node, flags, dam, coord):
# sets the blocked dofs vector to true in the desired axis
flags[int(self.axis)] = True
dam[int(self.axis)] = 0.0
# Dirichlet
solid.applyBC(aka.FixedValue(0., aka._x), 'top')
solid.applyBC(aka.FixedValue(0., aka._x), 'bottom')
solid.applyBC(aka.FixedValue(0., aka._x), 'left')
solid.applyBC(aka.FixedValue(0., aka._x), 'right')
solid.applyBC(aka.FixedValue(0.06e-3, aka._y), 'top')
solid.applyBC(aka.FixedValue(-0.06e-3, aka._y), 'bottom')
solid.solveStep('static')
solid.dump()
# #### **Damped dynamics resolution**
solid.setTimeStep(solid.getStableTimeStep()*0.8)
# set maximum number of iteration
maxsteps = 1000
# solve using staggered scheme
for i in range(0, maxsteps):
if i % 100 == 0:
print('step {0}/{1}'.format(i, maxsteps))
model.solve('explicit_lumped', '')
if i % 100 == 0:
model.dump()
diff --git a/examples/python/phase-field/phasefield-static.py b/examples/python/phase-field/phasefield-static.py
index 524a55d87..eea020c86 100644
--- a/examples/python/phase-field/phasefield-static.py
+++ b/examples/python/phase-field/phasefield-static.py
@@ -1,181 +1,124 @@
#!/usr/bin/env python
# coding: utf-8
+""" phasefield-static.py: Static phase field example"""
-import numpy as np
-import py11_akantu as aka
-
-
-import subprocess
-
-geometry_file = """
-element_size = 0.1;
-fine_element_size = element_size;
-
-Point(1) = {0.5, 0.5, 0, element_size};
-Point(2) = {-0.5, 0.5, 0, element_size};
-Point(3) = {-0.5, -0.5, 0, element_size};
-Point(4) = {0.5, -0.5, 0, element_size};
-Point(5) = {-0.5, 0.001, 0, element_size};
-Point(6) = {0., 0.0, 0, fine_element_size};
-Point(7) = {0.5, 0.0, 0, fine_element_size};
-Point(8) = {-0.5, -0.001, 0, element_size};
-
-Line(1) = {3, 4};
-Line(2) = {4, 7};
-Line(3) = {7, 1};
-Line(4) = {1, 2};
-Line(5) = {2, 5};
-Line(6) = {5, 6};
-Line(7) = {6, 8};
-Line(8) = {8, 3};
-
-Line Loop(1) = {1, 2, 3, 4, 5, 6, 7, 8};
-
-Plane Surface(1) = {1};
-
-Physical Surface("plate") = {1};
-
-Physical Line("bottom") = {1};
-Physical Line("right") = {2, 3};
-Physical Line("top") = {4};
-Physical Line("left") = {5,8};
-
-"""
-
-with open('plate.geo', 'w') as f:
- f.write(geometry_file)
-
-ret = subprocess.run("gmsh -2 -order 1 -o plate.msh plate.geo", shell=True)
-if ret.returncode:
- print("Beware, gmsh could not run: mesh is not regenerated")
-else:
- print("Mesh generated")
-
-material_file = """
-material phasefield [
-name = plate
- rho = 1.
- E = 210.0
- nu = 0.3
- eta = 0.0
- Plane_Stress = false
+__author__ = "Mohit Pundir"
+__credits__ = [
+ "Mohit Pundir <mohit.pundir@epfl.ch>",
]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
-phasefield exponential [
- name = plate
- l0 = 0.0075
- gc = 2.7e-3
- E = 210.0
- nu = 0.3
-]
-"""
-with open('material.dat', 'w') as f:
- f.write(material_file)
+import numpy as np
+import akantu as aka
+
-aka.parseInput("material.dat")
+aka.parseInput("material_static.dat")
dim = 2
mesh = aka.Mesh(dim)
-mesh.read("plate.msh")
+mesh.read("plate_static.msh")
model = aka.CouplerSolidPhaseField(mesh)
solid = model.getSolidMechanicsModel()
phase = model.getPhaseFieldModel()
solid.initFull(_analysis_method=aka._static)
solver = solid.getNonLinearSolver('static')
solver.set('max_iterations', 100)
-solver.set('threshold', 1e-8)
+solver.set('threshold', 1e-9)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
solid.getNewSolver("linear_static", aka.TimeStepSolverType.static,
aka.NonLinearSolverType.linear)
solid.setIntegrationScheme("linear_static", "displacement",
aka.IntegrationSchemeType.pseudo_time)
phase.initFull(_analysis_method=aka._static)
phase.getNewSolver("nonlinear_static", aka.TimeStepSolverType.static,
aka.NonLinearSolverType.newton_raphson)
phase.setIntegrationScheme("nonlinear_static", "damage",
aka.IntegrationSchemeType.pseudo_time)
+
solver = phase.getNonLinearSolver('nonlinear_static')
solver.set('max_iterations', 100)
solver.set('threshold', 1e-4)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
solid.applyBC(aka.FixedValue(0, aka._y), "bottom")
solid.applyBC(aka.FixedValue(0, aka._x), "left")
# Initialization for bulk vizualisation
solid.setBaseName('phasefield-static')
solid.addDumpFieldVector('displacement')
solid.addDumpFieldVector('external_force')
solid.addDumpField('strain')
solid.addDumpField('stress')
solid.addDumpField('damage')
solid.addDumpField('blocked_dofs')
-
nb_dofs = solid.getMesh().getNbNodes() * dim
increment = solid.getIncrement()
displacement = solid.getDisplacement()
displacement = displacement.reshape(nb_dofs)
blocked_dofs = solid.getBlockedDOFs()
blocked_dofs = blocked_dofs.reshape(nb_dofs)
damage = phase.getDamage()
-tolerance = 1e-8
+tolerance = 1e-6
steps = 1500
increment = 1e-5
for n in range(steps):
print("Computing iteration " + str(n + 1) + "/" + str(steps))
solid.applyBC(aka.IncrementValue(increment, aka._y), 'top')
- mask = blocked_dofs == False
+ mask = blocked_dofs == False # NOQA: E712
iiter = 0
error_disp = 1
error_dam = 1
displacement_prev = displacement[mask].copy()
damage_prev = damage.copy()
damage_prev = damage_prev
# solve using staggered scheme
while (error_disp > tolerance or error_dam > tolerance):
model.solve("linear_static", "")
displacement_new = displacement[mask]
damage_new = damage
delta_disp = displacement_new - displacement_prev
delta_dam = damage_new - damage_prev
error_disp = np.linalg.norm(delta_disp)
error_dam = np.linalg.norm(delta_dam)
iiter += 1
displacement_prev = displacement_new.copy()
damage_prev = damage_new.copy()
print(error_dam, error_disp)
if iiter > 500:
raise Exception('Convergence not reached')
if n % 50 == 0:
solid.dump()
solid.dump()
diff --git a/examples/python/phase-field/plate.geo b/examples/python/phase-field/plate.geo
new file mode 100644
index 000000000..3b8878ec6
--- /dev/null
+++ b/examples/python/phase-field/plate.geo
@@ -0,0 +1,38 @@
+h1 = 1e-4;
+h2 = 1e-3;
+L = 32e-3;
+H = 16e-3;
+l = 4e-3;
+Point(1) = {0, 0, 0, h1};
+Point(2) = {L, 0, 0, h1};
+Point(3) = {L, H/2, 0, h2};
+Point(4) = {0, H/2, 0, h2};
+Point(5) = {l, 0, 0, h1};
+
+Point(6) = {0, 0, 0, h1};
+Point(7) = {L, -H/2, 0, h2};
+Point(8) = {0, -H/2, 0, h2};
+
+
+Line(1) = {1, 5};
+Line(2) = {4, 1};
+Line(3) = {3, 4};
+Line(4) = {2, 3};
+Line(5) = {5, 2};
+
+Line Loop(1) = {2, 3, 4, 5, 1};
+Plane Surface(1) = {1};
+
+Line(6) = {5, 6};
+Line(7) = {6, 8};
+Line(8) = {8, 7};
+Line(9) = {7, 2};
+Line Loop(2) = {6, 7, 8, 9, -5};
+Plane Surface(2) = {2};
+
+
+Physical Surface(8) = {1,2};
+Physical Line("left") = {2,7};
+Physical Line("bottom") = {8};
+Physical Line("top") = {3};
+Physical Line("right") = {4,9};
diff --git a/examples/python/phase-field/plate_static.geo b/examples/python/phase-field/plate_static.geo
new file mode 100644
index 000000000..fbc2f095b
--- /dev/null
+++ b/examples/python/phase-field/plate_static.geo
@@ -0,0 +1,31 @@
+element_size = 0.1;
+fine_element_size = element_size;
+
+Point(1) = {0.5, 0.5, 0, element_size};
+Point(2) = {-0.5, 0.5, 0, element_size};
+Point(3) = {-0.5, -0.5, 0, element_size};
+Point(4) = {0.5, -0.5, 0, element_size};
+Point(5) = {-0.5, 0.001, 0, element_size};
+Point(6) = {0., 0.0, 0, fine_element_size};
+Point(7) = {0.5, 0.0, 0, fine_element_size};
+Point(8) = {-0.5, -0.001, 0, element_size};
+
+Line(1) = {3, 4};
+Line(2) = {4, 7};
+Line(3) = {7, 1};
+Line(4) = {1, 2};
+Line(5) = {2, 5};
+Line(6) = {5, 6};
+Line(7) = {6, 8};
+Line(8) = {8, 3};
+
+Line Loop(1) = {1, 2, 3, 4, 5, 6, 7, 8};
+
+Plane Surface(1) = {1};
+
+Physical Surface("plate") = {1};
+
+Physical Line("bottom") = {1};
+Physical Line("right") = {2, 3};
+Physical Line("top") = {4};
+Physical Line("left") = {5,8};
diff --git a/examples/python/plate-hole/CMakeLists.txt b/examples/python/plate-hole/CMakeLists.txt
index 64b2f0dec..3ab1dad5d 100644
--- a/examples/python/plate-hole/CMakeLists.txt
+++ b/examples/python/plate-hole/CMakeLists.txt
@@ -1,8 +1,40 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Jan 22 2016
+# @date last modification: Wed Aug 14 2019
+#
+# @brief CMakeLists for plate-hole example
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(plate_hole_mesh plate.geo DIM 2 ORDER 1)
register_example(plate-hole
SCRIPT plate.py
FILES_TO_COPY material.dat
DEPENDS plate_hole_mesh
PYTHON
)
diff --git a/examples/python/plate-hole/plate.py b/examples/python/plate-hole/plate.py
index efabe9628..4359fbf66 100644
--- a/examples/python/plate-hole/plate.py
+++ b/examples/python/plate-hole/plate.py
@@ -1,72 +1,83 @@
#!/usr/bin/env python3
+""" plate.py: Plate with hole linear elastic example"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
prank = comm.Get_rank()
except ImportError:
prank = 0
import akantu as aka
import numpy as np
# -----------------------------------------------------------------------------
def solve(material_file, mesh_file, traction):
aka.parseInput(material_file)
spatial_dimension = 2
# -------------------------------------------------------------------------
# Initialization
# -------------------------------------------------------------------------
mesh = aka.Mesh(spatial_dimension)
if prank == 0:
mesh.read(mesh_file)
mesh.distribute()
model = aka.SolidMechanicsModel(mesh)
model.initFull(_analysis_method=aka._static)
model.setBaseName("plate")
model.addDumpFieldVector("displacement")
model.addDumpFieldVector("external_force")
model.addDumpField("strain")
model.addDumpField("stress")
model.addDumpField("blocked_dofs")
# -------------------------------------------------------------------------
# Boundary conditions
# -------------------------------------------------------------------------
model.applyBC(aka.FixedValue(0.0, aka._x), "XBlocked")
model.applyBC(aka.FixedValue(0.0, aka._y), "YBlocked")
model.getExternalForce()[:] = 0
trac = np.zeros(spatial_dimension)
trac[1] = traction
model.applyBC(aka.FromTraction(trac), "Traction")
solver = model.getNonLinearSolver()
solver.set("max_iterations", 2)
solver.set("threshold", 1e-10)
solver.set("convergence_type", aka.SolveConvergenceCriteria.residual)
print("Solve for traction ", traction)
model.solveStep()
model.dump()
# -----------------------------------------------------------------------------
# main
# -----------------------------------------------------------------------------
def main():
mesh_file = 'plate.msh'
material_file = 'material.dat'
traction = 1.
solve(material_file, mesh_file, traction)
# -----------------------------------------------------------------------------
if __name__ == "__main__":
main()
diff --git a/examples/python/stiffness_matrix/CMakeLists.txt b/examples/python/stiffness_matrix/CMakeLists.txt
index bf55db522..3115a046f 100644
--- a/examples/python/stiffness_matrix/CMakeLists.txt
+++ b/examples/python/stiffness_matrix/CMakeLists.txt
@@ -1,8 +1,41 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Tue Mar 26 2019
+# @date last modification: Wed Aug 14 2019
+#
+# @brief CMakeLists for stiffness matrix extraction example
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(plate_stiffness_matrix plate.geo DIM 2)
register_example(stiffness_matrix
SCRIPT stiffness_matrix.py
FILES_TO_COPY material.dat
DEPENDS plate_stiffness_matrix
PYTHON
)
diff --git a/examples/python/stiffness_matrix/stiffness_matrix.py b/examples/python/stiffness_matrix/stiffness_matrix.py
index 9c13c37b8..ec54b2b97 100644
--- a/examples/python/stiffness_matrix/stiffness_matrix.py
+++ b/examples/python/stiffness_matrix/stiffness_matrix.py
@@ -1,39 +1,51 @@
#!/usr/bin/env python3
+""" stiffness_matrix.py: Example showing how to access the stifness matrix in
+python"""
+
+__author__ = "Guillaume Anciaux"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import akantu as aka
def getStiffnessMatrix(material_file, mesh_file, traction):
aka.parseInput(material_file)
spatial_dimension = 2
# --------------------------------------------------------------------------
# Initialization
# --------------------------------------------------------------------------
mesh = aka.Mesh(spatial_dimension)
mesh.read(mesh_file)
model = aka.SolidMechanicsModel(mesh)
model.initFull(_analysis_method=aka._static)
model.assembleStiffnessMatrix()
K = model.getDOFManager().getMatrix('K')
stiff = aka.AkantuSparseMatrix(K).toarray()
return stiff
# --------------------------------------------------------------------------
# main
# --------------------------------------------------------------------------
def main():
mesh_file = 'plate.msh'
material_file = 'material.dat'
traction = 1.
mat = getStiffnessMatrix(material_file, mesh_file, traction)
print(mat)
# --------------------------------------------------------------------------
if __name__ == "__main__":
main()
diff --git a/examples/python/structural_mechanics/CMakeLists.txt b/examples/python/structural_mechanics/CMakeLists.txt
index 7496e58f4..cae0cc6c0 100644
--- a/examples/python/structural_mechanics/CMakeLists.txt
+++ b/examples/python/structural_mechanics/CMakeLists.txt
@@ -1,14 +1,44 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Sat Mar 13 2021
+# @date last modification: Sun Mar 14 2021
+#
+# @brief CMakeLists for structural mechanics examples
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
register_example(structural_mechanics.py
SCRIPT structural_mechanics.py
PYTHON
)
register_example(structural_mechanics_softening.py
SCRIPT structural_mechanics_softening.py
PYTHON
)
register_example(structural_mechanics_dynamics.py
SCRIPT structural_mechanics_dynamics.py
PYTHON
)
diff --git a/examples/python/structural_mechanics/structural_mechanics.py b/examples/python/structural_mechanics/structural_mechanics.py
index d0706beda..4b65c2fd6 100644
--- a/examples/python/structural_mechanics/structural_mechanics.py
+++ b/examples/python/structural_mechanics/structural_mechanics.py
@@ -1,141 +1,151 @@
#!/usr/bin/env python
# coding: utf-8
+""" structural_mechanics.py: Simple structural mechanics example"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
# # Test of Structural Mechanics
# In this example a beam, consisting of two elements, three nodes, is created.
# The left most node is fixed and a force is applied at the right most node.
-import akantu as aka
-import numpy
import numpy as np
try:
import matplotlib.pyplot as plt
has_matplotlib = True
except ImportError:
has_matplotlib = False
+import akantu as aka
# ### Creating the Mesh
# Create a mesh for the two dimensional case
beam = aka.Mesh(2)
# We now create the connectivity array for the beam.
beam.addConnectivityType(aka._bernoulli_beam_2)
# We need a `MeshAccessor` in order to change the size of the mesh entities.
beamAcc = aka.MeshAccessor(beam)
# Now we create the array to store the nodes and the connectivities and give
# them their size.
beamAcc.resizeConnectivity(2, aka._bernoulli_beam_2)
beamAcc.resizeNodes(3)
Nodes = beam.getNodes()
Nodes[0, :] = [0., 0.]
Nodes[1, :] = [1., 0.]
Nodes[2, :] = [2., 0.]
# #### Setting the Connections
Conn = beam.getConnectivity(aka._bernoulli_beam_2)
Conn[0, :] = [0, 1]
Conn[1, :] = [1, 2]
# #### Ready
# We have to make the mesh ready.
beamAcc.makeReady()
# ### Creating the Model
model = aka.StructuralMechanicsModel(beam)
# #### Setting up the Modell
# ##### Creating and Inserting the Materials
mat1 = aka.StructuralMaterial()
mat1.E = 1e9
mat1.rho = 1.
mat1.I = 1. # noqa: E741
mat1.Iz = 1.
mat1.Iy = 1.
mat1.A = 1.
mat1.GJ = 1.
model.addMaterial(mat1)
mat2 = aka.StructuralMaterial()
mat2.E = 1e9
mat2.rho = 1.
mat2.I = 1. # noqa: E741
mat2.Iz = 1.
mat2.Iy = 1.
mat2.A = 1.
mat2.GJ = 1.
model.addMaterial(mat2)
# ##### Initializing the Model
model.initFull(aka._implicit_dynamic)
# ##### Assigning the Materials
materials = model.getElementMaterial(aka._bernoulli_beam_2)
materials[0][0] = 0
materials[1][0] = 1
# ##### Setting Boundaries
# Neumann
# Apply a force of `10` at the last (right most) node.
forces = model.getExternalForce()
forces[:] = 0
forces[2, 0] = 100.
# Dirichlets
# Block all dofs of the first node, since it is fixed.
# All other nodes have no restrictions
boundary = model.getBlockedDOFs()
boundary[0, :] = True
boundary[1, :] = False
boundary[2, :] = False
# ### Solving the System
# Set up the system
deltaT = 1e-10
model.setTimeStep(deltaT)
solver = model.getNonLinearSolver()
solver.set("max_iterations", 100)
solver.set("threshold", 1e-8)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
# Perform N time steps.
# At each step records the displacement of all three nodes in x direction.
N = 1000000
disp1 = np.zeros(N)
disp2 = np.zeros(N)
disp0 = np.zeros(N)
times = np.zeros(N)
for i in range(N):
model.solveStep()
disp = model.getDisplacement()
disp0[i] = disp[0, 0]
disp1[i] = disp[1, 0]
disp2[i] = disp[2, 0]
times[i] = deltaT * i
disps = [disp0, disp1, disp2]
maxMin = [-1.0, 1.0]
for d in disps:
maxMin[0] = max(np.max(d), maxMin[0])
maxMin[1] = min(np.min(d), maxMin[1])
if has_matplotlib:
plt.plot(disp1, times, color='g', label="middle node")
plt.plot(disp2, times, color='b', label="right node")
plt.title("Displacement in $x$ of the nodes")
plt.ylabel("Time [S]")
plt.xlabel("displacement [m]")
plt.xlim((maxMin[1] * 1.3, maxMin[0] * 1.1))
plt.legend()
plt.show()
diff --git a/examples/python/structural_mechanics/structural_mechanics_dynamics.py b/examples/python/structural_mechanics/structural_mechanics_dynamics.py
index 4a9745a3a..cdb3577cd 100644
--- a/examples/python/structural_mechanics/structural_mechanics_dynamics.py
+++ b/examples/python/structural_mechanics/structural_mechanics_dynamics.py
@@ -1,175 +1,185 @@
#!/usr/bin/env python
# coding: utf-8
-import akantu as aka
-import numpy
+""" structural_mechanics_dynamics.py: Dynamics structural mechanics example"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import numpy as np
try:
import matplotlib.pyplot as plt
has_matplotlib = True
except ImportError:
has_matplotlib = False
+import akantu as aka
# ### Creating the Mesh
# Create a mesh for the two dimensional case
el_type = aka._bernoulli_beam_2
beam = aka.Mesh(2)
# We now create the connectivity array for the beam.
beam.addConnectivityType(el_type)
# We need a `MeshAccessor` in order to change the size of the mesh entities.
beamAcc = aka.MeshAccessor(beam)
# Now we create the array to store the nodes and the connectivities and give
# them their size.
nb_elem = 40
L = 2
beamAcc.resizeConnectivity(nb_elem, el_type)
beamAcc.resizeNodes(nb_elem + 1)
# #### Setting the Nodes
Nodes = beam.getNodes()
length = L / nb_elem
Nodes[:, :] = 0.
Nodes[:, 0] = np.arange(nb_elem+1) * length
# #### Setting the Connections
Conn = beam.getConnectivity(el_type)
for e in range(nb_elem):
Conn[e, :] = [e, e + 1]
# #### Ready
# We have to make the mesh ready.
beamAcc.makeReady()
# ### Creating the Model
model = aka.StructuralMechanicsModel(beam)
if el_type == aka._bernoulli_beam_3:
normal = beam.getDataReal("extra_normal", el_type)
for e in range(nb_elem):
normal[e, :] = [0, 0, 1]
# #### Setting up the Modell
# ##### Creating and Inserting the Materials
mat1 = aka.StructuralMaterial()
mat1.E = 1e9
mat1.rho = 10.
mat1.I = 1. # noqa: E741
mat1.Iz = 1.
mat1.Iy = 1.
mat1.A = 1.
mat1.GJ = 1.
model.addMaterial(mat1, 'mat1')
# ##### Initializing the Model
model.initFull(aka.AnalysisMethod._implicit_dynamic)
# ##### Assigning the Materials
materials = model.getElementMaterial(el_type)
materials[:, :] = 0
# ##### Setting Boundaries
# Neumann
F = 1e4
no_print = int(nb_elem / 2)
# Apply a force of `10` at the last (right most) node.
forces = model.getExternalForce()
forces[:, :] = 0
forces[no_print, 1] = F
# Dirichlets
# Block all dofs of the first node, since it is fixed.
# All other nodes have no restrictions
boundary = model.getBlockedDOFs()
boundary[:, :] = False
boundary[0, 0] = True
boundary[0, 1] = True
if el_type == aka._bernoulli_beam_3:
boundary[0, 2] = True
boundary[nb_elem, 1] = True
# ### Solving the System
# Set up the system
deltaT = 1e-6
model.setTimeStep(deltaT)
solver = model.getNonLinearSolver()
solver.set("max_iterations", 100)
solver.set("threshold", 1e-8)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
model.assembleMatrix("M")
M_ = model.getDOFManager().getMatrix("M")
M = aka.AkantuSparseMatrix(M_)
model.assembleMatrix("K")
K_ = model.getDOFManager().getMatrix("K")
K = aka.AkantuSparseMatrix(K_)
C_ = model.getDOFManager().getMatrix("C")
C_.add(M_, 0.00001)
C_.add(K_, 0.00001)
def analytical_solution(time, L, rho, E, A, I, F): # noqa: E741
omega = np.pi**2 / L**2 * np.sqrt(E * I / rho)
sum = 0.
N = 110
for n in range(1, N, 2):
sum += (1. - np.cos(n * n * omega * time)) / n**4
return 2. * F * L**3 / np.pi**4 / E / I * sum
# Perform N time steps.
# At each step records the displacement of all three nodes in x direction.
N = 900
mat1 = model.getMaterial('mat1')
disp = model.getDisplacement()
velo = model.getVelocity()
disp[:, :] = 0.
displs = np.zeros(N)
ekin = np.zeros(N)
epot = np.zeros(N)
ework = np.zeros(N)
_ework = 0.
for i in range(1, N):
model.solveStep()
displs[i] = disp[no_print, 1]
_ework += F * velo[no_print, 1] * deltaT
ekin[i] = model.getEnergy("kinetic")
epot[i] = model.getEnergy("potential")
ework[i] = _ework
def sol(x):
return analytical_solution(x, L, mat1.rho, mat1.E,
mat1.A, mat1.I, F)
if has_matplotlib:
times = np.arange(N) * deltaT
plt.plot(times, sol(times))
plt.plot(times, displs)
plt.plot(times, displs - sol(times))
# What I do not fully understand is why the middle node first go backwards
# until it goes forward. I could imagine that there is some vibration,
# because everything is in rest.
np.max(displs - sol(times))
plt.plot(times, ekin+epot)
plt.plot(times, ework)
diff --git a/examples/python/structural_mechanics/structural_mechanics_softening.py b/examples/python/structural_mechanics/structural_mechanics_softening.py
index 602852693..8262f6261 100644
--- a/examples/python/structural_mechanics/structural_mechanics_softening.py
+++ b/examples/python/structural_mechanics/structural_mechanics_softening.py
@@ -1,189 +1,200 @@
#!/usr/bin/env python
# coding: utf-8
+""" structural_mechanics_softening.py: Structural mechanics with softening"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
# # Test of Structural Mechanics
# In this test there is a beam consisting of three parts, all have the same materials.
# The left most node is fixed.
# On the right most node a force is applied in x direction.
#
# After a certain time, the material of the middle _element_ is waekened, lower Young's modulus.
# In each step the modulus is lowered by a coinstant factor.
import akantu as aka
import numpy
import numpy as np
try:
import matplotlib.pyplot as plt
has_matplotlib = True
except ImportError:
has_matplotlib = False
# ### Creating the Mesh
# Create a mesh for the two dimensional case
beam = aka.Mesh(2)
# We now create the connectivity array for the beam.
beam.addConnectivityType(aka._bernoulli_beam_2)
# We need a `MeshAccessor` in order to change the size of the mesh entities.
beamAcc = aka.MeshAccessor(beam)
# Now we create the array to store the nodes and the connectivities and give them their size.
beamAcc.resizeConnectivity(3, aka._bernoulli_beam_2)
beamAcc.resizeNodes(4)
# #### Setting the Nodes
Nodes = beam.getNodes()
Nodes[0, :] = [0., 0.]
Nodes[1, :] = [1., 0.]
Nodes[2, :] = [2., 0.]
Nodes[3, :] = [3., 0.]
# Setting the Connections
Conn = beam.getConnectivity(aka._bernoulli_beam_2)
Conn[0, :] = [0, 1]
Conn[1, :] = [1, 2]
Conn[2, :] = [2, 3]
# Ready
# We have to make the mesh ready.
beamAcc.makeReady()
# Creating the Model
model = aka.StructuralMechanicsModel(beam)
# Setting up the Modell
# Creating and Inserting the Materials
mat1 = aka.StructuralMaterial()
mat1.E = 1e9
mat1.rho = 1.
mat1.I = 1. # noqa: E741
mat1.A = 1.
mat1.GJ = 1.
mat1ID = model.addMaterial(mat1, 'mat1')
mat2 = aka.StructuralMaterial()
mat2.E = 1e9
mat2.rho = 1.
mat2.I = 1. # noqa: E741
mat2.A = 1.
mat2.GJ = 1.
mat2ID = model.addMaterial(mat2, 'mat2')
mat3 = aka.StructuralMaterial()
mat3.E = mat2.E / 100000
mat3.rho = 1.
mat3.I = 1. # noqa: E741
mat3.A = mat2.A / 100
mat3.GJ = 1.
mat3ID = model.addMaterial(mat3, 'mat3')
# ##### Initializing the Model
model.initFull(aka.AnalysisMethod._implicit_dynamic)
# ##### Assigning the Materials
materials = model.getElementMaterial(aka._bernoulli_beam_2)
materials[0][0] = mat1ID
materials[1][0] = mat2ID
materials[2][0] = mat1ID
# ##### Setting Boundaries
# Neumann
# Apply a force of `10` at the last (right most) node.
forces = model.getExternalForce()
forces[:] = 0
forces[2, 0] = 100.
# Dirichlets
# Block all dofs of the first node, since it is fixed.
# All other nodes have no restrictions
boundary = model.getBlockedDOFs()
boundary[0, :] = True
boundary[1, :] = False
boundary[2, :] = False
boundary[3, :] = False
# ### Solving the System
# Set up the system
deltaT = 1e-9
model.setTimeStep(deltaT)
solver = model.getNonLinearSolver()
solver.set("max_iterations", 100)
solver.set("threshold", 1e-8)
solver.set("convergence_type", aka.SolveConvergenceCriteria.solution)
# Perform N time steps.
# At each step records the displacement of all three nodes in x direction.
N = 10000 * 60
disp0 = np.zeros(N)
disp1 = np.zeros(N)
disp2 = np.zeros(N)
disp3 = np.zeros(N)
times = np.zeros(N)
switchT = None
switchEnd = None
softDuration = 1000
SoftStart = (N // 2) - softDuration // 2
SoftEnd = SoftStart + softDuration
if(softDuration > 0):
softFactor = (model.getMaterial('mat3').E
/ model.getMaterial('mat2').E) ** (1.0 / softDuration)
mat2 = model.getMaterial('mat2')
for i in range(N):
times[i] = deltaT * i
if((SoftStart <= i <= SoftEnd) and (softDuration > 0)):
if switchT is None:
switchT = times[i]
elif(i == SoftEnd):
switchEnd = times[i]
#
mat2.E *= softFactor
#
model.solveStep()
disp = model.getDisplacement()
disp0[i] = disp[0, 0]
disp1[i] = disp[1, 0]
disp2[i] = disp[2, 0]
disp3[i] = disp[3, 0]
disps = [disp0, disp1, disp2, disp3]
maxMin = [-1.0, 1.0]
for d in disps:
maxMin[0] = max(np.max(d), maxMin[0])
maxMin[1] = min(np.min(d), maxMin[1])
if has_matplotlib:
# plt.plot(disp0, times, color='k', label = "left node (fix)")
plt.plot(disp1, times, color='g', label="middle, left node")
plt.plot(disp2, times, color='g', linestyle='--',
label="middle, right node")
plt.plot(disp3, times, color='b', label="right node")
if(softDuration > 0):
plt.plot((maxMin[1], maxMin[0]), (switchT, switchT),)
plt.plot((maxMin[1], maxMin[0]), (switchEnd, switchEnd), )
plt.title("Displacement in $x$ of the nodes")
plt.ylabel("Time [S]")
plt.xlabel("displacement [m]")
plt.xlim((maxMin[1] * 1.3, maxMin[0] * 1.1))
plt.legend()
plt.show()
# If the softening is disabled, then the displacement looks wierd.
# Because the displacement first increases and then decreases.
# In this case `softDuration > 0` holds.
#
# However if the softening is enabled, it looks rather good. The left middle
# node will start to vibrate, because it is not pulled in the other direction.
diff --git a/examples/static/CMakeLists.txt b/examples/static/CMakeLists.txt
index 6960f3cf2..6ecd37820 100644
--- a/examples/static/CMakeLists.txt
+++ b/examples/static/CMakeLists.txt
@@ -1,40 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
+# @author Oumaima Sabir <oumaima.sabir@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
-# @date last modification: Tue Jan 19 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Jun 08 2018
#
# @brief configuration implicit tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
add_mesh(static_mesh square.geo 2 2)
register_example(static
SOURCES static.cc
DEPENDS static_mesh
FILES_TO_COPY material.dat
)
diff --git a/examples/static/static.cc b/examples/static/static.cc
index 406f880ad..db9199bfd 100644
--- a/examples/static/static.cc
+++ b/examples/static/static.cc
@@ -1,77 +1,81 @@
/**
* @file static.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Oumaima Sabir <oumaima.sabir@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Mon Aug 09 2010
+ * @date last modification: Sun Dec 30 2018
*
* @brief This code refers to the implicit static example from the user manual
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
#define bar_length 0.01
#define bar_height 0.01
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("square.msh");
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _static);
model.setBaseName("static");
model.addDumpFieldVector("displacement");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.addDumpField("grad_u");
/// Dirichlet boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "Fixed_x");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "Fixed_y");
model.applyBC(BC::Dirichlet::FixedValue(0.0001, _y), "Traction");
model.dump();
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
model.solveStep();
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/examples/structural_mechanics/CMakeLists.txt b/examples/structural_mechanics/CMakeLists.txt
index fb1688a8d..7301ae3a9 100644
--- a/examples/structural_mechanics/CMakeLists.txt
+++ b/examples/structural_mechanics/CMakeLists.txt
@@ -1,37 +1,38 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
-# @date creation: Mon Jan 18 2016
-# @date last modification: Tue Jan 19 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Wed Jan 27 2021
#
# @brief configuration for structural mechanics example
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
register_example(bernoulli_beam_2_example
SOURCES bernoulli_beam_2_example.cc
)
diff --git a/examples/structural_mechanics/bernoulli_beam_2_example.cc b/examples/structural_mechanics/bernoulli_beam_2_example.cc
index e752a75a7..24712a721 100644
--- a/examples/structural_mechanics/bernoulli_beam_2_example.cc
+++ b/examples/structural_mechanics/bernoulli_beam_2_example.cc
@@ -1,139 +1,142 @@
/**
- * @file bernoulli_beam_2_exemple.cc
+ * @file bernoulli_beam_2_example.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
- * @date creation: Mon Jan 18 2016
+ * @date creation: Fri Jul 15 2011
+ * @date last modification: Mon Mar 15 2021
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#define TYPE _bernoulli_beam_2
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
// Defining the mesh
Mesh beams(2);
const auto q = 6000.;
const auto L = 10.;
const auto M = -3600.; // Momentum at 3
auto nb_nodes = 3;
auto nb_element = nb_nodes - 1;
MeshAccessor mesh_accessor(beams);
Array<Real> & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
beams.addConnectivityType(_bernoulli_beam_2);
Array<UInt> & connectivity = mesh_accessor.getConnectivity(_bernoulli_beam_2);
connectivity.resize(nb_element);
nodes.zero();
nodes(1, 0) = 10;
nodes(2, 0) = 18;
for (int i = 0; i < nb_element; ++i) {
connectivity(i, 0) = i;
connectivity(i, 1) = i + 1;
}
mesh_accessor.makeReady();
// Defining the materials
StructuralMechanicsModel model(beams);
StructuralMaterial mat1;
mat1.E = 3e10;
mat1.I = 0.0025;
mat1.A = 0.01;
model.addMaterial(mat1);
StructuralMaterial mat2;
mat2.E = 3e10;
mat2.I = 0.00128;
mat2.A = 0.01;
model.addMaterial(mat2);
// Defining the forces
model.initFull();
auto & forces = model.getExternalForce();
auto & displacement = model.getDisplacement();
auto & boundary = model.getBlockedDOFs();
const auto & N_M = model.getStress(_bernoulli_beam_2);
auto & element_material = model.getElementMaterial(_bernoulli_beam_2);
boundary.set(false);
forces.zero();
displacement.zero();
element_material(1) = 1;
forces(0, 1) = -q * L / 2.;
forces(0, 2) = -q * L * L / 12.;
forces(1, 1) = -q * L / 2.;
forces(1, 2) = q * L * L / 12.;
forces(2, 2) = M;
forces(2, 0) = mat2.E * mat2.A / 18;
// Defining the boundary conditions
boundary(0, 0) = true;
boundary(0, 1) = true;
boundary(0, 2) = true;
boundary(1, 1) = true;
boundary(2, 1) = true;
model.addDumpFieldVector("displacement");
model.addDumpField("rotation");
model.addDumpFieldVector("force");
model.addDumpField("momentum");
model.solveStep();
model.assembleResidual();
// Post-Processing
std::cout << " d1 = " << displacement(1, 2) << std::endl;
std::cout << " d2 = " << displacement(2, 2) << std::endl;
std::cout << " d3 = " << displacement(1, 0) << std::endl;
std::cout << " M1 = " << N_M(0, 1) << std::endl;
std::cout << " M2 = " << N_M(2 * (nb_nodes - 2), 1) << std::endl;
model.dump();
finalize();
}
diff --git a/extra_packages/extra-materials/package.cmake b/extra_packages/extra-materials/package.cmake
index 81377969f..8cc3e7719 100644
--- a/extra_packages/extra-materials/package.cmake
+++ b/extra_packages/extra-materials/package.cmake
@@ -1,109 +1,126 @@
#===============================================================================
# @file package.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
+# @date creation: Thu Mar 15 2018
+# @date last modification: Wed Dec 09 2020
#
# @brief package description for extra materials list
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
#===============================================================================
-package_declare(extra_materials
+
+package_declare(extra_materials ADVANCED
DESCRIPTION "Add the extra list of materials in Akantu"
DEPENDS lapack)
package_declare_sources(extra_materials
material_extra_includes.hh
material_damage/material_brittle.cc
material_damage/material_brittle.hh
material_damage/material_brittle_inline_impl.hh
material_damage/material_damage_iterative.cc
material_damage/material_damage_iterative.hh
material_damage/material_damage_iterative_inline_impl.hh
material_damage/material_iterative_stiffness_reduction.cc
material_damage/material_iterative_stiffness_reduction.hh
material_damage/material_damage_linear.cc
material_damage/material_damage_linear.hh
material_damage/material_damage_linear_inline_impl.hh
material_damage/material_vreepeerlings.hh
material_damage/material_vreepeerlings_inline_impl.hh
material_damage/material_vreepeerlings_tmpl.hh
material_plastic/material_viscoplastic.cc
material_plastic/material_viscoplastic.hh
material_plastic/material_viscoplastic_inline_impl.hh
material_viscoelastic/material_stiffness_proportional.cc
material_viscoelastic/material_stiffness_proportional.hh
material_damage/material_orthotropic_damage.hh
material_damage/material_orthotropic_damage_tmpl.hh
material_damage/material_orthotropic_damage_iterative.cc
material_damage/material_orthotropic_damage_iterative.hh
material_damage/material_orthotropic_damage_iterative_inline_impl.hh
material_FE2/material_FE2.hh
material_FE2/material_FE2.cc
material_FE2/material_FE2_inline_impl.hh
material_FE2/solid_mechanics_model_RVE.hh
material_FE2/solid_mechanics_model_RVE.cc
)
package_declare_material_infos(extra_materials
LIST AKANTU_EXTRA_MATERIAL_LIST
INCLUDE material_extra_includes.hh
)
package_declare_documentation_files(extra_materials
manual-extra_materials.tex
manual-appendix-materials-extra-materials.tex
figures/stress_strain_visco.pdf
)
package_declare_documentation(extra_materials
"This package activates additional constitutive laws:"
"\\begin{itemize}"
" \\item Linear anisotropy"
" \\item Linear orthotropy"
" \\item Visco-plastic"
"\\end{itemize}"
)
-package_declare(extra_materials_non_local
+package_declare(extra_materials_non_local ADVANCED
DESCRIPTION "Add the extra list of non local materials in Akantu"
DEPENDS extra_materials damage_non_local)
package_declare_sources(extra_materials_non_local
material_damage/material_orthotropic_damage_non_local.hh
material_damage/material_vreepeerlings_non_local.cc
material_damage/material_vreepeerlings_non_local.hh
material_damage/material_brittle_non_local.hh
material_damage/material_damage_iterative_non_local.hh
material_damage/material_damage_iterative_non_local.cc
material_damage/material_orthotropic_damage_iterative_non_local.hh
material_damage/material_vreepeerlings_non_local_inline_impl.hh
material_damage/material_brittle_non_local_inline_impl.hh
material_damage/material_damage_iterative_non_local_inline_impl.hh
material_damage/material_orthotropic_damage_iterative_non_local_inline_impl.hh
material_non_local_extra_includes.hh
)
package_declare_material_infos(extra_materials_non_local
LIST AKANTU_DAMAGE_NON_LOCAL_MATERIAL_EXTRA_LIST
INCLUDE material_extra_includes.hh
-)
+ )
diff --git a/extra_packages/igfem/package.cmake b/extra_packages/igfem/package.cmake
index 7092ba706..509f61cb0 100644
--- a/extra_packages/igfem/package.cmake
+++ b/extra_packages/igfem/package.cmake
@@ -1,104 +1,104 @@
#===============================================================================
# @file package.cmake
#
# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
#
# @brief package description for interface-enriched generalized IGFEM
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
#===============================================================================
-package_declare(IGFEM
+package_declare(IGFEM ADVANCED
DESCRIPTION "Use Interface-enriched generalized FEM"
DEPENDS CGAL)
package_declare_sources(igfem
element_class_igfem.cc
element_class_igfem.hh
element_classes_igfem/element_class_igfem_segment_3_inline_impl.hh
element_classes_igfem/element_class_igfem_triangle_4_inline_impl.hh
element_classes_igfem/element_class_igfem_triangle_5_inline_impl.hh
integrator_gauss_igfem.hh
integrator_gauss_igfem_inline_impl.hh
interpolation_element_igfem.cc
interpolation_element_igfem_tmpl.hh
geometrical_element_igfem.hh
shape_igfem.hh
shape_igfem.cc
shape_igfem_inline_impl.hh
fe_engine_template_tmpl_igfem.hh
dumper_igfem_connectivity.hh
dumper_igfem_elemental_field.hh
dumper_igfem_generic_elemental_field.hh
dumper_igfem_element_iterator.hh
dumper_igfem_material_internal_field.hh
dumper_igfem_quadrature_points_field.hh
dumper_igfem_element_partition.hh
igfem_helper.hh
igfem_helper.cc
igfem_enrichment.hh
igfem_enrichment.cc
igfem_enrichment_inline_impl.hh
solid_mechanics_model_igfem.hh
solid_mechanics_model_igfem.cc
solid_mechanics_model_igfem_inline_impl.hh
mesh_igfem_spherical_growing_gel.hh
mesh_igfem_spherical_growing_gel_tmpl.hh
material_igfem/material_igfem_includes.hh
material_igfem/material_igfem.hh
material_igfem/material_igfem.cc
material_igfem/material_igfem_inline_impl.hh
material_igfem/material_igfem_elastic.hh
material_igfem/material_igfem_elastic.cc
material_igfem/material_igfem_elastic_inline_impl.hh
material_igfem/material_igfem_saw_tooth_damage.hh
material_igfem/material_igfem_saw_tooth_damage.cc
material_igfem/material_igfem_saw_tooth_damage_inline_impl.hh
material_igfem/material_igfem_iterative_stiffness_reduction.hh
material_igfem/material_igfem_iterative_stiffness_reduction.cc
material_igfem/igfem_internal_field.hh
material_igfem/igfem_internal_field_tmpl.hh
non_local_manager_igfem.hh
non_local_manager_igfem.cc
)
package_declare_elements(igfem
ELEMENT_TYPES
_igfem_segment_3
_igfem_triangle_4
_igfem_triangle_5
KIND igfem
GEOMETRICAL_TYPES
_gt_igfem_segment_3
_gt_igfem_triangle_4
_gt_igfem_triangle_5
INTERPOLATION_TYPES
_itp_igfem_segment_3
_itp_igfem_triangle_4
_itp_igfem_triangle_5
INTERPOLATION_KIND
_itk_igfem
FE_ENGINE_LISTS
gradient_on_integration_points
interpolate_on_integration_points
interpolate
compute_normals_on_integration_points
inverse_map
contains
get_shapes_derivatives
)
package_declare_material_infos(igfem
LIST AKANTU_IGFEM_MATERIAL_LIST
INCLUDE material_igfem_includes.hh
)
diff --git a/extra_packages/traction-at-split-node-contact/README.txt b/extra_packages/traction-at-split-node-contact/README.txt
index b38a0de4b..67629602c 100644
--- a/extra_packages/traction-at-split-node-contact/README.txt
+++ b/extra_packages/traction-at-split-node-contact/README.txt
@@ -1,26 +1,37 @@
#===============================================================================
# @file README.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Tue Dec 02 2014
-# @date last modification: Mon Feb 01 2016
+# @date creation: Sat Jan 23 2016
+# @date last modification: Fri Mar 16 2018
#
# @brief kammer
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
Short explanation for AkantuSimTools:
Using ccmake for compilation, give the path to the build folder of akantu. By putting build_shared_libs on, the library is dynamic. Give a cmake_install_prefix (e.g., ./install).
When compiling use: make install (don't forget to create the folder in which you install)
diff --git a/extra_packages/traction-at-split-node-contact/package.cmake b/extra_packages/traction-at-split-node-contact/package.cmake
index acadcc21f..0703895b9 100644
--- a/extra_packages/traction-at-split-node-contact/package.cmake
+++ b/extra_packages/traction-at-split-node-contact/package.cmake
@@ -1,92 +1,95 @@
#===============================================================================
# @file package.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Tue Dec 02 2014
-# @date last modification: Wed Feb 03 2016
+# @date creation: Fri Mar 16 2018
+# @date last modification: Fri Mar 16 2018
+#
+# @brief Desciption of the traction-at-split-node-contact package
#
-# @brief
#
# @section LICENSE
#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(traction_at_split_node_contact
DESCRIPTION "The super contact of David"
DEPENDS iohelper)
package_declare_sources(traction_at_split_node_contact
common/synchronized_array.cc
common/parameter_reader.cc
common/manual_restart.cc
functions/boundary_functions.cc
ntn_contact/ntn_base_contact.cc
ntn_contact/ntn_contact.cc
ntn_contact/ntrf_contact.cc
ntn_contact/mIIasym_contact.cc
ntn_contact/ntn_base_friction.cc
ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc
ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc
ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc
ntn_contact/ntn_initiation_function.cc
tasn_contact.hh
# headers
common/synchronized_array.hh
common/parameter_reader.hh
common/manual_restart.hh
functions/boundary_functions.hh
functions/node_filter.hh
boundary_conditions/force_based_dirichlet.hh
boundary_conditions/spring_bc.hh
boundary_conditions/inclined_flat_dirichlet.hh
ntn_contact/ntn_base_contact.hh
ntn_contact/ntn_contact.hh
ntn_contact/ntrf_contact.hh
ntn_contact/mIIasym_contact.hh
ntn_contact/ntn_base_friction.hh
ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh
ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh
ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh
ntn_contact/ntn_friction.hh
ntn_contact/ntn_friction_tmpl.hh
ntn_contact/ntrf_friction.hh
ntn_contact/ntrf_friction_tmpl.hh
ntn_contact/ntn_initiation_function.hh
# inlines
common/synchronized_array_inline_impl.hh
ntn_contact/ntn_base_contact_inline_impl.hh
)
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
index 7f1cc31c4..3839869bf 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/force_based_dirichlet.hh
@@ -1,128 +1,130 @@
/**
* @file force_based_dirichlet.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
- * @brief dirichlet boundary condition that tries
- * to keep the force at a given value
+ * @brief dirichlet boundary condition that tries to keep the force at a given
+ * value
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_FORCE_BASED_DIRICHLET_HH_
#define AST_FORCE_BASED_DIRICHLET_HH_
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class ForceBasedDirichlet : public BC::Dirichlet::IncrementValue {
protected:
typedef const Array<Real> * RealArrayPtr;
typedef const Array<Int> * IntArrayPtr;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ForceBasedDirichlet(SolidMechanicsModel & model, BC::Axis ax, Real target_f,
Real mass = 0.)
: IncrementValue(0., ax), model(model), mass(mass), velocity(0.),
target_force(target_f), total_residual(0.) {}
virtual ~ForceBasedDirichlet() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void updateTotalResidual() {
this->total_residual = 0.;
for (auto && subboundary : this->subboundaries) {
this->total_residual +=
integrateResidual(subboundary, this->model, this->axis);
}
}
virtual Real update() {
AKANTU_DEBUG_IN();
this->updateTotalResidual();
Real total_force = this->target_force + this->total_residual;
Real a = total_force / this->mass;
Real dt = model.getTimeStep();
this->velocity += 0.5 * dt * a;
this->value =
this->velocity * dt + 0.5 * dt * dt * a; // increment position dx
this->velocity += 0.5 * dt * a;
AKANTU_DEBUG_OUT();
return this->total_residual;
}
Real applyYourself() {
AKANTU_DEBUG_IN();
Real reaction = this->update();
for (auto && subboundary : this->subboundaries) {
this->model.applyBC(*this, subboundary);
}
AKANTU_DEBUG_OUT();
return reaction;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_SET_MACRO(Mass, mass, Real);
AKANTU_SET_MACRO(TargetForce, target_force, Real);
void insertSubBoundary(const std::string & sb_name) {
this->subboundaries.insert(sb_name);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
typedef std::set<std::string> SubBoundarySet;
protected:
SolidMechanicsModel & model;
SubBoundarySet subboundaries;
Real mass;
Real velocity;
Real target_force;
Real total_residual;
};
} // namespace akantu
#endif /* AST_FORCE_BASED_DIRICHLET_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
index 3d88444a3..513ea3549 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/inclined_flat_dirichlet.hh
@@ -1,80 +1,82 @@
/**
* @file inclined_flat_dirichlet.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief inclined dirichlet
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_INCLINED_FLAT_DIRICHLET_HH_
#define AST_INCLINED_FLAT_DIRICHLET_HH_
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class InclinedFlatDirichlet : public BC::Dirichlet::DirichletFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InclinedFlatDirichlet(Real val, BC::Axis ax, BC::Axis incl_ax,
Real center_coord, Real tang)
: DirichletFunctor(ax), value(val), incl_ax(incl_ax),
center_coord(center_coord), tang(tang){};
virtual ~InclinedFlatDirichlet() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void operator()(UInt node, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
AKANTU_DEBUG_IN();
Real dist = coord(incl_ax) - this->center_coord;
flags(axis) = true;
primal(axis) = this->value + this->tang * dist;
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Real value;
BC::Axis incl_ax;
Real center_coord;
Real tang;
};
} // namespace akantu
#endif /* AST_INCLINED_FLAT_DIRICHLET_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
index 62c3f790b..e6105c662 100644
--- a/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
+++ b/extra_packages/traction-at-split-node-contact/src/boundary_conditions/spring_bc.hh
@@ -1,141 +1,143 @@
/**
* @file spring_bc.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief spring boundary condition
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_SPRING_BC_HH_
#define AST_SPRING_BC_HH_
// simtools
#include "force_based_dirichlet.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class SpringBC : public ForceBasedDirichlet {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SpringBC(SolidMechanicsModel & model, BC::Axis ax, Real stiffness,
Real mass = 0.)
: ForceBasedDirichlet(model, ax, 0., mass), stiffness(stiffness),
elongation(0.) {}
virtual ~SpringBC() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual Real update() {
AKANTU_DEBUG_IN();
this->target_force = -this->stiffness * this->elongation;
Real reaction = ForceBasedDirichlet::update();
this->elongation += this->value;
AKANTU_DEBUG_OUT();
return reaction;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Elongation, elongation, Real);
inline void setToEquilibrium() {
AKANTU_DEBUG_IN();
this->updateTotalResidual();
this->target_force = -this->total_residual;
this->elongation = -this->target_force / this->stiffness;
AKANTU_DEBUG_OUT();
}
/// change elongation
/// dx > 0 -> target_force < 0
inline void incrementElongation(Real dx) {
AKANTU_DEBUG_IN();
this->elongation += dx;
AKANTU_DEBUG_OUT();
}
// friend std::ostream& operator<<(std::ostream& out, const SpringBC &
// spring);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Real stiffness;
Real elongation;
};
// class SpringBCRestricted : public SpringBC {
// public:
// SpringBCRestricted(BC::Axis ax, Real target_force, BC::Axis surface_axis,
// Real min, Real max)
// :SpringBC(ax, target_force), surface_axis(surface_axis), min(min),
// max(max) {}
// virtual ~SpringBCRestricted() {}
// public:
// inline void operator()(UInt node, Vector<bool> & flags, Vector<Real> &
// primal, const Vector<Real> & coord) const {
// if(coord(surface_axis) > min && coord(surface_axis) < max) {
// SpringBC::operator()(node, flags, primal, coord);
// }
// }
// private:
// BC::Axis surface_axis;
// Real min;
// Real max;
// };
// std::ostream& operator<<(std::ostream& out, const SpringBC & spring) {
// out << "Real total_residual: " << *spring.total_residual << std::endl;
// out << "Real mass: " << spring.mass << std::endl;
// out << "Real k: " << spring.k << std::endl;
// out << "Real delta_x: " << spring.delta_x << std::endl;
// out << "Real dt: " << spring.dt << std::endl;
// out << "Real v: " << spring.v << std::endl;
// out << "Real dx: " << spring.dx << std::endl;
// out << "Real forcing_vel: " << spring.forcing_vel << std::endl;
// return out;
// }
} // namespace akantu
#endif /* AST_SPRING_BC_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/common/manual_restart.cc b/extra_packages/traction-at-split-node-contact/src/common/manual_restart.cc
index 04bfcf06f..4af44dc70 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/manual_restart.cc
+++ b/extra_packages/traction-at-split-node-contact/src/common/manual_restart.cc
@@ -1,133 +1,135 @@
/**
* @file manual_restart.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Mar 16 2018
*
- * @brief
+ * @brief Tools to do a restart
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "manual_restart.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
void dumpArray(const Array<Real> & array, const std::string & fname) {
std::ofstream outFile;
outFile.open(fname.c_str());
outFile.precision(9);
outFile.setf(std::ios::scientific);
UInt size = array.size();
UInt nb_component = array.getNbComponent();
outFile << size << std::endl;
outFile << nb_component << std::endl;
Array<Real>::const_iterator<Vector<Real>> tit = array.begin(nb_component);
Array<Real>::const_iterator<Vector<Real>> tend = array.end(nb_component);
for (; tit != tend; ++tit) {
for (UInt c = 0; c < nb_component; ++c) {
if (c != 0)
outFile << " ";
outFile << (*tit)(c);
}
outFile << std::endl;
}
outFile.close();
}
void loadArray(Array<Real> & array, const std::string & fname) {
std::ifstream inFile;
inFile.open(fname.c_str());
inFile.precision(9);
inFile.setf(std::ios::scientific);
UInt size(0), nb_comp(0);
inFile >> size;
inFile >> nb_comp;
AKANTU_DEBUG_ASSERT(array.getNbComponent() == nb_comp,
"BAD NUM OF COMPONENTS");
AKANTU_DEBUG_ASSERT(array.size() == size,
"loadArray: number of data points in file ("
<< size << ") does not correspond to array size ("
<< array.size() << ")!!");
Array<Real>::iterator<Vector<Real>> tit = array.begin(nb_comp);
Array<Real>::iterator<Vector<Real>> tend = array.end(nb_comp);
array.resize(size);
for (UInt i(0); i < size; ++i, ++tit) {
for (UInt c = 0; c < nb_comp; ++c) {
inFile >> (*tit)(c);
}
}
inFile.close();
}
/* -------------------------------------------------------------------------- */
void loadRestart(akantu::SolidMechanicsModel & model, const std::string & fname,
akantu::UInt prank) {
const akantu::Mesh & mesh = model.getMesh();
const akantu::UInt spatial_dimension = model.getMesh().getSpatialDimension();
auto & dof_manager = dynamic_cast<DOFManagerDefault &>(model.getDOFManager());
if (prank == 0) {
akantu::Array<akantu::Real> full_reload_array(mesh.getNbGlobalNodes(),
spatial_dimension);
loadArray(full_reload_array, fname);
dof_manager.getSynchronizer().scatter(model.getDisplacement(),
full_reload_array);
} else {
dof_manager.getSynchronizer().scatter(model.getDisplacement());
}
}
/* -------------------------------------------------------------------------- */
void loadRestart(akantu::SolidMechanicsModel & model,
const std::string & fname) {
loadArray(model.getDisplacement(), fname);
}
/* -------------------------------------------------------------------------- */
void dumpRestart(akantu::SolidMechanicsModel & model, const std::string & fname,
akantu::UInt prank) {
const akantu::Mesh & mesh = model.getMesh();
const akantu::UInt spatial_dimension = model.getMesh().getSpatialDimension();
auto & dof_manager = dynamic_cast<DOFManagerDefault &>(model.getDOFManager());
if (prank == 0) {
akantu::Array<akantu::Real> full_array(mesh.getNbGlobalNodes(),
spatial_dimension);
dof_manager.getSynchronizer().gather(model.getDisplacement(), full_array);
dumpArray(full_array, fname);
} else {
dof_manager.getSynchronizer().gather(model.getDisplacement());
}
}
/* -------------------------------------------------------------------------- */
void dumpRestart(akantu::SolidMechanicsModel & model,
const std::string & fname) {
dumpArray(model.getDisplacement(), fname);
}
diff --git a/extra_packages/traction-at-split-node-contact/src/common/manual_restart.hh b/extra_packages/traction-at-split-node-contact/src/common/manual_restart.hh
index 89eb065a8..5ee0ff94e 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/manual_restart.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/manual_restart.hh
@@ -1,51 +1,53 @@
/**
* @file manual_restart.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Mar 16 2018
*
- * @brief
+ * @brief Restart tools header
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/**
* @file manual_restart.hh
* @author Dana Christen <dana.christen@epfl.ch>
* @date May 15, 2013
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "solid_mechanics_model.hh"
void dumpArray(const akantu::Array<akantu::Real> & array,
const std::string & fname);
void loadArray(akantu::Array<akantu::Real> & array, const std::string & fname);
void loadRestart(akantu::SolidMechanicsModel & model, const std::string & fname,
akantu::UInt prank);
void loadRestart(akantu::SolidMechanicsModel & model,
const std::string & fname);
void dumpRestart(akantu::SolidMechanicsModel & model, const std::string & fname,
akantu::UInt prank);
void dumpRestart(akantu::SolidMechanicsModel & model,
const std::string & fname);
diff --git a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.cc b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.cc
index 1da58d35d..2727837d0 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.cc
+++ b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.cc
@@ -1,455 +1,457 @@
/**
* @file parameter_reader.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Mar 16 2018
*
* @brief implementation of parameter reader
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// std
#include <algorithm>
#include <fstream>
#include <iostream>
#include <utility>
// simtools
#include "parameter_reader.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
ParameterReader::ParameterReader()
: data_types(), element_type_data(), string_data(), int_data(), uint_data(),
real_data(), bool_data() {
AKANTU_DEBUG_IN();
// setup of types of element
data_types.insert("elementtype");
data_types.insert("string");
data_types.insert("uint");
data_types.insert("int");
data_types.insert("real");
data_types.insert("bool");
// data_types.insert("surface");
// define conversion maps
_input_to_akantu_element_types["_segment_2"] = akantu::_segment_2;
_input_to_akantu_element_types["_segment_3"] = akantu::_segment_3;
_input_to_akantu_element_types["_triangle_3"] = akantu::_triangle_3;
_input_to_akantu_element_types["_triangle_6"] = akantu::_triangle_6;
_input_to_akantu_element_types["_tetrahedron_4"] = akantu::_tetrahedron_4;
_input_to_akantu_element_types["_tetrahedron_10"] = akantu::_tetrahedron_10;
_input_to_akantu_element_types["_quadrangle_4"] = akantu::_quadrangle_4;
_input_to_akantu_element_types["_quadrangle_8"] = akantu::_quadrangle_8;
_input_to_akantu_element_types["_hexahedron_8"] = akantu::_hexahedron_8;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ParameterReader::readInputFile(std::string file_name) {
AKANTU_DEBUG_IN();
char comment_char = '#';
char equal_char = '=';
// open a file called file name
std::ifstream infile;
infile.open(file_name.c_str());
if (!infile.good()) {
std::cerr << "Cannot open file " << file_name << "!!!" << std::endl;
exit(EXIT_FAILURE);
}
std::string line;
std::string clean_line;
while (infile.good()) {
getline(infile, line);
clean_line = line;
// take out comments
size_t found_comment;
found_comment = line.find_first_of(comment_char);
if (found_comment != std::string::npos)
clean_line = line.substr(0, found_comment);
if (clean_line.empty())
continue;
std::stringstream sstr(clean_line);
// check if data type exists
std::string type;
sstr >> type;
std::transform(type.begin(), type.end(), type.begin(), ::tolower);
if (this->data_types.find(type) == this->data_types.end()) {
std::cerr << " *** WARNING *** Data type " << type << " does not exist"
<< " in this input data structure. Ignore line: ";
std::cerr << clean_line << std::endl;
continue;
}
std::string keyword;
std::string equal;
std::string value;
// get keyword
sstr >> keyword;
size_t equal_p = keyword.find_first_of(equal_char);
if (equal_p != std::string::npos) {
equal = keyword.substr(equal_p, std::string::npos);
keyword = keyword.substr(0, equal_p);
}
// get equal
if (equal.empty())
sstr >> equal;
if (equal.length() != 1) {
value = equal.substr(1, std::string::npos);
equal = equal[0];
}
if (equal[0] != equal_char) {
std::cerr << " *** WARNING *** Unrespected convention! Ignore line: ";
std::cerr << clean_line << std::endl;
continue;
}
// get value
if (value.empty())
sstr >> value;
// no value
if (value.empty()) {
std::cerr << " *** WARNING *** No value given! Ignore line: ";
std::cerr << clean_line << std::endl;
continue;
}
// put value in map
std::stringstream convert(value);
if (type.compare("elementtype") == 0) {
std::map<std::string, akantu::ElementType>::const_iterator it;
it = this->_input_to_akantu_element_types.find(value);
if (it != this->_input_to_akantu_element_types.end())
this->element_type_data.insert(std::make_pair(keyword, it->second));
else {
std::cerr << " *** WARNING *** ElementType " << value
<< " does not exist. Ignore line: ";
std::cerr << clean_line << std::endl;
continue;
}
} else if (type.compare("string") == 0) {
this->string_data.insert(std::make_pair(keyword, value));
}
/*
else if (type.compare("surface") == 0) {
//Surface surf;
UInt surf;
convert >> surf;
//this->surface_data.insert(std::make_pair(keyword,surf));
this->uint_data.insert(std::make_pair(keyword,surf));
}
*/
else if (type.compare("int") == 0) {
Int i;
convert >> i;
this->int_data.insert(std::make_pair(keyword, i));
} else if (type.compare("uint") == 0) {
UInt i;
convert >> i;
this->uint_data.insert(std::make_pair(keyword, i));
} else if (type.compare("real") == 0) {
Real r;
convert >> r;
this->real_data.insert(std::make_pair(keyword, r));
} else if (type.compare("bool") == 0) {
std::transform(value.begin(), value.end(), value.begin(), ::tolower);
bool b;
if (value.compare("true") == 0)
b = true;
else if (value.compare("false") == 0)
b = false;
else {
std::cerr << " *** WARNING *** boolean cannot be " << value
<< ". Ignore line: ";
std::cerr << clean_line << std::endl;
continue;
}
this->bool_data.insert(std::make_pair(keyword, b));
} else {
std::cerr << " *** ERROR *** Could not add data to InputData for line: ";
std::cerr << clean_line << std::endl;
continue;
exit(EXIT_FAILURE);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ParameterReader::writeInputFile(std::string file_name) const {
AKANTU_DEBUG_IN();
// open file to write input information
std::ofstream outfile;
outfile.open(file_name.c_str());
// element type
for (std::map<std::string, akantu::ElementType>::const_iterator it =
element_type_data.begin();
it != element_type_data.end(); ++it) {
for (std::map<std::string, ElementType>::const_iterator et =
_input_to_akantu_element_types.begin();
et != _input_to_akantu_element_types.end(); ++et) {
if (it->second == et->second) {
outfile << "ElementType " << it->first << " = " << et->first
<< std::endl;
continue;
}
}
}
// string
for (std::map<std::string, std::string>::const_iterator it =
string_data.begin();
it != string_data.end(); ++it)
outfile << "string " << it->first << " = " << it->second << std::endl;
// Surface
/*
for (std::map<std::string, akantu::Surface>::const_iterator it =
surface_data.begin();
it != surface_data.end(); ++it)
outfile << "Surface " << it->first << " = " << it->second << std::endl;
*/
// Int
for (std::map<std::string, akantu::Int>::const_iterator it = int_data.begin();
it != int_data.end(); ++it)
outfile << "Int " << it->first << " = " << it->second << std::endl;
// UInt
for (std::map<std::string, akantu::UInt>::const_iterator it =
uint_data.begin();
it != uint_data.end(); ++it)
outfile << "UInt " << it->first << " = " << it->second << std::endl;
// Real
for (std::map<std::string, akantu::Real>::const_iterator it =
real_data.begin();
it != real_data.end(); ++it)
outfile << "Real " << it->first << " = " << it->second << std::endl;
// Bool
for (std::map<std::string, bool>::const_iterator it = bool_data.begin();
it != bool_data.end(); ++it) {
std::string b = "false";
if (it->second)
b = "true";
outfile << "bool " << it->first << " = " << b << std::endl;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
akantu::UInt ParameterReader::get<akantu::UInt>(std::string key) const {
std::map<std::string, akantu::UInt>::const_iterator it;
it = this->uint_data.find(key);
// if not in map
if (it == this->uint_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "UInt " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
template <>
akantu::ElementType
ParameterReader::get<akantu::ElementType>(std::string key) const {
std::map<std::string, akantu::ElementType>::const_iterator it;
it = this->element_type_data.find(key);
// if not in map
if (it == this->element_type_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "ElementType " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
template <>
std::string ParameterReader::get<std::string>(std::string key) const {
std::map<std::string, std::string>::const_iterator it;
it = this->string_data.find(key);
// if not in map
if (it == this->string_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "string " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
/*
template<>
akantu::Surface ParameterData::get<akantu::Surface>(std::string key) const {
std::map<std::string,akantu::Surface>::const_iterator it;
it = this->surface_data.find(key);
// if not in map
if (it == this->surface_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "Surface " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
*/
/* -------------------------------------------------------------------------- */
template <>
akantu::Int ParameterReader::get<akantu::Int>(std::string key) const {
std::map<std::string, akantu::Int>::const_iterator it;
it = this->int_data.find(key);
// if not in map
if (it == this->int_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "Int " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
template <>
akantu::Real ParameterReader::get<akantu::Real>(std::string key) const {
std::map<std::string, akantu::Real>::const_iterator it;
it = this->real_data.find(key);
// if not in map
if (it == this->real_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "Real " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
template <> bool ParameterReader::get<bool>(std::string key) const {
std::map<std::string, bool>::const_iterator it;
it = this->bool_data.find(key);
// if not in map
if (it == this->bool_data.end()) {
std::cerr << " *** ERROR *** This data was not in input file. "
<< "You need the following line in your input file: ";
std::cerr << "bool " << key << " = ???" << std::endl;
exit(EXIT_FAILURE);
}
else
return it->second;
}
/* -------------------------------------------------------------------------- */
template <> bool ParameterReader::has<bool>(std::string key) const {
std::map<std::string, bool>::const_iterator it;
it = this->bool_data.find(key);
return (it != this->bool_data.end());
}
template <> bool ParameterReader::has<std::string>(std::string key) const {
std::map<std::string, std::string>::const_iterator it;
it = this->string_data.find(key);
return (it != this->string_data.end());
}
template <> bool ParameterReader::has<akantu::Int>(std::string key) const {
std::map<std::string, akantu::Int>::const_iterator it;
it = this->int_data.find(key);
return (it != this->int_data.end());
}
template <> bool ParameterReader::has<akantu::UInt>(std::string key) const {
std::map<std::string, akantu::UInt>::const_iterator it;
it = this->uint_data.find(key);
return (it != this->uint_data.end());
}
template <> bool ParameterReader::has<akantu::Real>(std::string key) const {
std::map<std::string, akantu::Real>::const_iterator it;
it = this->real_data.find(key);
return (it != this->real_data.end());
}
/* -------------------------------------------------------------------------- */
void ParameterReader::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ParameterReader [" << std::endl;
/*
stream << space << this->element_type_data << std::endl;
stream << space << this->string_data << std::endl;
stream << space << this->surface_data << std::endl;
stream << space << this->int_data << std::endl;
stream << space << this->uint_data << std::endl;
stream << space << this->real_data << std::endl;
stream << space << this->bool_data << std::endl;
*/
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
index 5dbaf6f2f..504218710 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/parameter_reader.hh
@@ -1,109 +1,111 @@
/**
* @file parameter_reader.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief for simulations to read parameters from an input file
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_PARAMETER_READER_HH_
#define AST_PARAMETER_READER_HH_
/* -------------------------------------------------------------------------- */
// std
#include <map>
#include <set>
// akantu
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class ParameterReader {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ParameterReader();
virtual ~ParameterReader(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read input file
void readInputFile(std::string file_name);
/// write input file
void writeInputFile(std::string file_name) const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
///
template <typename T> T get(std::string key) const;
template <typename T> bool has(std::string key) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// type of data available
std::set<std::string> data_types;
/// data
std::map<std::string, akantu::ElementType> element_type_data;
std::map<std::string, std::string> string_data;
std::map<std::string, akantu::Int> int_data;
std::map<std::string, akantu::UInt> uint_data;
std::map<std::string, akantu::Real> real_data;
std::map<std::string, bool> bool_data;
/// convert string to element type
std::map<std::string, ElementType> _input_to_akantu_element_types;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "parameter_reader_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ParameterReader & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_PARAMETER_READER_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
index 9b1ad7454..15bed027b 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
+++ b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.cc
@@ -1,241 +1,244 @@
/**
* @file synchronized_array.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of synchronized array function
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
- * You should have received a copy of the GNU Lesser General Public License
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// std
#include <fstream>
#include <iostream>
// simtools
#include "synchronized_array.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
SynchronizedArray<T>::SynchronizedArray(UInt size, UInt nb_component,
const_reference value, const ID & id,
const_reference default_value,
const std::string & restart_name)
: SynchronizedArrayBase(), Array<T>(size, nb_component, value, id),
default_value(default_value), restart_name(restart_name),
deleted_elements(0), nb_added_elements(size), depending_arrays(0) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
void SynchronizedArray<T>::syncElements(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
if (sync_choice == _deleted) {
- std::vector<SynchronizedArrayBase *>::iterator it;
- for (it = depending_arrays.begin(); it != depending_arrays.end(); ++it) {
- UInt vec_size = (*it)->syncDeletedElements(this->deleted_elements);
+ for (auto && array : depending_arrays) {
+ auto vec_size [[gnu::unused]] =
+ array->syncDeletedElements(this->deleted_elements);
AKANTU_DEBUG_ASSERT(vec_size == this->size_,
"Synchronized arrays do not have the same length"
<< "(may be a double synchronization)");
}
this->deleted_elements.clear();
}
else if (sync_choice == _added) {
- std::vector<SynchronizedArrayBase *>::iterator it;
- for (it = depending_arrays.begin(); it != depending_arrays.end(); ++it) {
- UInt vec_size = (*it)->syncAddedElements(this->nb_added_elements);
+ for (auto && array : depending_arrays) {
+ auto vec_size [[gnu::unused]] =
+ array->syncAddedElements(this->nb_added_elements);
AKANTU_DEBUG_ASSERT(vec_size == this->size_,
"Synchronized arrays do not have the same length"
<< "(may be a double synchronization)");
}
this->nb_added_elements = 0;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
UInt SynchronizedArray<T>::syncDeletedElements(
std::vector<UInt> & del_elements) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
nb_added_elements == 0 and deleted_elements.empty(),
"Cannot sync with a SynchronizedArray if it has already been modified");
- std::vector<UInt>::const_iterator it;
- for (it = del_elements.begin(); it != del_elements.end(); ++it) {
- erase(*it);
+ for (auto && el : del_elements) {
+ erase(el);
}
+
syncElements(_deleted);
AKANTU_DEBUG_OUT();
return this->size_;
}
/* -------------------------------------------------------------------------- */
template <class T>
UInt SynchronizedArray<T>::syncAddedElements(UInt nb_add_elements) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
nb_added_elements == 0 and deleted_elements.empty(),
"Cannot sync with a SynchronizedArray if it has already been modified");
for (UInt i = 0; i < nb_add_elements; ++i) {
push_back(this->default_value);
}
syncElements(_added);
AKANTU_DEBUG_OUT();
return this->size_;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SynchronizedArray<T>::registerDependingArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->depending_arrays.push_back(&array);
array.syncAddedElements(this->size_);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SynchronizedArray<T>::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space(indent, AKANTU_INDENT);
stream << space << "SynchronizedArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + default_value : " << this->default_value
<< std::endl;
stream << space << " + nb_added_elements : " << this->nb_added_elements
<< std::endl;
stream << space << " + deleted_elements : ";
for (auto && deleted_element : deleted_elements) {
stream << deleted_element << " ";
}
stream << std::endl;
stream << space << " + depending_arrays : ";
for (auto && depending_array : this->depending_arrays) {
stream << depending_array->getID() << " ";
}
stream << std::endl;
Array<T>::printself(stream, indent + 1);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
-void SynchronizedArray<T>::dumpRestartFile(const std::string & file_name) const {
+void SynchronizedArray<T>::dumpRestartFile(
+ const std::string & file_name) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
nb_added_elements == 0 and deleted_elements.empty(),
"Restart File for SynchronizedArray "
<< this->id << " should not be dumped as it is not synchronized yet");
std::stringstream name;
name << file_name << "-" << this->restart_name << ".rs";
std::ofstream out_restart;
out_restart.open(name.str().c_str());
out_restart << this->size_ << " " << this->nb_component << std::endl;
Real size_comp = this->size_ * this->nb_component;
for (UInt i = 0; i < size_comp; ++i) {
out_restart << std::setprecision(12) << this->values[i] << " ";
}
// out_restart << std::hex << std::setprecision(12) << this->values[i] << "
// ";
out_restart << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SynchronizedArray<T>::readRestartFile(const std::string & file_name) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
nb_added_elements == 0 and deleted_elements.empty(),
"Restart File for SynchronizedArray "
<< this->id << " should not be read as it is not synchronized yet");
std::stringstream name;
name << file_name << "-" << this->restart_name << ".rs";
std::ifstream infile;
infile.open(name.str().c_str());
std::string line;
// get size and nb_component info
AKANTU_DEBUG_ASSERT(infile.good(), "Could not read restart file for "
<< "SynchronizedArray " << this->id);
getline(infile, line);
std::stringstream size_comp(line);
size_comp >> this->size_;
size_comp >> this->nb_component;
// get elements in array
getline(infile, line);
std::stringstream data(line);
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
AKANTU_DEBUG_ASSERT(
!data.eof(),
"Read SynchronizedArray "
<< this->id
<< " got to the end of the file before having read all data!");
data >> this->values[i];
// data >> std::hex >> this->values[i];
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template class SynchronizedArray<Real>;
template class SynchronizedArray<UInt>;
template class SynchronizedArray<Int>;
template class SynchronizedArray<bool>;
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
index 70fa0eedf..7b8757f76 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array.hh
@@ -1,202 +1,204 @@
/**
* @file synchronized_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief synchronized array: a array can be registered to another (hereafter
* called top) array. If an element is added to or removed from the top array,
* the registered array removes or adds at the same position an element. The two
* arrays stay therefore synchronized.
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_SYNCHRONIZED_ARRAY_HH_
#define AST_SYNCHRONIZED_ARRAY_HH_
/* -------------------------------------------------------------------------- */
// std
#include <vector>
// akantu
#include "aka_array.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
enum SyncChoice { _added, _deleted };
/* -------------------------------------------------------------------------- */
class SynchronizedArrayBase {
public:
SynchronizedArrayBase() = default;
~SynchronizedArrayBase() = default;
virtual ID getID() const { return "call should be virtual"; };
virtual UInt syncDeletedElements(std::vector<UInt> & delete_el) = 0;
virtual UInt syncAddedElements(UInt nb_added_el) = 0;
};
/* -------------------------------------------------------------------------- */
template <class T>
class SynchronizedArray : public SynchronizedArrayBase, protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using value_type = typename Array<T>::value_type;
using reference = typename Array<T>::reference;
using pointer_type = typename Array<T>::pointer_type;
using const_reference = typename Array<T>::const_reference;
SynchronizedArray(UInt size, UInt nb_component, const_reference value,
const ID & id, const_reference default_value,
const std::string & restart_name);
~SynchronizedArray() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// push_back
template <typename P> inline void push_back(P && value);
/// erase
inline void erase(UInt i);
// template<typename R>
// inline void erase(const iterator<R> & it);
/// synchronize elements
void syncElements(SyncChoice sync_choice);
/// dump restart file
void dumpRestartFile(const std::string & file_name) const;
/// read restart file
void readRestartFile(const std::string & file_name);
/// register depending array
void registerDependingArray(SynchronizedArrayBase & array);
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// find position of element
Int find(const T & elem) const { return Array<T>::find(elem); };
/// set values to zero
inline void zero() { Array<T>::zero(); };
// inline void clear() { memset(values, 0, size*nb_component*sizeof(T)); };
/// set all entries of the array to the value t
/// @param t value to fill the array with
inline void set(T t) { Array<T>::set(t); }
/// set
template <template <typename> class C> inline void set(const C<T> & vm) {
Array<T>::set(vm);
}
/// set all entries of the array to value t and set default value
inline void setAndChangeDefault(T t) {
this->set(t);
this->default_value = t;
}
/// copy the content of an other array
void copy(const SynchronizedArray<T> & vect) { Array<T>::copy(vect); };
/// give the address of the memory allocated for this array
T * storage() const { return Array<T>::storage(); };
// T * storage() const { return this->values; };
// get nb component
UInt getNbComponent() const { return Array<T>::getNbComponent(); };
protected:
UInt syncDeletedElements(std::vector<UInt> & del_elements) override;
UInt syncAddedElements(UInt nb_add_elements) override;
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0) {
return Array<T>::operator()(i, j);
}
inline const_reference operator()(UInt i, UInt j = 0) const {
return Array<T>::operator()(i, j);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_SET_MACRO(DefaultValue, default_value, T);
UInt size() const { return this->size_; };
ID getID() const override { return Array<T>::getID(); };
const Array<T> & getArray() const {
const Array<T> & a = *(dynamic_cast<const Array<T> *>(this));
return a;
};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// init value when new elements added
T default_value;
/// restart file_name
const std::string restart_name;
/// elements that have been deleted
std::vector<UInt> deleted_elements;
/// number of elements to add
UInt nb_added_elements;
/// pointers to arrays to be updated
std::vector<SynchronizedArrayBase *> depending_arrays;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SynchronizedArray<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "synchronized_array_inline_impl.hh"
#endif /* AST_SYNCHRONIZED_ARRAY_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array_inline_impl.hh b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array_inline_impl.hh
index cacebf02d..bf5e6eadf 100644
--- a/extra_packages/traction-at-split-node-contact/src/common/synchronized_array_inline_impl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/common/synchronized_array_inline_impl.hh
@@ -1,67 +1,70 @@
/**
* @file synchronized_array_inline_impl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Mar 16 2018
*
* @brief inlined methods for the synchronized array
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "synchronized_array.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
template <typename P>
inline void SynchronizedArray<T>::push_back(P && value) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(deleted_elements.size() == 0,
"Cannot push_back element if SynchronizedArray"
<< " is already modified without synchronization");
Array<T>::push_back(std::forward<P>(value));
this->nb_added_elements++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T> inline void SynchronizedArray<T>::erase(UInt i) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(nb_added_elements == 0,
"Cannot erase element if SynchronizedArray"
<< " is already modified without synchronization");
for (UInt j = 0; j < this->nb_component; ++j)
this->values[i * this->nb_component + j] =
this->values[(this->size_ - 1) * this->nb_component + j];
this->size_--;
this->deleted_elements.push_back(i);
AKANTU_DEBUG_OUT();
}
}
diff --git a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc
index b80064f5a..b3250b05c 100644
--- a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc
+++ b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.cc
@@ -1,71 +1,73 @@
/**
* @file boundary_functions.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Tue Feb 20 2018
+ * @date last modification: Fri Jul 19 2019
*
- * @brief
+ * @brief functions for boundaries
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_functions.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "node_group.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Real integrateResidual(const std::string & sub_boundary_name,
const SolidMechanicsModel & model, UInt dir) {
Real int_res = 0.;
const Mesh & mesh = model.getMesh();
const Array<Real> & residual = model.getInternalForce();
const ElementGroup & boundary = mesh.getElementGroup(sub_boundary_name);
for (auto & node : boundary.getNodeGroup().getNodes()) {
bool is_local_node = mesh.isLocalOrMasterNode(node);
if (is_local_node) {
int_res += residual(node, dir);
}
}
mesh.getCommunicator().allReduce(int_res, SynchronizerOperation::_sum);
return int_res;
}
/* -------------------------------------------------------------------------- */
void boundaryFix(Mesh & mesh,
const std::vector<std::string> & sub_boundary_names) {
for (auto && eg : sub_boundary_names) {
if (mesh.elementGroupExists(eg)) {
mesh.createElementGroup(eg, mesh.getSpatialDimension() -
1); // empty element group
}
}
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
index 2652b1843..79505c795 100644
--- a/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
+++ b/extra_packages/traction-at-split-node-contact/src/functions/boundary_functions.hh
@@ -1,54 +1,56 @@
/**
* @file boundary_functions.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief functions for boundaries
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BOUNDARY_FUNCTIONS_HH_
#define AKANTU_BOUNDARY_FUNCTIONS_HH_
namespace akantu {
class SolidMechanicsModel;
}
namespace akantu {
Real integrateResidual(const std::string & sub_boundary_name,
const SolidMechanicsModel & model, UInt dir);
/// this is a fix so that all subboundaries exist on all procs
void boundaryFix(Mesh & mesh,
const std::vector<std::string> & sub_boundary_names);
} // namespace akantu
#endif /* AKANTU_BOUNDARY_FUNCTIONS_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh b/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
index 0cbc2f7ff..038b219ad 100644
--- a/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
+++ b/extra_packages/traction-at-split-node-contact/src/functions/node_filter.hh
@@ -1,112 +1,114 @@
/**
* @file node_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief to filter nodes with functors
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NODE_FILTER_HH_
#define AST_NODE_FILTER_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "aka_common.hh"
#include "mesh_filter.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class GeometryFilter : public NodeFilterFunctor {
public:
GeometryFilter(const Mesh & mesh, UInt dir, Real limit)
: NodeFilterFunctor(), mesh(mesh), dir(dir), limit(limit) {
this->positions = &(mesh.getNodes());
};
~GeometryFilter(){};
bool operator()(UInt node) { AKANTU_TO_IMPLEMENT(); };
protected:
const Mesh & mesh;
UInt dir;
Real limit;
const Array<Real> * positions;
};
/* -------------------------------------------------------------------------- */
class FilterPositionsGreaterThan : public GeometryFilter {
public:
FilterPositionsGreaterThan(const Mesh & mesh, UInt dir, Real limit)
: GeometryFilter(mesh, dir, limit){};
~FilterPositionsGreaterThan(){};
bool operator()(UInt node) {
AKANTU_DEBUG_IN();
bool to_filter = true;
if ((*this->positions)(node, this->dir) > this->limit)
to_filter = false;
AKANTU_DEBUG_OUT();
return to_filter;
};
};
/* -------------------------------------------------------------------------- */
class FilterPositionsLessThan : public GeometryFilter {
public:
FilterPositionsLessThan(const Mesh & mesh, UInt dir, Real limit)
: GeometryFilter(mesh, dir, limit){};
~FilterPositionsLessThan(){};
bool operator()(UInt node) {
AKANTU_DEBUG_IN();
bool to_filter = true;
if ((*this->positions)(node, this->dir) < this->limit)
to_filter = false;
AKANTU_DEBUG_OUT();
return to_filter;
};
};
/* -------------------------------------------------------------------------- */
// this filter is erase because the convention of filter has changed!!
// filter == true -> keep node
// template<class FilterType>
// void applyNodeFilter(Array<UInt> & nodes, FilterType & filter) {
// Array<UInt>::iterator<> it = nodes.begin();
// for (; it != nodes.end(); ++it) {
// if (filter(*it)) {
// it = nodes.erase(it);
// }
// }
// };
} // namespace akantu
#endif /* AST_NODE_FILTER_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
index cdb31ae9b..cbca0c8f5 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb.hh
@@ -1,106 +1,108 @@
/**
* @file ntn_friclaw_coulomb.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief coulomb friction with \mu_s = \mu_k (constant)
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICLAW_COULOMB_HH_
#define AST_NTN_FRICLAW_COULOMB_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawCoulomb : public Regularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawCoulomb(NTNBaseContact & contact, const ID & id = "coulomb");
virtual ~NTNFricLawCoulomb(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// friction coefficient
SynchronizedArray<Real> mu;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawCoulomb<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_coulomb_tmpl.hh"
#endif /* AST_NTN_FRICLAW_COULOMB_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh
index a1b626b67..df46a255d 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_coulomb_tmpl.hh
@@ -1,166 +1,168 @@
/**
* @file ntn_friclaw_coulomb_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of coulomb friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_nodal_field.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation>
NTNFricLawCoulomb<Regularisation>::NTNFricLawCoulomb(NTNBaseContact & contact,
const ID & id)
: Regularisation(contact, id),
mu(0, 1, 0., id + ":mu", 0., "mu") {
AKANTU_DEBUG_IN();
Regularisation::registerSynchronizedArray(this->mu);
this->registerParam("mu", this->mu, _pat_parsmod, "friction coefficient");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::computeFrictionalStrength() {
AKANTU_DEBUG_IN();
// get contact arrays
const SynchronizedArray<bool> & is_in_contact =
this->internalGetIsInContact();
const SynchronizedArray<Real> & pressure = this->internalGetContactPressure();
// array to fill
SynchronizedArray<Real> & strength = this->internalGetFrictionalStrength();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is NOT in contact
if (!is_in_contact(n))
strength(n) = 0.;
// node pair is in contact
else {
// compute frictional strength
strength(n) = this->mu(n) * pressure(n);
}
}
Regularisation::computeFrictionalStrength();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->mu.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::dumpRestart(
const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->mu.dumpRestartFile(file_name);
Regularisation::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::readRestart(
const std::string & file_name) {
AKANTU_DEBUG_IN();
this->mu.readRestartFile(file_name);
Regularisation::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricLawCoulomb [" << std::endl;
Regularisation::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawCoulomb<Regularisation>::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "mu") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->mu.getArray()));
}
/*
else if (field_id == "frictional_contact_pressure") {
this->internalAddDumpFieldToDumper(dumper_name,
field_id,
new
DumperIOHelper::NodalField<Real>(this->frictional_contact_pressure.getArray()));
}
*/
else {
Regularisation::addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
index c67547a1e..c1570427f 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive.hh
@@ -1,113 +1,115 @@
/**
* @file ntn_friclaw_linear_cohesive.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief linear cohesive law
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_
#define AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearCohesive : public Regularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearCohesive(NTNBaseContact & contact,
const ID & id = "linear_cohesive");
virtual ~NTNFricLawLinearCohesive(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// fracture energy
SynchronizedArray<Real> G_c;
// peak value of cohesive law
SynchronizedArray<Real> tau_c;
// residual value of cohesive law (for slip > d_c)
SynchronizedArray<Real> tau_r;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawLinearCohesive<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_cohesive_tmpl.hh"
#endif /* AST_NTN_FRICLAW_LINEAR_COHESIVE_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh
index ba169ee22..fee59ce33 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_cohesive_tmpl.hh
@@ -1,188 +1,190 @@
/**
* @file ntn_friclaw_linear_cohesive_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of linear cohesive law
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
//#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation>
NTNFricLawLinearCohesive<Regularisation>::NTNFricLawLinearCohesive(
NTNBaseContact & contact, const ID & id)
: Regularisation(contact, id),
G_c(0, 1, 0., id + ":G_c", 0., "G_c"),
tau_c(0, 1, 0., id + ":tau_c", 0., "tau_c"),
tau_r(0, 1, 0., id + ":tau_r", 0., "tau_r") {
AKANTU_DEBUG_IN();
Regularisation::registerSynchronizedArray(this->G_c);
Regularisation::registerSynchronizedArray(this->tau_c);
Regularisation::registerSynchronizedArray(this->tau_r);
this->registerParam("G_c", this->G_c, _pat_parsmod, "fracture energy");
this->registerParam("tau_c", this->tau_c, _pat_parsmod,
"peak shear strength");
this->registerParam("tau_r", this->tau_r, _pat_parsmod,
"residual shear strength");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::computeFrictionalStrength() {
AKANTU_DEBUG_IN();
// get arrays
const SynchronizedArray<bool> & is_in_contact =
this->internalGetIsInContact();
// const SynchronizedArray<Real> & slip = this->internalGetSlip();
const SynchronizedArray<Real> & slip = this->internalGetCumulativeSlip();
// array to fill
SynchronizedArray<Real> & strength = this->internalGetFrictionalStrength();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is NOT in contact
if (!is_in_contact(n))
strength(n) = 0.;
// node pair is in contact
else {
if (this->G_c(n) == 0.) {
// strength(n) = 0.;
strength(n) = this->tau_r(n);
} else {
Real slope = (this->tau_c(n) - this->tau_r(n)) *
(this->tau_c(n) - this->tau_r(n)) / (2 * this->G_c(n));
// no strength < tau_r
strength(n) =
std::max(this->tau_c(n) - slope * slip(n), this->tau_r(n));
// strength(n) = std::max(this->tau_c(n) - slope * slip(n), 0.); // no
// negative strength
}
}
}
Regularisation::computeFrictionalStrength();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->G_c.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::dumpRestart(
const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->G_c.dumpRestartFile(file_name);
this->tau_c.dumpRestartFile(file_name);
this->tau_r.dumpRestartFile(file_name);
Regularisation::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::readRestart(
const std::string & file_name) {
AKANTU_DEBUG_IN();
this->G_c.readRestartFile(file_name);
this->tau_c.readRestartFile(file_name);
this->tau_r.readRestartFile(file_name);
Regularisation::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricLawLinearCohesive [" << std::endl;
Regularisation::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearCohesive<Regularisation>::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "G_c") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->G_c.getArray()));
} else if (field_id == "tau_c") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->tau_c.getArray()));
} else if (field_id == "tau_r") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->tau_r.getArray()));
} else {
Regularisation::addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
index 60890c82c..88edfca2a 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening.hh
@@ -1,115 +1,117 @@
/**
* @file ntn_friclaw_linear_slip_weakening.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief linear slip weakening
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_
#define AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearSlipWeakening : public NTNFricLawCoulomb<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearSlipWeakening(NTNBaseContact & contact,
const ID & id = "linear_slip_weakening");
virtual ~NTNFricLawLinearSlipWeakening(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/// computes the friction coefficient as a function of slip
virtual void computeFrictionCoefficient();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// static coefficient of friction
SynchronizedArray<Real> mu_s;
// kinetic coefficient of friction
SynchronizedArray<Real> mu_k;
// Dc the length over which slip weakening happens
SynchronizedArray<Real> d_c;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricLawLinearSlipWeakening<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_slip_weakening_tmpl.hh"
#endif /* AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
index cc2c63f4f..7a7590daf 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing.hh
@@ -1,94 +1,96 @@
/**
* @file ntn_friclaw_linear_slip_weakening_no_healing.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief linear slip weakening
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_
#define AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_
/* -------------------------------------------------------------------------- */
#include "ntn_friclaw_linear_slip_weakening.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation = NTNFricRegNoRegularisation>
class NTNFricLawLinearSlipWeakeningNoHealing
: public NTNFricLawLinearSlipWeakening<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricLawLinearSlipWeakeningNoHealing(
NTNBaseContact & contact,
const ID & id = "linear_slip_weakening_no_healing");
virtual ~NTNFricLawLinearSlipWeakeningNoHealing(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// computes the friction coefficient as a function of slip
virtual void computeFrictionCoefficient();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Regularisation>
inline std::ostream & operator<<(
std::ostream & stream,
const NTNFricLawLinearSlipWeakeningNoHealing<Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh"
#endif /* AST_NTN_FRICLAW_LINEAR_SLIP_WEAKENING_NO_HEALING_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
index a8cc4cc41..ceeb3dd89 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
@@ -1,84 +1,86 @@
/**
* @file ntn_friclaw_linear_slip_weakening_no_healing_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Wed Oct 17 2018
*
* @brief implementation of linear slip weakening
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation>
NTNFricLawLinearSlipWeakeningNoHealing<Regularisation>::
NTNFricLawLinearSlipWeakeningNoHealing(NTNBaseContact & contact,
const ID & id)
: NTNFricLawLinearSlipWeakening<Regularisation>(contact, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakeningNoHealing<
Regularisation>::computeFrictionCoefficient() {
AKANTU_DEBUG_IN();
// get arrays
const SynchronizedArray<Real> & slip = this->internalGetCumulativeSlip();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (slip(n) >= this->d_c(n)) {
this->mu(n) = this->mu_k(n);
} else {
// mu = mu_k + (1 - slip / Dc) * (mu_s - mu_k)
this->mu(n) = this->mu_k(n) + (1 - (slip(n) / this->d_c(n))) *
(this->mu_s(n) - this->mu_k(n));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakeningNoHealing<Regularisation>::printself(
std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricLawLinearSlipWeakeningNoHealing [" << std::endl;
NTNFricLawLinearSlipWeakening<Regularisation>::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh
index 114143b36..7f9c8fd0a 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_laws/ntn_friclaw_linear_slip_weakening_tmpl.hh
@@ -1,189 +1,191 @@
/**
* @file ntn_friclaw_linear_slip_weakening_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of linear slip weakening
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Regularisation>
NTNFricLawLinearSlipWeakening<Regularisation>::NTNFricLawLinearSlipWeakening(
NTNBaseContact & contact, const ID & id)
: NTNFricLawCoulomb<Regularisation>(contact, id),
mu_s(0, 1, 0., id + ":mu_s", 0., "mu_s"),
mu_k(0, 1, 0., id + ":mu_k", 0., "mu_k"),
d_c(0, 1, 0., id + ":d_c", 0., "d_c") {
AKANTU_DEBUG_IN();
NTNFricLawCoulomb<Regularisation>::registerSynchronizedArray(this->mu_s);
NTNFricLawCoulomb<Regularisation>::registerSynchronizedArray(this->mu_k);
NTNFricLawCoulomb<Regularisation>::registerSynchronizedArray(this->d_c);
this->registerParam("mu_s", this->mu_s, _pat_parsmod,
"static friction coefficient");
this->registerParam("mu_k", this->mu_k, _pat_parsmod,
"kinetic friction coefficient");
this->registerParam("d_c", this->d_c, _pat_parsmod, "slip weakening length");
this->setParameterAccessType("mu", _pat_readable);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<
Regularisation>::computeFrictionalStrength() {
AKANTU_DEBUG_IN();
computeFrictionCoefficient();
NTNFricLawCoulomb<Regularisation>::computeFrictionalStrength();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<
Regularisation>::computeFrictionCoefficient() {
AKANTU_DEBUG_IN();
// get arrays
const SynchronizedArray<bool> & stick = this->internalGetIsSticking();
const SynchronizedArray<Real> & slip = this->internalGetSlip();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (stick(n)) {
this->mu(n) = this->mu_s(n);
} else {
if (slip(n) >= this->d_c(n)) {
this->mu(n) = this->mu_k(n);
} else {
// mu = mu_k + (1 - slip / Dc) * (mu_s - mu_k)
this->mu(n) = this->mu_k(n) + (1 - (slip(n) / this->d_c(n))) *
(this->mu_s(n) - this->mu_k(n));
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<Regularisation>::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->mu_s.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<Regularisation>::dumpRestart(
const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->mu_s.dumpRestartFile(file_name);
this->mu_k.dumpRestartFile(file_name);
this->d_c.dumpRestartFile(file_name);
NTNFricLawCoulomb<Regularisation>::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<Regularisation>::readRestart(
const std::string & file_name) {
AKANTU_DEBUG_IN();
this->mu_s.readRestartFile(file_name);
this->mu_k.readRestartFile(file_name);
this->d_c.readRestartFile(file_name);
NTNFricLawCoulomb<Regularisation>::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<Regularisation>::printself(
std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricLawLinearSlipWeakening [" << std::endl;
NTNFricLawCoulomb<Regularisation>::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Regularisation>
void NTNFricLawLinearSlipWeakening<Regularisation>::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "mu_s") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->mu_s.getArray()));
} else if (field_id == "mu_k") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->mu_k.getArray()));
} else if (field_id == "d_c") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->d_c.getArray()));
} else {
NTNFricLawCoulomb<Regularisation>::addDumpFieldToDumper(dumper_name,
field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc
index 76080511e..31f888ae6 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.cc
@@ -1,167 +1,169 @@
/**
* @file ntn_fricreg_no_regularisation.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of no regularisation
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNFricRegNoRegularisation::NTNFricRegNoRegularisation(
NTNBaseContact & contact, const ID & id)
: NTNBaseFriction(contact, id),
frictional_contact_pressure(0, 1, 0., id + ":frictional_contact_pressure",
0., "frictional_contact_pressure") {
AKANTU_DEBUG_IN();
NTNBaseFriction::registerSynchronizedArray(this->frictional_contact_pressure);
this->registerParam("frictional_contact_pressure",
this->frictional_contact_pressure, _pat_internal,
"contact pressure used for friction law");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const SynchronizedArray<Real> &
NTNFricRegNoRegularisation::internalGetContactPressure() {
AKANTU_DEBUG_IN();
this->computeFrictionalContactPressure();
AKANTU_DEBUG_OUT();
return this->frictional_contact_pressure;
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::computeFrictionalContactPressure() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
// get contact arrays
const SynchronizedArray<bool> & is_in_contact =
this->internalGetIsInContact();
const Array<Real> & pressure = this->contact.getContactPressure().getArray();
Array<Real>::const_iterator<Vector<Real>> it = pressure.begin(dim);
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is NOT in contact
if (!is_in_contact(n))
this->frictional_contact_pressure(n) = 0.;
// node pair is in contact
else {
// compute frictional contact pressure
const Vector<Real> & pres = it[n];
this->frictional_contact_pressure(n) = pres.norm();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->frictional_contact_pressure.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::dumpRestart(
const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->frictional_contact_pressure.dumpRestartFile(file_name);
NTNBaseFriction::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->frictional_contact_pressure.readRestartFile(file_name);
NTNBaseFriction::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricRegNoRegularisation [" << std::endl;
NTNBaseFriction::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegNoRegularisation::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "frictional_contact_pressure") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->frictional_contact_pressure.getArray()));
} else {
NTNBaseFriction::addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
index 75f399819..ffba2f5d5 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_no_regularisation.hh
@@ -1,132 +1,134 @@
/**
* @file ntn_fricreg_no_regularisation.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief regularisation that does nothing
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICREG_NO_REGULARISATION_HH_
#define AST_NTN_FRICREG_NO_REGULARISATION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegNoRegularisation : public NTNBaseFriction {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegNoRegularisation(NTNBaseContact & contact,
const ID & id = "no_regularisation");
virtual ~NTNFricRegNoRegularisation(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set to steady state for no regularisation -> do nothing
virtual void setToSteadyState(){};
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
virtual void computeFrictionalContactPressure();
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength(){};
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the is_in_contact array
virtual const SynchronizedArray<bool> & internalGetIsInContact() {
return this->contact.getIsInContact();
};
/// get the contact pressure (the norm: scalar value)
virtual const SynchronizedArray<Real> & internalGetContactPressure();
/// get the frictional strength array
virtual SynchronizedArray<Real> & internalGetFrictionalStrength() {
return this->frictional_strength;
};
/// get the is_sticking array
virtual SynchronizedArray<bool> & internalGetIsSticking() {
return this->is_sticking;
}
/// get the slip array
virtual SynchronizedArray<Real> & internalGetSlip() { return this->slip; }
/// get the slip array
virtual SynchronizedArray<Real> & internalGetCumulativeSlip() {
return this->cumulative_slip;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// contact pressure (absolut value) for computation of friction
SynchronizedArray<Real> frictional_contact_pressure;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_no_regularisation_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNFricRegNoRegularisation & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTN_FRICREG_NO_REGULARISATION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc
index 6877a5bf0..55ff516f0 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.cc
@@ -1,174 +1,176 @@
/**
* @file ntn_fricreg_rubin_ampuero.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of no regularisation
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_rubin_ampuero.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNFricRegRubinAmpuero::NTNFricRegRubinAmpuero(NTNBaseContact & contact,
const ID & id)
: NTNFricRegNoRegularisation(contact, id),
t_star(0, 1, 0., id + ":t_star", 0., "t_star") {
AKANTU_DEBUG_IN();
NTNFricRegNoRegularisation::registerSynchronizedArray(this->t_star);
this->registerParam("t_star", this->t_star, _pat_parsmod,
"time scale of regularization");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const SynchronizedArray<Real> &
NTNFricRegRubinAmpuero::internalGetContactPressure() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
Real delta_t = model.getTimeStep();
// get contact arrays
const SynchronizedArray<bool> & is_in_contact =
this->internalGetIsInContact();
const Array<Real> & pressure = this->contact.getContactPressure().getArray();
Array<Real>::const_iterator<Vector<Real>> it = pressure.begin(dim);
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is NOT in contact
if (!is_in_contact(n))
this->frictional_contact_pressure(n) = 0.;
// if t_star is too small compute like Coulomb friction (without
// regularization)
else if (Math::are_float_equal(this->t_star(n), 0.)) {
const Vector<Real> & pres = it[n];
this->frictional_contact_pressure(n) = pres.norm();
}
else {
// compute frictional contact pressure
// backward euler method: first order implicit numerical integration
// method
// \reg_pres_n+1 = (\reg_pres_n + \delta_t / \t_star * \cur_pres)
// / (1 + \delta_t / \t_star)
Real alpha = delta_t / this->t_star(n);
const Vector<Real> & pres = it[n];
this->frictional_contact_pressure(n) += alpha * pres.norm();
this->frictional_contact_pressure(n) /= 1 + alpha;
}
}
AKANTU_DEBUG_OUT();
return this->frictional_contact_pressure;
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::setToSteadyState() {
AKANTU_DEBUG_IN();
NTNFricRegNoRegularisation::computeFrictionalContactPressure();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->t_star.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->t_star.dumpRestartFile(file_name);
NTNFricRegNoRegularisation::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->t_star.readRestartFile(file_name);
NTNFricRegNoRegularisation::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricRegRubinAmpuero [" << std::endl;
NTNFricRegNoRegularisation::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegRubinAmpuero::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "t_star") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->t_star.getArray()));
} else {
NTNFricRegNoRegularisation::addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
index 2a6b85580..7df44ab25 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_rubin_ampuero.hh
@@ -1,100 +1,102 @@
/**
* @file ntn_fricreg_rubin_ampuero.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief regularisation that regularizes the contact pressure
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICREG_RUBIN_AMPUERO_HH_
#define AST_NTN_FRICREG_RUBIN_AMPUERO_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegRubinAmpuero : public NTNFricRegNoRegularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegRubinAmpuero(NTNBaseContact & contact,
const ID & id = "rubin_ampuero");
virtual ~NTNFricRegRubinAmpuero(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
virtual void setToSteadyState();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the contact pressure (the norm: scalar value)
virtual const SynchronizedArray<Real> & internalGetContactPressure();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
SynchronizedArray<Real> t_star;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_rubin_ampuero_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNFricRegRubinAmpuero & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTN_FRICREG_RUBIN_AMPUERO_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc
index dfacc1585..0837acb38 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.cc
@@ -1,162 +1,164 @@
/**
* @file ntn_fricreg_simplified_prakash_clifton.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Jul 19 2019
*
* @brief implementation of simplified prakash clifton with one parameter
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_simplified_prakash_clifton.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNFricRegSimplifiedPrakashClifton::NTNFricRegSimplifiedPrakashClifton(
NTNBaseContact & contact, const ID & id)
: NTNFricRegNoRegularisation(contact, id),
t_star(0, 1, 0., id + ":t_star", 0., "t_star"),
spc_internal(0, 1, 0., id + ":spc_internal", 0., "spc_internal") {
AKANTU_DEBUG_IN();
NTNFricRegNoRegularisation::registerSynchronizedArray(this->t_star);
NTNFricRegNoRegularisation::registerSynchronizedArray(this->spc_internal);
this->registerParam("t_star", this->t_star, _pat_parsmod,
"time scale of regularisation");
this->registerParam("spc_internal", this->spc_internal, _pat_internal, "");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::computeFrictionalStrength() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
Real delta_t = model.getTimeStep();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
Real alpha = delta_t / this->t_star(n);
this->frictional_strength(n) += alpha * this->spc_internal(n);
this->frictional_strength(n) /= 1 + alpha;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::setToSteadyState() {
AKANTU_DEBUG_IN();
/// fill the spc_internal array
computeFrictionalStrength();
/// set strength without regularisation
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
this->frictional_strength(n) = this->spc_internal(n);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::registerSynchronizedArray(
SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->t_star.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::dumpRestart(
const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->t_star.dumpRestartFile(file_name);
this->spc_internal.dumpRestartFile(file_name);
NTNFricRegNoRegularisation::dumpRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::readRestart(
const std::string & file_name) {
AKANTU_DEBUG_IN();
this->t_star.readRestartFile(file_name);
this->spc_internal.readRestartFile(file_name);
NTNFricRegNoRegularisation::readRestart(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFricRegSimplifiedPrakashClifton [" << std::endl;
NTNFricRegNoRegularisation::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNFricRegSimplifiedPrakashClifton::addDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "t_star") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->t_star.getArray()));
} else {
NTNFricRegNoRegularisation::addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
index e8d285288..ac7835dac 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/friction_regularisations/ntn_fricreg_simplified_prakash_clifton.hh
@@ -1,111 +1,113 @@
/**
* @file ntn_fricreg_simplified_prakash_clifton.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief regularisation that regularizes the frictional strength with one
* parameter
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_
#define AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_fricreg_no_regularisation.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNFricRegSimplifiedPrakashClifton : public NTNFricRegNoRegularisation {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFricRegSimplifiedPrakashClifton(
NTNBaseContact & contact, const ID & id = "simplified_prakash_clifton");
virtual ~NTNFricRegSimplifiedPrakashClifton(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
virtual void dumpRestart(const std::string & file_name) const;
virtual void readRestart(const std::string & file_name);
virtual void setToSteadyState();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength();
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// get the frictional strength array
virtual SynchronizedArray<Real> & internalGetFrictionalStrength() {
return this->spc_internal;
};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
SynchronizedArray<Real> t_star;
// to get the incremental frictional strength
SynchronizedArray<Real> spc_internal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_fricreg_simplified_prakash_clifton_inline_impl.hh"
/// standard output stream operator
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFricRegSimplifiedPrakashClifton & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTN_FRICREG_SIMPLIFIED_PRAKASH_CLIFTON_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc
index 014b71886..cd059e956 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.cc
@@ -1,118 +1,120 @@
/**
* @file mIIasym_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Wed Oct 17 2018
*
- * @brief
+ * @brief contact for mode II anti-symmetric simulations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "mIIasym_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
MIIASYMContact::MIIASYMContact(SolidMechanicsModel & model, const ID & id)
: NTRFContact(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MIIASYMContact::updateImpedance() {
AKANTU_DEBUG_IN();
NTRFContact::updateImpedance();
for (UInt i = 0; i < this->impedance.size(); ++i) {
this->impedance(i) *= 0.5;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// WARNING: this is only valid for the acceleration in equilibrium
void MIIASYMContact::computeRelativeNormalField(
const Array<Real> & field, Array<Real> & rel_normal_field) const {
AKANTU_DEBUG_IN();
NTRFContact::computeRelativeNormalField(field, rel_normal_field);
for (auto it_rtfield = rel_normal_field.begin();
it_rtfield != rel_normal_field.end(); ++it_rtfield) {
// in the anti-symmetric case
*it_rtfield *= 2.;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MIIASYMContact::computeRelativeTangentialField(
const Array<Real> & field, Array<Real> & rel_tang_field) const {
AKANTU_DEBUG_IN();
NTRFContact::computeRelativeTangentialField(field, rel_tang_field);
UInt dim = this->model.getSpatialDimension();
for (Array<Real>::iterator<Vector<Real>> it_rtfield =
rel_tang_field.begin(dim);
it_rtfield != rel_tang_field.end(dim); ++it_rtfield) {
// in the anti-symmetric case, the tangential fields become twice as large
*it_rtfield *= 2.;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MIIASYMContact::computeContactPressureInEquilibrium() {
AKANTU_DEBUG_IN();
NTRFContact::computeContactPressure();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MIIASYMContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "MIIASYMContact [" << std::endl;
NTRFContact::printself(stream, indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
index 5de74ea4d..ac35c2ac1 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/mIIasym_contact.hh
@@ -1,90 +1,92 @@
/**
* @file mIIasym_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief contact for mode II anti-symmetric simulations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_MIIASYM_CONTACT_HH_
#define AST_MIIASYM_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntrf_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class MIIASYMContact : public NTRFContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MIIASYMContact(SolidMechanicsModel & model, const ID & id = "contact");
~MIIASYMContact() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// update the impedance matrix
virtual void updateImpedance();
/// compute contact pressure -> do nothing because can only compute it in
/// equilibrium
void computeContactPressure() override{};
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// WARNING: this is only valid for the acceleration in equilibrium
void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const override;
/// compute relative tangential field (complet array)
/// relative to master nodes
void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const override;
/// compute contact pressure that is used over the entire time
virtual void computeContactPressureInEquilibrium();
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const MIIASYMContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_MIIASYM_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
index b2a7c43c2..fae762cb6 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.cc
@@ -1,565 +1,567 @@
/**
* @file ntn_base_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of ntn base contact
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "ntn_base_contact.hh"
#include "dof_manager_default.hh"
#include "dumpable_inline_impl.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
#include "non_linear_solver_lumped.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
// NTNContactSynchElementFilter::NTNContactSynchElementFilter(
// NTNBaseContact & contact)
// : contact(contact),
// connectivity(contact.getModel().getMesh().getConnectivities()) {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
// bool NTNContactSynchElementFilter::operator()(const Element & e) {
// AKANTU_DEBUG_IN();
// ElementType type = e.type;
// UInt element = e.element;
// GhostType ghost_type = e.ghost_type;
// // loop over all nodes of this element
// bool need_element = false;
// UInt nb_nodes = Mesh::getNbNodesPerElement(type);
// for (UInt n = 0; n < nb_nodes; ++n) {
// UInt nn = this->connectivity(type, ghost_type)(element, n);
// // if one nodes is in this contact, we need this element
// if (this->contact.getNodeIndex(nn) >= 0) {
// need_element = true;
// break;
// }
// }
// AKANTU_DEBUG_OUT();
// return need_element;
// }
/* -------------------------------------------------------------------------- */
NTNBaseContact::NTNBaseContact(SolidMechanicsModel & model, const ID & id)
: id(id), model(model),
slaves(0, 1, 0, id + ":slaves", std::numeric_limits<UInt>::quiet_NaN(),
"slaves"),
normals(0, model.getSpatialDimension(), 0, id + ":normals",
std::numeric_limits<Real>::quiet_NaN(), "normals"),
contact_pressure(
0, model.getSpatialDimension(), 0, id + ":contact_pressure",
std::numeric_limits<Real>::quiet_NaN(), "contact_pressure"),
is_in_contact(0, 1, false, id + ":is_in_contact", false, "is_in_contact"),
lumped_boundary_slaves(0, 1, 0, id + ":lumped_boundary_slaves",
std::numeric_limits<Real>::quiet_NaN(),
"lumped_boundary_slaves"),
impedance(0, 1, 0, id + ":impedance",
std::numeric_limits<Real>::quiet_NaN(), "impedance"),
slave_elements("slave_elements", id) {
AKANTU_DEBUG_IN();
auto & boundary_fem = this->model.getFEEngineBoundary();
for (auto && ghost_type : ghost_types) {
boundary_fem.initShapeFunctions(ghost_type);
}
auto & mesh = this->model.getMesh();
auto spatial_dimension = this->model.getSpatialDimension();
this->slave_elements.initialize(mesh,
_spatial_dimension = spatial_dimension - 1);
MeshUtils::buildNode2Elements(mesh, this->node_to_elements,
spatial_dimension - 1);
this->registerDumper<DumperText>("text_all", id, true);
this->addDumpFilteredMesh(mesh, slave_elements, slaves.getArray(),
spatial_dimension - 1, _not_ghost, _ek_regular);
// parallelisation
this->synch_registry = std::make_unique<SynchronizerRegistry>();
this->synch_registry->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NTNBaseContact::~NTNBaseContact() = default;
/* -------------------------------------------------------------------------- */
void NTNBaseContact::initParallel() {
AKANTU_DEBUG_IN();
this->synchronizer = std::make_unique<ElementSynchronizer>(
this->model.getMesh().getElementSynchronizer());
this->synchronizer->filterScheme([&](auto && element) {
// loop over all nodes of this element
Vector<UInt> conn = const_cast<const Mesh &>(this->model.getMesh())
.getConnectivity(element);
for (auto & node : conn) {
// if one nodes is in this contact, we need this element
if (this->getNodeIndex(node) >= 0) {
return true;
}
}
return false;
});
this->synch_registry->registerSynchronizer(*(this->synchronizer),
SynchronizationTag::_cf_nodal);
this->synch_registry->registerSynchronizer(*(this->synchronizer),
SynchronizationTag::_cf_incr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::findBoundaryElements(
const Array<UInt> & interface_nodes, ElementTypeMapArray<UInt> & elements) {
AKANTU_DEBUG_IN();
// add connected boundary elements that have all nodes on this contact
for (const auto & node : interface_nodes) {
for (const auto & element : this->node_to_elements.getRow(node)) {
Vector<UInt> conn = const_cast<const Mesh &>(this->model.getMesh())
.getConnectivity(element);
auto nb_nodes = conn.size();
decltype(nb_nodes) nb_found_nodes = 0;
for (auto & nn : conn) {
if (interface_nodes.find(nn) != UInt(-1)) {
nb_found_nodes++;
} else {
break;
}
}
// this is an element between all contact nodes
// and is not already in the elements
if ((nb_found_nodes == nb_nodes) &&
(elements(element.type, element.ghost_type).find(element.element) ==
UInt(-1))) {
elements(element.type, element.ghost_type).push_back(element.element);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::addSplitNode(UInt node, UInt) {
AKANTU_DEBUG_IN();
UInt dim = this->model.getSpatialDimension();
// add to node arrays
this->slaves.push_back(node);
// set contact as false
this->is_in_contact.push_back(false);
// before initializing
// set contact pressure, normal, lumped_boundary to Nan
this->contact_pressure.push_back(std::numeric_limits<Real>::quiet_NaN());
this->impedance.push_back(std::numeric_limits<Real>::quiet_NaN());
this->lumped_boundary_slaves.push_back(
std::numeric_limits<Real>::quiet_NaN());
Vector<Real> nan_normal(dim, std::numeric_limits<Real>::quiet_NaN());
this->normals.push_back(nan_normal);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::registerSynchronizedArray(SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->slaves.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->slaves.dumpRestartFile(file_name);
this->normals.dumpRestartFile(file_name);
this->is_in_contact.dumpRestartFile(file_name);
this->contact_pressure.dumpRestartFile(file_name);
this->lumped_boundary_slaves.dumpRestartFile(file_name);
this->impedance.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->slaves.readRestartFile(file_name);
this->normals.readRestartFile(file_name);
this->is_in_contact.readRestartFile(file_name);
this->contact_pressure.readRestartFile(file_name);
this->lumped_boundary_slaves.readRestartFile(file_name);
this->impedance.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt NTNBaseContact::getNbNodesInContact() const {
AKANTU_DEBUG_IN();
UInt nb_contact = 0;
UInt nb_nodes = this->getNbContactNodes();
const Mesh & mesh = this->model.getMesh();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(this->slaves(n));
bool is_pbc_slave_node = mesh.isPeriodicSlave(this->slaves(n));
if (is_local_node && !is_pbc_slave_node && this->is_in_contact(n)) {
nb_contact++;
}
}
mesh.getCommunicator().allReduce(nb_contact, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return nb_contact;
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::updateInternalData() {
AKANTU_DEBUG_IN();
updateNormals();
updateLumpedBoundary();
updateImpedance();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::updateLumpedBoundary() {
AKANTU_DEBUG_IN();
this->internalUpdateLumpedBoundary(this->slaves.getArray(),
this->slave_elements,
this->lumped_boundary_slaves);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::internalUpdateLumpedBoundary(
const Array<UInt> & nodes, const ElementTypeMapArray<UInt> & elements,
SynchronizedArray<Real> & boundary) {
AKANTU_DEBUG_IN();
// set all values in lumped_boundary to zero
boundary.zero();
UInt dim = this->model.getSpatialDimension();
// UInt nb_contact_nodes = getNbContactNodes();
const FEEngine & boundary_fem = this->model.getFEEngineBoundary();
const Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(dim - 1, ghost_type)) {
UInt nb_elements = mesh.getNbElement(type, ghost_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
// get shapes and compute integral
const Array<Real> & shapes = boundary_fem.getShapes(type, ghost_type);
Array<Real> area(nb_elements, nb_nodes_per_element);
boundary_fem.integrate(shapes, area, nb_nodes_per_element, type,
ghost_type);
if (this->contact_surfaces.size() == 0) {
AKANTU_DEBUG_WARNING(
"No surfaces in ntn base contact."
<< " You have to define the lumped boundary by yourself.");
}
Array<UInt>::const_iterator<UInt> elem_it =
(elements)(type, ghost_type).begin();
Array<UInt>::const_iterator<UInt> elem_it_end =
(elements)(type, ghost_type).end();
// loop over contact nodes
for (; elem_it != elem_it_end; ++elem_it) {
for (UInt q = 0; q < nb_nodes_per_element; ++q) {
UInt node = connectivity(*elem_it, q);
UInt node_index = nodes.find(node);
AKANTU_DEBUG_ASSERT(node_index != UInt(-1), "Could not find node "
<< node
<< " in the array!");
Real area_to_add = area(*elem_it, q);
boundary(node_index) += area_to_add;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::computeAcceleration(Array<Real> & acceleration) const {
auto && dof_manager =
dynamic_cast<DOFManagerDefault &>(model.getDOFManager());
const auto & b = dof_manager.getResidual();
acceleration.resize(b.size());
const auto & blocked_dofs = dof_manager.getGlobalBlockedDOFs();
const auto & A = dof_manager.getLumpedMatrix("M");
Array<bool> blocked_dofs_bool(blocked_dofs.size());
for (auto && data : zip(blocked_dofs, blocked_dofs_bool)) {
std::get<1>(data) = std::get<0>(data);
}
// pre-compute the acceleration
// (not increment acceleration, because residual is still Kf)
NonLinearSolverLumped::solveLumped(A, acceleration, b, this->model.getF_M2A(),
blocked_dofs_bool);
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::computeContactPressure() {
AKANTU_DEBUG_IN();
UInt dim = this->model.getSpatialDimension();
Real delta_t = this->model.getTimeStep();
UInt nb_contact_nodes = getNbContactNodes();
AKANTU_DEBUG_ASSERT(delta_t > 0.,
"Cannot compute contact pressure if no time step is set");
// synchronize data
this->synch_registry->synchronize(SynchronizationTag::_cf_nodal);
Array<Real> acceleration(0, dim);
this->computeAcceleration(acceleration);
// compute relative normal fields of displacement, velocity and acceleration
Array<Real> r_disp(0, 1);
Array<Real> r_velo(0, 1);
Array<Real> r_acce(0, 1);
Array<Real> r_old_acce(0, 1);
computeNormalGap(r_disp);
// computeRelativeNormalField(this->model.getCurrentPosition(), r_disp);
computeRelativeNormalField(this->model.getVelocity(), r_velo);
computeRelativeNormalField(acceleration, r_acce);
computeRelativeNormalField(this->model.getAcceleration(), r_old_acce);
AKANTU_DEBUG_ASSERT(r_disp.size() == nb_contact_nodes,
"computeRelativeNormalField does not give back arrays "
<< "size == nb_contact_nodes. nb_contact_nodes = "
<< nb_contact_nodes
<< " | array size = " << r_disp.size());
// compute gap array for all nodes
Array<Real> gap(nb_contact_nodes, 1);
Real * gap_p = gap.storage();
Real * r_disp_p = r_disp.storage();
Real * r_velo_p = r_velo.storage();
Real * r_acce_p = r_acce.storage();
Real * r_old_acce_p = r_old_acce.storage();
for (UInt i = 0; i < nb_contact_nodes; ++i) {
*gap_p = *r_disp_p + delta_t * *r_velo_p + delta_t * delta_t * *r_acce_p -
0.5 * delta_t * delta_t * *r_old_acce_p;
// increment pointers
gap_p++;
r_disp_p++;
r_velo_p++;
r_acce_p++;
r_old_acce_p++;
}
// check if gap is negative -> is in contact
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (gap(n) <= 0.) {
for (UInt d = 0; d < dim; ++d) {
this->contact_pressure(n, d) =
this->impedance(n) * gap(n) / (2 * delta_t) * this->normals(n, d);
}
this->is_in_contact(n) = true;
} else {
for (UInt d = 0; d < dim; ++d)
this->contact_pressure(n, d) = 0.;
this->is_in_contact(n) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::applyContactPressure() {
AKANTU_DEBUG_IN();
UInt nb_contact_nodes = getNbContactNodes();
UInt dim = this->model.getSpatialDimension();
Array<Real> & residual = this->model.getInternalForce();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt slave = this->slaves(n);
for (UInt d = 0; d < dim; ++d) {
// residual(master,d) += this->lumped_boundary(n,0) *
// this->contact_pressure(n,d);
residual(slave, d) -=
this->lumped_boundary_slaves(n) * this->contact_pressure(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int NTNBaseContact::getNodeIndex(UInt node) const {
return this->slaves.find(node);
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNBaseContact [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + slaves : " << std::endl;
this->slaves.printself(stream, indent + 2);
stream << space << " + normals : " << std::endl;
this->normals.printself(stream, indent + 2);
stream << space << " + contact_pressure : " << std::endl;
this->contact_pressure.printself(stream, indent + 2);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::syncArrays(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
this->slaves.syncElements(sync_choice);
this->normals.syncElements(sync_choice);
this->is_in_contact.syncElements(sync_choice);
this->contact_pressure.syncElements(sync_choice);
this->lumped_boundary_slaves.syncElements(sync_choice);
this->impedance.syncElements(sync_choice);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseContact::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
const Array<UInt> & nodal_filter = this->slaves.getArray();
#define ADD_FIELD(field_id, field, type) \
internalAddDumpFieldToDumper( \
dumper_name, field_id, \
std::make_unique< \
dumpers::NodalField<type, true, Array<type>, Array<UInt>>>( \
field, 0, 0, &nodal_filter))
if (field_id == "displacement") {
ADD_FIELD(field_id, this->model.getDisplacement(), Real);
} else if (field_id == "mass") {
ADD_FIELD(field_id, this->model.getMass(), Real);
} else if (field_id == "velocity") {
ADD_FIELD(field_id, this->model.getVelocity(), Real);
} else if (field_id == "acceleration") {
ADD_FIELD(field_id, this->model.getAcceleration(), Real);
} else if (field_id == "external_force") {
ADD_FIELD(field_id, this->model.getExternalForce(), Real);
} else if (field_id == "internal_force") {
ADD_FIELD(field_id, this->model.getInternalForce(), Real);
} else if (field_id == "blocked_dofs") {
ADD_FIELD(field_id, this->model.getBlockedDOFs(), bool);
} else if (field_id == "increment") {
ADD_FIELD(field_id, this->model.getIncrement(), Real);
} else if (field_id == "normal") {
internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->normals.getArray()));
} else if (field_id == "contact_pressure") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->contact_pressure.getArray()));
} else if (field_id == "is_in_contact") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<bool>>(
this->is_in_contact.getArray()));
} else if (field_id == "lumped_boundary_slave") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->lumped_boundary_slaves.getArray()));
} else if (field_id == "impedance") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->impedance.getArray()));
} else {
std::cerr << "Could not add field '" << field_id
<< "' to the dumper. Just ignored it." << std::endl;
}
#undef ADD_FIELD
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
index d786ccab5..8bfc075fb 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact.hh
@@ -1,250 +1,252 @@
/**
* @file ntn_base_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief base contact for ntn and ntrf contact
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_BASE_CONTACT_HH_
#define AST_NTN_BASE_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "aka_csr.hh"
#include "solid_mechanics_model.hh"
// simtools
#include "synchronized_array.hh"
namespace akantu {
class NTNBaseContact;
/* -------------------------------------------------------------------------- */
// class NTNContactSynchElementFilter : public SynchElementFilter {
// public:
// // constructor
// NTNContactSynchElementFilter(NTNBaseContact & contact);
// // answer to: do we need this element ?
// virtual bool operator()(const Element & e);
// private:
// const NTNBaseContact & contact;
// const ElementTypeMapArray<UInt> & connectivity;
// };
/* -------------------------------------------------------------------------- */
class NTNBaseContact : public DataAccessor<Element>, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNBaseContact(SolidMechanicsModel & model, const ID & id = "contact");
~NTNBaseContact() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initializes ntn contact parallel
virtual void initParallel();
/// add split node
virtual void addSplitNode(UInt node, UInt = 0);
/// update normals, lumped boundary, and impedance
virtual void updateInternalData();
/// update (compute the normals)
virtual void updateNormals() = 0;
/// update the lumped boundary B matrix
virtual void updateLumpedBoundary();
/// update the impedance matrix
virtual void updateImpedance() = 0;
/// compute the normal contact force
virtual void computeContactPressure();
/// impose the normal contact force
virtual void applyContactPressure();
/// register synchronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// compute the normal gap
virtual void computeNormalGap(Array<Real> & gap) const = 0;
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
virtual void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const = 0;
/// compute relative tangential field (complet array)
/// relative to master nodes
virtual void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const = 0;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// computes the acceleration
void computeAcceleration(Array<Real> & acceleration) const;
protected:
/// updateLumpedBoundary
virtual void
internalUpdateLumpedBoundary(const Array<UInt> & nodes,
const ElementTypeMapArray<UInt> & elements,
SynchronizedArray<Real> & boundary);
// to find the slave_elements or master_elements
virtual void findBoundaryElements(const Array<UInt> & interface_nodes,
ElementTypeMapArray<UInt> & elements);
/// synchronize arrays
virtual void syncArrays(SyncChoice sync_choice);
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Model, model, SolidMechanicsModel &)
AKANTU_GET_MACRO(Slaves, slaves, const SynchronizedArray<UInt> &)
AKANTU_GET_MACRO(Normals, normals, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(ContactPressure, contact_pressure,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(LumpedBoundarySlaves, lumped_boundary_slaves,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(Impedance, impedance, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(IsInContact, is_in_contact, const SynchronizedArray<bool> &)
AKANTU_GET_MACRO(SlaveElements, slave_elements,
const ElementTypeMapArray<UInt> &)
AKANTU_GET_MACRO(SynchronizerRegistry, *synch_registry,
SynchronizerRegistry &)
/// get number of nodes that are in contact (globally, on all procs together)
/// is_in_contact = true
virtual UInt getNbNodesInContact() const;
/// get index of node in either slaves or masters array
/// if node is in neither of them, return -1
virtual Int getNodeIndex(UInt node) const;
/// get number of contact nodes: nodes in the system locally (on this proc)
/// is_in_contact = true and false, because just in the system
virtual UInt getNbContactNodes() const { return this->slaves.size(); }
bool isNTNContact() const { return this->is_ntn_contact; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using SurfacePtrSet = std::set<const ElementGroup *>;
ID id;
SolidMechanicsModel & model;
/// array of slave nodes
SynchronizedArray<UInt> slaves;
/// array of normals
SynchronizedArray<Real> normals;
/// array indicating if nodes are in contact
SynchronizedArray<Real> contact_pressure;
/// array indicating if nodes are in contact
SynchronizedArray<bool> is_in_contact;
/// boundary matrix for slave nodes
SynchronizedArray<Real> lumped_boundary_slaves;
/// impedance matrix
SynchronizedArray<Real> impedance;
/// contact surface
SurfacePtrSet contact_surfaces;
/// element list for dump and lumped_boundary
ElementTypeMapArray<UInt> slave_elements;
CSR<Element> node_to_elements;
/// parallelisation
std::unique_ptr<SynchronizerRegistry> synch_registry;
std::unique_ptr<ElementSynchronizer> synchronizer;
bool is_ntn_contact{true};
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNBaseContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "ntn_base_contact_inline_impl.hh"
#endif /* AST_NTN_BASE_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact_inline_impl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact_inline_impl.hh
index 731303290..9168f051a 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact_inline_impl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_contact_inline_impl.hh
@@ -1,126 +1,129 @@
/**
* @file ntn_base_contact_inline_impl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief ntn base contact inline functions
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "ntn_base_contact.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt NTNBaseContact::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt spatial_dimension = this->model.getSpatialDimension();
UInt nb_nodes = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_nodes += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_cf_nodal: {
size += nb_nodes * spatial_dimension * sizeof(Real) *
3; // disp, vel and cur_pos
break;
}
case SynchronizationTag::_cf_incr: {
size += nb_nodes * spatial_dimension * sizeof(Real) * 1;
break;
}
default: {
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void NTNBaseContact::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_cf_nodal: {
DataAccessor::packNodalDataHelper(this->model.getDisplacement(), buffer,
elements, this->model.getMesh());
DataAccessor::packNodalDataHelper(this->model.getCurrentPosition(), buffer,
elements, this->model.getMesh());
DataAccessor::packNodalDataHelper(this->model.getVelocity(), buffer,
elements, this->model.getMesh());
break;
}
case SynchronizationTag::_cf_incr: {
DataAccessor::packNodalDataHelper(this->model.getIncrement(), buffer,
elements, this->model.getMesh());
break;
}
default: {
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void NTNBaseContact::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_cf_nodal: {
DataAccessor::unpackNodalDataHelper(this->model.getDisplacement(), buffer,
elements, this->model.getMesh());
DataAccessor::unpackNodalDataHelper(
const_cast<Array<Real> &>(this->model.getCurrentPosition()), buffer,
elements, this->model.getMesh());
DataAccessor::unpackNodalDataHelper(this->model.getVelocity(), buffer,
elements, this->model.getMesh());
break;
}
case SynchronizationTag::_cf_incr: {
DataAccessor::unpackNodalDataHelper(this->model.getIncrement(), buffer,
elements, this->model.getMesh());
break;
}
default: {
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
index e28e034fe..c66837db1 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.cc
@@ -1,379 +1,381 @@
/**
* @file ntn_base_friction.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of ntn base friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
#include "dof_manager_default.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
#include "non_linear_solver_lumped.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNBaseFriction::NTNBaseFriction(NTNBaseContact & contact, const ID & id)
: Parsable(ParserType::_friction, id), Dumpable(),
contact(contact),
is_sticking(0, 1, true, id + ":is_sticking", true, "is_sticking"),
frictional_strength(0, 1, 0., id + ":frictional_strength", 0.,
"frictional_strength"),
friction_traction(0, contact.getModel().getSpatialDimension(), 0.,
id + ":friction_traction", 0., "friction_traction"),
slip(0, 1, 0., id + ":slip", 0., "slip"),
cumulative_slip(0, 1, 0., id + ":cumulative_slip", 0., "cumulative_slip"),
slip_velocity(0, contact.getModel().getSpatialDimension(), 0.,
id + ":slip_velocity", 0., "slip_velocity") {
AKANTU_DEBUG_IN();
this->contact.registerSynchronizedArray(this->is_sticking);
this->contact.registerSynchronizedArray(this->frictional_strength);
this->contact.registerSynchronizedArray(this->friction_traction);
this->contact.registerSynchronizedArray(this->slip);
this->contact.registerSynchronizedArray(this->cumulative_slip);
this->contact.registerSynchronizedArray(this->slip_velocity);
this->registerExternalDumper(contact.getDumper().shared_from_this(),
contact.getDefaultDumperName(), true);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::updateSlip() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
// synchronize increment
this->contact.getSynchronizerRegistry().synchronize(
SynchronizationTag::_cf_incr);
Array<Real> rel_tan_incr(0, dim);
this->contact.computeRelativeTangentialField(model.getIncrement(),
rel_tan_incr);
Array<Real>::const_iterator<Vector<Real>> it = rel_tan_incr.begin(dim);
UInt nb_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->is_sticking(n)) {
this->slip(n) = 0.;
} else {
const Vector<Real> & rti = it[n];
this->slip(n) += rti.norm();
this->cumulative_slip(n) += rti.norm();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::computeFrictionTraction() {
AKANTU_DEBUG_IN();
this->computeStickTraction();
this->computeFrictionalStrength();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
// get contact arrays
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
Array<Real> & traction =
const_cast<Array<Real> &>(this->friction_traction.getArray());
Array<Real>::iterator<Vector<Real>> it_fric_trac = traction.begin(dim);
this->is_sticking.zero(); // set to not sticking
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// node pair is in contact
if (is_in_contact(n)) {
Vector<Real> fric_trac = it_fric_trac[n];
// check if it is larger than frictional strength
Real abs_fric = fric_trac.norm();
if (abs_fric != 0.) {
Real alpha = this->frictional_strength(n) / abs_fric;
// larger -> sliding
if (alpha < 1.) {
fric_trac *= alpha;
} else
this->is_sticking(n) = true;
} else {
// frictional traction is already zero
this->is_sticking(n) = true;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::computeStickTraction() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
UInt dim = model.getSpatialDimension();
Real delta_t = model.getTimeStep();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
// get contact arrays
const SynchronizedArray<Real> & impedance = this->contact.getImpedance();
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
Array<Real> acceleration(0, dim);
this->contact.computeAcceleration(acceleration);
// compute relative normal fields of velocity and acceleration
Array<Real> r_velo(0, dim);
Array<Real> r_acce(0, dim);
Array<Real> r_old_acce(0, dim);
this->contact.computeRelativeTangentialField(model.getVelocity(), r_velo);
this->contact.computeRelativeTangentialField(acceleration, r_acce);
this->contact.computeRelativeTangentialField(model.getAcceleration(),
r_old_acce);
AKANTU_DEBUG_ASSERT(r_velo.size() == nb_contact_nodes,
"computeRelativeNormalField does not give back arrays "
<< "size == nb_contact_nodes. nb_contact_nodes = "
<< nb_contact_nodes
<< " | array size = " << r_velo.size());
// compute tangential gap_dot array for all nodes
Array<Real> gap_dot(nb_contact_nodes, dim);
for (auto && data : zip(make_view(gap_dot), make_view(r_velo),
make_view(r_acce), make_view(r_old_acce))) {
auto & gap_dot = std::get<0>(data);
auto & r_velo = std::get<1>(data);
auto & r_acce = std::get<2>(data);
auto & r_old_acce = std::get<3>(data);
gap_dot = r_velo + delta_t * r_acce - 1. / 2. * delta_t * r_old_acce;
}
// compute friction traction to stop sliding
Array<Real> & traction =
const_cast<Array<Real> &>(this->friction_traction.getArray());
auto it_fric_trac = traction.begin(dim);
for (UInt n = 0; n < nb_contact_nodes; ++n) {
Vector<Real> fric_trac = it_fric_trac[n];
// node pair is NOT in contact
if (!is_in_contact(n)) {
fric_trac.zero(); // set to zero
}
// node pair is in contact
else {
// compute friction traction
for (UInt d = 0; d < dim; ++d)
fric_trac(d) = impedance(n) * gap_dot(n, d) / 2.;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::applyFrictionTraction() {
AKANTU_DEBUG_IN();
SolidMechanicsModel & model = this->contact.getModel();
Array<Real> & residual = model.getInternalForce();
UInt dim = model.getSpatialDimension();
const SynchronizedArray<UInt> & slaves = this->contact.getSlaves();
const SynchronizedArray<Real> & lumped_boundary_slaves =
this->contact.getLumpedBoundarySlaves();
UInt nb_contact_nodes = this->contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt slave = slaves(n);
for (UInt d = 0; d < dim; ++d) {
residual(slave, d) -=
lumped_boundary_slaves(n) * this->friction_traction(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::registerSynchronizedArray(SynchronizedArrayBase & array) {
AKANTU_DEBUG_IN();
this->frictional_strength.registerDependingArray(array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
this->is_sticking.dumpRestartFile(file_name);
this->frictional_strength.dumpRestartFile(file_name);
this->friction_traction.dumpRestartFile(file_name);
this->slip.dumpRestartFile(file_name);
this->cumulative_slip.dumpRestartFile(file_name);
this->slip_velocity.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
this->is_sticking.readRestartFile(file_name);
this->frictional_strength.readRestartFile(file_name);
this->friction_traction.readRestartFile(file_name);
this->cumulative_slip.readRestartFile(file_name);
this->slip_velocity.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::setParam(const std::string & name, UInt node,
Real value) {
AKANTU_DEBUG_IN();
SynchronizedArray<Real> & array =
this->get(name).get<SynchronizedArray<Real>>();
Int index = this->contact.getNodeIndex(node);
if (index < 0) {
AKANTU_DEBUG_WARNING("Node "
<< node << " is not a contact node. "
<< "Therefore, cannot set interface parameter!!");
} else {
array(index) = value; // put value
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt NTNBaseFriction::getNbStickingNodes() const {
AKANTU_DEBUG_IN();
UInt nb_stick = 0;
UInt nb_nodes = this->contact.getNbContactNodes();
const SynchronizedArray<UInt> & nodes = this->contact.getSlaves();
const SynchronizedArray<bool> & is_in_contact =
this->contact.getIsInContact();
const Mesh & mesh = this->contact.getModel().getMesh();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(nodes(n));
bool is_pbc_slave_node = mesh.isPeriodicSlave(nodes(n));
if (is_local_node && !is_pbc_slave_node && is_in_contact(n) &&
this->is_sticking(n)) {
nb_stick++;
}
}
mesh.getCommunicator().allReduce(nb_stick, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return nb_stick;
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNBaseFriction [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNBaseFriction::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
// &(this->contact.getSlaves());
if (field_id == "is_sticking") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<bool>>(
this->is_sticking.getArray()));
} else if (field_id == "frictional_strength") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->frictional_strength.getArray()));
} else if (field_id == "friction_traction") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->friction_traction.getArray()));
} else if (field_id == "slip") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(this->slip.getArray()));
} else if (field_id == "cumulative_slip") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->cumulative_slip.getArray()));
} else if (field_id == "slip_velocity") {
this->internalAddDumpFieldToDumper(
dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->slip_velocity.getArray()));
} else {
this->contact.addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
index 7b6ec0b96..e36eef799 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_base_friction.hh
@@ -1,176 +1,178 @@
/**
* @file ntn_base_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief base class for ntn and ntrf friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_BASE_FRICTION_HH_
#define AST_NTN_BASE_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// akantu
#include "parsable.hh"
// simtools
#include "ntn_base_contact.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<akantu::SynchronizedArray<Real>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setAndChangeDefault(r);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void ParameterTyped<akantu::SynchronizedArray<Real>>::setTyped<Real>(
const Real & value) {
param.setAndChangeDefault(value);
}
/* -------------------------------------------------------------------------- */
class NTNBaseFriction : public Parsable, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNBaseFriction(NTNBaseContact & contact, const ID & id = "friction");
virtual ~NTNBaseFriction() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute friction traction
virtual void computeFrictionTraction();
/// compute stick traction (friction traction needed to stick the nodes)
virtual void computeStickTraction();
/// apply the friction force
virtual void applyFrictionTraction();
/// compute slip
virtual void updateSlip();
/// register Syncronizedarrays for sync
virtual void registerSynchronizedArray(SynchronizedArrayBase & array);
/// dump restart file
virtual void dumpRestart(const std::string & file_name) const;
/// read restart file
virtual void readRestart(const std::string & file_name);
/// set to steady state
virtual void setToSteadyState() { AKANTU_TO_IMPLEMENT(); };
/// get the number of sticking nodes (in parallel)
/// a node that is not in contact does not count as sticking
virtual UInt getNbStickingNodes() const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// compute frictional strength according to friction law
virtual void computeFrictionalStrength() = 0;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Contact, contact, const NTNBaseContact &)
AKANTU_GET_MACRO(IsSticking, is_sticking, const SynchronizedArray<bool> &)
AKANTU_GET_MACRO(FrictionalStrength, frictional_strength,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(FrictionTraction, friction_traction,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(Slip, slip, const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(CumulativeSlip, cumulative_slip,
const SynchronizedArray<Real> &)
AKANTU_GET_MACRO(SlipVelocity, slip_velocity, const SynchronizedArray<Real> &)
/// set parameter of a given node
/// (if you need to set to all: used the setMixed function of the Parsable).
virtual void setParam(const std::string & name, UInt node, Real value);
// replaced by the setMixed of the Parsable
// virtual void setParam(const std::string & param, Real value) {
// AKANTU_ERROR("Friction does not know the following parameter: " <<
// param);
// };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
NTNBaseContact & contact;
// if node is sticking
SynchronizedArray<bool> is_sticking;
// frictional strength
SynchronizedArray<Real> frictional_strength;
// friction force
SynchronizedArray<Real> friction_traction;
// slip
SynchronizedArray<Real> slip;
SynchronizedArray<Real> cumulative_slip;
// slip velocity (tangential vector)
SynchronizedArray<Real> slip_velocity;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_base_friction_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNBaseFriction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTN_BASE_FRICTION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
index e5ad24f75..d633a0af8 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.cc
@@ -1,554 +1,556 @@
/**
* @file ntn_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of ntn_contact
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_contact.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTNContact::NTNContact(SolidMechanicsModel & model, const ID & id)
: NTNBaseContact(model, id),
masters(0, 1, 0, id + ":masters", std::numeric_limits<UInt>::quiet_NaN(),
"masters"),
lumped_boundary_masters(0, 1, 0, id + ":lumped_boundary_masters",
std::numeric_limits<Real>::quiet_NaN(),
"lumped_boundary_masters"),
master_elements("master_elements", id) {
AKANTU_DEBUG_IN();
const Mesh & mesh = this->model.getMesh();
UInt spatial_dimension = this->model.getSpatialDimension();
this->master_elements.initialize(mesh, _nb_component = 1,
_spatial_dimension = spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::pairInterfaceNodes(const ElementGroup & slave_boundary,
const ElementGroup & master_boundary,
UInt surface_normal_dir, const Mesh & mesh,
Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
pairs.resize(0);
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt dim = mesh.getSpatialDimension();
AKANTU_DEBUG_ASSERT(surface_normal_dir < dim,
"Mesh is of " << dim << " dimensions"
<< " and cannot have direction "
<< surface_normal_dir
<< " for surface normal");
// offset for projection computation
Vector<UInt> offset(dim - 1);
for (UInt i = 0, j = 0; i < dim; ++i) {
if (surface_normal_dir != i) {
offset(j) = i;
++j;
}
}
// find projected node coordinates
const Array<Real> & coordinates = mesh.getNodes();
// find slave nodes
Array<Real> proj_slave_coord(slave_boundary.getNbNodes(), dim - 1, 0.);
Array<UInt> slave_nodes(slave_boundary.getNbNodes());
UInt n(0);
for (auto && slave_node : slave_boundary.getNodeGroup().getNodes()) {
for (UInt d = 0; d < dim - 1; ++d) {
proj_slave_coord(n, d) = coordinates(slave_node, offset[d]);
slave_nodes(n) = slave_node;
}
++n;
}
// find master nodes
Array<Real> proj_master_coord(master_boundary.getNbNodes(), dim - 1, 0.);
Array<UInt> master_nodes(master_boundary.getNbNodes());
n = 0;
for (auto && master_node : master_boundary.getNodeGroup().getNodes()) {
for (UInt d = 0; d < dim - 1; ++d) {
proj_master_coord(n, d) = coordinates(master_node, offset[d]);
master_nodes(n) = master_node;
}
++n;
}
// find minimum distance between slave nodes to define tolerance
Real min_dist = std::numeric_limits<Real>::max();
for (UInt i = 0; i < proj_slave_coord.size(); ++i) {
for (UInt j = i + 1; j < proj_slave_coord.size(); ++j) {
Real dist = 0.;
for (UInt d = 0; d < dim - 1; ++d) {
dist += (proj_slave_coord(i, d) - proj_slave_coord(j, d)) *
(proj_slave_coord(i, d) - proj_slave_coord(j, d));
}
if (dist < min_dist) {
min_dist = dist;
}
}
}
min_dist = std::sqrt(min_dist);
Real local_tol = 0.1 * min_dist;
// find master slave node pairs
for (UInt i = 0; i < proj_slave_coord.size(); ++i) {
for (UInt j = 0; j < proj_master_coord.size(); ++j) {
Real dist = 0.;
for (UInt d = 0; d < dim - 1; ++d) {
dist += (proj_slave_coord(i, d) - proj_master_coord(j, d)) *
(proj_slave_coord(i, d) - proj_master_coord(j, d));
}
dist = std::sqrt(dist);
if (dist < local_tol) { // it is a pair
Vector<UInt> pair(2);
pair[0] = slave_nodes(i);
pair[1] = master_nodes(j);
pairs.push_back(pair);
continue; // found master do not need to search further for this slave
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addSurfacePair(const ID & slave, const ID & master,
UInt surface_normal_dir) {
AKANTU_DEBUG_IN();
const Mesh & mesh = this->model.getMesh();
const ElementGroup & slave_boundary = mesh.getElementGroup(slave);
const ElementGroup & master_boundary = mesh.getElementGroup(master);
this->contact_surfaces.insert(&slave_boundary);
this->contact_surfaces.insert(&master_boundary);
Array<UInt> pairs(0, 2);
NTNContact::pairInterfaceNodes(slave_boundary, master_boundary,
surface_normal_dir, this->model.getMesh(),
pairs);
// eliminate pairs which contain a pbc slave node
Array<UInt> pairs_no_PBC_slaves(0, 2);
Array<UInt>::const_vector_iterator it = pairs.begin(2);
Array<UInt>::const_vector_iterator end = pairs.end(2);
for (; it != end; ++it) {
const Vector<UInt> & pair = *it;
if (not mesh.isPeriodicSlave(pair(0)) and
not mesh.isPeriodicSlave(pair(1))) {
pairs_no_PBC_slaves.push_back(pair);
}
}
this->addNodePairs(pairs_no_PBC_slaves);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addNodePairs(const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt nb_pairs = pairs.size();
for (UInt n = 0; n < nb_pairs; ++n) {
this->addSplitNode(pairs(n, 0), pairs(n, 1));
}
// synchronize with depending nodes
findBoundaryElements(this->slaves.getArray(), this->slave_elements);
findBoundaryElements(this->masters.getArray(), this->master_elements);
updateInternalData();
syncArrays(_added);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::getNodePairs(Array<UInt> & pairs) const {
AKANTU_DEBUG_IN();
pairs.resize(0);
AKANTU_DEBUG_ASSERT(pairs.getNbComponent() == 2,
"Array of node pairs should have nb_component = 2,"
<< " but has nb_component = "
<< pairs.getNbComponent());
UInt nb_pairs = this->getNbContactNodes();
for (UInt n = 0; n < nb_pairs; ++n) {
Vector<UInt> pair{this->slaves(n), this->masters(n)};
pairs.push_back(pair);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addSplitNode(UInt slave, UInt master) {
AKANTU_DEBUG_IN();
NTNBaseContact::addSplitNode(slave);
this->masters.push_back(master);
this->lumped_boundary_masters.push_back(
std::numeric_limits<Real>::quiet_NaN());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/*
This function only works for surface elements with one quad point. For
surface elements with more quad points, it computes still, but the result
might not be what you are looking for.
*/
void NTNContact::updateNormals() {
AKANTU_DEBUG_IN();
// set normals to zero
this->normals.zero();
// contact information
UInt dim = this->model.getSpatialDimension();
UInt nb_contact_nodes = this->getNbContactNodes();
this->synch_registry->synchronize(
SynchronizationTag::_cf_nodal); // synchronize current pos
const Array<Real> & cur_pos = this->model.getCurrentPosition();
FEEngine & boundary_fem = this->model.getFEEngineBoundary();
const Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(dim - 1, ghost_type)) {
// compute the normals
Array<Real> quad_normals(0, dim);
boundary_fem.computeNormalsOnIntegrationPoints(cur_pos, quad_normals,
type, ghost_type);
UInt nb_quad_points =
boundary_fem.getNbIntegrationPoints(type, ghost_type);
// new version: compute normals only based on master elements (and not all
// boundary elements)
// -------------------------------------------------------------------------------------
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
// loop over contact nodes
for (auto & element : (this->master_elements)(type, ghost_type)) {
for (UInt q = 0; q < nb_nodes_per_element; ++q) {
UInt node = connectivity(element, q);
UInt node_index = this->masters.find(node);
AKANTU_DEBUG_ASSERT(node_index != UInt(-1), "Could not find node "
<< node
<< " in the array!");
for (UInt q = 0; q < nb_quad_points; ++q) {
// add quad normal to master normal
for (UInt d = 0; d < dim; ++d) {
this->normals(node_index, d) +=
quad_normals(element * nb_quad_points + q, d);
}
}
}
}
}
}
Real * master_normals = this->normals.storage();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
if (dim == 2)
Math::normalize2(&(master_normals[n * dim]));
else if (dim == 3)
Math::normalize3(&(master_normals[n * dim]));
}
// // normalize normals
// auto nit = this->normals.begin();
// auto nend = this->normals.end();
// for (; nit != nend; ++nit) {
// nit->normalize();
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::dumpRestart(const std::string & file_name) const {
AKANTU_DEBUG_IN();
NTNBaseContact::dumpRestart(file_name);
this->masters.dumpRestartFile(file_name);
this->lumped_boundary_masters.dumpRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::readRestart(const std::string & file_name) {
AKANTU_DEBUG_IN();
NTNBaseContact::readRestart(file_name);
this->masters.readRestartFile(file_name);
this->lumped_boundary_masters.readRestartFile(file_name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::updateImpedance() {
AKANTU_DEBUG_IN();
UInt nb_contact_nodes = getNbContactNodes();
Real delta_t = this->model.getTimeStep();
AKANTU_DEBUG_ASSERT(delta_t != NAN,
"Time step is NAN. Have you set it already?");
const Array<Real> & mass = this->model.getMass();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt master = this->masters(n);
UInt slave = this->slaves(n);
Real imp = (this->lumped_boundary_masters(n) / mass(master)) +
(this->lumped_boundary_slaves(n) / mass(slave));
imp = 2 / delta_t / imp;
this->impedance(n) = imp;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::updateLumpedBoundary() {
AKANTU_DEBUG_IN();
internalUpdateLumpedBoundary(this->slaves.getArray(), this->slave_elements,
this->lumped_boundary_slaves);
internalUpdateLumpedBoundary(this->masters.getArray(), this->master_elements,
this->lumped_boundary_masters);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::applyContactPressure() {
AKANTU_DEBUG_IN();
UInt nb_ntn_pairs = getNbContactNodes();
UInt dim = this->model.getSpatialDimension();
Array<Real> & residual = this->model.getInternalForce();
for (UInt n = 0; n < nb_ntn_pairs; ++n) {
UInt master = this->masters(n);
UInt slave = this->slaves(n);
for (UInt d = 0; d < dim; ++d) {
residual(master, d) +=
this->lumped_boundary_masters(n) * this->contact_pressure(n, d);
residual(slave, d) -=
this->lumped_boundary_slaves(n) * this->contact_pressure(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::computeRelativeTangentialField(
const Array<Real> & field, Array<Real> & rel_tang_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_tang_field.resize(0);
UInt dim = this->model.getSpatialDimension();
auto it_field = field.begin(dim);
auto it_normal = this->normals.getArray().begin(dim);
Vector<Real> rfv(dim);
Vector<Real> np_rfv(dim);
UInt nb_contact_nodes = this->slaves.size();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt slave = this->slaves(n);
UInt master = this->masters(n);
// relative field vector (slave - master)
rfv = Vector<Real>(it_field[slave]);
rfv -= Vector<Real>(it_field[master]);
// normal projection of relative field
const Vector<Real> normal_v = it_normal[n];
np_rfv = normal_v;
np_rfv *= rfv.dot(normal_v);
// subract normal projection from relative field to get the tangential
// projection
rfv -= np_rfv;
rel_tang_field.push_back(rfv);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::computeRelativeNormalField(
const Array<Real> & field, Array<Real> & rel_normal_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_normal_field.resize(0);
UInt dim = this->model.getSpatialDimension();
// Real * field_p = field.storage();
// Real * normals_p = this->normals.storage();
Array<Real>::const_iterator<Vector<Real>> it_field = field.begin(dim);
Array<Real>::const_iterator<Vector<Real>> it_normal =
this->normals.getArray().begin(dim);
Vector<Real> rfv(dim);
UInt nb_contact_nodes = this->getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt slave = this->slaves(n);
UInt master = this->masters(n);
// relative field vector (slave - master)
rfv = Vector<Real>(it_field[slave]);
rfv -= Vector<Real>(it_field[master]);
// length of normal projection of relative field
const Vector<Real> normal_v = it_normal[n];
rel_normal_field.push_back(rfv.dot(normal_v));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int NTNContact::getNodeIndex(UInt node) const {
AKANTU_DEBUG_IN();
Int slave_i = NTNBaseContact::getNodeIndex(node);
Int master_i = this->masters.find(node);
AKANTU_DEBUG_OUT();
return std::max(slave_i, master_i);
}
/* -------------------------------------------------------------------------- */
void NTNContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNContact [" << std::endl;
NTNBaseContact::printself(stream, indent);
stream << space << " + masters : " << std::endl;
this->masters.printself(stream, indent + 2);
stream << space << " + lumped_boundary_mastres : " << std::endl;
this->lumped_boundary_masters.printself(stream, indent + 2);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::syncArrays(SyncChoice sync_choice) {
AKANTU_DEBUG_IN();
NTNBaseContact::syncArrays(sync_choice);
this->masters.syncElements(sync_choice);
this->lumped_boundary_masters.syncElements(sync_choice);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTNContact::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
/*
#ifdef AKANTU_USE_IOHELPER
const Array<UInt> & nodal_filter = this->slaves.getArray();
#define ADD_FIELD(field_id, field, type) \
internalAddDumpFieldToDumper(dumper_name, \
field_id, \
new DumperIOHelper::NodalField< type, true, \
Array<type>, \
Array<UInt> >(field, 0, 0, &nodal_filter))
*/
if (field_id == "lumped_boundary_master") {
internalAddDumpFieldToDumper(dumper_name, field_id,
std::make_unique<dumpers::NodalField<Real>>(
this->lumped_boundary_masters.getArray()));
} else {
NTNBaseContact::addDumpFieldToDumper(dumper_name, field_id);
}
/*
#undef ADD_FIELD
#endif
*/
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
index dcd3beb69..39f69c8c3 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_contact.hh
@@ -1,165 +1,167 @@
/**
* @file ntn_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief contact for node to node discretization
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_CONTACT_HH_
#define AST_NTN_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTNContact : public NTNBaseContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNContact(SolidMechanicsModel & model, const ID & id = "contact");
~NTNContact() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// add surface pair and pair nodes according to the surface normal
void addSurfacePair(const ID & slave, const ID & master,
UInt surface_normal_dir);
/// fills the pairs vector with interface node pairs (*,0)=slaves,
/// (*,1)=masters
static void pairInterfaceNodes(const ElementGroup & slave_boundary,
const ElementGroup & master_boundary,
UInt surface_normal_dir, const Mesh & mesh,
Array<UInt> & pairs);
// add node pairs from a list with pairs(*,0)=slaves and pairs(*,1)=masters
void addNodePairs(const Array<UInt> & pairs);
/// add node pair
void addSplitNode(UInt slave, UInt master) override;
/// update (compute the normals on the master nodes)
void updateNormals() override;
/// update the lumped boundary B matrix
void updateLumpedBoundary() override;
/// update the impedance matrix
void updateImpedance() override;
/// impose the normal contact force
void applyContactPressure() override;
/// dump restart file
void dumpRestart(const std::string & file_name) const override;
/// read restart file
void readRestart(const std::string & file_name) override;
/// compute the normal gap
void computeNormalGap(Array<Real> & gap) const override {
this->computeRelativeNormalField(this->model.getCurrentPosition(), gap);
};
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const override;
/// compute relative tangential field (complet array)
/// relative to master nodes
void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const override;
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
protected:
/// synchronize arrays
void syncArrays(SyncChoice sync_choice) override;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) override;
// virtual void addDumpFieldVector(const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Masters, masters, const SynchronizedArray<UInt> &)
AKANTU_GET_MACRO(LumpedBoundaryMasters, lumped_boundary_masters,
const SynchronizedArray<Real> &)
/// get interface node pairs (*,0) are slaves, (*,1) are masters
void getNodePairs(Array<UInt> & pairs) const;
/// get index of node in either slaves or masters array
/// if node is in neither of them, return -1
Int getNodeIndex(UInt node) const override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of master nodes
SynchronizedArray<UInt> masters;
/// lumped boundary of master nodes
SynchronizedArray<Real> lumped_boundary_masters;
// element list for dump and lumped_boundary
ElementTypeMapArray<UInt> master_elements;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntn_contact_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTNContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTN_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
index a5f43b29a..58de04336 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction.hh
@@ -1,98 +1,100 @@
/**
* @file ntn_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of friction for node to node contact
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTN_FRICTION_HH_
#define AST_NTN_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw = NTNFricLawCoulomb,
class Regularisation = NTNFricRegNoRegularisation>
class NTNFriction : public FrictionLaw<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTNFriction(NTNBaseContact & contact, const ID & id = "friction");
virtual ~NTNFriction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// apply the friction force
virtual void applyFrictionTraction();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
// virtual void addDumpFieldToDumper(const std::string & dumper_name,
// const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <template <class> class FrictionLaw, class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTNFriction<FrictionLaw, Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntn_friction_tmpl.hh"
#endif /* AST_NTN_FRICTION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh
index af48546d3..c2b3c46d6 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_friction_tmpl.hh
@@ -1,95 +1,97 @@
/**
* @file ntn_friction_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Wed Oct 17 2018
*
- * @brief
+ * @brief base class for ntn and ntrf friction (template functions implementation)
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw, class Regularisation>
NTNFriction<FrictionLaw, Regularisation>::NTNFriction(
NTNBaseContact & contact, const ID & id)
: FrictionLaw<Regularisation>(contact, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw, class Regularisation>
void NTNFriction<FrictionLaw, Regularisation>::applyFrictionTraction() {
AKANTU_DEBUG_IN();
NTNContact & ntn_contact = dynamic_cast<NTNContact &>(this->contact);
SolidMechanicsModel & model = ntn_contact.getModel();
Array<Real> & residual = model.getInternalForce();
UInt dim = model.getSpatialDimension();
const SynchronizedArray<UInt> & masters = ntn_contact.getMasters();
const SynchronizedArray<UInt> & slaves = ntn_contact.getSlaves();
const SynchronizedArray<Real> & l_boundary_slaves =
ntn_contact.getLumpedBoundarySlaves();
const SynchronizedArray<Real> & l_boundary_masters =
ntn_contact.getLumpedBoundaryMasters();
UInt nb_contact_nodes = ntn_contact.getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt master = masters(n);
UInt slave = slaves(n);
for (UInt d = 0; d < dim; ++d) {
residual(master, d) +=
l_boundary_masters(n) * this->friction_traction(n, d);
residual(slave, d) -=
l_boundary_slaves(n) * this->friction_traction(n, d);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw, class Regularisation>
void NTNFriction<FrictionLaw, Regularisation>::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTNFriction [" << std::endl;
FrictionLaw<Regularisation>::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.cc
index b49f8de65..710905418 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.cc
@@ -1,144 +1,155 @@
/**
* @file ntn_initiation_function.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Tue Feb 20 2018
+ * @date last modification: Wed Oct 17 2018
*
* @brief implementation of initializing ntn and ntrf friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_initiation_function.hh"
#include "mIIasym_contact.hh"
#include "ntn_friction.hh"
#include "ntrf_friction.hh"
// friction regularisations
#include "ntn_fricreg_rubin_ampuero.hh"
#include "ntn_fricreg_simplified_prakash_clifton.hh"
// friction laws
#include "ntn_friclaw_linear_cohesive.hh"
#include "ntn_friclaw_linear_slip_weakening.hh"
#include "ntn_friclaw_linear_slip_weakening_no_healing.hh"
#include "aka_factory.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
std::unique_ptr<NTNBaseFriction>
initializeNTNFriction(NTNBaseContact & contact) {
AKANTU_DEBUG_IN();
auto sub_sect = getStaticParser().getSubSections(ParserType::_friction);
auto it = sub_sect.first;
const ParserSection & section = *it;
std::string friction_law = section.getName();
std::string friction_reg = section.getOption("no_regularisation");
std::unique_ptr<NTNBaseFriction> friction =
initializeNTNFriction(contact, friction_law, friction_reg);
friction->parseSection(section);
if (++it != sub_sect.second) {
AKANTU_DEBUG_WARNING("There were several friction sections in input file. "
<< "Only first one was used and all others ignored.");
}
AKANTU_DEBUG_OUT();
return friction;
}
namespace {
using NTNFactory =
Factory<NTNBaseFriction, std::tuple<bool, ID, ID>, NTNBaseContact &>;
// std::ostream & operator<<(std::ostream & stream,
// const std::tuple<bool, ID, ID> & tuple) {
// stream << "[" << std::get<0>(tuple) << ", " << std::get<1>(tuple) << ", "
// << std::get<2>(tuple) << ", "
// << "]" << std::endl;
// return stream;
// }
template <bool is_ntn, template <class> class FrictionLaw, class FrictionReg>
bool registerFriction(const ID & friction_law, const ID & friction_reg) {
NTNFactory::getInstance().registerAllocator(
std::make_tuple(is_ntn, friction_law, friction_reg),
[](NTNBaseContact & contact) -> std::unique_ptr<NTNBaseFriction> {
return std::make_unique<
std::conditional_t<is_ntn, NTNFriction<FrictionLaw, FrictionReg>,
NTRFFriction<FrictionLaw, FrictionReg>>>(
contact);
});
return true;
}
template <template <class> class FrictionLaw, class FrictionReg>
bool registerFrictionNTNandNTRF(const ID & friction_law,
const ID & friction_reg) {
registerFriction<true, FrictionLaw, FrictionReg>(friction_law,
friction_reg);
registerFriction<false, FrictionLaw, FrictionReg>(friction_law,
friction_reg);
return true;
}
template <template <class> class FrictionLaw>
bool registerFrictionRegs(const ID & friction_law) {
registerFrictionNTNandNTRF<FrictionLaw, NTNFricRegRubinAmpuero>(
friction_law, "no_regularisation");
registerFrictionNTNandNTRF<FrictionLaw, NTNFricRegRubinAmpuero>(
friction_law, "rubin_ampuero");
registerFrictionNTNandNTRF<FrictionLaw, NTNFricRegSimplifiedPrakashClifton>(
friction_law, "simplified_prakash_clifton");
return true;
}
bool registerFrictionLaws() {
registerFrictionRegs<NTNFricLawCoulomb>("coulomb");
registerFrictionRegs<NTNFricLawLinearSlipWeakening>(
"linear_slip_weakening");
registerFrictionRegs<NTNFricLawLinearSlipWeakeningNoHealing>(
"linear_slip_weakening_no_healing");
registerFrictionRegs<NTNFricLawLinearCohesive>("linear_cohesive");
return true;
}
static bool _ = registerFrictionLaws();
} // namespace
/* -------------------------------------------------------------------------- */
std::unique_ptr<NTNBaseFriction>
initializeNTNFriction(NTNBaseContact & contact,
const std::string & friction_law,
const std::string & friction_reg) {
bool is_ntn_contact = contact.isNTNContact();
return NTNFactory::getInstance().allocate(
std::make_tuple(is_ntn_contact, friction_law, friction_reg), contact);
}
} // namespace akantu
+
+namespace std {
+inline ostream & operator<<(ostream & stream,
+ const tuple<bool, string, string> & _this) {
+ stream << "<" << get<0>(_this) << ", " << get<1>(_this) << ", "
+ << get<2>(_this) << ">";
+ return stream;
+}
+} // namespace std
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.hh
index 53b57f6ef..9cdc4e0b4 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntn_initiation_function.hh
@@ -1,46 +1,48 @@
/**
* @file ntn_initiation_function.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Wed Oct 17 2018
*
* @brief initiation ntn and ntrf friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_friction.hh"
#include "ntrf_contact.hh"
#include "parameter_reader.hh"
namespace akantu {
std::unique_ptr<NTNBaseFriction>
initializeNTNFriction(NTNBaseContact & contact);
std::unique_ptr<NTNBaseFriction>
initializeNTNFriction(NTNBaseContact & contact,
const std::string & friction_law,
const std::string & friction_reg);
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
index c1ff7288f..c37967de4 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.cc
@@ -1,320 +1,322 @@
/**
* @file ntrf_contact.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Tue May 21 2019
*
- * @brief
+ * @brief contact for node to rigid flat interface
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// simtools
#include "ntrf_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
NTRFContact::NTRFContact(SolidMechanicsModel & model, const ID & id)
: NTNBaseContact(model, id),
reference_point(model.getSpatialDimension()),
normal(model.getSpatialDimension()) {
AKANTU_DEBUG_IN();
is_ntn_contact = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::setReferencePoint(Real x, Real y, Real z) {
AKANTU_DEBUG_IN();
Real coord[3];
coord[0] = x;
coord[1] = y;
coord[2] = z;
UInt dim = this->model.getSpatialDimension();
for (UInt d = 0; d < dim; ++d)
this->reference_point(d) = coord[d];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::setNormal(Real x, Real y, Real z) {
AKANTU_DEBUG_IN();
UInt dim = this->model.getSpatialDimension();
Real coord[3];
coord[0] = x;
coord[1] = y;
coord[2] = z;
for (UInt d = 0; d < dim; ++d)
this->normal(d) = coord[d];
this->normal.normalize();
this->updateNormals();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::addSurface(const ID & surf) {
AKANTU_DEBUG_IN();
const Mesh & mesh_ref = this->model.getMesh();
try {
const ElementGroup & boundary = mesh_ref.getElementGroup(surf);
this->contact_surfaces.insert(&boundary);
// find slave nodes
for (auto && node : boundary.getNodeGroup().getNodes()) {
if (not mesh_ref.isPeriodicSlave(node)) {
this->addSplitNode(node);
}
}
} catch (debug::Exception & e) {
AKANTU_DEBUG_INFO("NTRFContact addSurface did not found subboundary "
<< surf
<< " and ignored it. Other procs might have it :)");
}
// synchronize with depending nodes
findBoundaryElements(this->slaves.getArray(), this->slave_elements);
updateInternalData();
syncArrays(_added);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::addNodes(Array<UInt> & nodes) {
AKANTU_DEBUG_IN();
UInt nb_nodes = nodes.size();
UInt nb_compo = nodes.getNbComponent();
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt c = 0; c < nb_compo; ++c) {
this->addSplitNode(nodes(n, c));
}
}
// synchronize with depending nodes
findBoundaryElements(this->slaves.getArray(), this->slave_elements);
updateInternalData();
syncArrays(_added);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::updateNormals() {
AKANTU_DEBUG_IN();
// normal is the same for all slaves
this->normals.set(this->normal);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::updateImpedance() {
AKANTU_DEBUG_IN();
UInt nb_contact_nodes = getNbContactNodes();
Real delta_t = this->model.getTimeStep();
AKANTU_DEBUG_ASSERT(delta_t != NAN,
"Time step is NAN. Have you set it already?");
const Array<Real> & mass = this->model.getMass();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
UInt slave = this->slaves(n);
Real imp = this->lumped_boundary_slaves(n) / mass(slave);
imp = 2 / delta_t / imp;
this->impedance(n) = imp;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::computeRelativeTangentialField(
const Array<Real> & field, Array<Real> & rel_tang_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_tang_field.resize(0);
UInt dim = this->model.getSpatialDimension();
Array<Real>::const_iterator<Vector<Real>> it_field = field.begin(dim);
Array<Real>::const_iterator<Vector<Real>> it_normal =
this->normals.getArray().begin(dim);
Vector<Real> rfv(dim);
Vector<Real> np_rfv(dim);
UInt nb_contact_nodes = this->slaves.size();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt node = this->slaves(n);
// relative field vector
rfv = it_field[node];
;
// normal projection of relative field
const Vector<Real> & normal_v = it_normal[n];
np_rfv = normal_v;
np_rfv *= rfv.dot(normal_v);
// subtract normal projection from relative field to get the tangential
// projection
rfv -= np_rfv;
rel_tang_field.push_back(rfv);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::computeNormalGap(Array<Real> & gap) const {
AKANTU_DEBUG_IN();
gap.resize(0);
UInt dim = this->model.getSpatialDimension();
Array<Real>::const_iterator<Vector<Real>> it_cur_pos =
this->model.getCurrentPosition().begin(dim);
Array<Real>::const_iterator<Vector<Real>> it_normal =
this->normals.getArray().begin(dim);
Vector<Real> gap_v(dim);
UInt nb_contact_nodes = this->getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt node = this->slaves(n);
// gap vector
gap_v = it_cur_pos[node];
gap_v -= this->reference_point;
// length of normal projection of gap vector
const Vector<Real> & normal_v = it_normal[n];
gap.push_back(gap_v.dot(normal_v));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::computeRelativeNormalField(
const Array<Real> & field, Array<Real> & rel_normal_field) const {
AKANTU_DEBUG_IN();
// resize arrays to zero
rel_normal_field.resize(0);
UInt dim = this->model.getSpatialDimension();
Array<Real>::const_iterator<Vector<Real>> it_field = field.begin(dim);
Array<Real>::const_iterator<Vector<Real>> it_normal =
this->normals.getArray().begin(dim);
UInt nb_contact_nodes = this->getNbContactNodes();
for (UInt n = 0; n < nb_contact_nodes; ++n) {
// nodes
UInt node = this->slaves(n);
const Vector<Real> & field_v = it_field[node];
const Vector<Real> & normal_v = it_normal[n];
rel_normal_field.push_back(field_v.dot(normal_v));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::printself(std::ostream & stream, int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTRFContact [" << std::endl;
NTNBaseContact::printself(stream, indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NTRFContact::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
/*
#ifdef AKANTU_USE_IOHELPER
const Array<UInt> & nodal_filter = this->slaves.getArray();
#define ADD_FIELD(field_id, field, type) \
internalAddDumpFieldToDumper(dumper_name, \
field_id, \
new DumperIOHelper::NodalField< type, true, \
Array<type>, \
Array<UInt> >(field, 0, 0, &nodal_filter))
*/
/*
if(field_id == "displacement") {
ADD_FIELD(field_id, this->model.getDisplacement(), Real);
}
else if(field_id == "contact_pressure") {
internalAddDumpFieldToDumper(dumper_name,
field_id,
new
DumperIOHelper::NodalField<Real>(this->contact_pressure.getArray()));
}
else {*/
NTNBaseContact::addDumpFieldToDumper(dumper_name, field_id);
//}
/*
#undef ADD_FIELD
#endif
*/
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
index bd60a8761..c66b79f90 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_contact.hh
@@ -1,125 +1,127 @@
/**
* @file ntrf_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief contact for node to rigid flat interface
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTRF_CONTACT_HH_
#define AST_NTRF_CONTACT_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_base_contact.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
class NTRFContact : public NTNBaseContact {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTRFContact(SolidMechanicsModel & model, const ID & id = "contact");
~NTRFContact() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void setReferencePoint(Real x = 0., Real y = 0., Real z = 0.);
void setNormal(Real x = 1., Real y = 0., Real z = 0.);
/// add surface and nodes according to the surface normal
void addSurface(const ID & surf);
// add nodes from a list
void addNodes(Array<UInt> & nodes);
/// update (copy the normal to all normals)
void updateNormals() override;
/// update the impedance matrix
void updateImpedance() override;
/// compute the normal gap
void computeNormalGap(Array<Real> & gap) const override;
/// compute relative normal field (only value that has to be multiplied with
/// the normal)
/// relative to master nodes
void
computeRelativeNormalField(const Array<Real> & field,
Array<Real> & rel_normal_field) const override;
/// compute relative tangential field (complet array)
/// relative to master nodes
void
computeRelativeTangentialField(const Array<Real> & field,
Array<Real> & rel_tang_field) const override;
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) override;
// virtual void addDumpFieldVector(const std::string & field_id);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// reference point for rigid flat surface
Vector<Real> reference_point;
/// outpointing normal of rigid flat surface
Vector<Real> normal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "ntrf_contact_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NTRFContact & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AST_NTRF_CONTACT_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
index 55492b58b..d9bfbd10c 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction.hh
@@ -1,90 +1,92 @@
/**
* @file ntrf_friction.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief friction for node to rigid flat interface
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AST_NTRF_FRICTION_HH_
#define AST_NTRF_FRICTION_HH_
/* -------------------------------------------------------------------------- */
// simtools
#include "ntn_friclaw_coulomb.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw = NTNFricLawCoulomb,
class Regularisation = NTNFricRegNoRegularisation>
class NTRFFriction : public FrictionLaw<Regularisation> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NTRFFriction(NTNBaseContact & contact, const ID & id = "friction");
virtual ~NTRFFriction(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Dumpable */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operato
template <template <class> class FrictionLaw, class Regularisation>
inline std::ostream &
operator<<(std::ostream & stream,
const NTRFFriction<FrictionLaw, Regularisation> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "ntrf_friction_tmpl.hh"
#endif /* AST_NTRF_FRICTION_HH_ */
diff --git a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh
index 21debe0f7..00d8269bd 100644
--- a/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh
+++ b/extra_packages/traction-at-split-node-contact/src/ntn_contact/ntrf_friction_tmpl.hh
@@ -1,104 +1,106 @@
/**
* @file ntrf_friction_tmpl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Wed Oct 17 2018
*
* @brief implementation of node to rigid flat interface friction
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
//#include "ntrf_friction.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw, class Regularisation>
NTRFFriction<FrictionLaw, Regularisation>::NTRFFriction(
NTNBaseContact & contact, const ID & id)
: FrictionLaw<Regularisation>(contact, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <class> class FrictionLaw, class Regularisation>
void NTRFFriction<FrictionLaw, Regularisation>::printself(std::ostream & stream,
int indent) const {
AKANTU_DEBUG_IN();
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "NTRFFriction [" << std::endl;
FrictionLaw<Regularisation>::printself(stream, ++indent);
stream << space << "]" << std::endl;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/*
void NTRFFriction::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_IOHELPER
// const SynchronizedArray<UInt> * nodal_filter =
&(this->contact.getSlaves());
if(field_id == "is_sticking") {
this->internalAddDumpFieldToDumper(dumper_name,
field_id,
new
DumperIOHelper::NodalField<bool>(this->is_sticking.getArray()));
}
else if(field_id == "frictional_strength") {
this->internalAddDumpFieldToDumper(dumper_name,
field_id,
new
DumperIOHelper::NodalField<Real>(this->frictional_strength.getArray()));
}
else if(field_id == "friction_traction") {
this->internalAddDumpFieldToDumper(dumper_name,
field_id,
new
DumperIOHelper::NodalField<Real>(this->friction_traction.getArray()));
}
else if(field_id == "slip") {
this->internalAddDumpFieldToDumper(dumper_name,
field_id,
new DumperIOHelper::NodalField<Real>(this->slip.getArray()));
}
else {
this->contact.addDumpFieldToDumper(dumper_name, field_id);
}
#endif
AKANTU_DEBUG_OUT();
}
*/
} // namespace akantu
diff --git a/extra_packages/traction-at-split-node-contact/src/tasn_contact.hh b/extra_packages/traction-at-split-node-contact/src/tasn_contact.hh
index 42b0563fb..c6a5230b1 100644
--- a/extra_packages/traction-at-split-node-contact/src/tasn_contact.hh
+++ b/extra_packages/traction-at-split-node-contact/src/tasn_contact.hh
@@ -1,67 +1,69 @@
/**
* @file tasn_contact.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Dec 02 2014
- * @date last modification: Fri Feb 23 2018
+ * @date creation: Fri Mar 16 2018
+ * @date last modification: Fri Mar 16 2018
*
- * @brief
+ * @brief traction at split node main include
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
// ast common
#include "manual_restart.hh"
#include "parameter_reader.hh"
#include "synchronized_array.hh"
// functions
#include "boundary_functions.hh"
#include "node_filter.hh"
// boundary conditions
#include "force_based_dirichlet.hh"
#include "inclined_flat_dirichlet.hh"
#include "spring_bc.hh"
// ntn/ntrf contact
#include "mIIasym_contact.hh"
#include "ntn_base_contact.hh"
#include "ntn_contact.hh"
#include "ntrf_contact.hh"
// ntn/ntrf friction
#include "ntn_base_friction.hh"
#include "ntn_friction.hh"
#include "ntrf_friction.hh"
// friction regularisations
#include "ntn_fricreg_no_regularisation.hh"
#include "ntn_fricreg_rubin_ampuero.hh"
#include "ntn_fricreg_simplified_prakash_clifton.hh"
// friction laws
#include "ntn_friclaw_coulomb.hh"
#include "ntn_friclaw_linear_cohesive.hh"
#include "ntn_friclaw_linear_slip_weakening.hh"
#include "ntn_friclaw_linear_slip_weakening_no_healing.hh"
// initiation of friction
#include "ntn_initiation_function.hh"
diff --git a/packages/akantu_iterators.cmake b/packages/akantu_iterators.cmake
index 819d47be4..dd9cf6917 100644
--- a/packages/akantu_iterators.cmake
+++ b/packages/akantu_iterators.cmake
@@ -1,36 +1,38 @@
#===============================================================================
# @file akantu_iterators.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Mon Nov 21 2011
-# @date last modification: Mon Jan 18 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Wed Nov 27 2019
#
# @brief package description for akantu_iterators
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(akantu_iterators EXTERNAL
DESCRIPTION "Akantu's iterators hearder library"
SYSTEM OFF third-party/cmake/akantu_iterators.cmake
DEFAULT ON
)
diff --git a/packages/blackdynamite.cmake b/packages/blackdynamite.cmake
deleted file mode 100644
index 00f5cd853..000000000
--- a/packages/blackdynamite.cmake
+++ /dev/null
@@ -1,48 +0,0 @@
-#===============================================================================
-# @file blackdynamite.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Fri Mar 15 2013
-# @date last modification: Mon Jan 18 2016
-#
-# @brief package description for BlackDynamite support
-#
-# @section LICENSE
-#
-# Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-package_declare(BlackDynamite EXTERNAL
- DESCRIPTION "Use BlackDynamite library"
- SYSTEM OFF third-party/cmake/blackdynamite.cmake
- EXTRA_PACKAGE_OPTIONS FOUND BlackDynamite_FOUND)
-
-set(_version master)
-
-package_add_third_party_script_variable(BlackDynamite
- BLACKDYNAMITE_VERSION "${_version}")
-package_add_third_party_script_variable(BlackDynamite
- BLACKDYNAMITE_GIT "git@lsmssrv1.epfl.ch:blackdynamite.git")
-package_add_third_party_script_variable(BlackDynamite
- BLACKDYNAMITE_ARCHIVE "blackdynamite-${_version}.tar.gz")
-
-package_declare_extra_files_to_package(BlackDynamite
- PROJECT third-party/cmake/blackdynamite.cmake
- )
diff --git a/packages/blas.cmake b/packages/blas.cmake
index a41c05259..9056f6ea8 100644
--- a/packages/blas.cmake
+++ b/packages/blas.cmake
@@ -1,93 +1,85 @@
#===============================================================================
# @file blas.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Thu May 11 2017
#
# @brief package description for blas support
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(BLAS EXTERNAL
DESCRIPTION "Use BLAS for arithmetic operations"
EXTRA_PACKAGE_OPTIONS LANGUAGE Fortran
SYSTEM ON third-party/cmake/blas.cmake)
package_add_third_party_script_variable(BLAS BLAS_ARCHIVE "http://www.netlib.org/blas/blas-3.5.0.tgz")
package_add_third_party_script_variable(BLAS BLAS_VERSION "3.5.0")
set(_default_blas $ENV{BLA_VENDOR})
if(NOT _default_blas)
set(_default_blas All)
endif()
set(AKANTU_USE_BLAS_VENDOR "${_default_blas}" CACHE STRING "Version of blas to use")
mark_as_advanced(AKANTU_USE_BLAS_VENDOR)
set_property(CACHE AKANTU_USE_BLAS_VENDOR PROPERTY STRINGS
All
ACML
ACML_GPU
ACML_MP
ATLAS
Apple
CXML
DXML
Generic
Goto
IBMESSL
Intel
Intel10_32
Intel10_64lp
Intel10_64lp_seq
NAS
OpenBLAS
PhiPACK
SCSL
SGIMATH
SunPerf
)
set(ENV{BLA_VENDOR} ${AKANTU_USE_BLAS_VENDOR})
if(BLAS_mkl_core_LIBRARY)
set(AKANTU_USE_BLAS_MKL CACHE INTERNAL "" FORCE)
endif()
-package_declare_documentation(BLAS
- "This package provides access to a BLAS implementation."
- ""
- "Under Ubuntu (14.04 LTS), the installation can be performed using the following command:"
- "\\begin{command}"
- " > sudo apt-get install libatlas-base-dev"
- "\\end{command}"
- )
-
package_set_package_system_dependency(BLAS deb libblas3)
package_set_package_system_dependency(BLAS deb-src libblas3)
package_declare_extra_files_to_package(BLAS
PROJECT
third-party/cmake/blas.cmake
third-party/blas_3.5.0_make.inc.cmake
)
diff --git a/packages/boost.cmake b/packages/boost.cmake
index 67738520a..a5c2fe791 100644
--- a/packages/boost.cmake
+++ b/packages/boost.cmake
@@ -1,68 +1,59 @@
#===============================================================================
# @file boost.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Fri Mar 16 2018
#
# @brief package handling the dependencies to boost
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
set(Boost_NO_BOOST_CMAKE ON CACHE BOOL "" FORCE)
package_declare(Boost EXTERNAL
NOT_OPTIONAL
DESCRIPTION "Package handling boost components"
EXTRA_PACKAGE_OPTIONS PREFIX Boost
)
mask_package_options(Boost)
mark_as_advanced(AKANTU_USE_BOOST)
package_on_enabled_script(Boost
"if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER \"4.8\")
set(_boost_version \${Boost_MAJOR_VERSION}.\${Boost_MINOR_VERSION})
if(_boost_version VERSION_LESS 1.58 AND _boost_version VERSION_GREATER 1.53)
package_set_compile_flags(Boost CXX -DBOOST_SPIRIT_USE_PHOENIX_V3)
else()
package_unset_compile_flags(Boost CXX)
endif()
endif()
")
-
-package_declare_documentation(Boost
- "Akantu uses Boost header only for preprocessor and Spirit"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libboost"
- "\\end{command}"
- ""
-)
-
package_set_package_system_dependency(Boost deb-src libboost-dev)
# only build dependency
# package_set_package_system_dependency(Boost deb libboost)
# package_set_package_system_dependency(Boost rmp boost)
diff --git a/packages/cgal.cmake b/packages/cgal.cmake
index 80d0f5c80..4c9770900 100644
--- a/packages/cgal.cmake
+++ b/packages/cgal.cmake
@@ -1,85 +1,82 @@
#===============================================================================
# @file cgal.cmake
#
+# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
# @author Lucas Frerot <lucas.frerot@epfl.ch>
# @author Clement Roux <clement.roux@epfl.ch>
#
-# @date creation: Thu Feb 19 2015
-# @date last modification: Wed Jan 20 2016
+# @date creation: Fri Sep 03 2010
+# @date last modification: Tue Sep 29 2020
#
# @brief package description for CGAL
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(CGAL EXTERNAL
DESCRIPTION "Add CGAL support in akantu"
)
-package_is_activated(CGAL _is_activated)
package_on_enabled_script(CGAL
"
set(CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE TRUE
CACHE BOOL \"Tells CGAL cmake to shut up\")
set(CGAL_DISABLE_ROUNDING_MATH_CHECK ON
CACHE BOOL \"Disable rounding math check in CGAL. This permits Valgrind to run.\")
mark_as_advanced(
CGAL_DO_NOT_WARN_ABOUT_CMAKE_BUILD_TYPE
CGAL_DISABLE_ROUNDING_MATH_CHECK
)
")
package_declare_sources(CGAL
geometry/mesh_geom_common.hh
geometry/mesh_geom_abstract.hh
geometry/mesh_geom_factory.hh
geometry/mesh_geom_factory_tmpl.hh
geometry/mesh_abstract_intersector.hh
geometry/mesh_abstract_intersector_tmpl.hh
geometry/mesh_geom_intersector.hh
geometry/mesh_geom_intersector_tmpl.hh
geometry/mesh_segment_intersector.hh
geometry/mesh_segment_intersector_tmpl.hh
geometry/mesh_sphere_intersector.hh
geometry/mesh_sphere_intersector_tmpl.hh
geometry/tree_type_helper.hh
geometry/geom_helper_functions.hh
geometry/aabb_primitives/triangle.hh
geometry/aabb_primitives/line_arc.hh
geometry/aabb_primitives/tetrahedron.hh
geometry/aabb_primitives/aabb_primitive.hh
geometry/aabb_primitives/aabb_primitive.cc
)
-package_declare_documentation(CGAL
- "This package allows the use of CGAL's geometry algorithms in Akantu. Note that it needs a version of CGAL $\\geq$ 4.5 and needs activation of boost's system component."
- ""
- "CGAL checks with an assertion that the compilation flag \\shellcode{-frounding-math} is activated, which forbids the use of Valgrind on any code compilated with the package."
- )
-
package_set_package_system_dependency(CGAL deb-src "libcgal-dev >= 4.5")
diff --git a/packages/cohesive_element.cmake b/packages/cohesive_element.cmake
index 4fa27db0b..38c92873a 100644
--- a/packages/cohesive_element.cmake
+++ b/packages/cohesive_element.cmake
@@ -1,137 +1,116 @@
#===============================================================================
# @file cohesive_element.cmake
#
# @author Mauro Corrado <mauro.corrado@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
# @date creation: Tue Oct 16 2012
-# @date last modification: Tue Jan 12 2016
+# @date last modification: Thu Mar 11 2021
#
# @brief package description for cohesive elements
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(cohesive_element
DESCRIPTION "Use cohesive_element package of Akantu"
DEPENDS lapack solid_mechanics)
package_declare_sources(cohesive_element
fe_engine/cohesive_element.hh
fe_engine/fe_engine_template_cohesive.cc
fe_engine/shape_cohesive.hh
fe_engine/shape_cohesive_inline_impl.hh
mesh_utils/cohesive_element_inserter.cc
mesh_utils/cohesive_element_inserter.hh
mesh_utils/cohesive_element_inserter_inline_impl.hh
mesh_utils/cohesive_element_inserter_parallel.cc
mesh_utils/cohesive_element_inserter_helper.cc
mesh_utils/cohesive_element_inserter_helper.hh
model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.hh
model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
)
package_declare_elements(cohesive_element
ELEMENT_TYPES
_cohesive_1d_2
_cohesive_2d_4
_cohesive_2d_6
_cohesive_3d_12
_cohesive_3d_16
_cohesive_3d_6
_cohesive_3d_8
KIND cohesive
GEOMETRICAL_TYPES
_gt_cohesive_1d_2
_gt_cohesive_2d_4
_gt_cohesive_2d_6
_gt_cohesive_3d_12
_gt_cohesive_3d_16
_gt_cohesive_3d_6
_gt_cohesive_3d_8
FE_ENGINE_LISTS
compute_normals_on_integration_points
contains
get_shapes_derivatives
gradient_on_integration_points
interpolate_on_integration_points
inverse_map
lagrange_base
)
package_declare_material_infos(cohesive_element
LIST AKANTU_COHESIVE_MATERIAL_LIST
INCLUDE material_cohesive_includes.hh
)
-
-
-package_declare_documentation_files(cohesive_element
- manual-cohesive_elements.tex
- manual-cohesive_elements_insertion.tex
- manual-cohesive_laws.tex
- manual-appendix-materials-cohesive.tex
-
- figures/cohesive2d.pdf
- figures/cohesive_exponential.pdf
- figures/linear_cohesive_law.pdf
- figures/bilinear_cohesive_law.pdf
- )
-
-package_declare_documentation(cohesive_element
- "This package activates the cohesive elements engine within Akantu."
- "It depends on:"
- "\\begin{itemize}"
- " \\item A fortran compiler."
- " \\item An implementation of BLAS/LAPACK."
- "\\end{itemize}"
- )
diff --git a/packages/contact_mechanics.cmake b/packages/contact_mechanics.cmake
index f15c8affd..98609cf76 100644
--- a/packages/contact_mechanics.cmake
+++ b/packages/contact_mechanics.cmake
@@ -1,73 +1,75 @@
#===============================================================================
# @file contact_mechanics.cmake
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Sun Oct 21 2018
-# @date last modification: Sun Oct 21 2018
+# @date creation: Fri Sep 03 2010
+# @date last modification: Wed Jun 23 2021
#
# @brief package description for contact mechanics
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(contact_mechanics
DEPENDS model_couplers cohesive_element
DESCRIPTION "Use Contact Mechanics package of Akantu")
package_declare_sources(contact_mechanics
model/contact_mechanics/contact_mechanics_model.hh
model/contact_mechanics/contact_mechanics_model.cc
model/contact_mechanics/contact_detector.hh
model/contact_mechanics/contact_detector.cc
model/contact_mechanics/contact_detector_inline_impl.cc
model/contact_mechanics/contact_element.hh
model/contact_mechanics/geometry_utils.hh
model/contact_mechanics/geometry_utils.cc
model/contact_mechanics/geometry_utils_inline_impl.cc
model/contact_mechanics/resolution.hh
model/contact_mechanics/resolution.cc
model/contact_mechanics/resolution_utils.hh
model/contact_mechanics/resolution_utils.cc
model/contact_mechanics/resolutions/resolution_penalty.hh
model/contact_mechanics/resolutions/resolution_penalty.cc
model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh
model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc
model/contact_mechanics/surface_selector.hh
model/contact_mechanics/surface_selector.cc
model/model_couplers/coupler_solid_contact.hh
model/model_couplers/coupler_solid_contact_tmpl.hh
model/model_couplers/coupler_solid_contact.cc
model/model_couplers/coupler_solid_cohesive_contact.hh
model/model_couplers/coupler_solid_cohesive_contact.cc
model/model_couplers/cohesive_contact_solvercallback.hh
model/model_couplers/cohesive_contact_solvercallback.cc
)
package_declare_documentation_files(contact_mechanics
manual-contactmechanicsmodel.tex
manual-contact-detector.tex
)
package_declare_documentation(contact_mechanics
"This package activates the contact mechanics model")
diff --git a/packages/core.cmake b/packages/core.cmake
index ca7272e73..10660f10e 100644
--- a/packages/core.cmake
+++ b/packages/core.cmake
@@ -1,528 +1,433 @@
#===============================================================================
# @file core.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri Apr 09 2021
#
# @brief package description for core
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(core NOT_OPTIONAL
DESCRIPTION "core package for Akantu"
FEATURES_PUBLIC cxx_strong_enums cxx_defaulted_functions
cxx_deleted_functions cxx_auto_type cxx_decltype_auto
FEATURES_PRIVATE cxx_lambdas cxx_nullptr cxx_range_for
- cxx_delegating_constructors
- DEPENDS INTERFACE akantu_iterators Boost)
+ cxx_delegating_constructors
+ DEPENDS INTERFACE akantu_iterators Boost
+ )
+
+if (CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+ package_set_compile_flags(core "-Wall -Wextra -pedantic")
+else()
+ package_set_compile_flags(core "-Wall")
+endif()
package_declare_sources(core
common/aka_array.cc
common/aka_array.hh
common/aka_array_filter.hh
common/aka_array_tmpl.hh
common/aka_array_printer.hh
common/aka_bbox.hh
common/aka_blas_lapack.hh
common/aka_circular_array.hh
common/aka_circular_array_inline_impl.hh
common/aka_common.cc
common/aka_common.hh
common/aka_common_inline_impl.hh
common/aka_csr.hh
common/aka_element_classes_info_inline_impl.hh
common/aka_enum_macros.hh
common/aka_error.cc
common/aka_error.hh
common/aka_event_handler_manager.hh
common/aka_extern.cc
common/aka_factory.hh
common/aka_fwd.hh
common/aka_grid_dynamic.hh
common/aka_math.cc
common/aka_math.hh
common/aka_math_tmpl.hh
common/aka_named_argument.hh
common/aka_random_generator.hh
common/aka_safe_enum.hh
- common/aka_typelist.hh
common/aka_types.hh
- common/aka_visitor.hh
common/aka_voigthelper.hh
common/aka_voigthelper_tmpl.hh
common/aka_voigthelper.cc
common/aka_warning.hh
common/aka_warning_restore.hh
fe_engine/element_class.hh
fe_engine/element_class_helper.hh
fe_engine/element_class_tmpl.hh
fe_engine/element_classes/element_class_hexahedron_8_inline_impl.hh
fe_engine/element_classes/element_class_hexahedron_20_inline_impl.hh
fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
fe_engine/element_classes/element_class_pentahedron_15_inline_impl.hh
fe_engine/element_classes/element_class_point_1_inline_impl.hh
fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh
fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
fe_engine/element_classes/element_class_segment_2_inline_impl.hh
fe_engine/element_classes/element_class_segment_3_inline_impl.hh
fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.hh
fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.hh
fe_engine/element_classes/element_class_triangle_3_inline_impl.hh
fe_engine/element_classes/element_class_triangle_6_inline_impl.hh
fe_engine/element_type_conversion.hh
fe_engine/fe_engine.cc
fe_engine/fe_engine.hh
fe_engine/fe_engine_inline_impl.hh
fe_engine/fe_engine_template.hh
fe_engine/fe_engine_template_tmpl_field.hh
fe_engine/fe_engine_template_tmpl.hh
fe_engine/geometrical_element_property.hh
fe_engine/geometrical_element_property.cc
fe_engine/gauss_integration.cc
fe_engine/gauss_integration_tmpl.hh
fe_engine/integrator.hh
fe_engine/integrator_gauss.hh
fe_engine/integrator_gauss_inline_impl.hh
fe_engine/interpolation_element_tmpl.hh
fe_engine/integration_point.hh
fe_engine/shape_functions.hh
fe_engine/shape_functions.cc
fe_engine/shape_functions_inline_impl.hh
fe_engine/shape_lagrange_base.cc
fe_engine/shape_lagrange_base.hh
fe_engine/shape_lagrange_base_inline_impl.hh
fe_engine/shape_lagrange.hh
fe_engine/shape_lagrange_inline_impl.hh
fe_engine/element.hh
io/dumper/dumpable.hh
io/dumper/dumpable.cc
io/dumper/dumpable_dummy.hh
io/dumper/dumpable_inline_impl.hh
io/dumper/dumper_field.hh
io/dumper/dumper_material_padders.hh
io/dumper/dumper_filtered_connectivity.hh
io/dumper/dumper_element_partition.hh
io/mesh_io.cc
io/mesh_io.hh
io/mesh_io/mesh_io_diana.cc
io/mesh_io/mesh_io_diana.hh
io/mesh_io/mesh_io_msh.cc
io/mesh_io/mesh_io_msh.hh
#io/model_io.cc
#io/model_io.hh
io/parser/algebraic_parser.hh
io/parser/input_file_parser.hh
io/parser/parsable.cc
io/parser/parsable.hh
io/parser/parser.cc
io/parser/parser_real.cc
io/parser/parser_random.cc
io/parser/parser_types.cc
io/parser/parser_input_files.cc
io/parser/parser.hh
io/parser/parser_tmpl.hh
io/parser/parser_grammar_tmpl.hh
io/parser/cppargparse/cppargparse.hh
io/parser/cppargparse/cppargparse.cc
io/parser/cppargparse/cppargparse_tmpl.hh
io/parser/parameter_registry.cc
io/parser/parameter_registry.hh
io/parser/parameter_registry_tmpl.hh
mesh/element_group.cc
mesh/element_group.hh
mesh/element_group_inline_impl.hh
mesh/element_type_map.cc
mesh/element_type_map.hh
mesh/element_type_map_tmpl.hh
mesh/element_type_map_filter.hh
mesh/group_manager.cc
mesh/group_manager.hh
mesh/group_manager_inline_impl.hh
mesh/mesh.cc
mesh/mesh.hh
mesh/mesh_periodic.cc
mesh/mesh_accessor.hh
mesh/mesh_events.hh
mesh/mesh_filter.hh
mesh/mesh_global_data_updater.hh
mesh/mesh_data.cc
mesh/mesh_data.hh
mesh/mesh_data_tmpl.hh
mesh/mesh_inline_impl.hh
mesh/node_group.cc
mesh/node_group.hh
mesh/node_group_inline_impl.hh
mesh/mesh_iterators.hh
mesh_utils/mesh_partition.cc
mesh_utils/mesh_partition.hh
mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
mesh_utils/mesh_partition/mesh_partition_scotch.hh
mesh_utils/mesh_utils_pbc.cc
mesh_utils/mesh_utils.cc
mesh_utils/mesh_utils.hh
mesh_utils/mesh_utils_distribution.cc
mesh_utils/mesh_utils_distribution.hh
mesh_utils/mesh_utils.hh
mesh_utils/mesh_utils_inline_impl.hh
mesh_utils/global_ids_updater.hh
mesh_utils/global_ids_updater.cc
mesh_utils/global_ids_updater_inline_impl.hh
model/common/boundary_condition/boundary_condition.hh
model/common/boundary_condition/boundary_condition_functor.hh
model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
model/common/boundary_condition/boundary_condition_tmpl.hh
model/common/non_local_toolbox/neighborhood_base.hh
model/common/non_local_toolbox/neighborhood_base.cc
model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
model/common/non_local_toolbox/non_local_manager.hh
model/common/non_local_toolbox/non_local_manager.cc
model/common/non_local_toolbox/non_local_manager_inline_impl.hh
model/common/non_local_toolbox/non_local_manager_callback.hh
model/common/non_local_toolbox/non_local_neighborhood_base.hh
model/common/non_local_toolbox/non_local_neighborhood_base.cc
model/common/non_local_toolbox/non_local_neighborhood.hh
model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
model/common/non_local_toolbox/base_weight_function.hh
model/common/non_local_toolbox/base_weight_function_inline_impl.hh
model/common/model_solver.cc
model/common/model_solver.hh
model/common/solver_callback.hh
model/common/solver_callback.cc
model/common/dof_manager/dof_manager.cc
model/common/dof_manager/dof_manager.hh
model/common/dof_manager/dof_manager_default.cc
model/common/dof_manager/dof_manager_default.hh
model/common/dof_manager/dof_manager_default_inline_impl.hh
model/common/dof_manager/dof_manager_inline_impl.hh
model/common/non_linear_solver/non_linear_solver.cc
model/common/non_linear_solver/non_linear_solver.hh
model/common/non_linear_solver/non_linear_solver_default.hh
model/common/non_linear_solver/non_linear_solver_lumped.cc
model/common/non_linear_solver/non_linear_solver_lumped.hh
model/common/time_step_solvers/time_step_solver.hh
model/common/time_step_solvers/time_step_solver.cc
model/common/time_step_solvers/time_step_solver_default.cc
model/common/time_step_solvers/time_step_solver_default.hh
model/common/time_step_solvers/time_step_solver_default_explicit.hh
model/common/integration_scheme/generalized_trapezoidal.cc
model/common/integration_scheme/generalized_trapezoidal.hh
model/common/integration_scheme/integration_scheme.cc
model/common/integration_scheme/integration_scheme.hh
model/common/integration_scheme/integration_scheme_1st_order.cc
model/common/integration_scheme/integration_scheme_1st_order.hh
model/common/integration_scheme/integration_scheme_2nd_order.cc
model/common/integration_scheme/integration_scheme_2nd_order.hh
model/common/integration_scheme/newmark-beta.cc
model/common/integration_scheme/newmark-beta.hh
model/common/integration_scheme/pseudo_time.cc
model/common/integration_scheme/pseudo_time.hh
model/model.cc
model/model.hh
model/model_inline_impl.hh
model/model_options.hh
solver/solver_vector.hh
- solver/solver_vector_default.cc
solver/solver_vector_default.hh
solver/solver_vector_default_tmpl.hh
solver/solver_vector_distributed.cc
solver/solver_vector_distributed.hh
solver/sparse_matrix.cc
solver/sparse_matrix.hh
solver/sparse_matrix_aij.cc
solver/sparse_matrix_aij.hh
solver/sparse_matrix_aij_inline_impl.hh
solver/sparse_matrix_inline_impl.hh
solver/sparse_solver.cc
solver/sparse_solver.hh
solver/sparse_solver_inline_impl.hh
solver/terms_to_assemble.hh
synchronizer/communication_buffer_inline_impl.hh
synchronizer/communication_descriptor.hh
synchronizer/communication_descriptor_tmpl.hh
synchronizer/communication_request.hh
synchronizer/communication_tag.hh
synchronizer/communications.hh
synchronizer/communications_tmpl.hh
synchronizer/communicator.cc
synchronizer/communicator.hh
synchronizer/communicator_dummy_inline_impl.hh
synchronizer/communicator_event_handler.hh
synchronizer/communicator_inline_impl.hh
synchronizer/data_accessor.cc
synchronizer/data_accessor.hh
synchronizer/dof_synchronizer.cc
synchronizer/dof_synchronizer.hh
synchronizer/dof_synchronizer_inline_impl.hh
synchronizer/element_info_per_processor.cc
synchronizer/element_info_per_processor.hh
synchronizer/element_info_per_processor_tmpl.hh
synchronizer/element_synchronizer.cc
synchronizer/element_synchronizer.hh
synchronizer/facet_synchronizer.cc
synchronizer/facet_synchronizer.hh
synchronizer/facet_synchronizer_inline_impl.hh
synchronizer/grid_synchronizer.cc
synchronizer/grid_synchronizer.hh
synchronizer/grid_synchronizer_tmpl.hh
synchronizer/master_element_info_per_processor.cc
synchronizer/node_info_per_processor.cc
synchronizer/node_info_per_processor.hh
synchronizer/node_synchronizer.cc
synchronizer/node_synchronizer.hh
synchronizer/node_synchronizer_inline_impl.hh
synchronizer/periodic_node_synchronizer.cc
synchronizer/periodic_node_synchronizer.hh
synchronizer/slave_element_info_per_processor.cc
synchronizer/synchronizer.cc
synchronizer/synchronizer.hh
synchronizer/synchronizer_impl.hh
synchronizer/synchronizer_impl_tmpl.hh
synchronizer/synchronizer_registry.cc
synchronizer/synchronizer_registry.hh
synchronizer/synchronizer_tmpl.hh
synchronizer/communication_buffer.hh
)
set(AKANTU_SPIRIT_SOURCES
io/mesh_io/mesh_io_abaqus.cc
io/parser/parser_real.cc
io/parser/parser_random.cc
io/parser/parser_types.cc
io/parser/parser_input_files.cc
PARENT_SCOPE
)
package_declare_elements(core
ELEMENT_TYPES
_point_1
_segment_2
_segment_3
_triangle_3
_triangle_6
_quadrangle_4
_quadrangle_8
_tetrahedron_4
_tetrahedron_10
_pentahedron_6
_pentahedron_15
_hexahedron_8
_hexahedron_20
KIND regular
GEOMETRICAL_TYPES
_gt_point
_gt_segment_2
_gt_segment_3
_gt_triangle_3
_gt_triangle_6
_gt_quadrangle_4
_gt_quadrangle_8
_gt_tetrahedron_4
_gt_tetrahedron_10
_gt_hexahedron_8
_gt_hexahedron_20
_gt_pentahedron_6
_gt_pentahedron_15
INTERPOLATION_TYPES
_itp_lagrange_point_1
_itp_lagrange_segment_2
_itp_lagrange_segment_3
_itp_lagrange_triangle_3
_itp_lagrange_triangle_6
_itp_lagrange_quadrangle_4
_itp_serendip_quadrangle_8
_itp_lagrange_tetrahedron_4
_itp_lagrange_tetrahedron_10
_itp_lagrange_hexahedron_8
_itp_serendip_hexahedron_20
_itp_lagrange_pentahedron_6
_itp_lagrange_pentahedron_15
GEOMETRICAL_SHAPES
_gst_point
_gst_triangle
_gst_square
_gst_prism
GAUSS_INTEGRATION_TYPES
_git_point
_git_segment
_git_triangle
_git_tetrahedron
_git_pentahedron
INTERPOLATION_KIND _itk_lagrangian
FE_ENGINE_LISTS
gradient_on_integration_points
interpolate_on_integration_points
interpolate
compute_normals_on_integration_points
inverse_map
contains
compute_shapes
compute_shapes_derivatives
get_N
compute_dnds
compute_d2nds2
compute_jmat
get_shapes_derivatives
lagrange_base
assemble_fields
)
-package_declare_documentation_files(core
- manual.sty
- manual.cls
- manual.tex
- manual-macros.sty
- manual-titlepages.tex
- manual-authors.tex
- manual-changelog.tex
- manual-introduction.tex
- manual-gettingstarted.tex
- manual-io.tex
- manual-feengine.tex
- manual-elements.tex
- manual-appendix-elements.tex
- manual-appendix-packages.tex
- manual-backmatter.tex
- manual-bibliography.bib
- manual-bibliographystyle.bst
-
- figures/bc_and_ic_example.pdf
- figures/boundary.pdf
- figures/boundary.svg
- figures/dirichlet.pdf
- figures/dirichlet.svg
-# figures/doc_wheel.pdf
-# figures/doc_wheel.svg
- figures/hot-point-1.png
- figures/hot-point-2.png
- figures/insertion.pdf
- figures/interpolate.pdf
- figures/interpolate.svg
- figures/vectors.pdf
- figures/vectors.svg
-
- figures/elements/hexahedron_8.pdf
- figures/elements/hexahedron_8.svg
- figures/elements/quadrangle_4.pdf
- figures/elements/quadrangle_4.svg
- figures/elements/quadrangle_8.pdf
- figures/elements/quadrangle_8.svg
- figures/elements/segment_2.pdf
- figures/elements/segment_2.svg
- figures/elements/segment_3.pdf
- figures/elements/segment_3.svg
- figures/elements/tetrahedron_10.pdf
- figures/elements/tetrahedron_10.svg
- figures/elements/tetrahedron_4.pdf
- figures/elements/tetrahedron_4.svg
- figures/elements/triangle_3.pdf
- figures/elements/triangle_3.svg
- figures/elements/triangle_6.pdf
- figures/elements/triangle_6.svg
- figures/elements/xtemp.pdf
- )
-
-package_declare_documentation(core
- "This package is the core engine of \\akantu. It depends on:"
- "\\begin{itemize}"
- "\\item A C++ compiler (\\href{http://gcc.gnu.org/}{GCC} >= 4, or \\href{https://software.intel.com/en-us/intel-compilers}{Intel})."
- "\\item The cross-platform, open-source \\href{http://www.cmake.org/}{CMake} build system."
- "\\item The \\href{http://www.boost.org/}{Boost} C++ portable libraries."
- "\\item The \\href{http://www.zlib.net/}{zlib} compression library."
- "\\end{itemize}"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install cmake libboost-dev zlib1g-dev g++"
- "\\end{command}"
- ""
- "Under Mac OS X the installation requires the following steps:"
- "\\begin{itemize}"
- "\\item Install Xcode"
- "\\item Install the command line tools."
- "\\item Install the MacPorts project which allows to automatically"
- "download and install opensource packages."
- "\\end{itemize}"
- "Then the following commands should be typed in a terminal:"
- "\\begin{command}"
- " > sudo port install cmake gcc48 boost"
- "\\end{command}"
- )
-
find_program(READLINK_COMMAND readlink)
find_program(ADDR2LINE_COMMAND addr2line)
find_program(PATCH_COMMAND patch)
mark_as_advanced(READLINK_COMMAND)
mark_as_advanced(ADDR2LINE_COMMAND)
package_declare_extra_files_to_package(core
SOURCES
common/aka_element_classes_info.hh.in
common/aka_config.hh.in
)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" AND (NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.9))
package_set_compile_flags(core CXX "-Wno-undefined-var-template")
endif()
-
-if(DEFINED AKANTU_CXX11_FLAGS)
- package_declare(core_cxx11 NOT_OPTIONAL
- DESCRIPTION "C++ 11 additions for Akantu core"
- COMPILE_FLAGS CXX "${AKANTU_CXX11_FLAGS}")
-
- if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
- if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.6")
- set(AKANTU_CORE_CXX11 OFF CACHE BOOL "C++ 11 additions for Akantu core - not supported by the selected compiler" FORCE)
- endif()
- endif()
-
- package_declare_documentation(core_cxx11
- "This option activates some features of the C++11 standard. This is usable with GCC>=4.7 or Intel>=13.")
-else()
- if(CMAKE_VERSION VERSION_LESS 3.1)
- message(FATAL_ERROR "Since version 3.0 Akantu requires at least c++11 capable compiler")
- endif()
-endif()
diff --git a/packages/core_cxx11.cmake b/packages/core_cxx11.cmake
deleted file mode 100644
index 6d15c963c..000000000
--- a/packages/core_cxx11.cmake
+++ /dev/null
@@ -1,30 +0,0 @@
-#===============================================================================
-# @file core_cxx11.cmake
-#
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Tue Feb 26 2013
-# @date last modification: Fri Jan 22 2016
-#
-# @brief C++11 addition to the core package
-#
-# @section LICENSE
-#
-# Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
diff --git a/packages/damage_non_local.cmake b/packages/damage_non_local.cmake
index 7e0ad5e09..72b453f15 100644
--- a/packages/damage_non_local.cmake
+++ b/packages/damage_non_local.cmake
@@ -1,67 +1,61 @@
#===============================================================================
# @file damage_non_local.cmake
#
+# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Jun 15 2012
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Thu Dec 17 2020
#
# @brief package description for non-local materials
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(damage_non_local
DESCRIPTION "Package for Non-local damage constitutives laws Akantu"
DEPENDS lapack)
package_declare_sources(damage_non_local
model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc
model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh
model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.hh
model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
)
package_declare_material_infos(damage_non_local
LIST AKANTU_DAMAGE_NON_LOCAL_MATERIAL_LIST
INCLUDE material_non_local_includes.hh
)
-
-package_declare_documentation_files(damage_non_local
- manual-constitutive-laws-non_local.tex
- manual-appendix-materials-non-local.tex)
-
-package_declare_documentation(damage_non_local
-"This package activates the non local damage feature of AKANTU"
-"")
-
diff --git a/test/test_model/test_phase_field_model/CMakeLists.txt b/packages/documentation.cmake
similarity index 50%
copy from test/test_model/test_phase_field_model/CMakeLists.txt
copy to packages/documentation.cmake
index 6a2001030..5cd5a17d8 100644
--- a/test/test_model/test_phase_field_model/CMakeLists.txt
+++ b/packages/documentation.cmake
@@ -1,53 +1,46 @@
#===============================================================================
-# @file CMakeLists.txt
+# @file documentation_developer_manual.cmake
#
-# @author Mohit Pundir <mohit.pundir@epfl.ch>
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Thu Dec 20 2018
-# @date last modification: Thu Dec 20 2018
+# @date creation: Wed Jun 11 2014
+# @date last modification: Fri Jan 29 2021
+#
+# @brief Doxygen documentation of the code
#
-# @brief test for the phase field model
#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License along
# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
-register_test(test_phasefield_selector
- SOURCES test_phasefield_selector.cc
- FILES_TO_COPY phasefield_selector.dat phasefield_selector.msh
- PACKAGE phase_field
- )
-register_test(test_phase_solid_coupling
- SOURCES test_phase_solid_coupling.cc
- FILES_TO_COPY material_coupling.dat test_one_element.msh
- PACKAGE phase_field
- )
+package_declare(documentation
+ DESCRIPTION "Build source documentation using Sphinx/Doxygen.")
-register_test(test_phase_solid_explicit
- SOURCES test_phase_solid_explicit.cc
- FILES_TO_COPY material_coupling.dat test_one_element.msh
- PACKAGE phase_field
- )
+package_set_package_system_dependency(documentation deb-src
+ python3-sphinx python3-breathe doxygen graphviz)
-register_test(test_multi_material
- SOURCES test_multi_material.cc
- FILES_TO_COPY material_multiple.dat test_two_element.msh
- PACKAGE phase_field
+package_declare_extra_files_to_package(documentation
+ PROJECT doc/dev-doc/akantu.dox.j2
+ doc/dev-doc/conf.py
+ doc/dev-doc/index.rst
+ doc/dev-doc/reference.rst
+ cmake/Modules/FindSphinx.cmake
)
diff --git a/packages/documentation_developer_manual.cmake b/packages/documentation_developer_manual.cmake
deleted file mode 100644
index f933d41fa..000000000
--- a/packages/documentation_developer_manual.cmake
+++ /dev/null
@@ -1,58 +0,0 @@
-#===============================================================================
-# @file documentation_doxygen.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Wed Jun 11 2014
-# @date last modification: Mon Jan 18 2016
-#
-# @brief Doxygen documentation of the code
-#
-# @section LICENSE
-#
-# Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-package_declare(documentation
- DESCRIPTION "Build source documentation using Sphinx/Doxygen.")
-
-package_declare_documentation(documentation
- "This generates the Doxygen documantation of the source code."
- "It depends on:"
- "\\begin{itemize}"
- "\\item \\href{http://www.stack.nl/~dimitri/doxygen/}{Doxygen} an automated source code documentations system."
- "\\item Optional: \\href{http://www.graphviz.org/}{Graphviz} to generate the dependencies graph"
- "\\end{itemize}"
- ""
- "Under Ubuntu (14.04 LTS), the installation of the dependencies can be performed using the following command:"
- "\\begin{command}"
- " > sudo apt-get install doxygen"
- " > sudo apt-get install graphviz"
- "\\end{command}"
- )
-
-package_set_package_system_dependency(documentation deb-src
- python3-sphinx python3-breathe doxygen graphviz)
-
-package_declare_extra_files_to_package(documentation
- PROJECT doc/dev-doc/akantu.dox.j2
- doc/dev-doc/conf.py
- doc/dev-doc/index.rst
- doc/dev-doc/reference.rst
- cmake/Modules/FindSphinx.cmake
- )
diff --git a/packages/documentation_user_manual.cmake b/packages/documentation_user_manual.cmake
deleted file mode 100644
index d62b6a0bb..000000000
--- a/packages/documentation_user_manual.cmake
+++ /dev/null
@@ -1,55 +0,0 @@
-#===============================================================================
-# @file documentation_manual.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Tue Jun 10 2014
-# @date last modification: Mon Jan 18 2016
-#
-# @brief Akantu's manual package
-#
-# @section LICENSE
-#
-# Copyright (©) 2014, 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-package_declare(documentation_manual
- DESCRIPTION "Build the user manual.")
-
-package_declare_documentation(documentation_manual
-"This package alows to compile the user manual in the build folder \\shellcode{build/doc/manual/manual.pdf}."
-""
-"Under Ubuntu (14.04 LTS), the installation of the dependencies can be performed using the following command:"
-"\\begin{command}"
-" > sudo apt-get install install rubber texlive texlive-science texlive-latex-extra"
-"\\end{command}")
-
-package_set_package_system_dependency(documentation_manual deb-src
- rubber
- texlive-fonts-recommended
- texlive-science
- texlive-picture
- texlive-extra
- texlive-math-extra
- texlive-latex-extra
- texlive-bibtex-extra
- )
-
-package_declare_extra_files_to_package(documentation_manual
- MANUAL version-definition.tex.in
- PROJECT cmake/Modules/FindInkscape.cmake)
diff --git a/packages/dumpers.cmake b/packages/dumpers.cmake
index f4a4cfa2f..79fcfe832 100644
--- a/packages/dumpers.cmake
+++ b/packages/dumpers.cmake
@@ -1,37 +1,64 @@
+#===============================================================================
+# @file dumpers.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Tue Jan 16 2018
+# @date last modification: Fri Mar 16 2018
+#
+# @brief IO dumpers package description
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
package_declare(dumpers
DEFAULT ON
DESCRIPTION "Dumpers for Akantu"
DEPENDS INTERFACE IOHelper)
package_declare_sources(dumpers
io/dumper/dumpable_iohelper.hh
io/dumper/dumper_compute.hh
io/dumper/dumper_element_iterator.hh
io/dumper/dumper_elemental_field.hh
io/dumper/dumper_generic_elemental_field.hh
io/dumper/dumper_generic_elemental_field_tmpl.hh
io/dumper/dumper_homogenizing_field.hh
io/dumper/dumper_internal_material_field.hh
io/dumper/dumper_iohelper.cc
io/dumper/dumper_iohelper.hh
io/dumper/dumper_iohelper_paraview.cc
io/dumper/dumper_iohelper_paraview.hh
io/dumper/dumper_nodal_field.hh
io/dumper/dumper_padding_helper.hh
io/dumper/dumper_quadrature_point_iterator.hh
io/dumper/dumper_text.cc
io/dumper/dumper_text.hh
io/dumper/dumper_type_traits.hh
io/dumper/dumper_variable.hh
)
-package_declare_documentation(dumpers
- "This package activates the IOHelper facilities withing Akantu. This is mandatory if you want to be able to output Paraview files"
- "as well as any Dumper within Akantu."
- )
-
package_declare_extra_files_to_package(dumpers
PROJECT
third-party/cmake/iohelper.cmake
cmake/Modules/FindIOHelper.cmake
)
diff --git a/packages/embedded.cmake b/packages/embedded.cmake
index 75c2a1243..e67a88526 100644
--- a/packages/embedded.cmake
+++ b/packages/embedded.cmake
@@ -1,57 +1,53 @@
#===============================================================================
# @file embedded.cmake
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
-# @date last modification: Mon Dec 14 2015
+# @date last modification: Fri Mar 16 2018
#
# @brief package descrition for embedded model use
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(embedded
DESCRIPTION "Add support for the embedded solid mechanics model"
DEPENDS CGAL)
package_declare_sources(embedded
model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
)
package_declare_material_infos(embedded
LIST AKANTU_EMBEDDED_MATERIAL_LIST
INCLUDE material_embedded_includes.hh
)
-package_declare_documentation(embedded
-"This package allows the use of the embedded model in solid mechanics. This package depends on the CGAL package."
-)
-
-#add_example(embedded "Example on how to run embedded model simulation" PACKAGE embedded)
diff --git a/packages/google-benchmark.cmake b/packages/google-benchmark.cmake
deleted file mode 100644
index a33f54240..000000000
--- a/packages/google-benchmark.cmake
+++ /dev/null
@@ -1,11 +0,0 @@
-package_declare(gbenchmark EXTERNAL
- DESCRIPTION "Add Google Benchmark support"
- SYSTEM AUTO third-party/cmake/gbenchmark.cmake
- EXCLUDE_FROM_ALL
- )
-
-package_get_option_name(gbenchmark _opt_name)
-package_add_third_party_script_variable(gbenchmark
- GBENCHMARK_VERSION "master")
-package_add_third_party_script_variable(gbenchmark
- GBENCHMARK_GIT "https://github.com/google/benchmark.git")
diff --git a/packages/google-test.cmake b/packages/google-test.cmake
index 780afec72..010713667 100644
--- a/packages/google-test.cmake
+++ b/packages/google-test.cmake
@@ -1,15 +1,47 @@
+#===============================================================================
+# @file google-test.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Thu Nov 09 2017
+# @date last modification: Fri Mar 16 2018
+#
+# @brief package for external dependency to google tests
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
package_declare(gtest EXTERNAL
DESCRIPTION "Add GTest support for tests"
SYSTEM AUTO third-party/cmake/gtest.cmake
EXCLUDE_FROM_ALL
)
package_get_option_name(gtest _opt_name)
if(AKANTU_TESTS)
set(${_opt_name} ON CACHE BOOL "Add GTest support for tests (forced)" FORCE)
endif()
package_add_third_party_script_variable(google-test
GTEST_VERSION "master")
package_add_third_party_script_variable(google-test
GTEST_GIT "https://github.com/google/googletest.git")
diff --git a/packages/heat_transfer.cmake b/packages/heat_transfer.cmake
index 25651fac5..5c7eaef2e 100644
--- a/packages/heat_transfer.cmake
+++ b/packages/heat_transfer.cmake
@@ -1,49 +1,41 @@
#===============================================================================
# @file heat_transfer.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
# @date last modification: Mon Mar 30 2015
#
# @brief package description for heat transfer
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(heat_transfer
DESCRIPTION "Use Heat Transfer package of Akantu")
package_declare_sources(heat_transfer
model/heat_transfer/heat_transfer_model.cc
model/heat_transfer/heat_transfer_model.hh
model/heat_transfer/heat_transfer_model_inline_impl.hh
)
-
-package_declare_documentation_files(heat_transfer
- manual-heattransfermodel.tex
- )
-
-package_declare_documentation(heat_transfer
- "This package activates the heat transfer model within Akantu. "
- "It has no additional dependencies."
- )
diff --git a/packages/implicit.cmake b/packages/implicit.cmake
index 0a4f8d64c..289ea9e49 100644
--- a/packages/implicit.cmake
+++ b/packages/implicit.cmake
@@ -1,65 +1,57 @@
#===============================================================================
# @file implicit.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
-# @date last modification: Fri Aug 21 2015
+# @date last modification: Wed Dec 18 2019
#
# @brief package description for the implicit solver
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(implicit META
DESCRIPTION "Add support for implicit time scheme")
set(AKANTU_IMPLICIT_SOLVER "Mumps"
CACHE STRING "Solver activated in Akantu")
set_property(CACHE AKANTU_IMPLICIT_SOLVER PROPERTY STRINGS
Mumps
PETSc
Mumps+PETSc
)
if(AKANTU_IMPLICIT_SOLVER MATCHES "Mumps")
package_add_dependencies(implicit PRIVATE Mumps)
else()
package_remove_dependencies(implicit Mumps)
set(AKANTU_USE_MUMPS OFF CACHE BOOL "" FORCE)
endif()
if(AKANTU_IMPLICIT_SOLVER MATCHES "PETSc")
package_add_dependencies(implicit
PRIVATE PETSc)
else()
package_remove_dependency(implicit PETSc)
set(AKANTU_USE_PETSC OFF CACHE BOOL "" FORCE)
endif()
-
-package_declare_documentation(implicit
- "This package activates the sparse solver necessary to solve implicitely static/dynamic"
- "finite element problems."
- "It depends on:"
- "\\begin{itemize}"
- " \\item \\href{http://mumps.enseeiht.fr/}{MUMPS}, a parallel sparse direct solver."
- " \\item \\href{http://www.labri.fr/perso/pelegrin/scotch/}{Scotch}, a graph partitioner."
- "\\end{itemize}"
- )
diff --git a/packages/iohelper.cmake b/packages/iohelper.cmake
index 7f084c665..db89b78c6 100644
--- a/packages/iohelper.cmake
+++ b/packages/iohelper.cmake
@@ -1,42 +1,44 @@
#===============================================================================
# @file iohelper.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Nov 29 2011
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri Mar 16 2018
#
# @brief package description for iohelper
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(IOHelper EXTERNAL
DESCRIPTION "Add IOHelper support in akantu"
SYSTEM OFF third-party/cmake/iohelper.cmake
DEFAULT ON)
set(_version "1.1.1")
package_add_third_party_script_variable(IOHelper
IOHELPER_VERSION ${_version})
package_add_third_party_script_variable(IOHelper
IOHELPER_GIT "https://c4science.ch/source/iohelper.git")
package_add_third_party_script_variable(IOHelper
IOHELPER_ARCHIVE "iohelper_${_version}.tar.gz")
diff --git a/packages/lapack.cmake b/packages/lapack.cmake
index 69b50a87c..1a7f9387f 100644
--- a/packages/lapack.cmake
+++ b/packages/lapack.cmake
@@ -1,47 +1,39 @@
#===============================================================================
# @file lapack.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Oct 19 2012
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Mon Mar 30 2015
#
# @brief package description for lapack support
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(LAPACK EXTERNAL
DESCRIPTION "Use LAPACK for arithmetic operations"
EXTRA_PACKAGE_OPTIONS LANGUAGE Fortran)
-package_declare_documentation(LAPACK
- "This package provides access to a LAPACK implementation."
- ""
- "Under Ubuntu (14.04 LTS), the installation can be performed using the following command:"
- "\\begin{command}"
- " > sudo apt-get install libatlas-base-dev"
- "\\end{command}"
- )
-
package_set_package_system_dependency(LAPACK deb liblapack3)
package_set_package_system_dependency(LAPACK deb-src liblapack-dev)
diff --git a/packages/model_couplers.cmake b/packages/model_couplers.cmake
index 2b14e53a7..70a48cd2d 100644
--- a/packages/model_couplers.cmake
+++ b/packages/model_couplers.cmake
@@ -1,32 +1,35 @@
#===============================================================================
# @file model_couplers.cmake
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Sun Sep 30 2018
-# @date last modification: Sun Sep 28 2018
+# @date creation: Fri Oct 22 2010
+# @date last modification: Wed Jun 30 2021
#
# @brief package description for model couplers
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(model_couplers ADVANCED
DESCRIPTION "Use Model Couplers package of Akantu")
+
diff --git a/packages/mpi.cmake b/packages/mpi.cmake
index 2a355e31f..dd140b3c1 100644
--- a/packages/mpi.cmake
+++ b/packages/mpi.cmake
@@ -1,172 +1,160 @@
#===============================================================================
# @file mpi.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
-# @date last modification: Wed Jan 20 2016
+# @date last modification: Fri Dec 13 2019
#
# @brief package description for mpi
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
set(MPI_CXX_SKIP_MPICXX TRUE)
package_declare(MPI EXTERNAL
DESCRIPTION "Add MPI support in akantu"
EXTRA_PACKAGE_OPTIONS PREFIX MPI_C MPI
)
package_declare_sources(MPI
synchronizer/mpi_communicator_data.hh
synchronizer/communicator_mpi_inline_impl.hh
)
function(_add_to_mpi_preflags flag)
if(NOT MPIEXEC_PREFLAGS MATCHES "${flag}")
string(STRIP "${flag} ${MPIEXEC_PREFLAGS}" _preflags)
set(MPIEXEC_PREFLAGS "${_preflags}" CACHE STRING "" FORCE)
endif()
endfunction()
function(add_extra_mpi_options)
unset(MPI_ID CACHE)
package_get_include_dir(MPI _include_dir)
foreach(_inc_dir ${_include_dir})
if(EXISTS "${_inc_dir}/mpi.h")
if(NOT MPI_ID)
file(STRINGS "${_inc_dir}/mpi.h" _mpi_version REGEX "#define MPI_(SUB)?VERSION .*")
foreach(_ver ${_mpi_version})
string(REGEX MATCH "MPI_(VERSION|SUBVERSION) *([0-9]+)" _tmp "${_ver}")
set(_mpi_${CMAKE_MATCH_1} ${CMAKE_MATCH_2})
endforeach()
set(MPI_STD_VERSION "${_mpi_VERSION}.${_mpi_SUBVERSION}" CACHE INTERNAL "")
endif()
if(NOT MPI_ID)
# check if openmpi
file(STRINGS "${_inc_dir}/mpi.h" _ompi_version REGEX "#define OMPI_.*_VERSION .*")
if(_ompi_version)
set(MPI_ID "OpenMPI" CACHE INTERNAL "")
foreach(_version ${_ompi_version})
string(REGEX MATCH "OMPI_(.*)_VERSION (.*)" _tmp "${_version}")
if(_tmp)
set(MPI_VERSION_${CMAKE_MATCH_1} ${CMAKE_MATCH_2})
endif()
endforeach()
set(MPI_ID_VERSION "${MPI_VERSION_MAJOR}.${MPI_VERSION_MINOR}.${MPI_VERSION_RELEASE}"
CACHE INTERNAL "")
_add_to_mpi_preflags("--oversubscribe")
if(AKANTU_RUN_IN_DOCKER)
_add_to_mpi_preflags("--allow-run-as-root")
endif()
endif()
endif()
if(NOT MPI_ID)
# check if intelmpi
file(STRINGS "${_inc_dir}/mpi.h" _impi_version REGEX "#define I_MPI_VERSION .*")
if(_impi_version)
set(MPI_ID "IntelMPI" CACHE INTERNAL "")
string(REGEX MATCH "I_MPI_VERSION \"(.*)\"" _tmp "${_impi_version}")
if(_tmp)
set(MPI_ID_VERSION "${CMAKE_MATCH_1}" CACHE INTERNAL "")
endif()
endif()
endif()
if(NOT MPI_ID)
# check if mvapich2
file(STRINGS "${_inc_dir}/mpi.h" _mvapich2_version REGEX "#define MVAPICH2_VERSION .*")
if(_mvapich2_version)
set(MPI_ID "MPVAPICH2" CACHE INTERNAL "")
string(REGEX MATCH "MVAPICH2_VERSION \"(.*)\"" _tmp "${_mvapich2_version}")
if(_tmp)
set(MPI_ID_VERSION "${CMAKE_MATCH_1}" CACHE INTERNAL "")
endif()
endif()
endif()
if(NOT MPI_ID)
# check if mpich (mpich as to be checked after all the mpi that derives from it)
file(STRINGS "${_inc_dir}/mpi.h" _mpich_version REGEX "#define MPICH_VERSION .*")
if(_mpich_version)
set(MPI_ID "MPICH" CACHE INTERNAL "")
string(REGEX MATCH "I_MPI_VERSION \"(.*)\"" _tmp "${_mpich_version}")
if(_tmp)
set(MPI_ID_VERSION "${CMAKE_MATCH_1}" CACHE INTERNAL "")
endif()
endif()
endif()
endif()
endforeach()
if(MPI_ID STREQUAL "IntelMPI" OR
MPI_ID STREQUAL "MPICH" OR
MPI_ID STREQUAL "MVAPICH2")
set(_flags "-DMPICH_IGNORE_CXX_SEEK")
elseif(MPI_ID STREQUAL "OpenMPI")
set(_flags "-DOMPI_SKIP_MPICXX")
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
set( _flags "${_flags} -Wno-literal-suffix")
endif()
endif()
include(FindPackageMessage)
if(MPI_FOUND)
find_package_message(MPI "MPI ID: ${MPI_ID} ${MPI_ID_VERSION} (MPI standard ${MPI_STD_VERSION})" "${MPI_STD_VERSION}")
endif()
set(MPI_EXTRA_COMPILE_FLAGS "${_flags}" CACHE STRING "Extra flags for MPI" FORCE)
mark_as_advanced(MPI_EXTRA_COMPILE_FLAGS)
#package_get_source_files(MPI _srcs _pub _priv)
#list(APPEND _srcs "common/aka_error.cc")
#set_property(SOURCE ${_srcs} PROPERTY COMPILE_FLAGS "${_flags}")
package_set_compile_flags(MPI CXX ${_flags})
endfunction()
package_on_enabled_script(MPI
"
add_extra_mpi_options()
mask_package_options(MPI)
"
)
-package_declare_documentation(MPI
- "This is a meta package providing access to MPI."
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libopenmpi-dev"
- "\\end{command}"
- ""
- "Under Mac OS X the installation requires the following steps:"
- "\\begin{command}"
- " > sudo port install mpich-devel"
- "\\end{command}"
- )
-
package_set_package_system_dependency(MPI deb mpi-default-bin)
package_set_package_system_dependency(MPI deb-src mpi-default-dev)
diff --git a/packages/mumps.cmake b/packages/mumps.cmake
index e2967178a..2e86f9f25 100644
--- a/packages/mumps.cmake
+++ b/packages/mumps.cmake
@@ -1,114 +1,97 @@
#===============================================================================
# @file mumps.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Wed Dec 18 2019
#
# @brief package description for mumps support
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(Mumps EXTERNAL
DESCRIPTION "Add Mumps support in akantu"
SYSTEM ON
)
package_declare_sources(Mumps
model/common/non_linear_solver/non_linear_solver_linear.cc
model/common/non_linear_solver/non_linear_solver_linear.hh
model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
solver/sparse_solver_mumps.cc
solver/sparse_solver_mumps.hh
)
set(_mumps_float_type ${AKANTU_FLOAT_TYPE})
if(AKANTU_FLOAT_TYPE STREQUAL "float" OR
AKANTU_FLOAT_TYPE STREQUAL "double")
set(_mumps_components ${AKANTU_FLOAT_TYPE})
else()
if(DEFINED AKANTU_FLOAT_TYPE)
message(FATAL_ERROR "MUMPS doea not support floating point type \"${AKANTU_FLOAT_TYPE}\"")
endif()
endif()
package_get_option_name(parallel _par_option)
if(${_par_option})
package_set_find_package_extra_options(Mumps ARGS COMPONENTS "parallel" ${_mumps_components})
package_add_third_party_script_variable(Mumps MUMPS_TYPE "par")
package_set_package_system_dependency(Mumps deb libmumps)
package_set_package_system_dependency(Mumps deb-src libmumps-dev)
else()
package_set_find_package_extra_options(Mumps ARGS COMPONENTS "sequential" ${_mumps_components})
package_add_third_party_script_variable(Mumps MUMPS_TYPE "seq")
package_set_package_system_dependency(Mumps deb libmumps-seq)
package_set_package_system_dependency(Mumps deb-src libmumps-seq-dev)
endif()
package_use_system(Mumps _use_system)
if(NOT _use_system)
enable_language(Fortran)
set(AKANTU_USE_MUMPS_VERSION "4.10.0" CACHE STRING "Default Mumps version to compile")
mark_as_advanced(AKANTU_USE_MUMPS_VERSION)
set_property(CACHE AKANTU_USE_MUMPS_VERSION PROPERTY STRINGS "4.9.2" "4.10.0" "5.0.0")
package_get_option_name(MPI _mpi_option)
if(${_mpi_option})
package_add_dependencies(Mumps ScaLAPACK MPI)
endif()
package_add_dependencies(Mumps Scotch BLAS)
endif()
-package_declare_documentation(Mumps
- "This package enables the \\href{http://mumps.enseeiht.fr/}{MUMPS} parallel direct solver for sparce matrices."
- "This is necessary to solve static or implicit problems."
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- ""
- "\\begin{command}"
- " > sudo apt-get install libmumps-seq-dev # for sequential"
- " > sudo apt-get install libmumps-dev # for parallel"
- "\\end{command}"
- ""
- "Under Mac OS X the installation requires the following steps:"
- "\\begin{command}"
- " > sudo port install mumps"
- "\\end{command}"
- ""
- "If you activate the advanced option AKANTU\\_USE\\_THIRD\\_PARTY\\_MUMPS the make system of akantu can automatically compile MUMPS. For this you will have to download MUMPS from \\url{http://mumps.enseeiht.fr/} or \\url{http://graal.ens-lyon.fr/MUMPS} and place it in \\shellcode{<akantu source>/third-party}"
- )
-
package_declare_extra_files_to_package(MUMPS
PROJECT
third-party/MUMPS_4.10.0_make.inc.cmake
third-party/MUMPS_5.0.0.patch
third-party/MUMPS_4.10.0.patch
third-party/MUMPS_4.9.2_make.inc.cmake
third-party/cmake/mumps.cmake
cmake/Modules/FindMumps.cmake
)
diff --git a/packages/numpy.cmake b/packages/numpy.cmake
index 158ac82cb..25cabc4d7 100644
--- a/packages/numpy.cmake
+++ b/packages/numpy.cmake
@@ -1,48 +1,39 @@
#===============================================================================
# @file numpy.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Tue Nov 29 2011
-# @date last modification: Tue Jan 19 2016
+# @date creation: Fri Jan 04 2013
+# @date last modification: Sat Jan 23 2016
#
# @brief package description for the python library
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
-package_declare(Numpy EXTERNAL DESCRIPTION "Akantu's numpy dependance check")
-package_declare_documentation(Numpy
- "This package allows to wrap Akantu arrays to numpy arrays"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install python-numpy"
- "\\end{command}"
- ""
-)
+package_declare(Numpy EXTERNAL DESCRIPTION "Akantu's numpy dependance check")
package_set_package_system_dependency(Numpy deb python-numpy)
package_set_package_system_dependency(Numpy deb-src python-numpy)
package_declare_extra_files_to_package(Numpy
PROJECT cmake/Modules/FindNumpy.cmake)
diff --git a/packages/parallel.cmake b/packages/parallel.cmake
index 9c21d5d55..fc1fbf204 100644
--- a/packages/parallel.cmake
+++ b/packages/parallel.cmake
@@ -1,52 +1,46 @@
#===============================================================================
# @file parallel.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
-# @date last modification: Fri Jul 10 2015
+# @date last modification: Fri Mar 16 2018
#
# @brief meta package description for parallelization
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(parallel META
DESCRIPTION "Add parallel support in Akantu"
DEPENDS mpi scotch)
set(AKANTU_PARALLEL_TESTS
test_solid_mechanics_model_bar_traction2d_parallel
test_solid_mechanics_model_segment_parallel
test_solid_mechanics_model_pbc_parallel
test_synchronizer_communication
test_node_synchronizer
test_dof_synchronizer
test_dof_synchronizer_communication
test_solid_mechanics_model_reassign_material
)
-
-package_declare_documentation_files(parallel
- manual-parallel.tex
- )
-
-package_declare_documentation(parallel
- "This option activates the parallel features of AKANTU.")
diff --git a/packages/petsc.cmake b/packages/petsc.cmake
index 673cc86b2..d5ed21e14 100644
--- a/packages/petsc.cmake
+++ b/packages/petsc.cmake
@@ -1,90 +1,82 @@
#===============================================================================
# @file petsc.cmake
#
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
-# @date last modification: Tue Jan 19 2016
+# @date last modification: Sat May 23 2020
#
# @brief package description for PETSc support
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(PETSc EXTERNAL
DESCRIPTION "Add PETSc support in akantu"
EXTRA_PACKAGE_OPTIONS ARGS "VERSION;3.5"
DEPENDS parallel)
package_declare_sources(petsc
model/common/dof_manager/dof_manager_petsc.cc
model/common/dof_manager/dof_manager_petsc.hh
model/common/non_linear_solver/non_linear_solver_petsc.cc
model/common/non_linear_solver/non_linear_solver_petsc.hh
solver/petsc_wrapper.hh
solver/solver_petsc.cc
solver/solver_petsc.hh
solver/solver_vector_petsc.cc
solver/solver_vector_petsc.hh
solver/sparse_matrix_petsc.cc
solver/sparse_matrix_petsc.hh
)
package_declare_extra_files_to_package(PETSc
PROJECT cmake/Modules/FindPETSc.cmake
)
-package_declare_documentation(PETSc
- "This package enables PETSc as a solver in Akantu"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libpetsc3.4.2-dev"
- "\\end{command}"
- ""
-)
-
package_get_option_name(PETSc _opt_name)
if(${_opt_name})
include(CheckTypeSize)
package_get_include_dir(PETSc _petsc_include_dir)
if(_petsc_include_dir)
package_get_include_dir(MPI _mpi_include_dir)
set(CMAKE_EXTRA_INCLUDE_FILES petscsys.h)
set(CMAKE_REQUIRED_INCLUDES ${_petsc_include_dir} ${_mpi_include_dir})
check_type_size("PetscInt" PETSC_INT_SIZE)
if(PETSC_INT_SIZE AND NOT PETSC_INT_SIZE EQUAL AKANTU_INTEGER_SIZE)
message(SEND_ERROR "This version ofma PETSc cannot be used, it is compiled with the wrong size for PetscInt.")
endif()
check_type_size("PetscReal" PETSC_REAL_SIZE)
if(PETSC_REAL_SIZE AND NOT PETSC_REAL_SIZE EQUAL AKANTU_FLOAT_SIZE)
message(SEND_ERROR "This version of PETSc cannot be used, it is compiled with the wrong size for PetscInt.")
endif()
endif()
endif()
package_set_package_system_dependency(PETSc deb libpetsc3.4.2)
package_set_package_system_dependency(PETSc deb-src libpetsc3.4.2-dev)
diff --git a/packages/phase_field.cmake b/packages/phase_field.cmake
index f9dbd8560..c23b2e38d 100644
--- a/packages/phase_field.cmake
+++ b/packages/phase_field.cmake
@@ -1,60 +1,53 @@
#===============================================================================
# @file phase_field.cmake
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Sun Sep 30 2018
-# @date last modification: Sun Sep 30 2018
+# @date creation: Fri Sep 03 2010
+# @date last modification: Wed Jun 30 2021
#
# @brief package description for phase field model
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(phase_field
DEPENDS model_couplers
DESCRIPTION "Use Phase Field package of Akantu")
package_declare_sources(phase_field
model/phase_field/phasefield.cc
model/phase_field/phasefield.hh
model/phase_field/phasefield_inline_impl.cc
model/phase_field/phasefield_selector.hh
model/phase_field/phasefield_selector_tmpl.hh
model/phase_field/phasefields/phasefield_exponential.hh
model/phase_field/phasefields/phasefield_exponential.cc
model/phase_field/phase_field_model.cc
model/phase_field/phase_field_model.hh
model/phase_field/phase_field_model_inline_impl.cc
model/model_couplers/coupler_solid_phasefield.hh
model/model_couplers/coupler_solid_phasefield.cc
)
-
-package_declare_documentation_files(phase_field
- #
- )
-
-package_declare_documentation(phase_field
- "This package activates the phase field model within Akantu. "
- )
diff --git a/packages/pybind11.cmake b/packages/pybind11.cmake
index 0795aabbd..5e258169e 100644
--- a/packages/pybind11.cmake
+++ b/packages/pybind11.cmake
@@ -1,14 +1,47 @@
+#===============================================================================
+# @file pybind11.cmake
+#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Fri Dec 22 2017
+# @date last modification: Wed Dec 04 2019
+#
+# @brief package description for the pybind11 binding
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
set(PYBIND11_PYTHON_VERSION ${AKANTU_PREFERRED_PYTHON_VERSION} CACHE INTERNAL "")
package_declare(pybind11 EXTERNAL
EXTRA_PACKAGE_OPTIONS ARGS "2.4.2;CONFIG" LINK_LIBRARIES pybind11::embed PREFIX pybind11
DESCRIPTION "Akantu's pybind11 interface"
SYSTEM AUTO third-party/cmake/pybind11.cmake
DEPENDS PythonLibsNew
EXCLUDE_FROM_ALL
)
package_add_third_party_script_variable(pybind11
PYBIND11_VERSION "v2.4.2")
package_add_third_party_script_variable(pybind11
PYBIND11_GIT "https://github.com/pybind/pybind11.git")
diff --git a/packages/python_interface.cmake b/packages/python_interface.cmake
index 8e1fd72ea..ddc4988e2 100644
--- a/packages/python_interface.cmake
+++ b/packages/python_interface.cmake
@@ -1,43 +1,36 @@
#===============================================================================
# @file python_interface.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Nov 29 2011
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Wed Nov 27 2019
#
# @brief package description for the python interface
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(python_interface
DESCRIPTION "Akantu's python interface"
DEPENDS pybind11)
-
-package_declare_documentation(python_interface
- "This package enables the python interface of Akantu. It relies on pybind11"
-)
-
-package_declare_documentation_files(python_interface
- manual-python.tex
- )
diff --git a/packages/python_interpreter.cmake b/packages/python_interpreter.cmake
index 455a389c4..a4a1b3313 100644
--- a/packages/python_interpreter.cmake
+++ b/packages/python_interpreter.cmake
@@ -1,3 +1,35 @@
+#===============================================================================
+# @file python_interpreter.cmake
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Wed Oct 31 2018
+# @date last modification: Wed Oct 31 2018
+#
+# @brief packages description for the external dependency to the python interpreted
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
package_declare(PythonInterp EXTERNAL DESCRIPTION "Akantu's python interpreter"
EXTRA_PACKAGE_OPTIONS ARGS ${AKANTU_PREFERRED_PYTHON_VERSION}
)
diff --git a/packages/pythonlibs.cmake b/packages/pythonlibs.cmake
index 678abd195..efb89cbc7 100644
--- a/packages/pythonlibs.cmake
+++ b/packages/pythonlibs.cmake
@@ -1,59 +1,51 @@
#===============================================================================
# @file pythonlibs.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jan 22 2016
+# @date last modification: Fri Jul 24 2020
#
# @brief package description for the python library
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(PythonLibsNew EXTERNAL DESCRIPTION "Akantu's python interface"
DEPENDS numpy
EXTRA_PACKAGE_OPTIONS ARGS ${AKANTU_PREFERRED_PYTHON_VERSION} PREFIX PYTHON FOUND PYTHONLIBS_FOUND
)
package_on_enabled_script(PythonLibsNew
"set(PYTHON_MODULE_PREFIX \${PYTHON_MODULE_PREFIX} CACHE INTERNAL \"\")
set(PYTHON_MODULE_EXTENSION \${PYTHON_MODULE_EXTENSION} CACHE INTERNAL \"\")
set(PYTHON_VERSION_MAJOR \${PYTHON_VERSION_MAJOR} CACHE INTERNAL \"\")
set(PYTHON_VERSION_MINOR \${PYTHON_VERSION_MINOR} CACHE INTERNAL \"\")
set(PYTHON_SITE_PACKAGES \${PYTHON_SITE_PACKAGES} CACHE INTERNAL \"\")
")
if(AKANTU_PREFERRED_PYTHON_VERSION VERSION_GREATER 2.9)
package_set_package_system_dependency(PythonLibsNew deb libpython3)
package_set_package_system_dependency(PythonLibsNew deb-src libpython3-dev)
endif()
-
-package_declare_documentation(PythonLibsNew
- "This package is a dependency of the python interface"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libpython3-dev"
- "\\end{command}"
- ""
-)
diff --git a/packages/qview.cmake b/packages/qview.cmake
deleted file mode 100644
index 313a0ae3f..000000000
--- a/packages/qview.cmake
+++ /dev/null
@@ -1,41 +0,0 @@
-#===============================================================================
-# @file qview.cmake
-#
-# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
-# @author Nicolas Richart <nicolas.richart@epfl.ch>
-#
-# @date creation: Tue Nov 29 2011
-# @date last modification: Mon Jan 18 2016
-#
-# @brief package description for qview
-#
-# @section LICENSE
-#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation, either version 3 of the License, or (at your option) any
-# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
-#
-#===============================================================================
-
-package_declare(QVIEW EXTERNAL
- DESCRIPTION "Add QView support in akantu")
-
-set(AKANTU_QVIEW_DEB_DEPEND
- qview-client
- )
-
-package_declare_extra_files_to_package(QVIEW
- PROJECT cmake/Modules/FindQVIEW.cmake)
diff --git a/packages/scalapack.cmake b/packages/scalapack.cmake
index 384f24085..9164045af 100644
--- a/packages/scalapack.cmake
+++ b/packages/scalapack.cmake
@@ -1,64 +1,54 @@
#===============================================================================
# @file scalapack.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Oct 19 2012
-# @date last modification: Tue Jan 19 2016
+# @date last modification: Fri Jan 22 2016
#
# @brief package description for mumps support
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(ScaLAPACK EXTERNAL
DESCRIPTION "Add ScaLAPACK support in akantu"
SYSTEM OFF third-party/cmake/scalapack.cmake
DEPENDS MPI
)
package_add_third_party_script_variable(ScaLAPACK
SCALAPACK_VERSION "2.0.2")
package_add_third_party_script_variable(ScaLAPACK
SCALAPACK_ARCHIVE "http://www.netlib.org/scalapack/scalapack-${SCALAPACK_VERSION}.tgz")
package_add_third_party_script_variable(ScaLAPACK
SCALAPACK_ARCHIVE_HASH_2.0.2 "MD5=2f75e600a2ba155ed9ce974a1c4b536f")
package_set_package_system_dependency(ScaLAPACK deb-src libscalapack-mpi-dev)
package_declare_extra_files_to_package(ScaLAPACK
PROJECT
third-party/scalapack_2.0.2.patch
third-party/cmake/scalapack.cmake
cmake/Modules/FindScaLAPACK.cmake
)
-
-
-package_declare_documentation(ScaLAPACK
- "ScaLAPACK is used to compile mumps as a third-party"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libscalapack-mpi-dev"
- "\\end{command}"
- ""
-)
diff --git a/packages/scotch.cmake b/packages/scotch.cmake
index 0ec04f04c..af034c1f1 100644
--- a/packages/scotch.cmake
+++ b/packages/scotch.cmake
@@ -1,108 +1,79 @@
#===============================================================================
# @file scotch.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
# @date last modification: Mon Jan 18 2016
#
# @brief package description for scotch
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(Scotch EXTERNAL
DESCRIPTION "Add Scotch support in akantu"
SYSTEM ON third-party/cmake/scotch.cmake)
package_declare_sources(Scotch
mesh_utils/mesh_partition/mesh_partition_scotch.cc
)
package_add_third_party_script_variable(Scotch
SCOTCH_VERSION "5.1.12b")
package_add_third_party_script_variable(Scotch
SCOTCH_ARCHIVE_HASH "MD5=e13b49be804755470b159d7052764dc0")
package_add_third_party_script_variable(Scotch
SCOTCH_ARCHIVE "scotch_${SCOTCH_VERSION}_esmumps.tar.gz")
package_add_third_party_script_variable(Scotch
SCOTCH_URL "https://gforge.inria.fr/frs/download.php/28978/scotch_${SCOTCH_VERSION}_esmumps.tar.gz")
package_get_option_name(Scotch _opt_name)
package_use_system(Scotch _system)
if(${_opt_name} AND _system)
include(CheckTypeSize)
package_get_include_dir(Scotch _include_dir)
if(_include_dir)
set(CMAKE_EXTRA_INCLUDE_FILES stdio.h scotch.h)
set(CMAKE_REQUIRED_INCLUDES ${_include_dir})
check_type_size("SCOTCH_Num" SCOTCH_NUM)
if(SCOTCH_NUM AND NOT SCOTCH_NUM EQUAL AKANTU_INTEGER_SIZE)
math(EXPR _n "${AKANTU_INTEGER_SIZE} * 8")
message(SEND_ERROR "This version of Scotch cannot be used, it is compiled with the wrong size for SCOTCH_Num."
"Recompile Scotch with the define -DINTSIZE${_n}. The current scotch integer size is ${SCOTCH_NUM}")
endif()
endif()
endif()
-package_declare_documentation(Scotch
- "This package enables the use the \\href{http://www.labri.fr/perso/pelegrin/scotch/}{Scotch}"
- "library in order to perform a graph partitioning leading to the domain"
- "decomposition used within \\akantu"
- ""
- "Under Ubuntu (14.04 LTS) the installation can be performed using the commands:"
- "\\begin{command}"
- " > sudo apt-get install libscotch-dev"
- "\\end{command}"
- ""
- "If you activate the advanced option AKANTU\\_USE\\_THIRD\\_PARTY\\_SCOTCH"
- "the make system of akantu can automatically compile Scotch."
- ""
- "If the automated download fails due to a SSL access not supported by your"
- "version of CMake please download the file"
- "\\href{${SCOTCH_ARCHIVE}}{scotch\\_${SCOTCH_VERSION}\\_esmumps.tar.gz}"
- "and then place it in the directory \\shellcode{<akantu source>/third-party}"
- )
-
-# if(SCOTCH_INCLUDE_DIR)
-# file(STRINGS ${SCOTCH_INCLUDE_DIR}/scotch.h SCOTCH_INCLUDE_CONTENT)
-# string(REGEX MATCH "_cplusplus" _match ${SCOTCH_INCLUDE_CONTENT})
-# if(_match)
-# set(AKANTU_SCOTCH_NO_EXTERN ON)
-# list(APPEND AKANTU_DEFINITIONS AKANTU_SCOTCH_NO_EXTERN)
-# else()
-# set(AKANTU_SCOTCH_NO_EXTERN OFF)
-# endif()
-# endif()
-
package_set_package_system_dependency(Scotch deb libscotch)
package_set_package_system_dependency(Scotch deb-src libscotch-dev)
package_declare_extra_files_to_package(Scotch
PROJECT
third-party/cmake/scotch.cmake
third-party/scotch_5.1.12b.patch
third-party/scotch_5.1.12b_make.inc.cmake
cmake/Modules/FindScotch.cmake
)
diff --git a/packages/solid_mechanics.cmake b/packages/solid_mechanics.cmake
index e2c363359..113376256 100644
--- a/packages/solid_mechanics.cmake
+++ b/packages/solid_mechanics.cmake
@@ -1,143 +1,118 @@
#===============================================================================
# @file solid_mechanics.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Mon Nov 21 2011
-# @date last modification: Mon Jan 18 2016
+# @date creation: Mon Dec 04 2017
+# @date last modification: Fri Mar 26 2021
#
# @brief package description for core
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
package_declare(solid_mechanics DEFAULT ON
DESCRIPTION "Solid mechanics model"
DEPENDS core lapack
)
package_declare_sources(solid_mechanics
model/solid_mechanics/material.cc
model/solid_mechanics/material.hh
model/solid_mechanics/material_inline_impl.hh
model/solid_mechanics/material_selector.hh
model/solid_mechanics/material_selector_tmpl.hh
model/solid_mechanics/materials/internal_field.hh
model/solid_mechanics/materials/internal_field_tmpl.hh
model/solid_mechanics/materials/random_internal_field.hh
model/solid_mechanics/materials/random_internal_field_tmpl.hh
model/solid_mechanics/solid_mechanics_model.cc
model/solid_mechanics/solid_mechanics_model.hh
model/solid_mechanics/solid_mechanics_model_inline_impl.hh
model/solid_mechanics/solid_mechanics_model_io.cc
model/solid_mechanics/solid_mechanics_model_mass.cc
model/solid_mechanics/solid_mechanics_model_material.cc
model/solid_mechanics/solid_mechanics_model_tmpl.hh
model/solid_mechanics/solid_mechanics_model_event_handler.hh
model/solid_mechanics/materials/plane_stress_toolbox.hh
model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
model/solid_mechanics/materials/material_core_includes.hh
model/solid_mechanics/materials/material_elastic.cc
model/solid_mechanics/materials/material_elastic.hh
model/solid_mechanics/materials/material_elastic_inline_impl.hh
model/solid_mechanics/materials/material_thermal.cc
model/solid_mechanics/materials/material_thermal.hh
model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
model/solid_mechanics/materials/material_elastic_orthotropic.cc
model/solid_mechanics/materials/material_elastic_orthotropic.hh
model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
model/solid_mechanics/materials/material_damage/material_damage.hh
model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
model/solid_mechanics/materials/material_damage/material_marigo.cc
model/solid_mechanics/materials/material_damage/material_marigo.hh
model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
model/solid_mechanics/materials/material_damage/material_mazars.cc
model/solid_mechanics/materials/material_damage/material_mazars.hh
model/solid_mechanics/materials/material_damage/material_phasefield.cc
model/solid_mechanics/materials/material_damage/material_phasefield.hh
model/solid_mechanics/materials/material_damage/material_phasefield_inline_impl.cc
model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
model/solid_mechanics/materials/material_plastic/material_plastic.cc
model/solid_mechanics/materials/material_plastic/material_plastic.hh
model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.hh
model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc
model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh
model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc
model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh
model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh
model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
model/solid_mechanics/materials/material_non_local.hh
model/solid_mechanics/materials/material_non_local_tmpl.hh
model/solid_mechanics/materials/material_non_local_includes.hh
)
package_declare_material_infos(solid_mechanics
LIST AKANTU_CORE_MATERIAL_LIST
INCLUDE material_core_includes.hh
)
-package_declare_documentation_files(solid_mechanics
- manual-solidmechanicsmodel.tex
- manual-constitutive-laws.tex
- manual-lumping.tex
- manual-appendix-materials.tex
-
- figures/dynamic_analysis.png
- figures/explicit_dynamic.pdf
- figures/explicit_dynamic.svg
- figures/static.pdf
- figures/static.svg
- figures/hooke_law.pdf
- figures/implicit_dynamic.pdf
- figures/implicit_dynamic.svg
- figures/problemDomain.pdf_tex
- figures/problemDomain.pdf
- figures/static_analysis.png
- figures/stress_strain_el.pdf
- figures/tangent.pdf
- figures/tangent.svg
-
- figures/stress_strain_neo.pdf
- figures/visco_elastic_law.pdf
- figures/isotropic_hardening_plasticity.pdf
- figures/stress_strain_visco.pdf
- )
-
package_declare_extra_files_to_package(solid_mechanics
SOURCES
model/solid_mechanics/material_list.hh.in
)
diff --git a/packages/structural_mechanics.cmake b/packages/structural_mechanics.cmake
index 61624dbaa..7c908c2f3 100644
--- a/packages/structural_mechanics.cmake
+++ b/packages/structural_mechanics.cmake
@@ -1,91 +1,79 @@
#===============================================================================
# @file structural_mechanics.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Nov 21 2011
-# @date last modification: Sun Jul 19 2015
+# @date last modification: Mon Dec 02 2019
#
# @brief package description for structural mechanics
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2012, 2014, 2015 EPFL (Ecole Polytechnique Fédérale de
-# Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des
-# Solides)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
package_declare(structural_mechanics
DESCRIPTION "Use Structural mechanics model package of Akantu"
DEPENDS implicit)
package_declare_sources(structural_mechanics
fe_engine/element_class_structural.hh
fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
fe_engine/element_classes/element_class_hermite_inline_impl.hh
fe_engine/fe_engine_template_tmpl_struct.hh
fe_engine/shape_structural.cc
fe_engine/shape_structural.hh
fe_engine/shape_structural_inline_impl.hh
io/mesh_io/mesh_io_msh_struct.cc
io/mesh_io/mesh_io_msh_struct.hh
model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
model/structural_mechanics/structural_mechanics_model.cc
model/structural_mechanics/structural_mechanics_model.hh
model/structural_mechanics/structural_mechanics_model_boundary.cc
model/structural_mechanics/structural_mechanics_model_inline_impl.hh
model/structural_mechanics/structural_mechanics_model_mass.cc
)
package_declare_elements(structural_mechanics
ELEMENT_TYPES
_bernoulli_beam_2
_bernoulli_beam_3
_discrete_kirchhoff_triangle_18
KIND structural
INTERPOLATION_TYPES
_itp_hermite_2
_itp_bernoulli_beam_2
_itp_bernoulli_beam_3
_itp_discrete_kirchhoff_triangle_6
_itp_discrete_kirchhoff_triangle_18
INTERPOLATION_KIND
_itk_structural
FE_ENGINE_LISTS
gradient_on_integration_points
interpolate_on_integration_points
compute_shapes
compute_shapes_derivatives
get_shapes_derivatives
assemble_fields
)
-
-package_declare_documentation_files(structural_mechanics
- manual-structuralmechanicsmodel.tex
- manual-structuralmechanicsmodel-elements.tex
-
- figures/beam_example.pdf
- figures/elements/bernoulli_2.pdf
- figures/elements/bernoulli_2.svg
- )
-
-package_declare_documentation(structural_mechanics
- "This package activates the compilation for the Structural Mechanics engine of Akantu"
- )
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index f90ffb6bb..9cbc35a5d 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -1,147 +1,144 @@
-
#===============================================================================
# @file CMakeLists.txt
#
+# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Dec 12 2014
-# @date last modification: Mon Jan 18 2016
+# @date last modification: Fri May 07 2021
#
# @brief CMake file for the python wrapping of akantu
#
+#
# @section LICENSE
#
-# Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
-# (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the
-# terms of the GNU Lesser General Public License as published by the Free
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
-# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
+
if(NOT SKBUILD)
package_get_all_include_directories(
AKANTU_LIBRARY_INCLUDE_DIRS
)
package_get_all_external_informations(
PRIVATE_INCLUDE AKANTU_PRIVATE_EXTERNAL_INCLUDE_DIR
INTERFACE_INCLUDE AKANTU_INTERFACE_EXTERNAL_INCLUDE_DIR
LIBRARIES AKANTU_EXTERNAL_LIBRARIES
)
endif()
set(PYAKANTU_SRCS
py_aka_common.cc
py_aka_error.cc
py_akantu.cc
py_boundary_conditions.cc
py_fe_engine.cc
py_group_manager.cc
py_mesh.cc
py_model.cc
py_parser.cc
py_solver.cc
)
package_is_activated(iohelper _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_dumpable.cc
)
endif()
package_is_activated(solid_mechanics _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_solid_mechanics_model.cc
py_material.cc
py_material_selector.cc
)
endif()
package_is_activated(cohesive_element _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_solid_mechanics_model_cohesive.cc
py_fragment_manager.cc
)
endif()
package_is_activated(heat_transfer _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_heat_transfer_model.cc
)
endif()
package_is_activated(contact_mechanics _is_activated)
if(_is_activated)
list(APPEND PYAKANTU_SRCS
py_contact_mechanics_model.cc
- )
-endif()
-
-package_is_activated(model_couplers _is_activated)
-if(_is_activated)
- list(APPEND PYAKANTU_SRCS
py_model_couplers.cc
)
endif()
package_is_activated(phase_field _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_phase_field_model.cc
)
endif()
package_is_activated(structural_mechanics _is_activated)
if (_is_activated)
list(APPEND PYAKANTU_SRCS
py_structural_mechanics_model.cc
)
endif()
pybind11_add_module(py11_akantu ${PYAKANTU_SRCS})
# to avoid compilation warnings from pybind11
target_include_directories(py11_akantu
SYSTEM BEFORE
PRIVATE ${PYBIND11_INCLUDE_DIR}
PRIVATE ${pybind11_INCLUDE_DIR}
PRIVATE ${PYTHON_INCLUDE_DIRS})
target_link_libraries(py11_akantu PUBLIC akantu)
set_target_properties(py11_akantu PROPERTIES
DEBUG_POSTFIX ""
LIBRARY_OUTPUT_DIRECTORY akantu)
file(COPY akantu DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
if(NOT SKBUILD)
set(_python_install_dir
${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages)
else()
set(_python_install_dir .)
endif()
install(TARGETS py11_akantu
LIBRARY DESTINATION ${_python_install_dir})
if(NOT SKBUILD)
install(DIRECTORY akantu
DESTINATION ${_python_install_dir}
FILES_MATCHING PATTERN "*.py")
endif()
diff --git a/python/akantu/__init__.py b/python/akantu/__init__.py
index 00a25300d..7704446a4 100644
--- a/python/akantu/__init__.py
+++ b/python/akantu/__init__.py
@@ -1,60 +1,75 @@
+
+""" __init__.py: akantu python module"""
+
+__author__ = "Guillaume Anciaux and Nicolas Richart"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
+import warnings as _aka_warn
import scipy.sparse as _aka_sparse
import numpy as _aka_np
from . import py11_akantu as _py11_akantu
private_keys = set(dir(_py11_akantu)) - set(dir())
for k in private_keys:
globals()[k] = getattr(_py11_akantu, k)
if _py11_akantu.has_mpi():
try:
from mpi4py import MPI # noqa: F401
except Exception:
pass
def initialize(*args, **kwargs):
raise RuntimeError("No need to call initialize,"
" use parseInput to read an input file")
def finalize(*args, **kwargs):
- raise RuntimeError("No need to call finalize")
+ _aka_warn.warn("No need to call finalize", DeprecationWarning)
class AkantuSparseMatrix (_aka_sparse.coo_matrix):
def __init__(self, aka_sparse):
self.aka_sparse = aka_sparse
matrix_type = self.aka_sparse.getMatrixType()
sz = self.aka_sparse.size()
row = self.aka_sparse.getIRN()[:, 0] - 1
col = self.aka_sparse.getJCN()[:, 0] - 1
data = self.aka_sparse.getA()[:, 0]
row = row.copy()
col = col.copy()
data = data.copy()
if matrix_type == _py11_akantu._symmetric:
non_diags = (row != col)
row_sup = col[non_diags]
col_sup = row[non_diags]
data_sup = data[non_diags]
col = _aka_np.concatenate((col, col_sup))
row = _aka_np.concatenate((row, row_sup))
data = _aka_np.concatenate((data, data_sup))
_aka_sparse.coo_matrix.__init__(
self, (data, (row, col)), shape=(sz, sz))
FromStress = _py11_akantu.FromHigherDim
FromTraction = _py11_akantu.FromSameDim
_py11_akantu.__initialize()
from ._version import get_versions # NOQA(402@)
__version__ = get_versions()['version']
del get_versions
diff --git a/python/akantu/_version.py b/python/akantu/_version.py
index c85990081..04d3c3f97 100644
--- a/python/akantu/_version.py
+++ b/python/akantu/_version.py
@@ -1,525 +1,533 @@
+""" _version.py: _version file generated by versioneer"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains the computed version number.
# This file is released into the public domain. Generated by
# versioneer-0.19 (https://github.com/python-versioneer/python-versioneer)
-"""Git implementation of _version.py."""
-
import errno
import os
import re
import subprocess
import sys
def get_keywords():
"""Get the keywords needed to look up the version information."""
# these strings will be replaced by git during git-archive.
# setup.py/versioneer.py will grep for the variable names, so they must
# each be defined on a line of their own. _version.py will just call
# get_keywords().
git_refnames = "$Format:%d$"
git_full = "$Format:%H$"
git_date = "$Format:%ci$"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
class VersioneerConfig:
"""Container for Versioneer configuration parameters."""
def get_config():
"""Create, populate and return the VersioneerConfig() object."""
# these strings are filled in when 'setup.py versioneer' creates
# _version.py
cfg = VersioneerConfig()
cfg.VCS = "git"
cfg.style = "pep440"
cfg.tag_prefix = "v"
cfg.parentdir_prefix = "None"
cfg.versionfile_source = "akantu/python/akantu/_version.py"
cfg.verbose = False
return cfg
class NotThisMethod(Exception):
"""Exception raised if a method is not valid for the current scenario."""
LONG_VERSION_PY = {}
HANDLERS = {}
def register_vcs_handler(vcs, method): # decorator
"""Create decorator to mark a method as the handler of a VCS."""
def decorate(f):
"""Store f in HANDLERS[vcs][method]."""
if vcs not in HANDLERS:
HANDLERS[vcs] = {}
HANDLERS[vcs][method] = f
return f
return decorate
def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
env=None):
"""Call the given command(s)."""
assert isinstance(commands, list)
p = None
for c in commands:
try:
dispcmd = str([c] + args)
# remember shell=False, so use git.cmd on windows, not just git
p = subprocess.Popen([c] + args, cwd=cwd, env=env,
stdout=subprocess.PIPE,
stderr=(subprocess.PIPE if hide_stderr
else None))
break
except EnvironmentError:
e = sys.exc_info()[1]
if e.errno == errno.ENOENT:
continue
if verbose:
print("unable to run %s" % dispcmd)
print(e)
return None, None
else:
if verbose:
print("unable to find command, tried %s" % (commands,))
return None, None
stdout = p.communicate()[0].strip().decode()
if p.returncode != 0:
if verbose:
print("unable to run %s (error)" % dispcmd)
print("stdout was %s" % stdout)
return None, p.returncode
return stdout, p.returncode
def versions_from_parentdir(parentdir_prefix, root, verbose):
"""Try to determine the version from the parent directory name.
Source tarballs conventionally unpack into a directory that includes both
the project name and a version string. We will also support searching up
two directory levels for an appropriately named parent directory
"""
rootdirs = []
for i in range(3):
dirname = os.path.basename(root)
if dirname.startswith(parentdir_prefix):
return {"version": dirname[len(parentdir_prefix):],
"full-revisionid": None,
"dirty": False, "error": None, "date": None}
else:
rootdirs.append(root)
root = os.path.dirname(root) # up a level
if verbose:
print("Tried directories %s but none started with prefix %s" %
(str(rootdirs), parentdir_prefix))
raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
@register_vcs_handler("git", "get_keywords")
def git_get_keywords(versionfile_abs):
"""Extract version information from the given file."""
# the code embedded in _version.py can just fetch the value of these
# keywords. When used from setup.py, we don't want to import _version.py,
# so we do it with a regexp instead. This function is not used from
# _version.py.
keywords = {}
try:
f = open(versionfile_abs, "r")
for line in f.readlines():
if line.strip().startswith("git_refnames ="):
mo = re.search(r'=\s*"(.*)"', line)
if mo:
keywords["refnames"] = mo.group(1)
if line.strip().startswith("git_full ="):
mo = re.search(r'=\s*"(.*)"', line)
if mo:
keywords["full"] = mo.group(1)
if line.strip().startswith("git_date ="):
mo = re.search(r'=\s*"(.*)"', line)
if mo:
keywords["date"] = mo.group(1)
f.close()
except EnvironmentError:
pass
return keywords
@register_vcs_handler("git", "keywords")
def git_versions_from_keywords(keywords, tag_prefix, verbose):
"""Get version information from git keywords."""
if not keywords:
raise NotThisMethod("no keywords at all, weird")
date = keywords.get("date")
if date is not None:
# Use only the last line. Previous lines may contain GPG signature
# information.
date = date.splitlines()[-1]
# git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
# datestamp. However we prefer "%ci" (which expands to an "ISO-8601
# -like" string, which we must then edit to make compliant), because
# it's been around since git-1.5.3, and it's too difficult to
# discover which version we're using, or to work around using an
# older one.
date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
refnames = keywords["refnames"].strip()
if refnames.startswith("$Format"):
if verbose:
print("keywords are unexpanded, not using")
raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
refs = set([r.strip() for r in refnames.strip("()").split(",")])
# starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
# just "foo-1.0". If we see a "tag: " prefix, prefer those.
TAG = "tag: "
tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
if not tags:
# Either we're using git < 1.8.3, or there really are no tags. We use
# a heuristic: assume all version tags have a digit. The old git %d
# expansion behaves like git log --decorate=short and strips out the
# refs/heads/ and refs/tags/ prefixes that would let us distinguish
# between branches and tags. By ignoring refnames without digits, we
# filter out many common branch names like "release" and
# "stabilization", as well as "HEAD" and "master".
tags = set([r for r in refs if re.search(r'\d', r)])
if verbose:
print("discarding '%s', no digits" % ",".join(refs - tags))
if verbose:
print("likely tags: %s" % ",".join(sorted(tags)))
for ref in sorted(tags):
# sorting will prefer e.g. "2.0" over "2.0rc1"
if ref.startswith(tag_prefix):
r = ref[len(tag_prefix):]
if verbose:
print("picking %s" % r)
return {"version": r,
"full-revisionid": keywords["full"].strip(),
"dirty": False, "error": None,
"date": date}
# no suitable tags, so version is "0+unknown", but full hex is still there
if verbose:
print("no suitable tags, using unknown + full revision id")
return {"version": "0+unknown",
"full-revisionid": keywords["full"].strip(),
"dirty": False, "error": "no suitable tags", "date": None}
@register_vcs_handler("git", "pieces_from_vcs")
def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
"""Get version from 'git describe' in the root of the source tree.
This only gets called if the git-archive 'subst' keywords were *not*
expanded, and _version.py hasn't already been rewritten with a short
version string, meaning we're inside a checked out source tree.
"""
GITS = ["git"]
if sys.platform == "win32":
GITS = ["git.cmd", "git.exe"]
out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
hide_stderr=True)
if rc != 0:
if verbose:
print("Directory %s not under git control" % root)
raise NotThisMethod("'git rev-parse --git-dir' returned error")
# if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
# if there isn't one, this yields HEX[-dirty] (no NUM)
describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
"--always", "--long",
"--match", "%s*" % tag_prefix],
cwd=root)
# --long was added in git-1.5.5
if describe_out is None:
raise NotThisMethod("'git describe' failed")
describe_out = describe_out.strip()
full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
if full_out is None:
raise NotThisMethod("'git rev-parse' failed")
full_out = full_out.strip()
pieces = {}
pieces["long"] = full_out
pieces["short"] = full_out[:7] # maybe improved later
pieces["error"] = None
# parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
# TAG might have hyphens.
git_describe = describe_out
# look for -dirty suffix
dirty = git_describe.endswith("-dirty")
pieces["dirty"] = dirty
if dirty:
git_describe = git_describe[:git_describe.rindex("-dirty")]
# now we have TAG-NUM-gHEX or HEX
if "-" in git_describe:
# TAG-NUM-gHEX
mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
if not mo:
# unparseable. Maybe git-describe is misbehaving?
pieces["error"] = ("unable to parse git-describe output: '%s'"
% describe_out)
return pieces
# tag
full_tag = mo.group(1)
if not full_tag.startswith(tag_prefix):
if verbose:
fmt = "tag '%s' doesn't start with prefix '%s'"
print(fmt % (full_tag, tag_prefix))
pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
% (full_tag, tag_prefix))
return pieces
pieces["closest-tag"] = full_tag[len(tag_prefix):]
# distance: number of commits since tag
pieces["distance"] = int(mo.group(2))
# commit: short hex revision ID
pieces["short"] = mo.group(3)
else:
# HEX: no tags
pieces["closest-tag"] = None
count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
cwd=root)
pieces["distance"] = int(count_out) # total number of commits
# commit date: see ISO-8601 comment in git_versions_from_keywords()
date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
cwd=root)[0].strip()
# Use only the last line. Previous lines may contain GPG signature
# information.
date = date.splitlines()[-1]
pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
return pieces
def plus_or_dot(pieces):
"""Return a + if we don't already have one, else return a ."""
if "+" in pieces.get("closest-tag", ""):
return "."
return "+"
def render_pep440(pieces):
"""Build up version string, with post-release "local version identifier".
Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
Exceptions:
1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
if pieces["distance"] or pieces["dirty"]:
rendered += plus_or_dot(pieces)
rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
if pieces["dirty"]:
rendered += ".dirty"
else:
# exception #1
rendered = "0+untagged.%d.g%s" % (pieces["distance"],
pieces["short"])
if pieces["dirty"]:
rendered += ".dirty"
return rendered
def render_pep440_pre(pieces):
"""TAG[.post0.devDISTANCE] -- No -dirty.
Exceptions:
1: no tags. 0.post0.devDISTANCE
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
if pieces["distance"]:
rendered += ".post0.dev%d" % pieces["distance"]
else:
# exception #1
rendered = "0.post0.dev%d" % pieces["distance"]
return rendered
def render_pep440_post(pieces):
"""TAG[.postDISTANCE[.dev0]+gHEX] .
The ".dev0" means dirty. Note that .dev0 sorts backwards
(a dirty tree will appear "older" than the corresponding clean one),
but you shouldn't be releasing software with -dirty anyways.
Exceptions:
1: no tags. 0.postDISTANCE[.dev0]
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
if pieces["distance"] or pieces["dirty"]:
rendered += ".post%d" % pieces["distance"]
if pieces["dirty"]:
rendered += ".dev0"
rendered += plus_or_dot(pieces)
rendered += "g%s" % pieces["short"]
else:
# exception #1
rendered = "0.post%d" % pieces["distance"]
if pieces["dirty"]:
rendered += ".dev0"
rendered += "+g%s" % pieces["short"]
return rendered
def render_pep440_old(pieces):
"""TAG[.postDISTANCE[.dev0]] .
The ".dev0" means dirty.
Exceptions:
1: no tags. 0.postDISTANCE[.dev0]
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
if pieces["distance"] or pieces["dirty"]:
rendered += ".post%d" % pieces["distance"]
if pieces["dirty"]:
rendered += ".dev0"
else:
# exception #1
rendered = "0.post%d" % pieces["distance"]
if pieces["dirty"]:
rendered += ".dev0"
return rendered
def render_git_describe(pieces):
"""TAG[-DISTANCE-gHEX][-dirty].
Like 'git describe --tags --dirty --always'.
Exceptions:
1: no tags. HEX[-dirty] (note: no 'g' prefix)
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
if pieces["distance"]:
rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
else:
# exception #1
rendered = pieces["short"]
if pieces["dirty"]:
rendered += "-dirty"
return rendered
def render_git_describe_long(pieces):
"""TAG-DISTANCE-gHEX[-dirty].
Like 'git describe --tags --dirty --always -long'.
The distance/hash is unconditional.
Exceptions:
1: no tags. HEX[-dirty] (note: no 'g' prefix)
"""
if pieces["closest-tag"]:
rendered = pieces["closest-tag"]
rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
else:
# exception #1
rendered = pieces["short"]
if pieces["dirty"]:
rendered += "-dirty"
return rendered
def render(pieces, style):
"""Render the given version pieces into the requested style."""
if pieces["error"]:
return {"version": "unknown",
"full-revisionid": pieces.get("long"),
"dirty": None,
"error": pieces["error"],
"date": None}
if not style or style == "default":
style = "pep440" # the default
if style == "pep440":
rendered = render_pep440(pieces)
elif style == "pep440-pre":
rendered = render_pep440_pre(pieces)
elif style == "pep440-post":
rendered = render_pep440_post(pieces)
elif style == "pep440-old":
rendered = render_pep440_old(pieces)
elif style == "git-describe":
rendered = render_git_describe(pieces)
elif style == "git-describe-long":
rendered = render_git_describe_long(pieces)
else:
raise ValueError("unknown style '%s'" % style)
return {"version": rendered, "full-revisionid": pieces["long"],
"dirty": pieces["dirty"], "error": None,
"date": pieces.get("date")}
def get_versions():
"""Get version information or return default if unable to do so."""
# I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
# __file__, we can work backwards from there to the root. Some
# py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
# case we can only use expanded keywords.
cfg = get_config()
verbose = cfg.verbose
try:
return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
verbose)
except NotThisMethod:
pass
try:
root = os.path.realpath(__file__)
# versionfile_source is the relative path from the top of the source
# tree (where the .git directory might live) to this file. Invert
# this to find the root from __file__.
for i in cfg.versionfile_source.split('/'):
root = os.path.dirname(root)
except NameError:
return {"version": "0+unknown", "full-revisionid": None,
"dirty": None,
"error": "unable to find root of source tree",
"date": None}
try:
pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
return render(pieces, cfg.style)
except NotThisMethod:
pass
try:
if cfg.parentdir_prefix:
return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
except NotThisMethod:
pass
return {"version": "0+unknown", "full-revisionid": None,
"dirty": None,
"error": "unable to compute version", "date": None}
diff --git a/python/py11_akantu.cc b/python/py11_akantu.cc
deleted file mode 100644
index 60c98300b..000000000
--- a/python/py11_akantu.cc
+++ /dev/null
@@ -1 +0,0 @@
-// This file is only for cmake < 3.12
diff --git a/python/py_aka_array.hh b/python/py_aka_array.hh
index caf9ca460..e3868bd50 100644
--- a/python/py_aka_array.hh
+++ b/python/py_aka_array.hh
@@ -1,250 +1,282 @@
+/**
+ * @file py_aka_array.hh
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Oct 31 2018
+ * @date last modification: Fri Nov 13 2020
+ *
+ * @brief pybind11 interface to akantu Arrays
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include <aka_array.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace _aka = akantu;
namespace akantu {
namespace detail {
template <class T> struct is_array_type : public std::false_type {};
template <class T> struct is_array_type<Vector<T>> : public std::true_type {};
template <class T> struct is_array_type<Matrix<T>> : public std::true_type {};
template <class T> struct is_array_type<Array<T>> : public std::true_type {};
/* ------------------------------------------------------------------------ */
template <typename T> class ArrayProxy : public Array<T> {
protected:
// deallocate the memory
void deallocate() final {}
// allocate the memory
void allocate(UInt /*size*/, UInt /*nb_component*/) final {}
// allocate and initialize the memory
void allocate(UInt /*size*/, UInt /*nb_component*/,
const T & /*value*/) final {}
public:
ArrayProxy(T * data, UInt size, UInt nb_component) {
this->values = data;
this->size_ = size;
this->nb_component = nb_component;
}
ArrayProxy(const Array<T> & src) {
this->values = src.storage();
this->size_ = src.size();
this->nb_component = src.getNbComponent();
}
~ArrayProxy() override { this->values = nullptr; }
void resize(UInt size, const T & /*val*/) final {
if (size != this->size()) {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
//std::fill(this->begin(), this->end(), val);
}
void resize(UInt new_size) final {
if (new_size != this->size()) {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
}
void reserve(UInt /*size*/, UInt /*new_size*/) final {
AKANTU_EXCEPTION("cannot resize a temporary array");
}
};
/* ------------------------------------------------------------------------ */
template <typename T> struct ProxyType {};
template <typename T> struct ProxyType<Vector<T>> { using type = Vector<T>; };
template <typename T> struct ProxyType<Matrix<T>> { using type = Matrix<T>; };
template <typename T> struct ProxyType<Array<T>> {
using type = ArrayProxy<T>;
};
template <typename array> using ProxyType_t = typename ProxyType<array>::type;
} // namespace detail
} // namespace akantu
namespace pybind11 {
namespace detail {
template <typename T> struct AkaArrayType {
using type =
array_t<typename T::value_type, array::c_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Vector<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename T> struct AkaArrayType<_aka::Matrix<T>> {
using type = array_t<T, array::f_style | array::forcecast>;
};
template <typename U> using array_type_t = typename AkaArrayType<U>::type;
/* ------------------------------------------------------------------------ */
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Vector<T>> & ref,
const _aka::Vector<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Vector<T>>>(
ref.mutable_data(), ref.shape(0));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Matrix<T>> & ref,
const _aka::Matrix<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Matrix<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
template <typename T>
decltype(auto) create_proxy(array_type_t<_aka::Array<T>> & ref,
const _aka::Array<T> * /*unused*/) {
return std::make_unique<_aka::detail::ProxyType_t<_aka::Array<T>>>(
ref.mutable_data(), ref.shape(0), ref.shape(1));
}
/* ------------------------------------------------------------------------ */
template <typename T>
py::handle aka_array_cast(const _aka::Array<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Array<T>>({src.size(), src.getNbComponent()},
src.storage(), base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Vector<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Vector<T>>({src.size()}, src.storage(), base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
template <typename T>
py::handle aka_array_cast(const _aka::Matrix<T> & src,
py::handle base = handle(), bool writeable = true) {
array a;
a = array_type_t<_aka::Matrix<T>>({src.size(0), src.size(1)}, src.storage(),
base);
if (not writeable) {
array_proxy(a.ptr())->flags &= ~detail::npy_api::NPY_ARRAY_WRITEABLE_;
}
return a.release();
}
/* ------------------------------------------------------------------------ */
template <typename AkaArrayType>
class type_caster<
AkaArrayType,
std::enable_if_t<_aka::detail::is_array_type<AkaArrayType>::value>> {
protected:
using T = typename AkaArrayType::value_type;
using type = AkaArrayType;
using proxy_type = _aka::detail::ProxyType_t<AkaArrayType>;
using array_type = array_type_t<AkaArrayType>;
std::unique_ptr<proxy_type> array_proxy;
array_type_t<AkaArrayType> copy_or_ref;
public:
#if PYBIND11_VERSION_MAJOR >= 2 && PYBIND11_VERSION_MINOR >= 3
static constexpr auto name = _("AkaArray");
operator type &&() && { return std::move(*array_proxy); }
template <typename T_>
using cast_op_type = pybind11::detail::movable_cast_op_type<T_>;
#else
static PYBIND11_DESCR name() { return type_descr(_("AkaArray")); };
template <typename _T>
using cast_op_type = pybind11::detail::cast_op_type<_T>;
#endif
operator type *() { return array_proxy.get(); }
operator type &() { return *array_proxy; }
/**
* Conversion part 1 (Python->C++)
*/
bool load(handle src, bool convert) {
bool need_copy = not isinstance<array_type>(src);
auto && fits = [&](auto && aref) {
auto && dims = aref.ndim();
if (dims < 1 || dims > 2) {
return false;
}
return true;
};
if (not need_copy) {
// We don't need a converting copy, but we also need to check whether
// the strides are compatible with the Ref's stride requirements
auto aref = py::cast<array_type>(src);
if (not fits(aref)) {
return false;
}
copy_or_ref = std::move(aref);
} else {
if (not convert) {
return false;
}
auto copy = array_type::ensure(src);
if (not copy) {
return false;
}
if (not fits(copy)) {
return false;
}
copy_or_ref = std::move(array_type::ensure(src));
loader_life_support::add_patient(copy_or_ref);
}
AkaArrayType * dispatch = nullptr; // cannot detect T from the expression
array_proxy = create_proxy(copy_or_ref, dispatch);
return true;
}
/**
* Conversion part 2 (C++ -> Python)
*/
static handle cast(const type & src, return_value_policy policy,
handle parent) {
switch (policy) {
case return_value_policy::copy:
return aka_array_cast<T>(src);
case return_value_policy::reference_internal:
return aka_array_cast<T>(src, parent);
case return_value_policy::reference:
case return_value_policy::automatic:
case return_value_policy::automatic_reference:
return aka_array_cast<T>(src, none());
default:
pybind11_fail("Invalid return_value_policy for ArrayProxy type");
}
}
};
} // namespace detail
} // namespace pybind11
diff --git a/python/py_aka_common.cc b/python/py_aka_common.cc
index 22b86b372..9aa11d819 100644
--- a/python/py_aka_common.cc
+++ b/python/py_aka_common.cc
@@ -1,114 +1,147 @@
+/**
+ * @file py_aka_common.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Oct 31 2018
+ * @date last modification: Tue Mar 02 2021
+ *
+ * @brief pybind11 interface to aka_common.hh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include <aka_common.hh>
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace akantu {
/* -------------------------------------------------------------------------- */
#define PY_AKANTU_PP_VALUE(s, data, elem) \
.value(BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(data, elem))
#define PY_AKANTU_REGISTER_ENUM_(type_name, list, prefix, mod) \
py::enum_<type_name>(mod, BOOST_PP_STRINGIZE(type_name)) \
BOOST_PP_SEQ_FOR_EACH(PY_AKANTU_PP_VALUE, prefix, list) \
.export_values()
#define PY_AKANTU_REGISTER_CLASS_ENUM(type_name, list, mod) \
PY_AKANTU_REGISTER_ENUM_(type_name, list, type_name::_, mod)
#define PY_AKANTU_REGISTER_ENUM(type_name, list, mod) \
PY_AKANTU_REGISTER_ENUM_(type_name, list, , mod)
/* -------------------------------------------------------------------------- */
void register_initialize(py::module & mod) {
mod.def("__initialize", []() {
int nb_args = 0;
char ** null = nullptr;
initialize(nb_args, null);
});
}
void register_enums(py::module & mod) {
py::enum_<SpatialDirection>(mod, "SpatialDirection")
.value("_x", _x)
.value("_y", _y)
.value("_z", _z)
.export_values();
py::enum_<AnalysisMethod>(mod, "AnalysisMethod")
.value("_static", _static)
.value("_implicit_dynamic", _implicit_dynamic)
.value("_explicit_lumped_mass", _explicit_lumped_mass)
.value("_explicit_lumped_capacity", _explicit_lumped_capacity)
.value("_explicit_consistent_mass", _explicit_consistent_mass)
.value("_explicit_contact", _explicit_contact)
.value("_implicit_contact", _implicit_contact)
.export_values();
PY_AKANTU_REGISTER_CLASS_ENUM(ModelType, AKANTU_MODEL_TYPES, mod);
PY_AKANTU_REGISTER_CLASS_ENUM(NonLinearSolverType,
AKANTU_NON_LINEAR_SOLVER_TYPES, mod);
PY_AKANTU_REGISTER_CLASS_ENUM(TimeStepSolverType,
AKANTU_TIME_STEP_SOLVER_TYPE, mod);
PY_AKANTU_REGISTER_CLASS_ENUM(IntegrationSchemeType,
AKANTU_INTEGRATION_SCHEME_TYPE, mod);
PY_AKANTU_REGISTER_CLASS_ENUM(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA, mod);
py::enum_<CohesiveMethod>(mod, "CohesiveMethod")
.value("_intrinsic", _intrinsic)
.value("_extrinsic", _extrinsic)
.export_values();
py::enum_<GhostType>(mod, "GhostType")
.value("_not_ghost", _not_ghost)
.value("_ghost", _ghost)
.value("_casper", _casper)
.export_values();
py::enum_<MeshIOType>(mod, "MeshIOType")
.value("_miot_auto", _miot_auto)
.value("_miot_gmsh", _miot_gmsh)
.value("_miot_gmsh_struct", _miot_gmsh_struct)
.value("_miot_diana", _miot_diana)
.value("_miot_abaqus", _miot_abaqus)
.export_values();
py::enum_<MatrixType>(mod, "MatrixType")
.value("_unsymmetric", _unsymmetric)
.value("_symmetric", _symmetric)
.export_values();
PY_AKANTU_REGISTER_ENUM(ElementType, AKANTU_ALL_ELEMENT_TYPE(_not_defined),
mod);
PY_AKANTU_REGISTER_ENUM(ElementKind, AKANTU_ELEMENT_KIND(_ek_not_defined),
mod);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_PP_STR_TO_TYPE2(s, data, elem) ({BOOST_PP_STRINGIZE(elem), elem})
void register_functions(py::module & mod) {
mod.def("getElementTypes", []() {
std::map<std::string, akantu::ElementType> element_types{
BOOST_PP_SEQ_FOR_EACH_I(
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(AKANTU_ek_regular_ELEMENT_TYPE),
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_TYPE2, akantu,
AKANTU_ek_regular_ELEMENT_TYPE))};
return element_types;
});
}
#undef AKANTU_PP_STR_TO_TYPE2
} // namespace akantu
diff --git a/python/py_aka_common.hh b/python/py_aka_common.hh
index b0bdb21f3..2993bd566 100644
--- a/python/py_aka_common.hh
+++ b/python/py_aka_common.hh
@@ -1,14 +1,45 @@
+/**
+ * @file py_aka_common.hh
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ *
+ * @date creation: Fri May 03 2019
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to aka_common.hh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_AKA_COMMON_HH_
#define AKANTU_PY_AKA_COMMON_HH_
namespace akantu {
void register_enums(pybind11::module & mod);
void register_initialize(pybind11::module & mod);
void register_functions(pybind11::module & mod);
} // namespace akantu
#endif
diff --git a/python/py_aka_error.cc b/python/py_aka_error.cc
index 8012a913c..9e3e07caa 100644
--- a/python/py_aka_error.cc
+++ b/python/py_aka_error.cc
@@ -1,37 +1,69 @@
+/**
+ * @file py_aka_error.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue May 07 2019
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to aka_error
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_error.hh"
/* -------------------------------------------------------------------------- */
#include <aka_error.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_error(py::module & mod) {
mod.def("setDebugLevel", &debug::setDebugLevel);
mod.def("getDebugLevel", &debug::getDebugLevel);
mod.def("printBacktrace", [](bool flag) { debug::debugger.printBacktrace(flag); });
py::enum_<DebugLevel>(mod, "DebugLevel")
.value("dblError", dblError)
.value("dblException", dblException)
.value("dblCritical", dblCritical)
.value("dblMajor", dblMajor)
.value("dblWarning", dblWarning)
.value("dblInfo", dblInfo)
.value("dblTrace", dblTrace)
.value("dblAccessory", dblAccessory)
.value("dblDebug", dblDebug)
.value("dblDump", dblDump)
.value("dblTest", dblTest)
.export_values();
}
} // namespace akantu
diff --git a/python/py_aka_error.hh b/python/py_aka_error.hh
index 269bd5c4b..7f9296635 100644
--- a/python/py_aka_error.hh
+++ b/python/py_aka_error.hh
@@ -1,12 +1,43 @@
+/**
+ * @file py_aka_error.hh
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ *
+ * @date creation: Tue May 07 2019
+ * @date last modification: Mon Jan 18 2021
+ *
+ * @brief pybind11 interface to aka_error
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_AKA_ERROR_HH_
#define AKANTU_PY_AKA_ERROR_HH_
namespace akantu {
void register_error(pybind11::module & mod);
}
#endif
diff --git a/python/py_akantu.cc b/python/py_akantu.cc
index 8713b02d3..63db238f1 100644
--- a/python/py_akantu.cc
+++ b/python/py_akantu.cc
@@ -1,137 +1,171 @@
+/**
+ * @file py_akantu.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Oct 31 2018
+ * @date last modification: Mon Mar 29 2021
+ *
+ * @brief pybind11 interface to akantu main's file
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "py_aka_common.hh"
#include "py_aka_error.hh"
#include "py_boundary_conditions.hh"
#include "py_fe_engine.hh"
#include "py_group_manager.hh"
#include "py_mesh.hh"
#include "py_model.hh"
#include "py_parser.hh"
#include "py_solver.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "py_dumpable.hh"
#endif
#if defined(AKANTU_SOLID_MECHANICS)
#include "py_material.hh"
#include "py_material_selector.hh"
#include "py_solid_mechanics_model.hh"
#endif
#if defined(AKANTU_HEAT_TRANSFER)
#include "py_heat_transfer_model.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "py_fragment_manager.hh"
#include "py_solid_mechanics_model_cohesive.hh"
#endif
#if defined(AKANTU_CONTACT_MECHANICS)
#include "py_contact_mechanics_model.hh"
#include "py_model_couplers.hh"
#endif
#if defined(AKANTU_PHASE_FIELD)
#include "py_phase_field_model.hh"
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "py_structural_mechanics_model.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <aka_error.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace akantu {
void register_all(pybind11::module & mod) {
register_initialize(mod);
register_enums(mod);
register_error(mod);
register_functions(mod);
register_parser(mod);
register_solvers(mod);
register_group_manager(mod);
#if defined(AKANTU_USE_IOHELPER)
register_dumpable(mod);
#endif
register_mesh(mod);
register_fe_engine(mod);
register_boundary_conditions(mod);
register_model(mod);
#if defined(AKANTU_HEAT_TRANSFER)
register_heat_transfer_model(mod);
#endif
#if defined(AKANTU_SOLID_MECHANICS)
register_solid_mechanics_model(mod);
register_material(mod);
register_material_selector(mod);
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
register_solid_mechanics_model_cohesive(mod);
register_fragment_manager(mod);
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
register_structural_mechanics_model(mod);
#endif
#if defined(AKANTU_CONTACT_MECHANICS)
register_contact_mechanics_model(mod);
register_model_couplers(mod);
#endif
#if defined(AKANTU_PHASE_FIELD)
register_phase_field_model(mod);
register_phase_field_coupler(mod);
#endif
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
PYBIND11_MODULE(py11_akantu, mod) {
mod.doc() = "Akantu python interface";
static py::exception<akantu::debug::Exception> akantu_exception(mod,
"Exception");
py::register_exception_translator([](std::exception_ptr ptr) {
try {
if (ptr) {
std::rethrow_exception(ptr);
}
} catch (akantu::debug::Exception & e) {
if (akantu::debug::debugger.printBacktrace()) {
akantu::debug::printBacktrace();
}
akantu_exception(e.info().c_str());
}
});
akantu::register_all(mod);
mod.def("has_mpi", []() {
#if defined(AKANTU_USE_MPI)
return true;
#else
return false;
#endif
});
} // Module akantu
diff --git a/python/py_akantu.hh b/python/py_akantu.hh
index 73a65c297..b853b238c 100644
--- a/python/py_akantu.hh
+++ b/python/py_akantu.hh
@@ -1,14 +1,45 @@
+/**
+ * @file py_akantu.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to akantu main's file
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
#ifndef PY_AKANTU_HH_
#define PY_AKANTU_HH_
namespace akantu {
void register_all(pybind11::module & mod);
}
#endif /* PY_AKANTU_HH_ */
diff --git a/python/py_akantu_pybind11_compatibility.hh b/python/py_akantu_pybind11_compatibility.hh
index ea512ea51..83fa8619b 100644
--- a/python/py_akantu_pybind11_compatibility.hh
+++ b/python/py_akantu_pybind11_compatibility.hh
@@ -1,11 +1,42 @@
+/**
+ * @file py_akantu_pybind11_compatibility.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed May 26 2021
+ * @date last modification: Wed May 26 2021
+ *
+ * @brief Include for compatibility between pybind11 versions
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#ifndef PY_AKANTU_PYBIND11_COMPATIBILITY_HH_
#define PY_AKANTU_PYBIND11_COMPATIBILITY_HH_
#if not defined(PYBIND11_OVERRIDE)
#define PYBIND11_OVERRIDE PYBIND11_OVERLOAD
#define PYBIND11_OVERRIDE_NAME PYBIND11_OVERLOAD_NAME
#define PYBIND11_OVERRIDE_PURE PYBIND11_OVERLOAD_PURE
#define PYBIND11_OVERRIDE_PURE_NAME PYBIND11_OVERLOAD_PURE_NAME
#endif
#endif // PY_AKANTU_PYBIND11_COMPATIBILITY_HH_
diff --git a/python/py_boundary_conditions.cc b/python/py_boundary_conditions.cc
index 9db4b44b5..05c50abe7 100644
--- a/python/py_boundary_conditions.cc
+++ b/python/py_boundary_conditions.cc
@@ -1,98 +1,129 @@
+/**
+ * @file py_boundary_conditions.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ *
+ * @date creation: Mon Dec 02 2019
+ * @date last modification: Mon Dec 02 2019
+ *
+ * @brief pybind11 interface to boundary conditions
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_boundary_conditions.hh"
#include "py_aka_array.hh"
#include "py_akantu_pybind11_compatibility.hh"
/* -------------------------------------------------------------------------- */
#include <boundary_condition_functor.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace akantu {
namespace {
/* ------------------------------------------------------------------------ */
template <typename daughter = BC::Dirichlet::DirichletFunctor>
class PyDirichletFunctor : public daughter {
public:
/* Inherit the constructors */
using daughter::daughter;
/* Trampoline (need one for each virtual function) */
void operator()(UInt node, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE_NAME(void, daughter, "__call__", operator(), node,
flags, primal, coord);
}
};
/* ------------------------------------------------------------------------ */
template <typename daughter = BC::Neumann::NeumannFunctor>
class PyNeumannFunctor : public daughter {
public:
/* Inherit the constructors */
using daughter::daughter;
/* Trampoline (need one for each virtual function) */
void operator()(const IntegrationPoint & quad_point, Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE_PURE_NAME(void, daughter, "__call__", operator(),
quad_point, dual, coord, normals);
}
};
/* ------------------------------------------------------------------------ */
template <typename Functor, typename Constructor>
decltype(auto) register_dirichlet_functor(py::module mod, const char * name,
Constructor && cons) {
py::class_<Functor, PyDirichletFunctor<Functor>,
BC::Dirichlet::DirichletFunctor>(mod, name)
.def(cons);
}
/* ------------------------------------------------------------------------ */
template <typename Functor, typename Constructor>
decltype(auto) register_neumann_functor(py::module mod, const char * name,
Constructor && cons) {
py::class_<Functor, PyNeumannFunctor<Functor>, BC::Neumann::NeumannFunctor>(
mod, name)
.def(cons);
}
} // namespace
/* -------------------------------------------------------------------------- */
void register_boundary_conditions(py::module & mod) {
py::class_<BC::Functor>(mod, "BCFunctor");
py::class_<BC::Dirichlet::DirichletFunctor, PyDirichletFunctor<>,
BC::Functor>(mod, "DirichletFunctor")
.def(py::init())
.def(py::init<SpatialDirection>());
py::class_<BC::Neumann::NeumannFunctor, PyNeumannFunctor<>, BC::Functor>(
mod, "NeumannFunctor")
.def(py::init());
register_dirichlet_functor<BC::Dirichlet::FixedValue>(
mod, "FixedValue", py::init<Real, BC::Axis>());
register_dirichlet_functor<BC::Dirichlet::IncrementValue>(
mod, "IncrementValue", py::init<Real, BC::Axis>());
register_dirichlet_functor<BC::Dirichlet::Increment>(
mod, "Increment", py::init<Vector<Real> &>());
register_neumann_functor<BC::Neumann::FromHigherDim>(
mod, "FromHigherDim", py::init<Matrix<Real> &>());
register_neumann_functor<BC::Neumann::FromSameDim>(
mod, "FromSameDim", py::init<Vector<Real> &>());
register_neumann_functor<BC::Neumann::FreeBoundary>(mod, "FreeBoundary",
py::init());
}
} // namespace akantu
diff --git a/python/py_boundary_conditions.hh b/python/py_boundary_conditions.hh
index a5fee7649..03a774b91 100644
--- a/python/py_boundary_conditions.hh
+++ b/python/py_boundary_conditions.hh
@@ -1,12 +1,43 @@
+/**
+ * @file py_boundary_conditions.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to boundary conditions
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_BOUNDARY_CONDITIONS_HH_
#define AKANTU_PY_BOUNDARY_CONDITIONS_HH_
namespace akantu {
void register_boundary_conditions(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_BOUNDARY_CONDITIONS_HH_
diff --git a/python/py_contact_mechanics_model.cc b/python/py_contact_mechanics_model.cc
index 5f191a31e..1f2ed7dd2 100644
--- a/python/py_contact_mechanics_model.cc
+++ b/python/py_contact_mechanics_model.cc
@@ -1,130 +1,211 @@
+/**
+ * @file py_contact_mechanics_model.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Thu Jun 24 2021
+ *
+ * @brief Contact mechanics python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <contact_detector.hh>
+#include <contact_element.hh>
#include <contact_mechanics_model.hh>
#include <geometry_utils.hh>
#include <mesh_events.hh>
#include <parsable.hh>
#include <surface_selector.hh>
/* -------------------------------------------------------------------------- */
+#include <algorithm>
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_function_nocopy(func_name) \
def( \
#func_name, \
[](ContactMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](ContactMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
})
+namespace {
+ class ContactElementsView {
+ public:
+ ContactElementsView(const Array<ContactElement> & contact_elements)
+ : contact_elements(contact_elements) {}
+
+ auto begin() const { return contact_elements.begin(); }
+ auto end() const { return contact_elements.end(); }
+
+ auto size() const { return contact_elements.size(); }
+ auto operator[](size_t i) const { return contact_elements(i); }
+
+ auto contains(const ContactElement & contact_element) const {
+ return std::find(contact_elements.begin(), contact_elements.end(),
+ contact_element) != contact_elements.end();
+ }
+
+ private:
+ const Array<ContactElement> & contact_elements;
+ };
+} // namespace
+
/* -------------------------------------------------------------------------- */
void register_contact_mechanics_model(py::module & mod) {
py::class_<ContactDetector>(mod, "ContactDetector",
py::multiple_inheritance())
.def(py::init<Mesh &, const ID &>(), py::arg("mesh"),
py::arg("id") = "contact_detector")
.def(py::init<Mesh &, Array<Real>, const ID &>(), py::arg("mesh"),
py::arg("positions"), py::arg("id") = "contact_detector")
.def("setSurfaceSelector", &ContactDetector::setSurfaceSelector);
py::class_<SurfaceSelector, std::shared_ptr<SurfaceSelector>>(
mod, "SurfaceSelector", py::multiple_inheritance())
.def(py::init<Mesh &>(), py::arg("mesh"));
py::class_<PhysicalSurfaceSelector, SurfaceSelector,
std::shared_ptr<PhysicalSurfaceSelector>>(
mod, "PhysicalSurfaceSelector")
.def(py::init<Mesh &>(), py::arg("mesh"));
py::class_<CohesiveSurfaceSelector, SurfaceSelector,
std::shared_ptr<CohesiveSurfaceSelector>>(
mod, "CohesiveSurfaceSelector")
.def(py::init<Mesh &>(), py::arg("mesh"));
py::class_<AllSurfaceSelector, SurfaceSelector,
std::shared_ptr<AllSurfaceSelector>>(mod, "AllSurfaceSelector")
.def(py::init<Mesh &>(), py::arg("mesh"));
py::class_<ContactMechanicsModelOptions>(mod, "ContactMechanicsModelOptions")
.def(py::init<AnalysisMethod>(),
py::arg("analysis_method") = _explicit_contact);
+ /* ------------------------------------------------------------------------ */
+ py::class_<ContactElementsView>(mod, "ContactElementsView")
+ .def("__iter__",
+ [](const ContactElementsView & self) {
+ return py::make_iterator(self.begin(), self.end());
+ })
+ .def("__size__",
+ [](const ContactElementsView & self) { return self.size(); })
+ .def(
+ "__contains__",
+ [](const ContactElementsView & self, const ContactElement & element) {
+ return self.contains(element);
+ })
+ .def("__getitem__",
+ [](const ContactElementsView & self, size_t i) { return self[i]; });
+
/* ------------------------------------------------------------------------ */
py::class_<ContactMechanicsModel, Model>(mod, "ContactMechanicsModel",
py::multiple_inheritance())
.def(py::init<Mesh &, UInt, const ID &, std::shared_ptr<DOFManager>,
const ModelType>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "contact_mechanics_model",
py::arg("dof_manager") = nullptr,
py::arg("model_type") = ModelType::_contact_mechanics_model)
.def(
"initFull",
[](ContactMechanicsModel & self,
const ContactMechanicsModelOptions & options) {
self.initFull(options);
},
py::arg("options") = ContactMechanicsModelOptions())
.def(
"initFull",
[](ContactMechanicsModel & self,
const AnalysisMethod & analysis_method) {
self.initFull(_analysis_method = analysis_method);
},
py::arg("_analysis_method"))
.def_function(search)
.def_function(assembleStiffnessMatrix)
.def_function(assembleInternalForces)
.def_function_nocopy(getExternalForce)
.def_function_nocopy(getNormalForce)
.def_function_nocopy(getTangentialForce)
.def_function_nocopy(getInternalForce)
.def_function_nocopy(getGaps)
.def_function_nocopy(getNormals)
.def_function_nocopy(getNodalArea)
- .def_function_nocopy(getContactDetector);
+ .def_function_nocopy(getContactDetector)
+ .def("getContactElements", [](ContactMechanicsModel & self) {
+ return ContactElementsView(self.getContactElements());
+ });
py::class_<ContactElement>(mod, "ContactElement")
.def(py::init<>())
.def_readwrite("master", &ContactElement::master)
- .def_readwrite("slave", &ContactElement::slave);
+ .def_readwrite("slave", &ContactElement::slave)
+ .def("__repr__", [](ContactElement & self) {
+ return "{master: " + std::to_string(self.master) +
+ ", slave: " + std::to_string(self.slave) + "}";
+ });
py::class_<GeometryUtils>(mod, "GeometryUtils")
.def_static(
"normal",
py::overload_cast<const Mesh &, const Array<Real> &, const Element &,
Vector<Real> &, bool>(&GeometryUtils::normal),
py::arg("mesh"), py::arg("positions"), py::arg("element"),
py::arg("normal"), py::arg("outward") = true)
.def_static(
"covariantBasis",
py::overload_cast<const Mesh &, const Array<Real> &, const Element &,
const Vector<Real> &, Vector<Real> &,
Matrix<Real> &>(&GeometryUtils::covariantBasis),
py::arg("mesh"), py::arg("positions"), py::arg("element"),
py::arg("normal"), py::arg("natural_projection"), py::arg("basis"))
.def_static("curvature", &GeometryUtils::curvature)
.def_static("contravariantBasis", &GeometryUtils::contravariantBasis,
py::arg("covariant_basis"), py::arg("basis"))
.def_static("realProjection",
py::overload_cast<const Mesh &, const Array<Real> &,
const Vector<Real> &, const Element &,
const Vector<Real> &, Vector<Real> &>(
&GeometryUtils::realProjection),
py::arg("mesh"), py::arg("positions"), py::arg("slave"),
py::arg("element"), py::arg("normal"), py::arg("projection"))
.def_static("isBoundaryElement", &GeometryUtils::isBoundaryElement);
}
} // namespace akantu
diff --git a/python/py_contact_mechanics_model.hh b/python/py_contact_mechanics_model.hh
index cec86c46a..8856c8318 100644
--- a/python/py_contact_mechanics_model.hh
+++ b/python/py_contact_mechanics_model.hh
@@ -1,10 +1,41 @@
+/**
+ * @file py_contact_mechanics_model.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Sat Dec 12 2020
+ *
+ * @brief Contact mechanics python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef __AKANTU_PY_CONTACT_MECHANICS_MODEL_HH__
#define __AKANTU_PY_CONTACT_MECHANICS_MODEL_HH__
namespace akantu {
void register_contact_mechanics_model(pybind11::module & mod);
} // namespace akantu
#endif // __AKANTU_PY_CONTACT_MECHANICS_MODEL_HH__
diff --git a/python/py_dumpable.cc b/python/py_dumpable.cc
index 480c95e84..fb8233845 100644
--- a/python/py_dumpable.cc
+++ b/python/py_dumpable.cc
@@ -1,92 +1,135 @@
+/**
+ * @file py_dumpable.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Thu Nov 12 2020
+ *
+ * @brief pybind11 interface to Dumpers
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <dumper_iohelper_paraview.hh>
#include <mesh.hh>
/* -------------------------------------------------------------------------- */
#include <dumpable_inline_impl.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
std::vector<detail::ArrayProxy<Real>> tmp_array;
void register_dumpable(py::module & mod) {
/* ------------------------------------------------------------------------ */
py::class_<Dumpable>(mod, "Dumpable")
.def("registerDumperParaview", &Dumpable::registerDumper<DumperParaview>,
py::arg("dumper_name"), py::arg("file_name"),
py::arg("is_default") = false)
.def("addDumpMeshToDumper", &Dumpable::addDumpMeshToDumper,
py::arg("dumper_name"), py::arg("mesh"), py::arg("dimension"),
py::arg("ghost_type") = _not_ghost,
py::arg("element_kind") = _ek_regular)
.def("addDumpMesh", &Dumpable::addDumpMesh, py::arg("mesh"),
py::arg("dimension"), py::arg("ghost_type") = _not_ghost,
py::arg("element_kind") = _ek_regular)
.def("addDumpField", &Dumpable::addDumpField, py::arg("field_id"))
.def("addDumpFieldToDumper", &Dumpable::addDumpFieldToDumper,
py::arg("dumper_name"), py::arg("field_id"))
.def(
"addDumpFieldExternal",
[](Dumpable & _this, const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
return _this.addDumpFieldExternal(field_id, field);
},
py::arg("field_id"), py::arg("field"))
.def(
"addDumpFieldExternal",
[](Dumpable & _this, const std::string & field_id,
Array<Real> & field) {
auto & tmp = dynamic_cast<detail::ArrayProxy<Real> &>(field);
tmp_array.push_back(tmp);
return _this.addDumpFieldExternal(field_id, tmp_array.back());
},
py::arg("field_id"), py::arg("field"))
.def(
"addDumpFieldExternalToDumper",
[](Dumpable & _this, const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
return _this.addDumpFieldExternalToDumper(dumper_name, field_id,
field);
},
py::arg("dumper_name"), py::arg("field_id"), py::arg("field"))
- .def("dump", py::overload_cast<>(&Dumpable::dump))
- .def("dump", py::overload_cast<Real, UInt>(&Dumpable::dump),
- py::arg("time"), py::arg("step"))
- .def("dump", py::overload_cast<UInt>(&Dumpable::dump), py::arg("step"))
- .def("dump",
- py::overload_cast<const std::string &, UInt>(&Dumpable::dump),
- py::arg("dumper_name"), py::arg("step"))
- .def("dump",
- py::overload_cast<const std::string &, Real, UInt>(&Dumpable::dump),
- py::arg("dumper_name"), py::arg("time"), py::arg("step"))
- .def("dump", py::overload_cast<const std::string &>(&Dumpable::dump),
- py::arg("dumper_name"));
+ .def("dump", [](Dumpable & self) { self.dump(); })
+ .def(
+ "dump", [](Dumpable & self, UInt step) { self.dump(step); },
+ py::arg("step"))
+ .def(
+ "dump",
+ [](Dumpable & self, Real time, UInt step) { self.dump(time, step); },
+ py::arg("time"), py::arg("step"))
+ .def(
+ "dump",
+ [](Dumpable & self, const std::string & dumper) { self.dump(dumper); },
+ py::arg("dumper_name"))
+ .def(
+ "dump",
+ [](Dumpable & self, const std::string & dumper, UInt step) {
+ self.dump(dumper, step);
+ },
+ py::arg("dumper_name"), py::arg("step"))
+ .def(
+ "dump",
+ [](Dumpable & self, const std::string & dumper, Real time, UInt step) {
+ self.dump(dumper, time, step);
+ },
+ py::arg("dumper_name"), py::arg("time"), py::arg("step"));
}
/* -------------------------------------------------------------------------- */
PYBIND11_MODULE(dumper_module, mod) {
mod.attr("__name__") = "py11_akantu.dumper";
/* ------------------------------------------------------------------------ */
py::class_<dumpers::Field, std::shared_ptr<dumpers::Field>>(mod, "Field");
/* ------------------------------------------------------------------------ */
py::class_<dumpers::ElementalField<UInt>, dumpers::Field,
std::shared_ptr<dumpers::ElementalField<UInt>>>(
mod, "ElementalFieldUInt", py::multiple_inheritance())
.def(py::init<dumpers::ElementalField<UInt>::field_type &, UInt,
GhostType, ElementKind>(),
py::arg("field"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("ghost_type") = _not_ghost,
py::arg("element_kind") = _ek_not_defined);
}
} // namespace akantu
diff --git a/python/py_dumpable.hh b/python/py_dumpable.hh
index df09c66ac..a5d5fe386 100644
--- a/python/py_dumpable.hh
+++ b/python/py_dumpable.hh
@@ -1,12 +1,43 @@
+/**
+ * @file py_dumpable.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to Dumpers
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_DUMPABLE_HH_
#define AKANTU_PY_DUMPABLE_HH_
namespace akantu {
void register_dumpable(pybind11::module & mod);
} // namespace akantu
#endif /* AKANTU_PY_DUMPABLE_HH_ */
diff --git a/python/py_fe_engine.cc b/python/py_fe_engine.cc
index 021539fc7..c17e05a49 100644
--- a/python/py_fe_engine.cc
+++ b/python/py_fe_engine.cc
@@ -1,120 +1,155 @@
+/**
+ * @file py_fe_engine.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Nov 27 2019
+ * @date last modification: Sat Dec 12 2020
+ *
+ * @brief pybind11 interface to FEEngine
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include "py_aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <element.hh>
#include <fe_engine.hh>
#include <integration_point.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/functional.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
void register_fe_engine(py::module & mod) {
py::class_<Element>(mod, "Element")
.def(py::init([](ElementType type, UInt id) {
return new Element{type, id, _not_ghost};
}))
.def(py::init([](ElementType type, UInt id, GhostType ghost_type) {
return new Element{type, id, ghost_type};
}))
.def("__lt__",
[](Element & self, const Element & other) { return (self < other); })
.def("__repr__", [](Element & self) { return std::to_string(self); });
mod.attr("ElementNull") = ElementNull;
py::class_<FEEngine>(mod, "FEEngine")
.def(
"getNbIntegrationPoints",
[](FEEngine & fem, const ElementType & type,
const GhostType & ghost_type) {
return fem.getNbIntegrationPoints(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def(
"gradientOnIntegrationPoints",
[](FEEngine & fem, const Array<Real> & u, Array<Real> & nablauq,
UInt nb_degree_of_freedom, ElementType type, GhostType ghost_type,
const Array<UInt> * filter_elements) {
if (filter_elements == nullptr) {
// This is due to the ArrayProxy that looses the
// empty_filter information
filter_elements = &empty_filter;
}
fem.gradientOnIntegrationPoints(u, nablauq, nb_degree_of_freedom,
type, ghost_type, *filter_elements);
},
py::arg("u"), py::arg("nablauq"), py::arg("nb_degree_of_freedom"),
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::arg("filter_elements") = nullptr)
.def(
"interpolateOnIntegrationPoints",
[](FEEngine & self, const Array<Real> & u, Array<Real> & uq,
UInt nb_degree_of_freedom, ElementType type, GhostType ghost_type,
const Array<UInt> * filter_elements) {
if (filter_elements == nullptr) {
// This is due to the ArrayProxy that looses the
// empty_filter information
filter_elements = &empty_filter;
}
self.interpolateOnIntegrationPoints(u, uq, nb_degree_of_freedom,
type, ghost_type,
*filter_elements);
},
py::arg("u"), py::arg("uq"), py::arg("nb_degree_of_freedom"),
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::arg("filter_elements") = nullptr)
.def(
"interpolateOnIntegrationPoints",
[](FEEngine & self, const Array<Real> & u,
ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) {
self.interpolateOnIntegrationPoints(u, uq, filter_elements);
},
py::arg("u"), py::arg("uq"), py::arg("filter_elements") = nullptr)
.def(
"computeIntegrationPointsCoordinates",
[](FEEngine & self, ElementTypeMapArray<Real> & coordinates,
const ElementTypeMapArray<UInt> * filter_elements)
-> decltype(auto) {
return self.computeIntegrationPointsCoordinates(coordinates,
filter_elements);
},
py::arg("coordinates"), py::arg("filter_elements") = nullptr)
.def(
"assembleFieldLumped",
[](FEEngine & fem,
const std::function<void(Matrix<Real> &, const Element &)> &
field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type) {
fem.assembleFieldLumped(field_funct, matrix_id, dof_id, dof_manager,
type, ghost_type);
},
py::arg("field_funct"), py::arg("matrix_id"), py::arg("dof_id"),
py::arg("dof_manager"), py::arg("type"),
py::arg("ghost_type") = _not_ghost)
.def(
"assembleFieldMatrix",
[](FEEngine & fem,
const std::function<void(Matrix<Real> &, const Element &)> &
field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type = _not_ghost) {
fem.assembleFieldMatrix(field_funct, matrix_id, dof_id, dof_manager,
type, ghost_type);
},
py::arg("field_funct"), py::arg("matrix_id"), py::arg("dof_id"),
py::arg("dof_manager"), py::arg("type"),
- py::arg("ghost_type") = _not_ghost);
+ py::arg("ghost_type") = _not_ghost)
+ .def("getElementInradius", [](FEEngine & self, const Element & element) {
+ return self.getElementInradius(element);
+ });
py::class_<IntegrationPoint>(mod, "IntegrationPoint");
}
} // namespace akantu
diff --git a/python/py_fe_engine.hh b/python/py_fe_engine.hh
index feaafd1a1..c65b4f1d7 100644
--- a/python/py_fe_engine.hh
+++ b/python/py_fe_engine.hh
@@ -1,12 +1,45 @@
+/**
+ * @file py_fe_engine.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to FEEngine
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_FE_ENGINE_HH_
#define AKANTU_PY_FE_ENGINE_HH_
namespace akantu {
void register_fe_engine(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_FE_ENGINE_HH_
diff --git a/python/py_fragment_manager.cc b/python/py_fragment_manager.cc
index cd2a48e9b..a44b29b49 100644
--- a/python/py_fragment_manager.cc
+++ b/python/py_fragment_manager.cc
@@ -1,50 +1,82 @@
+/**
+ * @file py_fragment_manager.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Mar 29 2021
+ * @date last modification: Mon Mar 29 2021
+ *
+ * @brief pybind11 interface to FragmentManager
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include <fragment_manager.hh>
#include <solid_mechanics_model_cohesive.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
def( \
#func_name, \
[](SolidMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](FragmentManager & self) -> decltype(auto) { \
return self.func_name(); \
})
void register_fragment_manager(py::module & mod) {
py::class_<FragmentManager, GroupManager>(mod, "FragmentManager")
.def(py::init<SolidMechanicsModelCohesive &, bool, const ID &>(),
py::arg("model"), py::arg("dump_data") = true,
py::arg("ID") = "fragment_manager")
.def("buildFragments", &FragmentManager::buildFragments,
py::arg("damage_limit") = 1.)
.def_function(computeCenterOfMass)
.def_function(computeVelocity)
.def_function(computeInertiaMoments)
.def("computeAllData", &FragmentManager::computeAllData,
py::arg("damage_limit") = 1.)
.def_function(computeNbElementsPerFragment)
.def_function(getNbFragment)
.def_function(getMass)
.def_function(getVelocity)
.def_function(getMomentsOfInertia)
.def_function(getPrincipalDirections)
.def_function(getNbElementsPerFragment);
}
} // namespace akantu
diff --git a/python/py_fragment_manager.hh b/python/py_fragment_manager.hh
index 2cbbed1d8..d7cc6476f 100644
--- a/python/py_fragment_manager.hh
+++ b/python/py_fragment_manager.hh
@@ -1,12 +1,46 @@
+/**
+ * @file py_fragment_manager.hh
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Mar 29 2021
+ * @date last modification: Mon Mar 29 2021
+ *
+ * @brief pybind11 interface to FragmentManager
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_FRAGMENT_MANAGER_HH_
#define AKANTU_PY_FRAGMENT_MANAGER_HH_
namespace akantu {
void register_fragment_manager(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_FRAGMENT_MANAGER_HH_
diff --git a/python/py_group_manager.cc b/python/py_group_manager.cc
index 305d77889..02bd999da 100644
--- a/python/py_group_manager.cc
+++ b/python/py_group_manager.cc
@@ -1,143 +1,178 @@
+/**
+ * @file py_group_manager.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Mon Dec 02 2019
+ *
+ * @brief pybind11 interface to GroupManager, ElementGroup and NodeGroup
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <element_group.hh>
#include <node_group.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_group_manager(py::module & mod) {
/* ------------------------------------------------------------------------ */
py::class_<NodeGroup>(mod, "NodeGroup")
.def(
"getNodes",
[](NodeGroup & self) -> decltype(auto) { return self.getNodes(); },
py::return_value_policy::reference)
.def("__len__", &NodeGroup::size)
.def(
"__iter__",
[](const NodeGroup & self) {
return py::make_iterator(self.begin(), self.end());
},
py::keep_alive<0, 1>())
.def("__contains__",
[](const NodeGroup & self, UInt node) {
return self.find(node) != UInt(-1);
})
.def("getName", &NodeGroup::getName)
.def("clear", &NodeGroup::clear)
.def("empty", &NodeGroup::empty)
.def("append", &NodeGroup::append)
.def("add", &NodeGroup::add, py::arg("node"),
py::arg("check_for_duplicate") = true)
.def("remove", &NodeGroup::add);
/* ------------------------------------------------------------------------ */
py::class_<ElementGroup>(mod, "ElementGroup")
.def(
"getNodeGroup",
[](ElementGroup & self) -> decltype(auto) {
return self.getNodeGroup();
},
py::return_value_policy::reference)
.def("getName", &ElementGroup::getName)
.def(
"getElements",
[](ElementGroup & self) -> decltype(auto) {
return self.getElements();
},
py::return_value_policy::reference)
.def(
"getNodeGroup",
[](ElementGroup & self) -> decltype(auto) {
return self.getNodeGroup();
},
py::return_value_policy::reference)
.def("__len__", [](const ElementGroup & self) { return self.size(); })
.def("clear", [](ElementGroup & self) { self.clear(); })
.def("empty", &ElementGroup::empty)
.def("append", &ElementGroup::append)
.def(
"add",
[](ElementGroup & self, const Element & element, bool add_nodes,
bool check_for_duplicate) {
self.add(element, add_nodes, check_for_duplicate);
},
py::arg("element"), py::arg("add_nodes") = false,
py::arg("check_for_duplicate") = true)
.def("fillFromNodeGroup", &ElementGroup::fillFromNodeGroup)
.def("addDimension", &ElementGroup::addDimension);
/* ------------------------------------------------------------------------ */
py::class_<GroupManager>(mod, "GroupManager")
.def(
"getElementGroup",
[](GroupManager & self, const std::string & name) -> decltype(auto) {
return self.getElementGroup(name);
},
py::return_value_policy::reference)
.def("iterateElementGroups",
[](GroupManager & self) -> decltype(auto) {
std::vector<std::reference_wrapper<ElementGroup>> groups;
for (auto & group : self.iterateElementGroups()) {
groups.emplace_back(group);
}
return groups;
})
.def("iterateNodeGroups",
[](GroupManager & self) -> decltype(auto) {
std::vector<std::reference_wrapper<NodeGroup>> groups;
for (auto & group : self.iterateNodeGroups()) {
groups.emplace_back(group);
}
return groups;
})
.def("createNodeGroup", &GroupManager::createNodeGroup,
py::return_value_policy::reference)
- .def("createElementGroup",
- py::overload_cast<const std::string &, UInt, bool>(
- &GroupManager::createElementGroup),
- py::return_value_policy::reference)
+ .def(
+ "createElementGroup",
+ [](GroupManager & self, const std::string & id,
+ UInt spatial_dimension, bool b) -> decltype(auto) {
+ return self.createElementGroup(id, spatial_dimension, b);
+ },
+ py::return_value_policy::reference)
.def("createGroupsFromMeshDataUInt",
&GroupManager::createGroupsFromMeshData<UInt>)
.def("createElementGroupFromNodeGroup",
&GroupManager::createElementGroupFromNodeGroup, py::arg("name"),
py::arg("node_group"), py::arg("dimension") = _all_dimensions)
.def(
"getNodeGroup",
[](GroupManager & self, const std::string & name) -> decltype(auto) {
return self.getNodeGroup(name);
},
py::return_value_policy::reference)
.def(
"nodeGroups",
[](GroupManager & self) {
std::vector<NodeGroup *> groups;
for (auto & g : self.iterateNodeGroups()) {
groups.push_back(&g);
}
return groups;
},
py::return_value_policy::reference)
.def(
"elementGroups",
[](GroupManager & self) {
std::vector<ElementGroup *> groups;
for (auto & g : self.iterateElementGroups()) {
groups.push_back(&g);
}
return groups;
},
py::return_value_policy::reference)
.def("createBoundaryGroupFromGeometry",
&GroupManager::createBoundaryGroupFromGeometry);
}
} // namespace akantu
diff --git a/python/py_group_manager.hh b/python/py_group_manager.hh
index 9b1917b6d..8ad3edce0 100644
--- a/python/py_group_manager.hh
+++ b/python/py_group_manager.hh
@@ -1,10 +1,42 @@
+/**
+ * @file py_group_manager.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to GroupManager, ElementGroup and NodeGroup
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_GROUP_MANAGER_HH_
#define AKANTU_PY_GROUP_MANAGER_HH_
namespace akantu {
void register_group_manager(pybind11::module & mod);
} // namespace akantu
#endif /* AKANTU_PY_GROUP_MANAGER_HH_ */
diff --git a/python/py_heat_transfer_model.cc b/python/py_heat_transfer_model.cc
index d37cae96b..44b2df682 100644
--- a/python/py_heat_transfer_model.cc
+++ b/python/py_heat_transfer_model.cc
@@ -1,68 +1,99 @@
+/**
+ * @file py_heat_transfer_model.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Sun Jun 16 2019
+ *
+ * @brief pybind11 interface to HeatTransferModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <heat_transfer_model.hh>
#include <non_linear_solver.hh>
/* -------------------------------------------------------------------------- */
//#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
//#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
def(#func_name, \
[](HeatTransferModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](HeatTransferModel & self) -> decltype(auto) { \
return self.func_name(); \
})
/* -------------------------------------------------------------------------- */
void register_heat_transfer_model(py::module & mod) {
py::class_<HeatTransferModelOptions>(mod, "HeatTransferModelOptions")
.def(py::init<AnalysisMethod>(),
py::arg("analysis_method") = _explicit_lumped_mass);
py::class_<HeatTransferModel, Model>(mod, "HeatTransferModel",
py::multiple_inheritance())
.def(py::init<Mesh &, UInt, const ID &>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "heat_transfer_model")
.def("initFull",
[](HeatTransferModel & self,
const HeatTransferModelOptions & options) {
self.initFull(options);
},
py::arg("_analysis_method") = HeatTransferModelOptions())
.def("initFull",
[](HeatTransferModel & self,
const AnalysisMethod & _analysis_method) {
self.initFull(HeatTransferModelOptions(_analysis_method));
},
py::arg("_analysis_method"))
.def("setTimeStep", &HeatTransferModel::setTimeStep, py::arg("time_step"),
py::arg("solver_id") = "")
.def_function(getStableTimeStep)
.def_function_nocopy(getTemperature)
.def_function_nocopy(getBlockedDOFs)
.def("getTemperatureGradient", &HeatTransferModel::getTemperatureGradient,
py::arg("el_type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def("getKgradT", &HeatTransferModel::getKgradT, py::arg("el_type"),
py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference);
}
} // namespace akantu
diff --git a/python/py_heat_transfer_model.hh b/python/py_heat_transfer_model.hh
index 634c15f8a..e953101d5 100644
--- a/python/py_heat_transfer_model.hh
+++ b/python/py_heat_transfer_model.hh
@@ -1,12 +1,44 @@
+/**
+ * @file py_heat_transfer_model.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to HeatTransferModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
#define AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
namespace akantu {
void register_heat_transfer_model(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_HEAT_TRANSFERT_MODEL_HH_
diff --git a/python/py_material.cc b/python/py_material.cc
index fdc0528e0..e07f137c6 100644
--- a/python/py_material.cc
+++ b/python/py_material.cc
@@ -1,178 +1,213 @@
+/**
+ * @file py_material.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Fri Apr 09 2021
+ *
+ * @brief pybind11 interface to Material
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include "py_akantu_pybind11_compatibility.hh"
/* -------------------------------------------------------------------------- */
#include <material_selector.hh>
#include <solid_mechanics_model.hh>
#if defined(AKANTU_COHESIVE_ELEMENT)
#include <solid_mechanics_model_cohesive.hh>
#endif
#include <material_elastic.cc>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
template <typename _Material> class PyMaterial : public _Material {
public:
/* Inherit the constructors */
using _Material::_Material;
~PyMaterial() override = default;
void initMaterial() override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE(void, _Material, initMaterial, );
};
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE_PURE(void, _Material, computeStress, el_type,
ghost_type);
}
void computeTangentModuli(ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE(void, _Material, computeTangentModuli, el_type,
tangent_matrix, ghost_type);
}
void computePotentialEnergy(ElementType el_type) override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE(void, _Material, computePotentialEnergy, el_type);
}
Real getPushWaveSpeed(const Element & element) const override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE(Real, _Material, getPushWaveSpeed, element);
}
Real getShearWaveSpeed(const Element & element) const override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE(Real, _Material, getShearWaveSpeed, element);
}
template <typename T>
void registerInternal(const std::string & name, UInt nb_component) {
auto && internal = std::make_shared<InternalField<T>>(name, *this);
AKANTU_DEBUG_INFO("alloc internal " << name << " "
<< &this->internals[name]);
internal->initialize(nb_component);
this->internals[name] = internal;
}
protected:
std::map<std::string, std::shared_ptr<ElementTypeMapBase>> internals;
};
/* ------------------------------------------------------------------------ */
template <typename T>
void register_internal_field(py::module & mod, const std::string & name) {
py::class_<InternalField<T>, ElementTypeMapArray<T>,
std::shared_ptr<InternalField<T>>>(
mod, ("InternalField" + name).c_str());
}
/* ------------------------------------------------------------------------ */
template <typename _Material>
void register_material_classes(py::module & mod, const std::string & name) {
py::class_<_Material, Material, Parsable, PyMaterial<_Material>>(
mod, name.c_str(), py::multiple_inheritance())
.def(py::init<SolidMechanicsModel &, const ID &>());
}
} // namespace
/* -------------------------------------------------------------------------- */
void register_material(py::module & mod) {
py::class_<MaterialFactory>(mod, "MaterialFactory")
.def_static(
"getInstance",
[]() -> MaterialFactory & { return Material::getFactory(); },
py::return_value_policy::reference)
.def("registerAllocator",
[](MaterialFactory & self, const std::string id, py::function func) {
self.registerAllocator(
id,
[func, id](UInt dim, const ID & /*unused*/,
SolidMechanicsModel & model,
const ID & option) -> std::unique_ptr<Material> {
py::object obj = func(dim, id, model, option);
auto & ptr = py::cast<Material &>(obj);
obj.release();
return std::unique_ptr<Material>(&ptr);
});
})
.def("getPossibleAllocators", &MaterialFactory::getPossibleAllocators);
register_internal_field<Real>(mod, "Real");
register_internal_field<UInt>(mod, "UInt");
py::class_<Material, Parsable, PyMaterial<Material>>(
mod, "Material", py::multiple_inheritance())
.def(py::init<SolidMechanicsModel &, const ID &>())
.def(
"getGradU",
[](Material & self, ElementType el_type,
GhostType ghost_type = _not_ghost) -> decltype(auto) {
return self.getGradU(el_type, ghost_type);
},
py::arg("el_type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"getStress",
[](Material & self, ElementType el_type,
GhostType ghost_type = _not_ghost) -> decltype(auto) {
return self.getStress(el_type, ghost_type);
},
py::arg("el_type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"getPotentialEnergy",
[](Material & self, ElementType el_type) -> decltype(auto) {
return self.getPotentialEnergy(el_type);
},
py::return_value_policy::reference)
.def("initMaterial", &Material::initMaterial)
.def("getModel", &Material::getModel)
.def("registerInternalReal",
[](Material & self, const std::string & name, UInt nb_component) {
return dynamic_cast<PyMaterial<Material> &>(self)
.registerInternal<Real>(name, nb_component);
})
.def("registerInternalUInt",
[](Material & self, const std::string & name, UInt nb_component) {
return dynamic_cast<PyMaterial<Material> &>(self)
.registerInternal<UInt>(name, nb_component);
})
.def(
"getInternalReal",
[](Material & self, const ID & id) -> decltype(auto) {
return self.getInternal<Real>(id);
},
py::arg("id"), py::return_value_policy::reference)
.def(
"getInternalUInt",
[](Material & self, const ID & id) -> decltype(auto) {
return self.getInternal<UInt>(id);
},
py::arg("id"), py::return_value_policy::reference)
.def(
"getElementFilter",
[](Material & self) -> decltype(auto) {
return self.getElementFilter();
},
- py::return_value_policy::reference);
+ py::return_value_policy::reference)
+ .def("getPushWaveSpeed", &Material::getPushWaveSpeed)
+ .def("getShearWaveSpeed", &Material::getShearWaveSpeed);
register_material_classes<MaterialElastic<2>>(mod, "MaterialElastic2D");
register_material_classes<MaterialElastic<3>>(mod, "MaterialElastic3D");
}
} // namespace akantu
diff --git a/python/py_material.hh b/python/py_material.hh
index 910a95843..ff6751264 100644
--- a/python/py_material.hh
+++ b/python/py_material.hh
@@ -1,12 +1,44 @@
+/**
+ * @file py_material.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to Material
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_MATERIAL_HH_
#define AKANTU_PY_MATERIAL_HH_
namespace akantu {
void register_material(pybind11::module & mod);
void register_material_selector(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_MATERIAL_HH_
diff --git a/python/py_material_selector.cc b/python/py_material_selector.cc
index 81a58bc43..1601109ce 100644
--- a/python/py_material_selector.cc
+++ b/python/py_material_selector.cc
@@ -1,86 +1,117 @@
+/**
+ * @file py_material_selector.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed May 26 2021
+ * @date last modification: Wed May 26 2021
+ *
+ * @brief Material selector python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_material_selector.hh"
#include "py_akantu_pybind11_compatibility.hh"
/* -------------------------------------------------------------------------- */
#include <material_selector.hh>
#include <solid_mechanics_model.hh>
#if defined(AKANTU_COHESIVE_ELEMENT)
#include <material_selector_cohesive.hh>
#include <solid_mechanics_model_cohesive.hh>
#endif
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
template <class Base = MaterialSelector>
class PyMaterialSelector : public Base {
public:
/* Inherit the constructors */
using Base::Base;
~PyMaterialSelector() override = default;
UInt operator()(const Element & element) override {
// NOLINTNEXTLINE
PYBIND11_OVERRIDE_NAME(UInt, MaterialSelector, "__call__", operator(),
element);
}
};
template <class MaterialSelectorDaughter>
decltype(auto) register_material_selectors(py::module & mod,
const std::string & class_name) {
return py::class_<MaterialSelectorDaughter, MaterialSelector,
PyMaterialSelector<MaterialSelectorDaughter>,
std::shared_ptr<MaterialSelectorDaughter>>(
mod, class_name.c_str());
}
} // namespace
void register_material_selector(py::module & mod) {
py::class_<MaterialSelector, PyMaterialSelector<>,
std::shared_ptr<MaterialSelector>>(mod, "MaterialSelector")
.def(py::init())
.def("setFallback",
[](MaterialSelector & self, UInt f) { self.setFallback(f); })
.def("setFallback",
[](MaterialSelector & self,
const std::shared_ptr<MaterialSelector> & fallback_selector) {
self.setFallback(fallback_selector);
})
.def("__call__", &MaterialSelector::operator());
register_material_selectors<DefaultMaterialSelector>(
mod, "DefaultMaterialSelector")
.def(py::init<const ElementTypeMapArray<UInt>>());
register_material_selectors<MeshDataMaterialSelector<std::string>>(
mod, "MeshDataMaterialSelectorString")
.def(py::init<const std::string &, const SolidMechanicsModel &, UInt>(),
py::arg("name"), py::arg("model"), py::arg("first_index") = 1);
#if defined(AKANTU_COHESIVE_ELEMENT)
register_material_selectors<DefaultMaterialCohesiveSelector>(
mod, "DefaultMaterialCohesiveSelector")
.def(py::init<const SolidMechanicsModelCohesive &>());
register_material_selectors<MeshDataMaterialCohesiveSelector>(
mod, "MeshDataMaterialCohesiveSelector")
.def(py::init<const SolidMechanicsModelCohesive &>());
register_material_selectors<MaterialCohesiveRulesSelector>(
mod, "MaterialCohesiveRulesSelector")
.def(py::init<const SolidMechanicsModelCohesive &,
const MaterialCohesiveRules &, const ID &>(),
py::arg("model"), py::arg("rules"),
py::arg("mesh_data_id") = "physical_names");
#endif
}
} // namespace akantu
diff --git a/python/py_material_selector.hh b/python/py_material_selector.hh
index e4fcde441..a76575cba 100644
--- a/python/py_material_selector.hh
+++ b/python/py_material_selector.hh
@@ -1,12 +1,43 @@
+/**
+ * @file py_material_selector.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed May 26 2021
+ * @date last modification: Wed May 26 2021
+ *
+ * @brief Material selector python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_MATERIAL_SELECTOR_HH_
#define AKANTU_PY_MATERIAL_SELECTOR_HH_
namespace akantu {
void register_material_selector(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_MATERIAL_SELECTOR_HH_
diff --git a/python/py_mesh.cc b/python/py_mesh.cc
index 25ea2e8c4..b3b90270e 100644
--- a/python/py_mesh.cc
+++ b/python/py_mesh.cc
@@ -1,160 +1,194 @@
+/**
+ * @file py_mesh.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Mon Mar 15 2021
+ *
+ * @brief pybind11 interface to Mesh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <mesh.hh>
#include <mesh_accessor.hh>
#include <mesh_utils.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
/* ------------------------------------------------------------------------ */
template <typename T>
void register_element_type_map_array(py::module & mod,
const std::string & name) {
py::class_<ElementTypeMapArray<T>, std::shared_ptr<ElementTypeMapArray<T>>>(
mod, ("ElementTypeMapArray" + name).c_str())
.def(
"__call__",
[](ElementTypeMapArray<T> & self, ElementType type,
GhostType ghost_type) -> decltype(auto) {
return self(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"elementTypes",
[](ElementTypeMapArray<T> & self, UInt _dim, GhostType _ghost_type,
ElementKind _kind) -> std::vector<ElementType> {
auto types = self.elementTypes(_dim, _ghost_type, _kind);
std::vector<ElementType> _types;
for (auto && t : types) {
_types.push_back(t);
}
return _types;
},
py::arg("dim") = _all_dimensions,
py::arg("ghost_type") = _not_ghost, py::arg("kind") = _ek_regular);
}
} // namespace
/* -------------------------------------------------------------------------- */
void register_mesh(py::module & mod) {
register_element_type_map_array<Real>(mod, "Real");
register_element_type_map_array<UInt>(mod, "UInt");
//register_element_type_map_array<std::string>(mod, "String");
py::class_<MeshData>(mod, "MeshData")
.def(
"getElementalDataUInt",
[](MeshData & _this, const ID & name) -> decltype(auto) {
return _this.getElementalData<UInt>(name);
},
py::return_value_policy::reference)
.def(
"getElementalDataReal",
[](MeshData & _this, const ID & name) -> decltype(auto) {
return _this.getElementalData<Real>(name);
},
py::return_value_policy::reference);
py::class_<Mesh, GroupManager, Dumpable, MeshData>(mod, "Mesh",
py::multiple_inheritance())
.def(py::init<UInt, const ID &>(), py::arg("spatial_dimension"),
py::arg("id") = "mesh")
.def("read", &Mesh::read, py::arg("filename"),
py::arg("mesh_io_type") = _miot_auto, "read the mesh from a file")
.def(
"getNodes",
[](Mesh & self) -> decltype(auto) { return self.getNodes(); },
py::return_value_policy::reference)
.def("getNbNodes", &Mesh::getNbNodes)
.def(
"getConnectivity",
[](Mesh & self, ElementType type) -> decltype(auto) {
return self.getConnectivity(type);
},
py::return_value_policy::reference)
.def(
"addConnectivityType",
[](Mesh & self, ElementType type, GhostType ghost_type) -> void {
self.addConnectivityType(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def("distribute", [](Mesh & self) { self.distribute(); })
.def("fillNodesToElements", &Mesh::fillNodesToElements,
py::arg("dimension") = _all_dimensions)
.def("getAssociatedElements",
[](Mesh & self, const UInt & node, py::list list) {
Array<Element> elements;
self.getAssociatedElements(node, elements);
for (auto && element : elements) {
list.append(element);
}
})
.def("makePeriodic",
[](Mesh & self, const SpatialDirection & direction) {
self.makePeriodic(direction);
})
.def(
"getNbElement",
[](Mesh & self, const UInt spatial_dimension, GhostType ghost_type,
ElementKind kind) {
return self.getNbElement(spatial_dimension, ghost_type, kind);
},
py::arg("spatial_dimension") = _all_dimensions,
py::arg("ghost_type") = _not_ghost, py::arg("kind") = _ek_not_defined)
.def(
"getNbElement",
[](Mesh & self, ElementType type, GhostType ghost_type) {
return self.getNbElement(type, ghost_type);
},
py::arg("type"), py::arg("ghost_type") = _not_ghost)
.def_static(
"getSpatialDimension",
[](ElementType & type) { return Mesh::getSpatialDimension(type); })
.def(
"getDataReal",
[](Mesh & _this, const ID & name, ElementType type,
GhostType ghost_type) -> decltype(auto) {
return _this.getData<Real>(name, type, ghost_type);
},
py::arg("name"), py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"hasDataReal",
[](Mesh & _this, const ID & name, ElementType type,
GhostType ghost_type) -> bool {
return _this.hasData<Real>(name, type, ghost_type);
},
py::arg("name"), py::arg("type"), py::arg("ghost_type") = _not_ghost);
/* ------------------------------------------------------------------------ */
py::class_<MeshUtils>(mod, "MeshUtils")
.def_static("buildFacets", &MeshUtils::buildFacets);
py::class_<MeshAccessor>(mod, "MeshAccessor")
.def(py::init<Mesh &>(), py::arg("mesh"))
.def(
"resizeConnectivity",
[](MeshAccessor & self, UInt new_size, ElementType type, GhostType gt)
-> void { self.resizeConnectivity(new_size, type, gt); },
py::arg("new_size"), py::arg("type"),
py::arg("ghost_type") = _not_ghost)
.def(
"resizeNodes",
[](MeshAccessor & self, UInt new_size) -> void {
self.resizeNodes(new_size);
},
py::arg("new_size"))
.def("makeReady", &MeshAccessor::makeReady);
}
} // namespace akantu
diff --git a/python/py_mesh.hh b/python/py_mesh.hh
index 2efe88e06..ae7142252 100644
--- a/python/py_mesh.hh
+++ b/python/py_mesh.hh
@@ -1,10 +1,42 @@
+/**
+ * @file py_mesh.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to Mesh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_MESH_HH_
#define AKANTU_PY_MESH_HH_
namespace akantu {
void register_mesh(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_MESH_HH_
diff --git a/python/py_model.cc b/python/py_model.cc
index ab06474f6..01c123893 100644
--- a/python/py_model.cc
+++ b/python/py_model.cc
@@ -1,107 +1,159 @@
+/**
+ * @file py_model.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Sat Mar 13 2021
+ *
+ * @brief pybind11 interface to Model and parent classes
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <model.hh>
#include <non_linear_solver.hh>
#include <sparse_matrix_aij.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_model(py::module & mod) {
py::class_<DOFManager>(mod, "DOFManager")
.def("getMatrix", &DOFManager::getMatrix,
py::return_value_policy::reference)
.def(
"getNewMatrix",
[](DOFManager & self, const std::string & name,
const std::string & matrix_to_copy_id) -> decltype(auto) {
return self.getNewMatrix(name, matrix_to_copy_id);
},
py::return_value_policy::reference)
.def(
"getResidual",
[](DOFManager & self) -> decltype(auto) {
return self.getResidual();
},
py::return_value_policy::reference)
.def("getArrayPerDOFs", &DOFManager::getArrayPerDOFs)
.def(
"hasMatrix",
[](DOFManager & self, const ID & name) -> bool {
return self.hasMatrix(name);
},
py::arg("name"))
.def("assembleToResidual", &DOFManager::assembleToResidual);
py::class_<NonLinearSolver>(mod, "NonLinearSolver")
.def(
"set",
[](NonLinearSolver & self, const std::string & id, const Real & val) {
if (id == "max_iterations") {
self.set(id, int(val));
} else {
self.set(id, val);
}
})
.def("set",
[](NonLinearSolver & self, const std::string & id,
const SolveConvergenceCriteria & val) { self.set(id, val); });
py::class_<ModelSolver, Parsable>(mod, "ModelSolver",
py::multiple_inheritance())
.def("getNonLinearSolver",
(NonLinearSolver & (ModelSolver::*)(const ID &)) &
ModelSolver::getNonLinearSolver,
py::arg("solver_id") = "", py::return_value_policy::reference)
.def("solveStep", [](ModelSolver & self) { self.solveStep(); })
.def("solveStep", [](ModelSolver & self, const ID & solver_id) {
self.solveStep(solver_id);
});
py::class_<Model, ModelSolver>(mod, "Model", py::multiple_inheritance())
.def("setBaseName", &Model::setBaseName)
.def("setDirectory", &Model::setDirectory)
.def("getFEEngine", &Model::getFEEngine, py::arg("name") = "",
py::return_value_policy::reference)
.def("getFEEngineBoundary", &Model::getFEEngine, py::arg("name") = "",
py::return_value_policy::reference)
.def("addDumpFieldVector", &Model::addDumpFieldVector)
.def("addDumpField", &Model::addDumpField)
.def("setBaseNameToDumper", &Model::setBaseNameToDumper)
.def("addDumpFieldVectorToDumper", &Model::addDumpFieldVectorToDumper)
.def("addDumpFieldToDumper", &Model::addDumpFieldToDumper)
- .def("dump", py::overload_cast<>(&Model::dump))
- .def("dump", py::overload_cast<UInt>(&Model::dump))
- .def("dump", py::overload_cast<Real, UInt>(&Model::dump))
- .def("dump", py::overload_cast<const std::string &>(&Model::dump))
- .def("dump", py::overload_cast<const std::string &, UInt>(&Model::dump))
- .def("dump",
- py::overload_cast<const std::string &, Real, UInt>(&Model::dump))
+ .def("dump", [](Model & self) { self.dump(); })
+ .def(
+ "dump", [](Model & self, UInt step) { self.dump(step); },
+ py::arg("step"))
+ .def(
+ "dump",
+ [](Model & self, Real time, UInt step) { self.dump(time, step); },
+ py::arg("time"), py::arg("step"))
+ .def(
+ "dump",
+ [](Model & self, const std::string & dumper) { self.dump(dumper); },
+ py::arg("dumper_name"))
+ .def(
+ "dump",
+ [](Model & self, const std::string & dumper, UInt step) {
+ self.dump(dumper, step);
+ },
+ py::arg("dumper_name"), py::arg("step"))
+ .def(
+ "dump",
+ [](Model & self, const std::string & dumper, Real time, UInt step) {
+ self.dump(dumper, time, step);
+ },
+ py::arg("dumper_name"), py::arg("time"), py::arg("step"))
.def("initNewSolver", &Model::initNewSolver)
.def(
"getNewSolver",
[](Model & self, const std::string id,
const TimeStepSolverType & time,
const NonLinearSolverType & type) {
self.getNewSolver(id, time, type);
},
py::return_value_policy::reference)
.def("setIntegrationScheme",
[](Model & self, const std::string id, const std::string primal,
const IntegrationSchemeType & scheme) {
self.setIntegrationScheme(id, primal, scheme);
})
.def("getDOFManager", &Model::getDOFManager,
py::return_value_policy::reference)
.def("assembleMatrix", &Model::assembleMatrix);
}
} // namespace akantu
diff --git a/python/py_model.hh b/python/py_model.hh
index 11e329094..1f356847c 100644
--- a/python/py_model.hh
+++ b/python/py_model.hh
@@ -1,12 +1,44 @@
+/**
+ * @file py_model.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to Model and parent classes
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_AKA_MODEL_HH_
#define AKANTU_PY_AKA_MODEL_HH_
namespace akantu {
void register_model(pybind11::module & mod);
}
#endif
diff --git a/python/py_model_couplers.cc b/python/py_model_couplers.cc
index b461d19d8..d5b250f71 100644
--- a/python/py_model_couplers.cc
+++ b/python/py_model_couplers.cc
@@ -1,90 +1,122 @@
+/**
+ * @file py_model_couplers.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Thu Jun 24 2021
+ *
+ * @brief Model Coupler python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <cohesive_contact_solvercallback.hh>
#include <coupler_solid_cohesive_contact.hh>
#include <coupler_solid_contact.hh>
#include <non_linear_solver.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
template <class CouplerSolidContact_>
auto register_coupler_solid_contact(py::module & mod,
const std::string & name)
-> py::class_<CouplerSolidContact_, Model> {
return py::class_<CouplerSolidContact_, Model>(mod, name.c_str(),
py::multiple_inheritance())
.def(py::init<Mesh &, UInt, const ID &, std::shared_ptr<DOFManager>,
const ModelType>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "coupler_solid_contact",
py::arg("dof_manager") = nullptr,
py::arg("model_type") = ModelType::_coupler_solid_contact)
.def("applyBC",
[](CouplerSolidContact_ & self,
BC::Dirichlet::DirichletFunctor & func,
const std::string & element_group) {
self.applyBC(func, element_group);
})
.def("applyBC",
[](CouplerSolidContact_ & self, BC::Neumann::NeumannFunctor & func,
const std::string & element_group) {
self.applyBC(func, element_group);
})
.def("setTimeStep", &CouplerSolidContact_::setTimeStep,
py::arg("time_step"), py::arg("solver_id") = "")
.def("getContactMechanicsModel",
&CouplerSolidContact_::getContactMechanicsModel,
py::return_value_policy::reference);
}
} // namespace
/* -------------------------------------------------------------------------- */
void register_model_couplers(py::module & mod) {
register_coupler_solid_contact<CouplerSolidContact>(mod,
"CouplerSolidContact")
.def(
"getSolidMechanicsModel",
[](CouplerSolidContact & self) -> decltype(auto) {
return self.getSolidMechanicsModel();
},
py::return_value_policy::reference)
.def(
"initFull",
[](CouplerSolidContact & self,
const AnalysisMethod & analysis_method) {
self.initFull(_analysis_method = analysis_method);
},
py::arg("_analysis_method") = _explicit_lumped_mass);
register_coupler_solid_contact<CouplerSolidCohesiveContact>(
mod, "CouplerSolidCohesiveContact")
.def(
"initFull",
[](CouplerSolidCohesiveContact & self,
const AnalysisMethod & analysis_method, bool is_extrinsic) {
self.initFull(_analysis_method = analysis_method,
_is_extrinsic = is_extrinsic);
},
py::arg("_analysis_method") = _explicit_lumped_mass,
py::arg("_is_extrinsic") = false)
.def("checkCohesiveStress",
[](CouplerSolidCohesiveContact & self) {
return self.checkCohesiveStress();
})
.def(
"getSolidMechanicsModelCohesive",
[](CouplerSolidCohesiveContact & self) -> decltype(auto) {
return self.getSolidMechanicsModelCohesive();
},
py::return_value_policy::reference);
}
} // namespace akantu
diff --git a/python/py_model_couplers.hh b/python/py_model_couplers.hh
index bb517af36..1d4e67ed1 100644
--- a/python/py_model_couplers.hh
+++ b/python/py_model_couplers.hh
@@ -1,10 +1,41 @@
+/**
+ * @file py_model_couplers.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Thu Jun 20 2019
+ * @date last modification: Sat Dec 12 2020
+ *
+ * @brief Model Coupler python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef __AKANTU_PY_MODEL_COUPLERS_HH__
#define __AKANTU_PY_MODEL_COUPLERS_HH__
namespace akantu {
void register_model_couplers(pybind11::module & mod);
} // namespace akantu
#endif // __AKANTU_PY_MODEL_COUPLERS_HH__
diff --git a/python/py_parser.cc b/python/py_parser.cc
index 2c8fc9dbf..1c9b7b496 100644
--- a/python/py_parser.cc
+++ b/python/py_parser.cc
@@ -1,70 +1,102 @@
+/**
+ * @file py_parser.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Mon Mar 01 2021
+ *
+ * @brief pybind11 interface to Mesh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <aka_common.hh>
#include <parameter_registry.hh>
#include <parsable.hh>
#include <parser.hh>
/* -------------------------------------------------------------------------- */
#include <map>
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
std::map<void *, std::map<std::string, void *>> map_params;
void register_parser(py::module & mod) {
py::enum_<ParameterAccessType>(mod, "ParameterAccessType", py::arithmetic())
.value("_pat_internal", _pat_internal)
.value("_pat_writable", _pat_writable)
.value("_pat_readable", _pat_readable)
.value("_pat_modifiable", _pat_modifiable)
.value("_pat_parsable", _pat_parsable)
.value("_pat_parsmod", _pat_parsmod)
.export_values();
py::class_<ParameterRegistry>(mod, "ParameterRegistry",
py::multiple_inheritance())
.def("registerParamReal",
[](ParameterRegistry & self, const std::string & name, UInt type,
const std::string & description) {
Real * p = new Real;
map_params[&self][name] = p;
self.registerParam<Real>(name, *p, ParameterAccessType(type),
description);
})
.def("registerParamReal",
[](ParameterRegistry & self, const Real & _default,
const std::string & name, UInt type,
const std::string & description) {
Real * p = new Real;
map_params[&self][name] = p;
self.registerParam<Real>(name, *p, _default,
ParameterAccessType(type), description);
})
.def("getReal",
[](ParameterRegistry & self, const std::string & name) {
return Real(self.get(name));
})
.def("getMatrix",
[](ParameterRegistry & self, const std::string & name) {
const Matrix<Real> & res =
static_cast<const Matrix<Real> &>(self.get(name));
return res;
},
py::return_value_policy::copy);
py::class_<Parsable, ParameterRegistry>(mod, "Parsable",
py::multiple_inheritance())
.def(py::init<const ParserType &, const ID &>());
mod.def("parseInput",
[](const std::string & input_file) {
getStaticParser().parse(input_file);
},
"Parse an Akantu input file");
}
} // namespace akantu
diff --git a/python/py_parser.hh b/python/py_parser.hh
index 66fec2b42..d7a6d60b0 100644
--- a/python/py_parser.hh
+++ b/python/py_parser.hh
@@ -1,12 +1,44 @@
+/**
+ * @file py_parser.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to Mesh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_AKA_PARSER_HH_
#define AKANTU_PY_AKA_PARSER_HH_
namespace akantu {
void register_parser(pybind11::module & mod);
}
#endif
diff --git a/python/py_phase_field_model.cc b/python/py_phase_field_model.cc
index 77a3da1e7..45e2ef393 100644
--- a/python/py_phase_field_model.cc
+++ b/python/py_phase_field_model.cc
@@ -1,123 +1,144 @@
+/**
+ * @file py_phase_field_model.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Fri Jun 25 2021
+ *
+ * @brief Phase field python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
+#include <coupler_solid_phasefield.hh>
#include <non_linear_solver.hh>
#include <phase_field_model.hh>
-#include <coupler_solid_phasefield.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
- def(#func_name, \
+ def( \
+ #func_name, \
[](PhaseFieldModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](PhaseFieldModel & self) -> decltype(auto) { \
return self.func_name(); \
})
/* -------------------------------------------------------------------------- */
-
[[gnu::visibility("default")]] void
register_phase_field_model(py::module & mod) {
py::class_<PhaseFieldModelOptions>(mod, "PhaseFieldModelOptions")
- .def(py::init<AnalysisMethod>(),
- py::arg("analysis_method") = _static);
+ .def(py::init<AnalysisMethod>(), py::arg("analysis_method") = _static);
-
py::class_<PhaseFieldModel, Model>(mod, "PhaseFieldModel",
- py::multiple_inheritance())
- .def(py::init<Mesh &, UInt, const ID &, const ModelType>(),
- py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
- py::arg("id") = "phase_field_model",
- py::arg("model_type") = ModelType::_phase_field_model)
- .def("initFull",
- [](PhaseFieldModel & self,
- const PhaseFieldModelOptions & options) {
- self.initFull(options);
- },
- py::arg("_analysis_method") = PhaseFieldModelOptions())
- .def("initFull",
- [](PhaseFieldModel & self,
- const AnalysisMethod & analysis_method) {
- self.initFull(_analysis_method = analysis_method);
- },
- py::arg("_analysis_method"))
- .def_deprecated("applyDirichletBC", "Deprecated: use applyBC")
- .def("applyBC",
- [](PhaseFieldModel & self,
- BC::Dirichlet::DirichletFunctor & func,
- const std::string & element_group) {
- self.applyBC(func, element_group);
- })
- .def("applyBC",
- [](PhaseFieldModel & self, BC::Neumann::NeumannFunctor & func,
- const std::string & element_group) {
- self.applyBC(func, element_group);
- })
- .def("setTimeStep", &PhaseFieldModel::setTimeStep,
- py::arg("time_step"), py::arg("solver_id") = "")
- .def_function(assembleStiffnessMatrix)
- .def_function(assembleInternalForces)
- .def_function_nocopy(getDamage)
- .def_function_nocopy(getInternalForce)
- .def_function_nocopy(getBlockedDOFs)
- .def_function_nocopy(getMesh)
- .def("dump", py::overload_cast<>(&PhaseFieldModel::dump))
- .def("dump",
- py::overload_cast<const std::string &>(&PhaseFieldModel::dump))
- .def("dump", py::overload_cast<const std::string &, UInt>(
- &PhaseFieldModel::dump))
- .def("dump", py::overload_cast<const std::string &, Real, UInt>(
- &PhaseFieldModel::dump))
- .def("getPhaseField",
- py::overload_cast<UInt>(&PhaseFieldModel::getPhaseField),
- py::return_value_policy::reference)
- .def("getPhaseField",
- py::overload_cast<const std::string &>(
- &PhaseFieldModel::getPhaseField),
- py::return_value_policy::reference)
- .def("getPhaseFieldIndex", &PhaseFieldModel::getPhaseFieldIndex)
- .def("setPhaseFieldSelector", &PhaseFieldModel::setPhaseFieldSelector);
-
+ py::multiple_inheritance())
+ .def(py::init<Mesh &, UInt, const ID &, const ModelType>(),
+ py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
+ py::arg("id") = "phase_field_model",
+ py::arg("model_type") = ModelType::_phase_field_model)
+ .def(
+ "initFull",
+ [](PhaseFieldModel & self, const PhaseFieldModelOptions & options) {
+ self.initFull(options);
+ },
+ py::arg("_analysis_method") = PhaseFieldModelOptions())
+ .def(
+ "initFull",
+ [](PhaseFieldModel & self, const AnalysisMethod & analysis_method) {
+ self.initFull(_analysis_method = analysis_method);
+ },
+ py::arg("_analysis_method"))
+ .def_deprecated("applyDirichletBC", "Deprecated: use applyBC")
+ .def("applyBC",
+ [](PhaseFieldModel & self, BC::Dirichlet::DirichletFunctor & func,
+ const std::string & element_group) {
+ self.applyBC(func, element_group);
+ })
+ .def("applyBC",
+ [](PhaseFieldModel & self, BC::Neumann::NeumannFunctor & func,
+ const std::string & element_group) {
+ self.applyBC(func, element_group);
+ })
+ .def("setTimeStep", &PhaseFieldModel::setTimeStep, py::arg("time_step"),
+ py::arg("solver_id") = "")
+ .def_function(assembleStiffnessMatrix)
+ .def_function(assembleInternalForces)
+ .def_function_nocopy(getDamage)
+ .def_function_nocopy(getInternalForce)
+ .def_function_nocopy(getBlockedDOFs)
+ .def_function_nocopy(getMesh)
+ .def(
+ "getPhaseField",
+ [](PhaseFieldModel & self, UInt phase_field_id) -> decltype(auto) {
+ return self.getPhaseField(phase_field_id);
+ },
+ py::arg("phase_field_id"), py::return_value_policy::reference)
+ .def(
+ "getPhaseField",
+ [](PhaseFieldModel & self,
+ const ID & phase_field_name) -> decltype(auto) {
+ return self.getPhaseField(phase_field_name);
+ },
+ py::arg("phase_field_name"), py::return_value_policy::reference)
+ .def("getPhaseFieldIndex", &PhaseFieldModel::getPhaseFieldIndex)
+ .def("setPhaseFieldSelector", &PhaseFieldModel::setPhaseFieldSelector);
}
-
[[gnu::visibility("default")]] void
register_phase_field_coupler(py::module & mod) {
-
+
py::class_<CouplerSolidPhaseField, Model>(mod, "CouplerSolidPhaseField")
- .def(py::init<Mesh &, UInt, const ID &,
- const ModelType>(),
+ .def(py::init<Mesh &, UInt, const ID &, const ModelType>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "coupler_solid_phasefield",
- py::arg("model_type") = ModelType::_coupler_solid_phasefield)
- .def("solve", [](CouplerSolidPhaseField & self, const ID & solid_solver_id,
- const ID & phase_solver_id) {
- self.solve(solid_solver_id, phase_solver_id);
- })
+ py::arg("model_type") = ModelType::_coupler_solid_phasefield)
+ .def("solve",
+ [](CouplerSolidPhaseField & self, const ID & solid_solver_id,
+ const ID & phase_solver_id) {
+ self.solve(solid_solver_id, phase_solver_id);
+ })
.def("getSolidMechanicsModel",
&CouplerSolidPhaseField::getSolidMechanicsModel,
py::return_value_policy::reference)
- .def("getPhaseFieldModel",
- &CouplerSolidPhaseField::getPhaseFieldModel,
+ .def("getPhaseFieldModel", &CouplerSolidPhaseField::getPhaseFieldModel,
py::return_value_policy::reference);
-
}
-
-
-}
+} // namespace akantu
diff --git a/python/py_phase_field_model.hh b/python/py_phase_field_model.hh
index 541f2a10a..27aaea328 100644
--- a/python/py_phase_field_model.hh
+++ b/python/py_phase_field_model.hh
@@ -1,11 +1,42 @@
+/**
+ * @file py_phase_field_model.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Feb 26 2021
+ * @date last modification: Fri May 14 2021
+ *
+ * @brief Phase field python binding
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include <pybind11/pybind11.h>
#ifndef __AKANTU_PY_PHASE_FIELD_MODEL_HH__
#define __AKANTU_PY_PHASE_FIELD_MODEL_HH__
namespace akantu {
void register_phase_field_model(pybind11::module & mod);
void register_phase_field_coupler(pybind11::module & mod);
} // namespace akantu
#endif // __AKANTU_PY_PHASE_FIELD_MODEL_HH__
diff --git a/python/py_solid_mechanics_model.cc b/python/py_solid_mechanics_model.cc
index 9166c4319..26d35c75e 100644
--- a/python/py_solid_mechanics_model.cc
+++ b/python/py_solid_mechanics_model.cc
@@ -1,122 +1,166 @@
+/**
+ * @file py_solid_mechanics_model.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Sun Jun 16 2019
+ * @date last modification: Sat Mar 13 2021
+ *
+ * @brief pybind11 interface to SolidMechanicsModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <non_linear_solver.hh>
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
def( \
#func_name, \
[](SolidMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](SolidMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
})
/* -------------------------------------------------------------------------- */
void register_solid_mechanics_model(py::module & mod) {
py::class_<SolidMechanicsModelOptions>(mod, "SolidMechanicsModelOptions")
.def(py::init<AnalysisMethod>(),
py::arg("_analysis_method") = _explicit_lumped_mass);
py::class_<SolidMechanicsModel, Model>(mod, "SolidMechanicsModel",
py::multiple_inheritance())
.def(py::init<Mesh &, UInt, const ID &, std::shared_ptr<DOFManager>,
const ModelType>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "solid_mechanics_model",
py::arg("dof_manager") = nullptr,
py::arg("model_type") = ModelType::_solid_mechanics_model)
.def(
"initFull",
[](SolidMechanicsModel & self,
const SolidMechanicsModelOptions & options) {
self.initFull(options);
},
py::arg("option") = SolidMechanicsModelOptions())
.def(
"initFull",
[](SolidMechanicsModel & self,
const AnalysisMethod & analysis_method) {
self.initFull(_analysis_method = analysis_method);
},
py::arg("_analysis_method"))
.def_deprecated("applyDirichletBC", "Deprecated: use applyBC")
.def("applyBC",
[](SolidMechanicsModel & self,
BC::Dirichlet::DirichletFunctor & func,
const std::string & element_group) {
self.applyBC(func, element_group);
})
.def("applyBC",
[](SolidMechanicsModel & self, BC::Neumann::NeumannFunctor & func,
const std::string & element_group) {
self.applyBC(func, element_group);
})
.def("setTimeStep", &SolidMechanicsModel::setTimeStep,
py::arg("time_step"), py::arg("solver_id") = "")
- .def("getEnergy",
- py::overload_cast<const std::string &>(
- &SolidMechanicsModel::getEnergy),
- py::arg("energy_id"))
- .def("getEnergy",
- py::overload_cast<const std::string &, const std::string &>(
- &SolidMechanicsModel::getEnergy),
- py::arg("energy_id"), py::arg("group_id"))
+ .def(
+ "getEnergy",
+ [](SolidMechanicsModel & self, const std::string & energy_id) {
+ return self.getEnergy(energy_id);
+ },
+ py::arg("energy_id"))
+ .def(
+ "getEnergy",
+ [](SolidMechanicsModel & self, const std::string & energy_id,
+ const std::string & group_id) {
+ return self.getEnergy(energy_id, group_id);
+ },
+ py::arg("energy_id"), py::arg("group_id"))
.def_function(assembleStiffnessMatrix)
.def_function(assembleInternalForces)
.def_function(assembleMass)
.def_function(assembleMassLumped)
.def_function(getStableTimeStep)
.def_function_nocopy(getExternalForce)
.def_function_nocopy(getDisplacement)
.def_function_nocopy(getPreviousDisplacement)
.def_function_nocopy(getCurrentPosition)
.def_function_nocopy(getIncrement)
.def_function_nocopy(getInternalForce)
.def_function_nocopy(getMass)
.def_function_nocopy(getVelocity)
.def_function_nocopy(getAcceleration)
.def_function_nocopy(getInternalForce)
.def_function_nocopy(getBlockedDOFs)
.def_function_nocopy(getMesh)
- .def("getMaterial",
- py::overload_cast<UInt>(&SolidMechanicsModel::getMaterial),
- py::return_value_policy::reference)
- .def("getMaterial",
- py::overload_cast<const std::string &>(
- &SolidMechanicsModel::getMaterial),
- py::return_value_policy::reference)
+ .def(
+ "getMaterial",
+ [](SolidMechanicsModel & self, UInt material_id) -> decltype(auto) {
+ return self.getMaterial(material_id);
+ },
+ py::arg("material_id"),
+ py::return_value_policy::reference)
+ .def(
+ "getMaterial",
+ [](SolidMechanicsModel & self, const ID & material_name)
+ -> decltype(auto) { return self.getMaterial(material_name); },
+ py::arg("material_name"),
+ py::return_value_policy::reference)
.def("getMaterialIndex", &SolidMechanicsModel::getMaterialIndex)
// .def(
// "setMaterialSelector",
// [](SolidMechanicsModel & self, MaterialSelector &
// material_selector) {
// self.setMaterialSelector(material_selector.shared_from_this());
// })
.def("setMaterialSelector",
[](SolidMechanicsModel & self,
std::shared_ptr<MaterialSelector> material_selector) {
std::cout << (*material_selector)(ElementNull) << std::endl;
self.setMaterialSelector(material_selector);
})
.def("getMaterialSelector", &SolidMechanicsModel::getMaterialSelector);
}
} // namespace akantu
diff --git a/python/py_solid_mechanics_model.hh b/python/py_solid_mechanics_model.hh
index e344e65f1..95508fb39 100644
--- a/python/py_solid_mechanics_model.hh
+++ b/python/py_solid_mechanics_model.hh
@@ -1,13 +1,45 @@
+/**
+ * @file py_solid_mechanics_model.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to SolidMechanicsModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
#define AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
namespace akantu {
void register_solid_mechanics_model(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_SOLID_MECHANICS_MODEL_HH_
diff --git a/python/py_solid_mechanics_model_cohesive.cc b/python/py_solid_mechanics_model_cohesive.cc
index d5495117d..0d11e800c 100644
--- a/python/py_solid_mechanics_model_cohesive.cc
+++ b/python/py_solid_mechanics_model_cohesive.cc
@@ -1,64 +1,95 @@
+/**
+ * @file py_solid_mechanics_model_cohesive.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Jul 21 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to SolidMechanicsModelCohesive
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <non_linear_solver.hh>
#include <solid_mechanics_model_cohesive.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
def( \
#func_name, \
[](SolidMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function(func_name) \
def(#func_name, [](SolidMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
})
void register_solid_mechanics_model_cohesive(py::module & mod) {
py::class_<CohesiveElementInserter>(mod, "CohesiveElementInserter")
.def("setLimit", &CohesiveElementInserter::setLimit);
py::class_<SolidMechanicsModelCohesiveOptions, SolidMechanicsModelOptions>(
mod, "SolidMechanicsModelCohesiveOptions")
.def(py::init<AnalysisMethod, bool>(),
py::arg("analysis_method") = _explicit_lumped_mass,
py::arg("is_extrinsic") = false);
py::class_<SolidMechanicsModelCohesive, SolidMechanicsModel>(
mod, "SolidMechanicsModelCohesive")
.def(py::init<Mesh &, UInt, const ID &>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "solid_mechanics_model")
.def(
"initFull",
[](SolidMechanicsModel & self, const AnalysisMethod & analysis_method,
bool is_extrinsic) {
self.initFull(_analysis_method = analysis_method,
_is_extrinsic = is_extrinsic);
},
py::arg("_analysis_method"), py::arg("_is_extrinsic") = false)
.def("checkCohesiveStress",
&SolidMechanicsModelCohesive::checkCohesiveStress)
.def("getElementInserter",
&SolidMechanicsModelCohesive::getElementInserter,
py::return_value_policy::reference)
.def("updateAutomaticInsertion",
&SolidMechanicsModelCohesive::updateAutomaticInsertion);
}
} // namespace akantu
diff --git a/python/py_solid_mechanics_model_cohesive.hh b/python/py_solid_mechanics_model_cohesive.hh
index c0c883d61..42a94cfcc 100644
--- a/python/py_solid_mechanics_model_cohesive.hh
+++ b/python/py_solid_mechanics_model_cohesive.hh
@@ -1,13 +1,45 @@
+/**
+ * @file py_solid_mechanics_model_cohesive.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Tue Sep 29 2020
+ *
+ * @brief pybind11 interface to SolidMechanicsModelCohesive
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
#define AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
namespace akantu {
void register_solid_mechanics_model_cohesive(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_SOLID_MECHANICS_MODEL_COHESIVE_HH_
diff --git a/python/py_solver.cc b/python/py_solver.cc
index a0146642d..962445f78 100644
--- a/python/py_solver.cc
+++ b/python/py_solver.cc
@@ -1,53 +1,84 @@
+/**
+ * @file py_solver.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Sat Mar 06 2021
+ *
+ * @brief pybind11 interface to Solver and SparseMatrix
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_solver.hh"
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <model.hh>
#include <non_linear_solver.hh>
#include <sparse_matrix_aij.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/operators.h>
#include <pybind11/pybind11.h>
#include <pybind11/stl.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void register_solvers(py::module & mod) {
py::class_<SparseMatrix>(mod, "SparseMatrix")
.def("getMatrixType", &SparseMatrix::getMatrixType)
.def("size", &SparseMatrix::size)
.def("zero", &SparseMatrix::zero)
.def("saveProfile", &SparseMatrix::saveProfile)
.def("saveMatrix", &SparseMatrix::saveMatrix)
.def(
"add", [](SparseMatrix & self, UInt i, UInt j) { self.add(i, j); },
"Add entry in the profile")
.def(
"add",
[](SparseMatrix & self, UInt i, UInt j, Real value) {
self.add(i, j, value);
},
"Add the value to the matrix")
.def(
"add",
[](SparseMatrix & self, SparseMatrix & A, Real alpha) {
self.add(A, alpha);
},
"Add a matrix to the matrix", py::arg("A"), py::arg("alpha") = 1.)
.def("__call__", [](const SparseMatrix & self, UInt i, UInt j) {
return self(i, j);
});
py::class_<SparseMatrixAIJ, SparseMatrix>(mod, "SparseMatrixAIJ")
.def("getIRN", &SparseMatrixAIJ::getIRN)
.def("getJCN", &SparseMatrixAIJ::getJCN)
.def("getA", &SparseMatrixAIJ::getA);
py::class_<SolverVector>(mod, "SolverVector");
}
} // namespace akantu
diff --git a/python/py_solver.hh b/python/py_solver.hh
index 41e1124e8..f28b18303 100644
--- a/python/py_solver.hh
+++ b/python/py_solver.hh
@@ -1,12 +1,44 @@
+/**
+ * @file py_solver.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Tue Sep 29 2020
+ * @date last modification: Wed Feb 24 2021
+ *
+ * @brief pybind11 interface to Solver and SparseMatrix
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_AKA_SOLVER_HH_
#define AKANTU_PY_AKA_SOLVER_HH_
namespace akantu {
void register_solvers(pybind11::module & mod);
}
#endif
diff --git a/python/py_structural_mechanics_model.cc b/python/py_structural_mechanics_model.cc
index 05ec73e83..8fbef76e5 100644
--- a/python/py_structural_mechanics_model.cc
+++ b/python/py_structural_mechanics_model.cc
@@ -1,129 +1,162 @@
+/**
+ * @file py_structural_mechanics_model.cc
+ *
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Feb 03 2021
+ * @date last modification: Thu Apr 01 2021
+ *
+ * @brief pybind11 interface to StructuralMechanicsModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <structural_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#define def_deprecated(func_name, mesg) \
def(func_name, [](py::args, py::kwargs) { AKANTU_ERROR(mesg); })
#define def_function_nocopy(func_name) \
def( \
#func_name, \
[](StructuralMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
}, \
py::return_value_policy::reference)
#define def_function_(func_name) \
def(#func_name, [](StructuralMechanicsModel & self) -> decltype(auto) { \
return self.func_name(); \
})
#define def_plainmember(M) def_readwrite(#M, &StructuralMaterial::M)
/* -------------------------------------------------------------------------- */
void register_structural_mechanics_model(pybind11::module & mod) {
/* First we have to register the material class
* The wrapper aims to mimic the behaviour of the real material.
*/
py::class_<StructuralMaterial>(mod, "StructuralMaterial")
.def(py::init<>())
.def(py::init<const StructuralMaterial &>())
.def_plainmember(E)
.def_plainmember(A)
.def_plainmember(I)
.def_plainmember(Iz)
.def_plainmember(Iy)
.def_plainmember(GJ)
.def_plainmember(rho)
.def_plainmember(t)
.def_plainmember(nu);
/* Now we create the structural model wrapper
* Note that this is basically a port from the solid mechanic part.
*/
py::class_<StructuralMechanicsModel, Model>(mod, "StructuralMechanicsModel")
.def(py::init<Mesh &, UInt, const ID &>(),
py::arg("mesh"), py::arg("spatial_dimension") = _all_dimensions,
py::arg("id") = "structural_mechanics_model")
.def(
"initFull",
[](StructuralMechanicsModel & self,
const AnalysisMethod & analysis_method) -> void {
self.initFull(_analysis_method = analysis_method);
},
py::arg("_analysis_method"))
.def("initFull",
[](StructuralMechanicsModel & self) -> void { self.initFull(); })
.def_function_nocopy(getExternalForce)
.def_function_nocopy(getDisplacement)
.def_function_nocopy(getInternalForce)
.def_function_nocopy(getVelocity)
.def_function_nocopy(getAcceleration)
.def_function_nocopy(getInternalForce)
.def_function_nocopy(getBlockedDOFs)
.def_function_nocopy(getMesh)
.def("setTimeStep", &StructuralMechanicsModel::setTimeStep,
py::arg("time_step"), py::arg("solver_id") = "")
.def(
"getElementMaterial",
[](StructuralMechanicsModel & self, const ElementType & type,
GhostType ghost_type) -> decltype(auto) {
return self.getElementMaterial(type, ghost_type);
},
"This function returns the map that maps elements to materials.",
py::arg("type"), py::arg("ghost_type") = _not_ghost,
py::return_value_policy::reference)
.def(
"getMaterialByElement",
[](StructuralMechanicsModel & self, Element element)
-> decltype(auto) { return self.getMaterialByElement(element); },
"This function returns the `StructuralMaterial` instance that is "
"associated with element `element`.",
py::arg("element"), py::return_value_policy::reference)
.def(
"addMaterial",
[](StructuralMechanicsModel & self, StructuralMaterial & mat,
const ID & name) -> UInt { return self.addMaterial(mat, name); },
"This function adds the `StructuralMaterial` `mat` to `self`."
" The function returns the ID of the new material.",
py::arg("mat"), py::arg("name") = "")
.def(
"getMaterial",
[](StructuralMechanicsModel & self, UInt material_index)
-> decltype(auto) { return self.getMaterial(material_index); },
"This function returns the `i`th material of `self`."
" Note a reference is returned which allows to modify the material inside `self`.",
py::arg("i"),
py::return_value_policy::reference)
.def(
"getMaterial",
[](StructuralMechanicsModel & self, const ID & name)
-> decltype(auto) { return self.getMaterial(name); },
"This function returns the material with name `i` of `self`."
" Note a reference is returned which allows to modify the material inside `self`.",
py::arg("i"),
py::return_value_policy::reference)
.def(
"getNbMaterials",
[](StructuralMechanicsModel & self) { return self.getNbMaterials(); },
"Returns the number of different materials inside `self`.")
.def("getKineticEnergy", &StructuralMechanicsModel::getKineticEnergy,
"Compute kinetic energy")
.def("getPotentialEnergy", &StructuralMechanicsModel::getPotentialEnergy,
"Compute potential energy")
.def("getEnergy", &StructuralMechanicsModel::getEnergy,
"Compute the specified energy");
} // End: register structural mechanical model
} // namespace akantu
diff --git a/python/py_structural_mechanics_model.hh b/python/py_structural_mechanics_model.hh
index a859cd1f4..462f03f79 100644
--- a/python/py_structural_mechanics_model.hh
+++ b/python/py_structural_mechanics_model.hh
@@ -1,12 +1,45 @@
+/**
+ * @file py_structural_mechanics_model.hh
+ *
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Feb 03 2021
+ * @date last modification: Mon Feb 08 2021
+ *
+ * @brief pybind11 interface to StructuralMechanicsModel
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
#ifndef AKANTU_PY_STRUCTURAL_MECHANICS_MODEL_HH_
#define AKANTU_PY_STRUCTURAL_MECHANICS_MODEL_HH_
namespace akantu {
void register_structural_mechanics_model(pybind11::module & mod);
} // namespace akantu
#endif // AKANTU_PY_STRUCTURAL_MECHANICS_MODEL_HH_
diff --git a/src/common/aka_array.cc b/src/common/aka_array.cc
index 48d7bda57..98a7cf9fb 100644
--- a/src/common/aka_array.cc
+++ b/src/common/aka_array.cc
@@ -1,96 +1,98 @@
/**
* @file aka_array.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Implementation of akantu::Array
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <memory>
#include <utility>
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Functions ArrayBase */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> UInt Array<Real>::find(const Real & elem) const {
AKANTU_DEBUG_IN();
Real epsilon = std::numeric_limits<Real>::epsilon();
auto it = std::find_if(begin(), end(), [&elem, &epsilon](auto && a) {
return std::abs(a - elem) <= epsilon;
});
AKANTU_DEBUG_OUT();
return (it != end()) ? end() - it : UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <>
Array<ElementType> &
Array<ElementType>::operator*=(const ElementType &/*alpha*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> &
Array<ElementType>::operator-=(const Array<ElementType> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> &
Array<ElementType>::operator+=(const Array<ElementType> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <> Array<char> & Array<char>::operator*=(const char & /*alpha*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator-=(const Array<char> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator+=(const Array<char> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
return *this;
}
} // namespace akantu
diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh
index 9f93dc68c..74a245513 100644
--- a/src/common/aka_array.hh
+++ b/src/common/aka_array.hh
@@ -1,443 +1,446 @@
/**
* @file aka_array.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 16 2018
+ * @date last modification: Sun Nov 22 2020
*
- * @brief Array container for Akantu
- * This container differs from the std::vector from the fact it as 2 dimensions
- * a main dimension and the size stored per entries
+ * @brief Array container for Akantu This container differs from the std::vector
+ * from the fact it as 2 dimensions a main dimension and the size stored per
+ * entries
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
#include <vector>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ARRAY_HH_
#define AKANTU_ARRAY_HH_
namespace akantu {
/// class that afford to store vectors in static memory
// NOLINTNEXTLINE(cppcoreguidelines-special-member-functions)
class ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit ArrayBase(const ID &id = "") : id(id) {}
ArrayBase(const ArrayBase & other, const ID & id = "") {
this->id = (id.empty()) ? other.id : id;
}
ArrayBase(ArrayBase && other) = default;
ArrayBase & operator=(const ArrayBase & other) = default;
ArrayBase & operator=(ArrayBase && other) noexcept = default;
virtual ~ArrayBase() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the amount of space allocated in bytes
virtual UInt getMemorySize() const = 0;
// changed empty to match std::vector empty
inline bool empty() const __attribute__((warn_unused_result)) {
return size_ == 0;
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the Size of the Array
UInt size() const { return size_; }
/// Get the number of components
AKANTU_GET_MACRO(NbComponent, nb_component, UInt);
/// Get the name of th array
AKANTU_GET_MACRO(ID, id, const ID &);
/// Set the name of th array
AKANTU_SET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the vector
ID id;
/// the size used
UInt size_{0};
/// number of components
UInt nb_component{1};
};
/* -------------------------------------------------------------------------- */
namespace {
template <std::size_t dim, typename T> struct IteratorHelper {};
template <typename T> struct IteratorHelper<0, T> { using type = T; };
template <typename T> struct IteratorHelper<1, T> { using type = Vector<T>; };
template <typename T> struct IteratorHelper<2, T> { using type = Matrix<T>; };
template <typename T> struct IteratorHelper<3, T> {
using type = Tensor3<T>;
};
template <std::size_t dim, typename T>
using IteratorHelper_t = typename IteratorHelper<dim, T>::type;
} // namespace
/* -------------------------------------------------------------------------- */
/* Memory handling layer */
/* -------------------------------------------------------------------------- */
enum class ArrayAllocationType {
_default,
_pod,
};
template <typename T>
struct ArrayAllocationTrait
: public std::conditional_t<
std::is_scalar<T>::value,
std::integral_constant<ArrayAllocationType,
ArrayAllocationType::_pod>,
std::integral_constant<ArrayAllocationType,
ArrayAllocationType::_default>> {};
/* -------------------------------------------------------------------------- */
template <typename T,
ArrayAllocationType allocation_trait = ArrayAllocationTrait<T>::value>
class ArrayDataLayer : public ArrayBase {
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
public:
~ArrayDataLayer() override = default;
/// Allocation of a new vector
explicit ArrayDataLayer(UInt size = 0, UInt nb_component = 1,
const ID & id = "");
/// Allocation of a new vector with a default value
ArrayDataLayer(UInt size, UInt nb_component, const_reference value,
const ID & id = "");
/// Copy constructor (deep copy)
ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = "");
/// Copy constructor (deep copy)
explicit ArrayDataLayer(const std::vector<value_type> & vect);
// copy operator
ArrayDataLayer & operator=(const ArrayDataLayer & other);
// move constructor
ArrayDataLayer(ArrayDataLayer && other) noexcept = default;
// move assign
ArrayDataLayer & operator=(ArrayDataLayer && other) noexcept = default;
protected:
// deallocate the memory
virtual void deallocate() {}
// allocate the memory
virtual void allocate(UInt size, UInt nb_component);
// allocate and initialize the memory
virtual void allocate(UInt size, UInt nb_component, const T & value);
public:
/// append a tuple of size nb_component containing value
inline void push_back(const_reference value);
/// append a vector
// inline void push_back(const value_type new_elem[]);
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem);
/// changes the allocated size but not the size, if new_size = 0, the size is
/// set to min(current_size and reserve size)
virtual void reserve(UInt size, UInt new_size = UInt(-1));
/// change the size of the Array
virtual void resize(UInt size);
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val);
/// get the amount of space allocated in bytes
inline UInt getMemorySize() const override;
/// Get the real size allocated in memory
inline UInt getAllocatedSize() const;
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
protected:
/// allocation type agnostic data access
T * values{nullptr};
/// data storage
std::vector<T> data_storage;
};
/* -------------------------------------------------------------------------- */
/* Actual Array */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array : public ArrayDataLayer<T> {
private:
using parent = ArrayDataLayer<T>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using value_type = typename parent::value_type;
using reference = typename parent::reference;
using pointer_type = typename parent::pointer_type;
using const_reference = typename parent::const_reference;
using array_type = Array<T>;
~Array() override;
Array() : Array(0){};
/// Allocation of a new vector
explicit Array(UInt size, UInt nb_component = 1, const ID & id = "");
/// Allocation of a new vector with a default value
explicit Array(UInt size, UInt nb_component, const_reference value,
const ID & id = "");
/// Copy constructor
Array(const Array & vect, const ID & id = "");
/// Copy constructor (deep copy)
explicit Array(const std::vector<T> & vect);
// copy operator
Array & operator=(const Array & other);
// move constructor
Array(Array && other) noexcept = default;
// move assign
Array & operator=(Array && other) noexcept = default;
/* ------------------------------------------------------------------------ */
/* Iterator */
/* ------------------------------------------------------------------------ */
/// \todo protected: does not compile with intel check why
public:
template <class R, class it, class IR = R,
bool is_tensor_ = aka::is_tensor<std::decay_t<R>>::value>
class iterator_internal;
public:
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
template <typename R = T> class const_iterator;
template <typename R = T> class iterator;
/* ------------------------------------------------------------------------ */
/// iterator for Array of nb_component = 1
using scalar_iterator = iterator<T>;
/// const_iterator for Array of nb_component = 1
using const_scalar_iterator = const_iterator<T>;
/// iterator returning Vectors of size n on entries of Array with
/// nb_component = n
using vector_iterator = iterator<Vector<T>>;
/// const_iterator returning Vectors of n size on entries of Array with
/// nb_component = n
using const_vector_iterator = const_iterator<Vector<T>>;
/// iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using matrix_iterator = iterator<Matrix<T>>;
/// const iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using const_matrix_iterator = const_iterator<Matrix<T>>;
/// iterator returning Tensor3 of size (m, n, k) on entries of Array with
/// nb_component = m*n*k
using tensor3_iterator = iterator<Tensor3<T>>;
/// const iterator returning Tensor3 of size (m, n, k) on entries of Array
/// with nb_component = m*n*k
using const_tensor3_iterator = const_iterator<Tensor3<T>>;
/* ------------------------------------------------------------------------ */
template <typename... Ns> inline decltype(auto) begin(Ns &&... n);
template <typename... Ns> inline decltype(auto) end(Ns &&... n);
template <typename... Ns> inline decltype(auto) begin(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) end(Ns &&... n) const;
template <typename... Ns> inline decltype(auto) begin_reinterpret(Ns &&... n);
template <typename... Ns> inline decltype(auto) end_reinterpret(Ns &&... n);
template <typename... Ns>
inline decltype(auto) begin_reinterpret(Ns &&... n) const;
template <typename... Ns>
inline decltype(auto) end_reinterpret(Ns &&... n) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// search elem in the vector, return the position of the first occurrence or
/// -1 if not found
UInt find(const_reference elem) const;
/// @see Array::find(const_reference elem) const
// UInt find(T elem[]) const;
/// append a value to the end of the Array
inline void push_back(const_reference value) { parent::push_back(value); }
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem) {
parent::push_back(new_elem);
}
/// append the content of the iterator at the end of the Array
template <typename Ret> inline void push_back(const iterator<Ret> & it) {
push_back(*it);
}
/// erase the value at position i
inline void erase(UInt i);
/// ask Nico, clarify
template <typename R> inline iterator<R> erase(const iterator<R> & it);
/// @see Array::find(const_reference elem) const
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline UInt find(const C<T> & elem);
/// set all entries of the array to the value t
/// @param t value to fill the array with
inline void set(T t) {
std::fill_n(this->values, this->size_ * this->nb_component, t);
}
/// set the array to T{}
inline void zero() { this->set({}); }
/// resize the array to 0
inline void clear() { this->resize(0); }
/// set all tuples of the array to a given vector or matrix
/// @param vm Matrix or Vector to fill the array with
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void set(const C<T> & vm);
/// Append the content of the other array to the current one
void append(const Array<T> & other);
/// copy another Array in the current Array, the no_sanity_check allows you to
/// force the copy in cases where you know what you do with two non matching
/// Arrays in terms of n
void copy(const Array<T, is_scal> & other, bool no_sanity_check = false);
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// substraction entry-wise
Array<T, is_scal> & operator-=(const Array<T, is_scal> & other);
/// addition entry-wise
Array<T, is_scal> & operator+=(const Array<T, is_scal> & other);
/// multiply evry entry by alpha
Array<T, is_scal> & operator*=(const T & alpha);
/// check if the array are identical entry-wise
bool operator==(const Array<T, is_scal> & other) const;
/// @see Array::operator==(const Array<T, is_scal> & other) const
bool operator!=(const Array<T, is_scal> & other) const;
/// return a reference to the j-th entry of the i-th tuple
inline reference operator()(UInt i, UInt j = 0);
/// return a const reference to the j-th entry of the i-th tuple
inline const_reference operator()(UInt i, UInt j = 0) const;
/// return a reference to the ith component of the 1D array
inline reference operator[](UInt i);
/// return a const reference to the ith component of the 1D array
inline const_reference operator[](UInt i) const;
};
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal>
inline std::ostream & operator<<(std::ostream & stream,
const Array<T, is_scal> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream,
const ArrayBase & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_array_tmpl.hh"
#endif /* AKANTU_ARRAY_HH_ */
diff --git a/src/common/aka_array_printer.hh b/src/common/aka_array_printer.hh
index cd0030613..c9d5d53ec 100644
--- a/src/common/aka_array_printer.hh
+++ b/src/common/aka_array_printer.hh
@@ -1,100 +1,104 @@
/**
* @file aka_array_printer.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mer jun 19 2019
+ * @date creation: Wed Jul 03 2019
+ * @date last modification: Tue Sep 29 2020
*
- * @brief A Documented file.
+ * @brief Helper to print arrays on screen
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_ARRAY_PRINTER_HH_
#define AKANTU_AKA_ARRAY_PRINTER_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class container, bool no_explicit = true> class ArrayPrinter {
public:
ArrayPrinter(const container & cont) : cont(cont) {}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "{";
for (UInt i = 0; i < this->cont.size(); ++i) {
stream << this->cont[i];
if (i != this->cont.size() - 1)
stream << ", ";
}
stream << "}";
}
private:
const container & cont;
};
/* -------------------------------------------------------------------------- */
template <class T> class ArrayPrinter<Array<T>> {
public:
ArrayPrinter(const Array<T> & cont) : cont(cont) {}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "{";
for (UInt i = 0; i < this->cont.size(); ++i) {
stream << "{";
for (UInt j = 0; j < this->cont.getNbComponent(); ++j) {
stream << this->cont(i, j);
if (j != this->cont.getNbComponent() - 1)
stream << ", ";
}
stream << "}";
if (i != this->cont.size() - 1)
stream << ", ";
}
stream << "}";
}
private:
const Array<T> & cont;
};
template <class container>
decltype(auto) make_printer(const container & array) {
return ArrayPrinter<container>(array);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline std::ostream & operator<<(std::ostream & stream,
const ArrayPrinter<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_AKA_ARRAY_PRINTER_HH_ */
diff --git a/src/common/aka_array_tmpl.hh b/src/common/aka_array_tmpl.hh
index cd716dab0..11994d8e8 100644
--- a/src/common/aka_array_tmpl.hh
+++ b/src/common/aka_array_tmpl.hh
@@ -1,1361 +1,1364 @@
/**
* @file aka_array_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Feb 26 2021
*
* @brief Inline functions of the classes Array<T> and ArrayBase
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T> */
/* -------------------------------------------------------------------------- */
#include "aka_array.hh" // NOLINT
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_ARRAY_TMPL_HH_
#define AKANTU_AKA_ARRAY_TMPL_HH_
namespace akantu {
namespace debug {
struct ArrayException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(UInt size,
UInt nb_component,
const ID & id)
: ArrayBase(id) {
allocate(size, nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(UInt size,
UInt nb_component,
const_reference value,
const ID & id)
: ArrayBase(id) {
allocate(size, nb_component, value);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(const ArrayDataLayer & vect,
const ID & id)
: ArrayBase(vect, id) {
this->data_storage = vect.data_storage;
this->size_ = vect.size_;
this->nb_component = vect.nb_component;
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait>::ArrayDataLayer(
const std::vector<value_type> & vect) {
this->data_storage = vect;
this->size_ = vect.size();
this->nb_component = 1;
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
ArrayDataLayer<T, allocation_trait> &
ArrayDataLayer<T, allocation_trait>::operator=(const ArrayDataLayer & other) {
if (this != &other) {
this->data_storage = other.data_storage;
this->nb_component = other.nb_component;
this->size_ = other.size_;
this->values = this->data_storage.data();
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::allocate(UInt new_size,
UInt nb_component) {
this->nb_component = nb_component;
this->resize(new_size);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::allocate(UInt new_size,
UInt nb_component,
const T & val) {
this->nb_component = nb_component;
this->resize(new_size, val);
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::resize(UInt new_size) {
this->data_storage.resize(new_size * this->nb_component);
this->values = this->data_storage.data();
this->size_ = new_size;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::resize(UInt new_size,
const T & value) {
this->data_storage.resize(new_size * this->nb_component, value);
this->values = this->data_storage.data();
this->size_ = new_size;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
void ArrayDataLayer<T, allocation_trait>::reserve(UInt size, UInt new_size) {
if (new_size != UInt(-1)) {
this->data_storage.resize(new_size * this->nb_component);
}
this->data_storage.reserve(size * this->nb_component);
this->values = this->data_storage.data();
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array with the value value for all components
* @param value the new last tuple or the array will contain nb_component copies
* of value
*/
template <typename T, ArrayAllocationType allocation_trait>
inline void ArrayDataLayer<T, allocation_trait>::push_back(const T & value) {
this->data_storage.push_back(value);
this->values = this->data_storage.data();
this->size_ += 1;
}
/* -------------------------------------------------------------------------- */
/**
* append a matrix or a vector to the array
* @param new_elem a reference to a Matrix<T> or Vector<T> */
template <typename T, ArrayAllocationType allocation_trait>
template <template <typename> class C, typename>
inline void
ArrayDataLayer<T, allocation_trait>::push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
for (UInt i = 0; i < new_elem.size(); ++i) {
this->data_storage.push_back(new_elem[i]);
}
this->values = this->data_storage.data();
this->size_ += 1;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
inline UInt ArrayDataLayer<T, allocation_trait>::getAllocatedSize() const {
return this->data_storage.capacity() / this->nb_component;
}
/* -------------------------------------------------------------------------- */
template <typename T, ArrayAllocationType allocation_trait>
inline UInt ArrayDataLayer<T, allocation_trait>::getMemorySize() const {
return this->data_storage.capacity() * sizeof(T);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T>
class ArrayDataLayer<T, ArrayAllocationType::_pod> : public ArrayBase {
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
public:
~ArrayDataLayer() override { deallocate(); }
/// Allocation of a new vector
ArrayDataLayer(UInt size = 0, UInt nb_component = 1, const ID & id = "")
: ArrayBase(id) {
allocate(size, nb_component);
}
/// Allocation of a new vector with a default value
ArrayDataLayer(UInt size, UInt nb_component, const_reference value,
const ID & id = "")
: ArrayBase(id) {
allocate(size, nb_component, value);
}
/// Copy constructor (deep copy)
ArrayDataLayer(const ArrayDataLayer & vect, const ID & id = "")
: ArrayBase(vect, id) {
allocate(vect.size(), vect.getNbComponent());
std::copy_n(vect.storage(), this->size_ * this->nb_component, values);
}
/// Copy constructor (deep copy)
explicit ArrayDataLayer(const std::vector<value_type> & vect) {
allocate(vect.size(), 1);
std::copy_n(vect.data(), this->size_ * this->nb_component, values);
}
// copy operator
inline ArrayDataLayer & operator=(const ArrayDataLayer & other) {
if (this != &other) {
allocate(other.size(), other.getNbComponent());
std::copy_n(other.storage(), this->size_ * this->nb_component, values);
}
return *this;
}
// move constructor
inline ArrayDataLayer(ArrayDataLayer && other) noexcept = default;
// move assign
inline ArrayDataLayer & operator=(ArrayDataLayer && other) noexcept = default;
protected:
// deallocate the memory
virtual void deallocate() {
// NOLINTNEXTLINE(cppcoreguidelines-owning-memory,
// cppcoreguidelines-no-malloc)
free(this->values);
}
// allocate the memory
virtual inline void allocate(UInt size, UInt nb_component) {
if (size != 0) { // malloc can return a non NULL pointer in case size is 0
this->values = static_cast<T *>( // NOLINT
std::malloc(nb_component * size * sizeof(T))); // NOLINT
}
if (this->values == nullptr and size != 0) {
throw std::bad_alloc();
}
this->nb_component = nb_component;
this->allocated_size = this->size_ = size;
}
// allocate and initialize the memory
virtual inline void allocate(UInt size, UInt nb_component, const T & value) {
allocate(size, nb_component);
std::fill_n(values, size * nb_component, value);
}
public:
/// append a tuple of size nb_component containing value
inline void push_back(const_reference value) {
resize(this->size_ + 1, value);
}
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<aka::is_tensor<C<T>>::value or
aka::is_tensor_proxy<C<T>>::value>>
inline void push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
this->resize(this->size_ + 1);
std::copy_n(new_elem.storage(), new_elem.size(),
values + this->nb_component * (this->size_ - 1));
}
/// changes the allocated size but not the size
virtual void reserve(UInt size, UInt new_size = UInt(-1)) {
UInt tmp_size = this->size_;
if (new_size != UInt(-1)) {
tmp_size = new_size;
}
this->resize(size);
this->size_ = std::min(this->size_, tmp_size);
}
/// change the size of the Array
virtual void resize(UInt size) {
if (size * this->nb_component == 0) {
free(values); // NOLINT: cppcoreguidelines-no-malloc
values = nullptr;
this->allocated_size = 0;
} else {
if (this->values == nullptr) {
this->allocate(size, this->nb_component);
return;
}
Int diff = size - allocated_size;
UInt size_to_allocate = (std::abs(diff) > AKANTU_MIN_ALLOCATION)
? size
: (diff > 0)
? allocated_size + AKANTU_MIN_ALLOCATION
: allocated_size;
if (size_to_allocate ==
allocated_size) { // otherwhy the reserve + push_back might fail...
this->size_ = size;
return;
}
auto * tmp_ptr = reinterpret_cast<T *>( // NOLINT
realloc(this->values,
size_to_allocate * this->nb_component * sizeof(T)));
if (tmp_ptr == nullptr) {
throw std::bad_alloc();
}
this->values = tmp_ptr;
this->allocated_size = size_to_allocate;
}
this->size_ = size;
}
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val) {
UInt tmp_size = this->size_;
this->resize(size);
if (size > tmp_size) {
// NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
std::fill_n(values + this->nb_component * tmp_size,
(size - tmp_size) * this->nb_component, val);
}
}
/// get the amount of space allocated in bytes
inline UInt getMemorySize() const final {
return this->allocated_size * this->nb_component * sizeof(T);
}
/// Get the real size allocated in memory
inline UInt getAllocatedSize() const { return this->allocated_size; }
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
protected:
/// allocation type agnostic data access
T * values{nullptr};
UInt allocated_size{0};
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator()(UInt i, UInt j) -> reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_) && (j < this->nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< this->id << "\"");
return this->values[i * this->nb_component + j];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator()(UInt i, UInt j) const
-> const_reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_) && (j < this->nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< this->id << "\"");
// NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
return this->values[i * this->nb_component + j];
}
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator[](UInt i) -> reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_ * this->nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << this->id
<< "\"");
return this->values[i];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline auto Array<T, is_scal>::operator[](UInt i) const -> const_reference {
AKANTU_DEBUG_ASSERT(this->size_ > 0,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < this->size_ * this->nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << this->id
<< "\"");
return this->values[i];
}
/* -------------------------------------------------------------------------- */
/**
* erase an element. If the erased element is not the last of the array, the
* last element is moved into the hole in order to maintain contiguity. This
* may invalidate existing iterators (For instance an iterator obtained by
* Array::end() is no longer correct) and will change the order of the
* elements.
* @param i index of element to erase
*/
template <class T, bool is_scal> inline void Array<T, is_scal>::erase(UInt i) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT((this->size_ > 0), "The array is empty");
AKANTU_DEBUG_ASSERT((i < this->size_), "The element at position ["
<< i << "] is out of range (" << i
<< ">=" << this->size_ << ")");
if (i != (this->size_ - 1)) {
for (UInt j = 0; j < this->nb_component; ++j) {
// NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
this->values[i * this->nb_component + j] =
this->values[(this->size_ - 1) * this->nb_component + j];
}
}
this->resize(this->size_ - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Subtract another array entry by entry from this array in place. Both arrays
* must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to subtract from this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> &
Array<T, is_scal>::operator-=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_ASSERT((this->size_ == other.size_) &&
(this->nb_component == other.nb_component),
"The too array don't have the same sizes");
T * a = this->values;
T * b = other.storage();
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a -= *b;
++a;
++b;
}
return *this;
}
/* --------------------------------------------------------------------------
*/
/**
* Add another array entry by entry to this array in
* place. Both arrays must have the same size and
* nb_component. If the arrays have different shapes, code
* compiled in debug mode will throw an expeption and
* optimised code will behave in an unpredicted manner
* @param other array to add to this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> &
Array<T, is_scal>::operator+=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_ASSERT((this->size_ == other.size()) &&
(this->nb_component == other.nb_component),
"The too array don't have the same sizes");
T * a = this->values;
T * b = other.storage();
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a++ += *b++;
}
return *this;
}
/* --------------------------------------------------------------------------
*/
/**
* Multiply all entries of this array by a scalar in place
* @param alpha scalar multiplicant
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::operator*=(const T & alpha) {
T * a = this->values;
for (UInt i = 0; i < this->size_ * this->nb_component; ++i) {
*a++ *= alpha;
}
return *this;
}
/* --------------------------------------------------------------------------
*/
/**
* Compare this array element by element to another.
* @param other array to compare to
* @return true it all element are equal and arrays have
* the same shape, else false
*/
template <class T, bool is_scal>
bool Array<T, is_scal>::operator==(const Array<T, is_scal> & other) const {
bool equal = this->nb_component == other.nb_component &&
this->size_ == other.size_ && this->id == other.id;
if (not equal) {
return false;
}
if (this->values == other.storage()) {
return true;
}
// NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-pointer-arithmetic)
return std::equal(this->values,
this->values + this->size_ * this->nb_component,
other.storage());
}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & other) const {
return !operator==(other);
}
/* --------------------------------------------------------------------------
*/
/**
* set all tuples of the array to a given vector or matrix
* @param vm Matrix or Vector to fill the array with
*/
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::set(const C<T> & vm) {
AKANTU_DEBUG_ASSERT(this->nb_component == vm.size(),
"The size of the object does not "
"match the number of components");
for (T * it = this->values;
it < this->values + this->nb_component * this->size_;
it += this->nb_component) {
std::copy_n(vm.storage(), this->nb_component, it);
}
}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
void Array<T, is_scal>::append(const Array<T> & other) {
AKANTU_DEBUG_ASSERT(this->nb_component == other.nb_component,
"Cannot append an array with a "
"different number of component");
UInt old_size = this->size_;
this->resize(this->size_ + other.size());
T * tmp = this->values + this->nb_component * old_size;
std::copy_n(other.storage(), other.size() * this->nb_component, tmp);
}
/* --------------------------------------------------------------------------
*/
/* Functions Array<T, is_scal> */
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const ID & id)
: parent(size, nb_component, id) {}
template <>
inline Array<std::string, false>::Array(UInt size, UInt nb_component,
const ID & id)
: parent(size, nb_component, "", id) {}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const_reference value,
const ID & id)
: parent(size, nb_component, value, id) {}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
Array<T, is_scal>::Array(const Array & vect, const ID & id)
: parent(vect, id) {}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
Array<T, is_scal> &
Array<T, is_scal>::operator=(const Array<T, is_scal> & other) {
AKANTU_DEBUG_WARNING("You are copying the array "
<< this->id << " are you sure it is on purpose");
if (&other == this) {
return *this;
}
parent::operator=(other);
return *this;
}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
Array<T, is_scal>::Array(const std::vector<T> & vect) : parent(vect) {}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal> Array<T, is_scal>::~Array() = default;
/* --------------------------------------------------------------------------
*/
/**
* search elem in the array, return the position of the
* first occurrence or -1 if not found
* @param elem the element to look for
* @return index of the first occurrence of elem or -1 if
* elem is not present
*/
template <class T, bool is_scal>
UInt Array<T, is_scal>::find(const_reference elem) const {
AKANTU_DEBUG_IN();
auto begin = this->begin();
auto end = this->end();
auto it = std::find(begin, end, elem);
AKANTU_DEBUG_OUT();
return (it != end) ? it - begin : UInt(-1);
}
/* --------------------------------------------------------------------------
*/
// template <class T, bool is_scal> UInt Array<T,
// is_scal>::find(T elem[]) const
// {
// AKANTU_DEBUG_IN();
// T * it = this->values;
// UInt i = 0;
// for (; i < this->size_; ++i) {
// if (*it == elem[0]) {
// T * cit = it;
// UInt c = 0;
// for (; (c < this->nb_component) && (*cit ==
// elem[c]); ++c, ++cit)
// ;
// if (c == this->nb_component) {
// AKANTU_DEBUG_OUT();
// return i;
// }
// }
// it += this->nb_component;
// }
// return UInt(-1);
// }
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline UInt Array<T, is_scal>::find(const C<T> & elem) {
AKANTU_DEBUG_ASSERT(elem.size() == this->nb_component,
"Cannot find an element with a wrong size ("
<< elem.size() << ") != " << this->nb_component);
return this->find(*elem.storage());
}
/* --------------------------------------------------------------------------
*/
/**
* copy the content of another array. This overwrites the
* current content.
* @param other Array to copy into this array. It has to
* have the same nb_component as this. If compiled in
* debug mode, an incorrect other will result in an
* exception being thrown. Optimised code may result in
* unpredicted behaviour.
* @param no_sanity_check turns off all checkes
*/
template <class T, bool is_scal>
void Array<T, is_scal>::copy(const Array<T, is_scal> & other,
bool no_sanity_check) {
AKANTU_DEBUG_IN();
if (not no_sanity_check and (other.nb_component != this->nb_component)) {
AKANTU_ERROR("The two arrays do not have the same "
"number of components");
}
this->resize((other.size_ * other.nb_component) / this->nb_component);
std::copy_n(other.storage(), this->size_ * this->nb_component, this->values);
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
template <bool is_scal> class ArrayPrintHelper {
public:
template <typename T>
static void print_content(const Array<T> & vect, std::ostream & stream,
int indent) {
std::string space(indent, AKANTU_INDENT);
stream << space << " + values : {";
for (UInt i = 0; i < vect.size(); ++i) {
stream << "{";
for (UInt j = 0; j < vect.getNbComponent(); ++j) {
stream << vect(i, j);
if (j != vect.getNbComponent() - 1) {
stream << ", ";
}
}
stream << "}";
if (i != vect.size() - 1) {
stream << ", ";
}
}
stream << "}" << std::endl;
}
};
template <> class ArrayPrintHelper<false> {
public:
template <typename T>
static void print_content(__attribute__((unused)) const Array<T> & vect,
__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent) {}
};
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
void Array<T, is_scal>::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(2);
stream << space << "Array<" << debug::demangle(typeid(T).name()) << "> ["
<< std::endl;
stream << space << " + id : " << this->id << std::endl;
stream << space << " + size : " << this->size_ << std::endl;
stream << space << " + nb_component : " << this->nb_component << std::endl;
stream << space << " + allocated size : " << this->getAllocatedSize()
<< std::endl;
stream << space
<< " + memory size : " << printMemorySize<T>(this->getMemorySize())
<< std::endl;
if (not AKANTU_DEBUG_LEVEL_IS_TEST()) {
stream << space << " + address : " << std::hex << this->values
<< std::dec << std::endl;
}
stream.precision(prec);
stream.flags(ff);
if (AKANTU_DEBUG_TEST(dblDump) || AKANTU_DEBUG_LEVEL_IS_TEST()) {
ArrayPrintHelper<is_scal or std::is_enum<T>::value>::print_content(
*this, stream, indent);
}
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
/* Inline Functions ArrayBase */
/* --------------------------------------------------------------------------
*/
// inline bool ArrayBase::empty() { return (this->size_ ==
// 0); }
/* --------------------------------------------------------------------------
*/
/* Iterators */
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
template <class R, class daughter, class IR, bool is_tensor>
class Array<T, is_scal>::iterator_internal {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
static_assert(not is_tensor, "Cannot handle tensors");
public:
iterator_internal(pointer data = nullptr) : ret(data), initial(data){};
iterator_internal(const iterator_internal & it) = default;
iterator_internal(iterator_internal && it) noexcept = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) = default;
inline iterator_internal &
operator=(iterator_internal && it) noexcept = default;
UInt getCurrentIndex() { return (this->ret - this->initial); };
inline reference operator*() { return *ret; };
inline const_reference operator*() const { return *ret; };
inline pointer operator->() { return ret; };
inline daughter & operator++() {
++ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
--ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret += n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret -= n;
return static_cast<daughter &>(*this);
}
inline reference operator[](const UInt n) { return ret[n]; }
inline bool operator==(const iterator_internal & other) const {
return ret == other.ret;
}
inline bool operator!=(const iterator_internal & other) const {
return ret != other.ret;
}
inline bool operator<(const iterator_internal & other) const {
return ret < other.ret;
}
inline bool operator<=(const iterator_internal & other) const {
return ret <= other.ret;
}
inline bool operator>(const iterator_internal & other) const {
return ret > other.ret;
}
inline bool operator>=(const iterator_internal & other) const {
return ret >= other.ret;
}
inline daughter operator-(difference_type n) { return daughter(ret - n); }
inline daughter operator+(difference_type n) { return daughter(ret + n); }
inline difference_type operator-(const iterator_internal & b) {
return ret - b.ret;
}
inline pointer data() const { return ret; }
protected:
pointer ret{nullptr};
pointer initial{nullptr};
};
/* --------------------------------------------------------------------------
*/
/**
* Specialization for scalar types
*/
template <class T, bool is_scal>
template <class R, class daughter, class IR>
class Array<T, is_scal>::iterator_internal<R, daughter, IR, true> {
public:
using value_type = R;
using pointer = R *;
using pointer_type = typename Array<T, is_scal>::pointer_type;
using reference = R &;
using proxy = typename R::proxy;
using const_proxy = const typename R::proxy;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
public:
iterator_internal() = default;
iterator_internal(pointer_type data, UInt _offset)
: _offset(_offset), initial(data), ret(nullptr), ret_ptr(data) {
AKANTU_ERROR("The constructor should never be called "
"it is just an ugly trick...");
}
iterator_internal(std::unique_ptr<internal_value_type> && wrapped)
: _offset(wrapped->size()), initial(wrapped->storage()),
ret(std::move(wrapped)), ret_ptr(ret->storage()) {}
iterator_internal(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
}
iterator_internal(iterator_internal && it) noexcept = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
if (this->ret) {
this->ret->shallowCopy(*it.ret);
} else {
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
}
return *this;
}
inline iterator_internal &
operator=(iterator_internal && it) noexcept = default;
UInt getCurrentIndex() {
return (this->ret_ptr - this->initial) / this->_offset;
};
inline reference operator*() {
ret->values = ret_ptr;
return *ret;
};
inline const_reference operator*() const {
ret->values = ret_ptr;
return *ret;
};
inline pointer operator->() {
ret->values = ret_ptr;
return ret.get();
};
inline daughter & operator++() {
ret_ptr += _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
ret_ptr -= _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret_ptr += _offset * n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret_ptr -= _offset * n;
return static_cast<daughter &>(*this);
}
inline proxy operator[](const UInt n) {
ret->values = ret_ptr + n * _offset;
return proxy(*ret);
}
inline const_proxy operator[](const UInt n) const { // NOLINT
ret->values = ret_ptr + n * _offset;
return const_proxy(*ret);
}
inline bool operator==(const iterator_internal & other) const {
return this->ret_ptr == other.ret_ptr;
}
inline bool operator!=(const iterator_internal & other) const {
return this->ret_ptr != other.ret_ptr;
}
inline bool operator<(const iterator_internal & other) const {
return this->ret_ptr < other.ret_ptr;
}
inline bool operator<=(const iterator_internal & other) const {
return this->ret_ptr <= other.ret_ptr;
}
inline bool operator>(const iterator_internal & other) const {
return this->ret_ptr > other.ret_ptr;
}
inline bool operator>=(const iterator_internal & other) const {
return this->ret_ptr >= other.ret_ptr;
}
inline daughter operator+(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp += n;
return tmp;
}
inline daughter operator-(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp -= n;
return tmp;
}
inline difference_type operator-(const iterator_internal & b) {
return (this->ret_ptr - b.ret_ptr) / _offset;
}
inline pointer_type data() const { return ret_ptr; }
inline difference_type offset() const { return _offset; }
protected:
UInt _offset{0};
pointer_type initial{nullptr};
std::unique_ptr<internal_value_type> ret{nullptr};
pointer_type ret_ptr{nullptr};
};
/* -------------------------------------------------------------------------- */
/* Iterators */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::const_iterator
: public iterator_internal<const R, Array<T, is_scal>::const_iterator<R>,
R> {
public:
using parent = iterator_internal<const R, const_iterator, R>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
~const_iterator() override = default;
const_iterator() = default;
const_iterator(const const_iterator & it) = default;
const_iterator(const_iterator && it) noexcept = default;
const_iterator & operator=(const const_iterator & it) = default;
const_iterator & operator=(const_iterator && it) noexcept = default;
template <typename P,
typename = std::enable_if_t<not aka::is_tensor<P>::value>>
const_iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<aka::is_tensor<
typename UP_P::element_type>::value>>
const_iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
};
/* -------------------------------------------------------------------------- */
template <class T, class R, bool is_tensor_ = aka::is_tensor<R>::value>
struct ConstConverterIteratorHelper {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(std::unique_ptr<R>(new R(*it, false)));
}
};
template <class T, class R> struct ConstConverterIteratorHelper<T, R, false> {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(it.data());
}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::iterator
: public iterator_internal<R, Array<T, is_scal>::iterator<R>> {
public:
using parent = iterator_internal<R, iterator>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
~iterator() override = default;
iterator() = default;
iterator(const iterator & it) = default;
iterator(iterator && it) noexcept = default;
iterator & operator=(const iterator & it) = default;
iterator & operator=(iterator && it) noexcept = default;
template <typename P,
typename = std::enable_if_t<not aka::is_tensor<P>::value>>
iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<aka::is_tensor<
typename UP_P::element_type>::value>>
iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
operator const_iterator<R>() {
return ConstConverterIteratorHelper<T, R>::convert(*this);
}
};
/* -------------------------------------------------------------------------- */
/* Begin/End functions implementation */
/* -------------------------------------------------------------------------- */
namespace detail {
template <class Tuple, size_t... Is>
constexpr auto take_front_impl(Tuple && t,
std::index_sequence<Is...> /*idxs*/) {
return std::make_tuple(std::get<Is>(std::forward<Tuple>(t))...);
}
template <size_t N, class Tuple> constexpr auto take_front(Tuple && t) {
return take_front_impl(std::forward<Tuple>(t),
std::make_index_sequence<N>{});
}
template <typename... V> constexpr auto product_all(V &&... v) {
std::common_type_t<int, V...> result = 1;
(void)std::initializer_list<int>{(result *= v, 0)...};
return result;
}
template <typename... T> std::string to_string_all(T &&... t) {
if (sizeof...(T) == 0) {
return "";
}
std::stringstream ss;
bool noComma = true;
ss << "(";
(void)std::initializer_list<bool>{
(ss << (noComma ? "" : ", ") << t, noComma = false)...};
ss << ")";
return ss.str();
}
template <std::size_t N> struct InstantiationHelper {
template <typename type, typename T, typename... Ns>
static auto instantiate(T && data, Ns... ns) {
return std::make_unique<type>(data, ns...);
}
};
template <> struct InstantiationHelper<0> {
template <typename type, typename T> static auto instantiate(T && data) {
return data;
}
};
template <typename Arr, typename T, typename... Ns>
decltype(auto) get_iterator(Arr && array, T * data, Ns &&... ns) {
using type = IteratorHelper_t<sizeof...(Ns) - 1, T>;
using array_type = std::decay_t<Arr>;
using iterator =
std::conditional_t<std::is_const<std::remove_reference_t<Arr>>::value,
typename array_type::template const_iterator<type>,
typename array_type::template iterator<type>>;
static_assert(sizeof...(Ns), "You should provide a least one size");
if (array.getNbComponent() * array.size() !=
product_all(std::forward<Ns>(ns)...)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::ArrayException(),
"The iterator on "
<< debug::demangle(typeid(Arr).name())
<< to_string_all(array.size(), array.getNbComponent())
<< "is not compatible with the type "
<< debug::demangle(typeid(type).name()) << to_string_all(ns...));
}
auto && wrapped = aka::apply(
[&](auto... n) {
return InstantiationHelper<sizeof...(n)>::template instantiate<type>(
data, n...);
},
take_front<sizeof...(Ns) - 1>(std::make_tuple(ns...)));
return iterator(std::move(wrapped));
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...,
this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) {
return detail::get_iterator(*this,
this->values + this->nb_component * this->size_,
std::forward<Ns>(ns)..., this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) const {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...,
this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) const {
return detail::get_iterator(*this,
this->values + this->nb_component * this->size_,
std::forward<Ns>(ns)..., this->size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) {
return detail::get_iterator(
*this, this->values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) const {
return detail::get_iterator(*this, this->values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) const {
return detail::get_iterator(
*this, this->values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
/* -------------------------------------------------------------------------- */
/* Views */
/* -------------------------------------------------------------------------- */
namespace detail {
template <typename Array, typename... Ns> class ArrayView {
using tuple = std::tuple<Ns...>;
public:
~ArrayView() = default;
ArrayView(Array && array, Ns... ns) noexcept
: array(array), sizes(std::move(ns)...) {}
ArrayView(const ArrayView & array_view) = default;
ArrayView & operator=(const ArrayView & array_view) = default;
ArrayView(ArrayView && array_view) noexcept = default;
ArrayView & operator=(ArrayView && array_view) noexcept = default;
decltype(auto) begin() {
return aka::apply(
[&](auto &&... ns) { return array.get().begin_reinterpret(ns...); },
sizes);
}
decltype(auto) begin() const {
return aka::apply(
[&](auto &&... ns) { return array.get().begin_reinterpret(ns...); },
sizes);
}
decltype(auto) end() {
return aka::apply(
[&](auto &&... ns) { return array.get().end_reinterpret(ns...); },
sizes);
}
decltype(auto) end() const {
return aka::apply(
[&](auto &&... ns) { return array.get().end_reinterpret(ns...); },
sizes);
}
decltype(auto) size() const {
return std::get<std::tuple_size<tuple>::value - 1>(sizes);
}
decltype(auto) dims() const { return std::tuple_size<tuple>::value - 1; }
private:
std::reference_wrapper<std::remove_reference_t<Array>> array;
tuple sizes;
};
} // namespace detail
/* -------------------------------------------------------------------------- */
template <typename Array, typename... Ns>
decltype(auto) make_view(Array && array, const Ns... ns) {
static_assert(aka::conjunction<std::is_integral<std::decay_t<Ns>>...>::value,
"Ns should be integral types");
AKANTU_DEBUG_ASSERT((detail::product_all(ns...) != 0),
"You must specify non zero dimensions");
auto size = std::forward<decltype(array)>(array).size() *
std::forward<decltype(array)>(array).getNbComponent() /
detail::product_all(ns...);
return detail::ArrayView<Array, std::common_type_t<size_t, Ns>...,
std::common_type_t<size_t, decltype(size)>>(
std::forward<Array>(array), std::move(ns)..., size);
}
/* --------------------------------------------------------------------------
*/
template <class T, bool is_scal>
template <typename R>
inline typename Array<T, is_scal>::template iterator<R>
Array<T, is_scal>::erase(const iterator<R> & it) {
T * curr = it.data();
UInt pos = (curr - this->values) / this->nb_component;
erase(pos);
iterator<R> rit = it;
return --rit;
}
} // namespace akantu
#endif /* AKANTU_AKA_ARRAY_TMPL_HH_ */
diff --git a/src/common/aka_bbox.hh b/src/common/aka_bbox.hh
index f6a15ee5d..1d7424420 100644
--- a/src/common/aka_bbox.hh
+++ b/src/common/aka_bbox.hh
@@ -1,273 +1,278 @@
/**
* @file aka_bbox.hh
*
- * @author Nicolas Richart
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Mon Feb 12 2018
+ * @date creation: Wed Feb 14 2018
+ * @date last modification: Tue Sep 29 2020
*
- * @brief A simple bounding box class
+ * @brief A simple bounding box class
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "aka_types.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_BBOX_HH_
#define AKANTU_AKA_BBOX_HH_
namespace akantu {
class BBox {
public:
BBox() = default;
BBox(UInt spatial_dimension)
: dim(spatial_dimension),
lower_bounds(spatial_dimension, std::numeric_limits<Real>::max()),
upper_bounds(spatial_dimension, std::numeric_limits<Real>::lowest()) {}
BBox(const BBox & other)
: dim(other.dim), empty{false}, lower_bounds(other.lower_bounds),
upper_bounds(other.upper_bounds) {}
BBox & operator=(const BBox & other) {
if (this != &other) {
this->dim = other.dim;
this->lower_bounds = other.lower_bounds;
this->upper_bounds = other.upper_bounds;
this->empty = other.empty;
}
return *this;
}
inline BBox & operator+=(const Vector<Real> & position) {
AKANTU_DEBUG_ASSERT(
this->dim == position.size(),
"You are adding a point of a wrong dimension to the bounding box");
this->empty = false;
for (auto s : arange(dim)) {
lower_bounds(s) = std::min(lower_bounds(s), position(s));
upper_bounds(s) = std::max(upper_bounds(s), position(s));
}
return *this;
}
/* ------------------------------------------------------------------------ */
inline bool intersects(const BBox & other,
const SpatialDirection & direction) const {
AKANTU_DEBUG_ASSERT(
this->dim == other.dim,
"You are intersecting bounding boxes of different dimensions");
return Math::intersects(lower_bounds(direction), upper_bounds(direction),
other.lower_bounds(direction),
other.upper_bounds(direction));
}
inline bool intersects(const BBox & other) const {
if (this->empty or other.empty) {
return false;
}
bool intersects_ = true;
for (auto s : arange(this->dim)) {
intersects_ &= this->intersects(other, SpatialDirection(s));
}
return intersects_;
}
/* ------------------------------------------------------------------------ */
inline BBox intersection(const BBox & other) const {
AKANTU_DEBUG_ASSERT(
this->dim == other.dim,
"You are intersecting bounding boxes of different dimensions");
BBox intersection_(this->dim);
intersection_.empty = not this->intersects(other);
if (intersection_.empty) {
return intersection_;
}
for (auto s : arange(this->dim)) {
// is lower point in range ?
bool point1 = Math::is_in_range(other.lower_bounds(s), lower_bounds(s),
upper_bounds(s));
// is upper point in range ?
bool point2 = Math::is_in_range(other.upper_bounds(s), lower_bounds(s),
upper_bounds(s));
if (point1 and not point2) {
// |-----------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = other.lower_bounds(s);
intersection_.upper_bounds(s) = upper_bounds(s);
} else if (point1 && point2) {
// |-----------------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = other.lower_bounds(s);
intersection_.upper_bounds(s) = other.upper_bounds(s);
} else if (!point1 && point2) {
// |-----------| this (i)
// |-----------| other(i)
// 1 2
intersection_.lower_bounds(s) = this->lower_bounds(s);
intersection_.upper_bounds(s) = other.upper_bounds(s);
} else {
// |-----------| this (i)
// |-----------------| other(i)
// 1 2
intersection_.lower_bounds(s) = this->lower_bounds(s);
intersection_.upper_bounds(s) = this->upper_bounds(s);
}
}
return intersection_;
}
/* ------------------------------------------------------------------------ */
inline bool contains(const Vector<Real> & point) const {
return (point >= lower_bounds) and (point <= upper_bounds);
}
/* ------------------------------------------------------------------------ */
inline void reset() {
lower_bounds.set(std::numeric_limits<Real>::max());
upper_bounds.set(std::numeric_limits<Real>::lowest());
}
/* -------------------------------------------------------------------------- */
inline void getCenter(Vector<Real> & center) {
center = upper_bounds;
center += lower_bounds;
center /= 2.;
}
/* ------------------------------------------------------------------------ */
const Vector<Real> & getLowerBounds() const { return lower_bounds; }
const Vector<Real> & getUpperBounds() const { return upper_bounds; }
Vector<Real> & getLowerBounds() { return lower_bounds; }
Vector<Real> & getUpperBounds() { return upper_bounds; }
/* ------------------------------------------------------------------------ */
inline Real size(const SpatialDirection & direction) const {
return upper_bounds(direction) - lower_bounds(direction);
}
Vector<Real> size() const {
Vector<Real> size_(dim);
for (auto s : arange(this->dim)) {
size_(s) = this->size(SpatialDirection(s));
}
return size_;
}
inline operator bool() const { return not empty; }
/* ------------------------------------------------------------------------ */
BBox allSum(const Communicator & communicator) const {
Matrix<Real> reduce_bounds(dim, 2);
Vector<Real>(reduce_bounds(0)) = lower_bounds;
Vector<Real>(reduce_bounds(1)) = Real(-1.) * upper_bounds;
communicator.allReduce(reduce_bounds, SynchronizerOperation::_min);
BBox global(dim);
global.lower_bounds = Vector<Real>(reduce_bounds(0));
global.upper_bounds = Real(-1.) * Vector<Real>(reduce_bounds(1));
global.empty = false;
return global;
}
std::vector<BBox> allGather(const Communicator & communicator) const {
auto prank = communicator.whoAmI();
auto nb_proc = communicator.getNbProc();
Array<Real> bboxes_data(nb_proc, dim * 2 + 1);
auto * base = bboxes_data.storage() + prank * (2 * dim + 1);
Vector<Real>(base + dim * 0, dim) = lower_bounds;
Vector<Real>(base + dim * 1, dim) = upper_bounds;
base[dim * 2] = empty ? 1. : 0.; // ugly trick
communicator.allGather(bboxes_data);
std::vector<BBox> bboxes;
bboxes.reserve(nb_proc);
for (auto p : arange(nb_proc)) {
bboxes.emplace_back(dim);
auto & bbox = bboxes.back();
auto * base = bboxes_data.storage() + p * (2 * dim + 1);
bbox.lower_bounds = Vector<Real>(base + dim * 0, dim);
bbox.upper_bounds = Vector<Real>(base + dim * 1, dim);
bbox.empty = (base[dim * 2] == 1.);
}
return bboxes;
}
std::map<UInt, BBox> intersection(const BBox & other,
const Communicator & communicator) const {
// todo: change for a custom reduction algorithm
auto other_bboxes = other.allGather(communicator);
std::map<UInt, BBox> intersections;
for (const auto & bbox : enumerate(other_bboxes)) {
auto && tmp = this->intersection(std::get<1>(bbox));
if (tmp) {
intersections[std::get<0>(bbox)] = tmp;
}
}
return intersections;
}
void printself(std::ostream & stream) const {
stream << "BBox[";
if (not empty) {
stream << lower_bounds << " - " << upper_bounds;
}
stream << "]";
}
protected:
UInt dim{0};
bool empty{true};
Vector<Real> lower_bounds;
Vector<Real> upper_bounds;
};
inline std::ostream & operator<<(std::ostream & stream, const BBox & bbox) {
bbox.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_AKA_BBOX_HH_ */
diff --git a/src/common/aka_blas_lapack.hh b/src/common/aka_blas_lapack.hh
index 57c199263..cd077caa2 100644
--- a/src/common/aka_blas_lapack.hh
+++ b/src/common/aka_blas_lapack.hh
@@ -1,343 +1,346 @@
/**
* @file aka_blas_lapack.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 06 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Interface of the Fortran BLAS/LAPACK libraries
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_BLAS_LAPACK_HH_
#define AKANTU_AKA_BLAS_LAPACK_HH_
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_BLAS
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
double AKA_FC_GLOBAL(ddot, DDOT)(int *, double *, int *, double *, int *);
void AKA_FC_GLOBAL(daxpy, DAXPY)(int *, double *, double *, int *, double *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(dgemv, DGEMV)(char *, int *, int *, double *, double *,
int *, double *, int *, double *, double *,
int *);
// LEVEL 3
void AKA_FC_GLOBAL(dgemm, DGEMM)(char *, char *, int *, int *, int *, double *,
double *, int *, double *, int *, double *,
double *, int *);
/* ------------------------------------------------------------------------ */
/* Simple precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
float AKA_FC_GLOBAL(sdot, SDOT)(int *, float *, int *, float *, int *);
void AKA_FC_GLOBAL(saxpy, SAXPY)(int *, float *, float *, int *, float *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(sgemv, SGEMV)(char *, int *, int *, float *, float *, int *,
float *, int *, float *, float *, int *);
// LEVEL 3
void AKA_FC_GLOBAL(sgemm, SGEMM)(char *, char *, int *, int *, int *, float *,
float *, int *, float *, int *, float *,
float *, int *);
}
#endif
namespace akantu {
#define AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
#include "aka_warning.hh"
/// Wrapper around the S/DDOT BLAS function that returns the dot product of two
/// vectors
template <typename T>
inline T aka_dot(int * n, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DAXPY BLAS function that computes \f$y := \alpha x +
/// y\f$
template <typename T>
inline void aka_axpy(int * n, T * alpha, T * x, int * incx, T * y, int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMV BLAS function that computes matrix-vector product
/// \f$y := \alpha A^{(T)}x + \beta y \f$
template <typename T>
inline void aka_gemv(char * trans, int * m, int * n, T * alpha, T * a,
int * lda, T * x, int * incx, T * beta, T * y,
int * incy) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMM BLAS function that computes the product of two
/// matrices \f$C := \alpha A^{(T)} B^{(T)} + \beta C \f$
template <typename T>
inline void aka_gemm(char * transa, char * transb, int * m, int * n, int * k,
T * alpha, T * a, int * lda, T * b, int * ldb, T * beta,
T * c, int * ldc) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
#if defined(AKANTU_USE_BLAS)
template <>
inline double aka_dot<double>(int * n, double * x, int * incx, double * y,
int * incy) {
return AKA_FC_GLOBAL(ddot, DDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, double * alpha, double * x, int * incx,
double * y, int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<double>(char * trans, int * m, int * n, double * alpha,
double * a, int * lda, double * x, int * incx,
double * beta, double * y, int * incy) {
return AKA_FC_GLOBAL(dgemv, DGEMV)(trans, m, n, alpha, a, lda, x, incx, beta,
y, incy);
}
template <>
inline void aka_gemm<double>(char * transa, char * transb, int * m, int * n,
int * k, double * alpha, double * a, int * lda,
double * b, int * ldb, double * beta, double * c,
int * ldc) {
AKA_FC_GLOBAL(dgemm, DGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline float aka_dot<float>(int * n, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(sdot, SDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, float * alpha, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<float>(char * trans, int * m, int * n, float * alpha,
float * a, int * lda, float * x, int * incx,
float * beta, float * y, int * incy) {
AKA_FC_GLOBAL(sgemv, SGEMV)
(trans, m, n, alpha, a, lda, x, incx, beta, y, incy);
}
template <>
inline void aka_gemm<float>(char * transa, char * transb, int * m, int * n,
int * k, float * alpha, float * a, int * lda,
float * b, int * ldb, float * beta, float * c,
int * ldc) {
AKA_FC_GLOBAL(sgemm, SGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
#endif
} // namespace akantu
#ifdef AKANTU_USE_LAPACK
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(dgeev, DGEEV)(char * jobvl, char * jobvr, int * n,
double * a, int * lda, double * wr,
double * wi, double * vl, int * ldvl,
double * vr, int * ldvr, double * work,
int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(dgetrf, DGETRF)(int * m, int * n, double * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(dgetri, DGETRI)(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(dgetrs, DGETRS)(char * trans, int * n, int * nrhs,
double * A, int * lda, int * ipiv,
double * b, int * ldb, int * info);
/* ------------------------------------------------------------------------ */
/* Simple general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(sgeev, SGEEV)(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr,
float * work, int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(sgetrf, SGETRF)(int * m, int * n, float * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(sgetri, SGETRI)(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(sgetrs, SGETRS)(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info);
}
#endif // AKANTU_USE_LAPACK
namespace akantu {
/// Wrapper around the S/DGEEV BLAS function that computes the eigenvalues and
/// eigenvectors of a matrix
template <typename T>
inline void aka_geev(char * jobvl, char * jobvr, int * n, T * a, int * lda,
T * wr, T * wi, T * vl, int * ldvl, T * vr, int * ldvr,
T * work, int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRF BLAS function that computes the LU decomposition
/// of a matrix
template <typename T>
inline void aka_getrf(int * m, int * n, T * a, int * lda, int * ipiv,
int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRI BLAS function that computes the inverse of a
/// matrix given its LU decomposition
template <typename T>
inline void aka_getri(int * n, T * a, int * lda, int * ipiv, T * work,
int * lwork, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRS BLAS function that solves \f$A^{(T)}x = b\f$
/// using LU decomposition
template <typename T>
inline void aka_getrs(char * trans, int * n, int * nrhs, T * A, int * lda,
int * ipiv, T * b, int * ldb, int * info) {
AKANTU_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
#include "aka_warning_restore.hh"
#ifdef AKANTU_USE_LAPACK
template <>
inline void aka_geev<double>(char * jobvl, char * jobvr, int * n, double * a,
int * lda, double * wr, double * wi, double * vl,
int * ldvl, double * vr, int * ldvr, double * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(dgeev, DGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<double>(int * m, int * n, double * a, int * lda,
int * ipiv, int * info) {
AKA_FC_GLOBAL(dgetrf, DGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<double>(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info) {
AKA_FC_GLOBAL(dgetri, DGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<double>(char * trans, int * n, int * nrhs, double * A,
int * lda, int * ipiv, double * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(dgetrs, DGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline void aka_geev<float>(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr, float * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(sgeev, SGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<float>(int * m, int * n, float * a, int * lda, int * ipiv,
int * info) {
AKA_FC_GLOBAL(sgetrf, SGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<float>(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info) {
AKA_FC_GLOBAL(sgetri, SGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<float>(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(sgetrs, SGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
#endif
} // namespace akantu
#endif /* AKANTU_AKA_BLAS_LAPACK_HH_ */
diff --git a/src/common/aka_circular_array.hh b/src/common/aka_circular_array.hh
index 08a391564..ae97900ee 100644
--- a/src/common/aka_circular_array.hh
+++ b/src/common/aka_circular_array.hh
@@ -1,120 +1,123 @@
/**
* @file aka_circular_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief class of circular array
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_CIRCULAR_ARRAY_HH_
#define AKANTU_AKA_CIRCULAR_ARRAY_HH_
namespace akantu {
template <class T> class CircularArray : protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef typename Array<T>::value_type value_type;
typedef typename Array<T>::reference reference;
typedef typename Array<T>::pointer_type pointer_type;
typedef typename Array<T>::const_reference const_reference;
/// Allocation of a new array with a default value
CircularArray(UInt size, UInt nb_component = 1,
const_reference value = value_type(), const ID & id = "")
: Array<T>(size, nb_component, value, id), start_position(0),
end_position(size - 1) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
virtual ~CircularArray() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
advance start and end position by one:
the first element is now at the end of the array
**/
inline void makeStep();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0);
inline const_reference operator()(UInt i, UInt j = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
UInt size() const { return this->size_; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// indice of first element in this circular array
UInt start_position;
/// indice of last element in this circular array
UInt end_position;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const CircularArray<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_circular_array_inline_impl.hh"
#endif /* AKANTU_AKA_CIRCULAR_ARRAY_HH_ */
diff --git a/src/common/aka_circular_array_inline_impl.hh b/src/common/aka_circular_array_inline_impl.hh
index 6d68e657e..6651ec6a7 100644
--- a/src/common/aka_circular_array_inline_impl.hh
+++ b/src/common/aka_circular_array_inline_impl.hh
@@ -1,100 +1,103 @@
/**
* @file aka_circular_array_inline_impl.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Nov 11 2011
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Fri Mar 16 2018
*
* @brief implementation of circular array
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_circular_array.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
inline typename CircularArray<T>::reference CircularArray<T>::
operator()(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(end_position != start_position,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT(
(i < (end_position - start_position + this->allocated_size) %
this->allocated_size +
1) &&
(j < this->nb_component),
"The value at position [" << i << "," << j
<< "] is out of range in array \"" << this->id
<< "\"");
return this->values[((i + start_position) % this->allocated_size) *
this->nb_component +
j];
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline typename CircularArray<T>::const_reference CircularArray<T>::
operator()(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(end_position != start_position,
"The array \"" << this->id << "\" is empty");
AKANTU_DEBUG_ASSERT(
(i < (end_position - start_position + this->allocated_size) %
this->allocated_size +
1) &&
(j < this->nb_component),
"The value at position [" << i << "," << j
<< "] is out of range in array \"" << this->id
<< "\"");
return this->values[((i + start_position) % this->allocated_size) *
this->nb_component +
j];
}
/* -------------------------------------------------------------------------- */
template <class T> inline void CircularArray<T>::makeStep() {
AKANTU_DEBUG_IN();
start_position = (start_position + 1) % this->allocated_size;
end_position = (end_position + 1) % this->allocated_size;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T>
void CircularArray<T>::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CircularArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + start_position : " << this->start_position
<< std::endl;
stream << space << " + end_position : " << this->end_position << std::endl;
Array<T>::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
}
diff --git a/src/common/aka_common.cc b/src/common/aka_common.cc
index 4687f3fa6..530ce8df5 100644
--- a/src/common/aka_common.cc
+++ b/src/common/aka_common.cc
@@ -1,153 +1,155 @@
/**
* @file aka_common.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Mon Feb 05 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief Initialization of global variables
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "communication_tag.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <ctime>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void initialize(int & argc, char **& argv) {
AKANTU_DEBUG_IN();
initialize("", argc, argv);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void initialize(const std::string & input_file, int & argc, char **& argv) {
AKANTU_DEBUG_IN();
Communicator & comm = Communicator::getStaticCommunicator(argc, argv);
Tag::setMaxTag(comm.getMaxTag());
debug::debugger.setParallelContext(comm.whoAmI(), comm.getNbProc());
debug::setDebugLevel(dblError);
static_argparser.setParallelContext(comm.whoAmI(), comm.getNbProc());
static_argparser.setExternalExitFunction(debug::exit);
static_argparser.addArgument("--aka_input_file", "Akantu's input file", 1,
cppargparse::_string, std::string());
static_argparser.addArgument(
"--aka_debug_level",
std::string("Akantu's overall debug level") +
std::string(" (0: error, 1: exceptions, 4: warnings, 5: info, ..., "
"100: dump") +
std::string(" more info on levels can be foind in aka_error.hh)"),
1, cppargparse::_integer, (long int)(dblWarning));
static_argparser.addArgument(
"--aka_print_backtrace",
"Should Akantu print a backtrace in case of error", 0,
cppargparse::_boolean, false, true);
static_argparser.addArgument("--aka_seed", "The seed to use on prank 0", 1,
cppargparse::_integer);
static_argparser.parse(argc, argv, cppargparse::_remove_parsed);
std::string infile = static_argparser["aka_input_file"];
if (infile.empty()) {
infile = input_file;
}
debug::debugger.printBacktrace(static_argparser["aka_print_backtrace"]);
if (not infile.empty()) {
readInputFile(infile);
}
long int seed;
if (static_argparser.has("aka_seed")) {
seed = static_argparser["aka_seed"];
} else {
seed =
static_parser.getParameter("seed", time(nullptr), _ppsc_current_scope);
}
seed *= (comm.whoAmI() + 1);
RandomGenerator<UInt>::seed(seed);
long int dbl_level = static_argparser["aka_debug_level"];
debug::setDebugLevel(DebugLevel(dbl_level));
AKANTU_DEBUG_INFO("Random seed set to " << seed);
std::atexit(finalize);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void finalize() { }
/* -------------------------------------------------------------------------- */
void readInputFile(const std::string & input_file) {
static_parser.parse(input_file);
}
/* -------------------------------------------------------------------------- */
cppargparse::ArgumentParser & getStaticArgumentParser() {
return static_argparser;
}
/* -------------------------------------------------------------------------- */
Parser & getStaticParser() { return static_parser; }
/* -------------------------------------------------------------------------- */
const ParserSection & getUserParser() {
return *(static_parser.getSubSections(ParserType::_user).first);
}
std::unique_ptr<Communicator> Communicator::static_communicator;
std::ostream & operator<<(std::ostream & stream, NodeFlag flag) {
using under = std::underlying_type_t<NodeFlag>;
auto digits = static_cast<int>(std::log(std::numeric_limits<under>::max() + 1) / std::log(16));
std::ios_base::fmtflags ff;
ff = stream.flags();
auto value = static_cast<std::common_type_t<under, unsigned int>>(flag);
stream << "0x" << std::hex << std::setw(digits) << std::setfill('0') << value;
stream.flags(ff);
return stream;
}
} // namespace akantu
diff --git a/src/common/aka_common.hh b/src/common/aka_common.hh
index 759f7a746..1492dbe02 100644
--- a/src/common/aka_common.hh
+++ b/src/common/aka_common.hh
@@ -1,711 +1,713 @@
/**
* @file aka_common.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Mon Feb 12 2018
+ * @date last modification: Sat May 01 2021
*
* @brief common type descriptions for akantu
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMON_HH_
#define AKANTU_COMMON_HH_
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#if defined(WIN32)
#define __attribute__(x)
#endif
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
#include "aka_error.hh"
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
#include <limits>
#include <list>
#include <memory>
#include <string>
#include <type_traits>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Constants */
/* -------------------------------------------------------------------------- */
namespace {
[[gnu::unused]] constexpr UInt _all_dimensions{
std::numeric_limits<UInt>::max()};
#ifdef AKANTU_NDEBUG
[[gnu::unused]] constexpr Real REAL_INIT_VALUE{0.};
#else
[[gnu::unused]] constexpr Real REAL_INIT_VALUE{
std::numeric_limits<Real>::quiet_NaN()};
#endif
} // namespace
/* -------------------------------------------------------------------------- */
/* Common types */
/* -------------------------------------------------------------------------- */
using ID = std::string;
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "aka_enum_macros.hh"
/* -------------------------------------------------------------------------- */
#include "aka_element_classes_info.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Mesh/FEM/Model types */
/* -------------------------------------------------------------------------- */
/// small help to use names for directions
enum SpatialDirection { _x = 0, _y = 1, _z = 2 };
/// enum MeshIOType type of mesh reader/writer
enum MeshIOType {
_miot_auto, ///< Auto guess of the reader to use based on the extension
_miot_gmsh, ///< Gmsh files
_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has
/// structures elements
_miot_diana, ///< TNO Diana mesh format
_miot_abaqus ///< Abaqus mesh format
};
/// enum MeshEventHandlerPriority defines relative order of execution of
/// events
enum EventHandlerPriority {
_ehp_highest = 0,
_ehp_mesh = 5,
_ehp_fe_engine = 9,
_ehp_synchronizer = 10,
_ehp_dof_manager = 20,
_ehp_model = 94,
_ehp_non_local_manager = 100,
_ehp_lowest = 100
};
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_MODEL_TYPES \
(model) \
(solid_mechanics_model) \
(solid_mechanics_model_cohesive) \
(heat_transfer_model) \
(structural_mechanics_model) \
(embedded_model) \
(contact_mechanics_model) \
(coupler_solid_contact) \
(coupler_solid_cohesive_contact) \
(phase_field_model) \
(coupler_solid_phasefield)
// clang-format on
/// enum ModelType defines which type of physics is solved
AKANTU_CLASS_ENUM_DECLARE(ModelType, AKANTU_MODEL_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(ModelType, AKANTU_MODEL_TYPES)
#else
enum class ModelType {
model,
solid_mechanics_model,
solid_mechanics_model_cohesive,
heat_transfer_model,
structural_mechanics_model,
embedded_model,
};
#endif
/// enum AnalysisMethod type of solving method used to solve the equation of
/// motion
enum AnalysisMethod {
_static = 0,
_implicit_dynamic = 1,
_explicit_lumped_mass = 2,
_explicit_lumped_capacity = 2,
_explicit_consistent_mass = 3,
_explicit_contact = 4,
_implicit_contact = 5
};
/// enum DOFSupportType defines which kind of dof that can exists
enum DOFSupportType { _dst_nodal, _dst_generic };
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_NON_LINEAR_SOLVER_TYPES \
(linear) \
(newton_raphson) \
(newton_raphson_modified) \
(lumped) \
(gmres) \
(bfgs) \
(cg) \
(newton_raphson_contact) \
(auto)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(NonLinearSolverType, AKANTU_NON_LINEAR_SOLVER_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(NonLinearSolverType,
AKANTU_NON_LINEAR_SOLVER_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(NonLinearSolverType,
AKANTU_NON_LINEAR_SOLVER_TYPES)
#else
/// Type of non linear resolution available in akantu
enum class NonLinearSolverType {
_linear, ///< No non linear convergence loop
_newton_raphson, ///< Regular Newton-Raphson
_newton_raphson_modified, ///< Newton-Raphson with initial tangent
_lumped, ///< Case of lumped mass or equivalent matrix
_gmres,
_bfgs,
_cg,
_newton_raphson_contact, ///< Regular Newton-Raphson modified
/// for contact problem
_auto, ///< This will take a default value that make sense in case of
/// model::getNewSolver
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_TIME_STEP_SOLVER_TYPE \
(static) \
(dynamic) \
(dynamic_lumped) \
(not_defined)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(TimeStepSolverType, AKANTU_TIME_STEP_SOLVER_TYPE)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(TimeStepSolverType,
AKANTU_TIME_STEP_SOLVER_TYPE)
AKANTU_CLASS_ENUM_INPUT_STREAM(TimeStepSolverType, AKANTU_TIME_STEP_SOLVER_TYPE)
#else
/// Type of time stepping solver
enum class TimeStepSolverType {
_static, ///< Static solution
_dynamic, ///< Dynamic solver
_dynamic_lumped, ///< Dynamic solver with lumped mass
_not_defined, ///< For not defined cases
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_INTEGRATION_SCHEME_TYPE \
(pseudo_time) \
(forward_euler) \
(trapezoidal_rule_1) \
(backward_euler) \
(central_difference) \
(fox_goodwin) \
(trapezoidal_rule_2) \
(linear_acceleration) \
(newmark_beta) \
(generalized_trapezoidal)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(IntegrationSchemeType, AKANTU_INTEGRATION_SCHEME_TYPE)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(IntegrationSchemeType,
AKANTU_INTEGRATION_SCHEME_TYPE)
AKANTU_CLASS_ENUM_INPUT_STREAM(IntegrationSchemeType,
AKANTU_INTEGRATION_SCHEME_TYPE)
#else
/// Type of integration scheme
enum class IntegrationSchemeType {
_pseudo_time, ///< Pseudo Time
_forward_euler, ///< GeneralizedTrapezoidal(0)
_trapezoidal_rule_1, ///< GeneralizedTrapezoidal(1/2)
_backward_euler, ///< GeneralizedTrapezoidal(1)
_central_difference, ///< NewmarkBeta(0, 1/2)
_fox_goodwin, ///< NewmarkBeta(1/6, 1/2)
_trapezoidal_rule_2, ///< NewmarkBeta(1/2, 1/2)
_linear_acceleration, ///< NewmarkBeta(1/3, 1/2)
_newmark_beta, ///< generic NewmarkBeta with user defined
/// alpha and beta
_generalized_trapezoidal ///< generic GeneralizedTrapezoidal with user
/// defined alpha
};
#endif
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SOLVE_CONVERGENCE_CRITERIA \
(residual) \
(solution) \
(residual_mass_wgh)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
AKANTU_CLASS_ENUM_INPUT_STREAM(SolveConvergenceCriteria,
AKANTU_SOLVE_CONVERGENCE_CRITERIA)
#else
/// enum SolveConvergenceCriteria different convergence criteria
enum class SolveConvergenceCriteria {
_residual, ///< Use residual to test the convergence
_solution, ///< Use solution to test the convergence
_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to
///< testb
};
#endif
/// enum CohesiveMethod type of insertion of cohesive elements
enum CohesiveMethod { _intrinsic, _extrinsic };
/// @enum MatrixType type of sparse matrix used
enum MatrixType { _unsymmetric, _symmetric, _mt_not_defined };
/// @enum Type of contact detection
enum DetectionType { _explicit, _implicit };
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_CONTACT_STATE \
(no_contact) \
(stick) \
(slip)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(ContactState,
AKANTU_CONTACT_STATE)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(ContactState,
AKANTU_CONTACT_STATE)
AKANTU_CLASS_ENUM_INPUT_STREAM(ContactState,
AKANTU_CONTACT_STATE)
#else
/// @enum no contact or stick or slip state
enum class ContactState {
_no_contact = 0,
_stick = 1,
_slip = 2,
};
#endif
/* -------------------------------------------------------------------------- */
/* Ghosts handling */
/* -------------------------------------------------------------------------- */
/// @enum CommunicatorType type of communication method to use
enum CommunicatorType { _communicator_mpi, _communicator_dummy };
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SYNCHRONIZATION_TAG \
(whatever) \
(update) \
(ask_nodes) \
(size) \
(smm_mass) \
(smm_for_gradu) \
(smm_boundary) \
(smm_uv) \
(smm_res) \
(smm_init_mat) \
(smm_stress) \
(smmc_facets) \
(smmc_facets_conn) \
(smmc_facets_stress) \
(smmc_damage) \
(giu_global_conn) \
(ce_groups) \
(ce_insertion_order) \
(gm_clusters) \
(htm_temperature) \
(htm_gradient_temperature) \
(htm_phi) \
(htm_gradient_phi) \
(pfm_damage) \
(pfm_driving) \
(pfm_history) \
(pfm_energy) \
(csp_damage) \
(csp_strain) \
(mnl_for_average) \
(mnl_weight) \
(nh_criterion) \
(test) \
(user_1) \
(user_2) \
(material_id) \
(for_dump) \
(cf_nodal) \
(cf_incr) \
(solver_solution)
// clang-format on
AKANTU_CLASS_ENUM_DECLARE(SynchronizationTag, AKANTU_SYNCHRONIZATION_TAG)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(SynchronizationTag, AKANTU_SYNCHRONIZATION_TAG)
#else
/// @enum SynchronizationTag type of synchronizations
enum class SynchronizationTag {
//--- Generic tags ---
_whatever,
_update,
_ask_nodes,
_size,
//--- SolidMechanicsModel tags ---
_smm_mass, ///< synchronization of the SolidMechanicsModel.mass
_smm_for_gradu, ///< synchronization of the
/// SolidMechanicsModel.displacement
_smm_boundary, ///< synchronization of the boundary, forces, velocities
/// and displacement
_smm_uv, ///< synchronization of the nodal velocities and displacement
_smm_res, ///< synchronization of the nodal residual
_smm_init_mat, ///< synchronization of the data to initialize materials
_smm_stress, ///< synchronization of the stresses to compute the
///< internal
/// forces
_smmc_facets, ///< synchronization of facet data to setup facet synch
_smmc_facets_conn, ///< synchronization of facet global connectivity
_smmc_facets_stress, ///< synchronization of facets' stress to setup
///< facet
/// synch
_smmc_damage, ///< synchronization of damage
// --- GlobalIdsUpdater tags ---
_giu_global_conn, ///< synchronization of global connectivities
// --- CohesiveElementInserter tags ---
_ce_groups, ///< synchronization of cohesive element insertion depending
/// on facet groups
_ce_insertion_order, ///< synchronization of the order of insertion of
/// cohesive elements
// --- GroupManager tags ---
_gm_clusters, ///< synchronization of clusters
// --- HeatTransfer tags ---
_htm_temperature, ///< synchronization of the nodal temperature
_htm_gradient_temperature, ///< synchronization of the element gradient
/// temperature
// --- PhaseFieldModel tags ---
_pfm_damage, ///< synchronization of the nodal damage
_pfm_driving, ///< synchronization of the driving forces to
/// compute the internal
_pfm_history, ///< synchronization of the damage history to
/// compute the internal
_pfm_energy, ///< synchronization of the damage energy
/// density to compute the internal
// --- CouplerSolidPhaseField tags ---
_csp_damage, ///< synchronization of the damage from phase
/// model to solid model
_csp_strain, ///< synchronization of the strain from solid
/// model to phase model
// --- LevelSet tags ---
_htm_phi, ///< synchronization of the nodal level set value phi
_htm_gradient_phi, ///< synchronization of the element gradient phi
//--- Material non local ---
_mnl_for_average, ///< synchronization of data to average in non local
/// material
_mnl_weight, ///< synchronization of data for the weight computations
// --- NeighborhoodSynchronization tags ---
_nh_criterion,
// --- General tags ---
_test, ///< Test tag
_user_1, ///< tag for user simulations
_user_2, ///< tag for user simulations
_material_id, ///< synchronization of the material ids
_for_dump, ///< everything that needs to be synch before dump
// --- Contact & Friction ---
_cf_nodal, ///< synchronization of disp, velo, and current position
_cf_incr, ///< synchronization of increment
// --- Solver tags ---
_solver_solution ///< synchronization of the solution obained with the
/// PETSc solver
};
#endif
/// @enum GhostType type of ghost
enum GhostType {
_not_ghost = 0,
_ghost = 1,
_casper // not used but a real cute ghost
};
/// Define the flag that can be set to a node
enum class NodeFlag : std::uint8_t {
_normal = 0x00,
_distributed = 0x01,
_master = 0x03,
_slave = 0x05,
_pure_ghost = 0x09,
_shared_mask = 0x0F,
_periodic = 0x10,
_periodic_master = 0x30,
_periodic_slave = 0x50,
_periodic_mask = 0xF0,
_local_master_mask = 0xCC, // ~(_master & _periodic_mask)
};
inline NodeFlag operator&(const NodeFlag & a, const NodeFlag & b) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(under(a) & under(b));
}
inline NodeFlag operator|(const NodeFlag & a, const NodeFlag & b) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(under(a) | under(b));
}
inline NodeFlag & operator|=(NodeFlag & a, const NodeFlag & b) {
a = a | b;
return a;
}
inline NodeFlag & operator&=(NodeFlag & a, const NodeFlag & b) {
a = a & b;
return a;
}
inline NodeFlag operator~(const NodeFlag & a) {
using under = std::underlying_type_t<NodeFlag>;
return NodeFlag(~under(a));
}
std::ostream & operator<<(std::ostream & stream, NodeFlag flag);
} // namespace akantu
AKANTU_ENUM_HASH(GhostType)
namespace akantu {
/* -------------------------------------------------------------------------- */
struct GhostType_def {
using type = GhostType;
static const type _begin_ = _not_ghost;
static const type _end_ = _casper;
};
using ghost_type_t = safe_enum<GhostType_def>;
namespace {
constexpr ghost_type_t ghost_types{_casper};
}
/// standard output stream operator for GhostType
// inline std::ostream & operator<<(std::ostream & stream, GhostType type);
/* -------------------------------------------------------------------------- */
/* Global defines */
/* -------------------------------------------------------------------------- */
#define AKANTU_MIN_ALLOCATION 2000
#define AKANTU_INDENT ' '
#define AKANTU_INCLUDE_INLINE_IMPL
/* -------------------------------------------------------------------------- */
#define AKANTU_SET_MACRO(name, variable, type) \
inline void set##name(type variable) { this->variable = variable; }
#define AKANTU_GET_MACRO(name, variable, type) \
inline type get##name() const { return variable; }
#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
inline type get##name() { return variable; }
#define AKANTU_GET_MACRO_DEREF_PTR(name, ptr) \
inline const auto & get##name() const { \
if (not(ptr)) { \
AKANTU_EXCEPTION("The member " << #ptr << " is not initialized"); \
} \
return (*(ptr)); \
}
#define AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(name, ptr) \
inline auto & get##name() { \
if (not(ptr)) { \
AKANTU_EXCEPTION("The member " << #ptr << " is not initialized"); \
} \
return (*(ptr)); \
}
#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, support, con) \
inline con Array<type> & get##name(const support & el_type, \
GhostType ghost_type = _not_ghost) \
con { /* NOLINT */ \
return variable(el_type, ghost_type); \
} // NOLINT
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, )
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, )
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)
/* -------------------------------------------------------------------------- */
/// initialize the static part of akantu
void initialize(int & argc, char **& argv);
/// initialize the static part of akantu and read the global input_file
void initialize(const std::string & input_file, int & argc, char **& argv);
/* -------------------------------------------------------------------------- */
/// finilize correctly akantu and clean the memory
void finalize();
/* -------------------------------------------------------------------------- */
/// Read an new input file
void readInputFile(const std::string & input_file);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* string manipulation */
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str);
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim);
inline std::string trim(const std::string & to_trim, char c);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// give a string representation of the a human readable size in bit
template <typename T> std::string printMemorySize(UInt size);
/* -------------------------------------------------------------------------- */
struct TensorTrait {};
struct TensorProxyTrait {};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Type traits */
/* -------------------------------------------------------------------------- */
namespace aka {
/* ------------------------------------------------------------------------ */
template <typename T> using is_tensor = std::is_base_of<akantu::TensorTrait, T>;
template <typename T>
using is_tensor_proxy = std::is_base_of<akantu::TensorProxyTrait, T>;
/* ------------------------------------------------------------------------ */
template <typename T> using is_scalar = std::is_arithmetic<T>;
/* ------------------------------------------------------------------------ */
template <typename R, typename T,
std::enable_if_t<std::is_reference<T>::value> * = nullptr>
bool is_of_type(T && t) {
return (
dynamic_cast<std::add_pointer_t<
std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
std::add_const_t<R>, R>>>(&t) != nullptr);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T> bool is_of_type(std::unique_ptr<T> & t) {
return (
dynamic_cast<std::add_pointer_t<
std::conditional_t<std::is_const<T>::value, std::add_const_t<R>, R>>>(
t.get()) != nullptr);
}
/* ------------------------------------------------------------------------ */
template <typename R, typename T,
std::enable_if_t<std::is_reference<T>::value> * = nullptr>
decltype(auto) as_type(T && t) {
static_assert(
disjunction<
std::is_base_of<std::decay_t<T>, std::decay_t<R>>, // down-cast
std::is_base_of<std::decay_t<R>, std::decay_t<T>> // up-cast
>::value,
"Type T and R are not valid for a as_type conversion");
return dynamic_cast<std::add_lvalue_reference_t<
std::conditional_t<std::is_const<std::remove_reference_t<T>>::value,
std::add_const_t<R>, R>>>(t);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T,
std::enable_if_t<std::is_pointer<T>::value> * = nullptr>
decltype(auto) as_type(T && t) {
return &as_type<R>(*t);
}
/* -------------------------------------------------------------------------- */
template <typename R, typename T>
decltype(auto) as_type(const std::shared_ptr<T> & t) {
return std::dynamic_pointer_cast<R>(t);
}
} // namespace aka
#include "aka_common_inline_impl.hh"
#include "aka_fwd.hh"
namespace akantu {
/// get access to the internal argument parser
cppargparse::ArgumentParser & getStaticArgumentParser();
/// get access to the internal input file parser
Parser & getStaticParser();
/// get access to the user part of the internal input file parser
const ParserSection & getUserParser();
#define AKANTU_CURRENT_FUNCTION \
(std::string(__func__) + "():" + std::to_string(__LINE__))
} // namespace akantu
/* -------------------------------------------------------------------------- */
#if AKANTU_INTEGER_SIZE == 4
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b9
#elif AKANTU_INTEGER_SIZE == 8
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b97f4a7c13LL
#endif
namespace std {
/**
* Hashing function for pairs based on hash_combine from boost The magic
* number is coming from the golden number @f[\phi = \frac{1 + \sqrt5}{2}@f]
* @f[\frac{2^32}{\phi} = 0x9e3779b9@f]
* http://stackoverflow.com/questions/4948780/magic-number-in-boosthash-combine
* http://burtleburtle.net/bob/hash/doobs.html
*/
template <typename a, typename b> struct hash<std::pair<a, b>> {
hash() = default;
size_t operator()(const std::pair<a, b> & p) const {
size_t seed = ah(p.first);
return bh(p.second) + AKANTU_HASH_COMBINE_MAGIC_NUMBER + (seed << 6) +
(seed >> 2);
}
private:
const hash<a> ah{};
const hash<b> bh{};
};
} // namespace std
#endif // AKANTU_COMMON_HH_
diff --git a/src/common/aka_common_inline_impl.hh b/src/common/aka_common_inline_impl.hh
index 31a34b97f..c50502cc3 100644
--- a/src/common/aka_common_inline_impl.hh
+++ b/src/common/aka_common_inline_impl.hh
@@ -1,129 +1,131 @@
/**
* @file aka_common_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 09 2021
*
* @brief inline implementations of common akantu type descriptions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <cctype>
#include <cmath>
#include <iomanip>
#include <iostream>
#include <array>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// standard output stream operator for GhostType
inline std::ostream & operator<<(std::ostream & stream, GhostType type) {
switch (type) {
case _not_ghost:
stream << "not_ghost";
break;
case _ghost:
stream << "ghost";
break;
case _casper:
stream << "Casper the friendly ghost";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(), (int (*)(int))tolower);
return lstr;
}
namespace {
template <typename pred>
inline std::string trim_p(const std::string & to_trim, pred && p) {
std::string trimed = to_trim;
auto && not_ = [&](auto && a) { return not p(a); };
// left trim
trimed.erase(trimed.begin(),
std::find_if(trimed.begin(), trimed.end(), not_));
// right trim
trimed.erase(std::find_if(trimed.rbegin(), trimed.rend(), not_).base(),
trimed.end());
return trimed;
}
} // namespace
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim) {
return trim_p(to_trim, [&](auto && a) { return std::isspace(a); });
}
inline std::string trim(const std::string & to_trim, char c) {
return trim_p(to_trim, [&c](auto && a) { return (a == c); });
}
/* -------------------------------------------------------------------------- */
template <typename T> std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt mult = 0;
if (real_size != 0) {
mult = (std::log(real_size) / std::log(2)) / 10;
}
std::stringstream sstr;
real_size /= Real(1 << (10 * mult));
sstr << std::setprecision(2) << std::fixed << real_size;
std::string size_prefix;
std::array<std::string, 9> ratio = {
"", "Ki", "Mi",
"Gi", // I started on this type of machines (32bit computers) (Nicolas)
"Ti", "Pi",
"Ei", // theoritical limit of RAM of the current computers in 2014 (64bit
// computers) (Nicolas)
"Zi", "Yi"};
if (mult >= ratio.size()) {
AKANTU_ERROR(
"The programmer in 2014 didn't thought so far (even wikipedia does not "
"go further)."
<< " You have at least 1024 times more than a yobibit of RAM!!!"
<< " Just add the prefix corresponding in the ratio array.");
}
sstr << ratio[mult] << "Byte";
return sstr.str();
}
} // namespace akantu
diff --git a/src/common/aka_csr.hh b/src/common/aka_csr.hh
index 8724edca6..4f7f9f163 100644
--- a/src/common/aka_csr.hh
+++ b/src/common/aka_csr.hh
@@ -1,285 +1,287 @@
/**
* @file aka_csr.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 20 2011
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief A compresed sparse row structure based on akantu Arrays
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_CSR_HH_
#define AKANTU_AKA_CSR_HH_
namespace akantu {
/**
* This class can be used to store the structure of a sparse matrix or for
* vectors with variable number of component per element
*
* @param nb_rows number of rows of a matrix or size of a vector.
*/
template <typename T> class CSR {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CSR(UInt nb_rows = 0)
: nb_rows(nb_rows), rows_offsets(nb_rows + 1, 1, "rows_offsets"),
rows(0, 1, "rows") {
rows_offsets.zero();
};
virtual ~CSR() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// does nothing
inline void beginInsertions(){};
/// insert a new entry val in row row
inline UInt insertInRow(UInt row, const T & val) {
UInt pos = rows_offsets(row)++;
rows(pos) = val;
return pos;
}
/// access an element of the matrix
inline const T & operator()(UInt row, UInt col) const {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
/// access an element of the matrix
inline T & operator()(UInt row, UInt col) {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
inline void endInsertions() {
for (UInt i = nb_rows; i > 0; --i) {
rows_offsets(i) = rows_offsets(i - 1);
}
rows_offsets(0) = 0;
}
inline void countToCSR() {
for (UInt i = 1; i < nb_rows; ++i) {
rows_offsets(i) += rows_offsets(i - 1);
}
for (UInt i = nb_rows; i >= 1; --i) {
rows_offsets(i) = rows_offsets(i - 1);
}
rows_offsets(0) = 0;
}
inline void clearRows() {
rows_offsets.zero();
rows.resize(0);
};
inline void resizeRows(UInt nb_rows) {
this->nb_rows = nb_rows;
rows_offsets.resize(nb_rows + 1);
rows_offsets.zero();
}
inline void resizeCols() { rows.resize(rows_offsets(nb_rows)); }
inline void copy(Array<UInt> & offsets, Array<T> & values) {
offsets.copy(rows_offsets);
values.copy(rows);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// returns the number of rows
inline UInt getNbRows() const { return rows_offsets.size() - 1; };
/// returns the number of non-empty columns in a given row
inline UInt getNbCols(UInt row) const {
return rows_offsets(row + 1) - rows_offsets(row);
};
/// returns the offset (start of columns) for a given row
inline UInt & rowOffset(UInt row) { return rows_offsets(row); };
// /// iterator on a row
// template <class array_iterator>
// class iterator_internal
// : public std::iterator<std::bidirectional_iterator_tag, typename
// array_iterator::value_type> {
// public:
// using _parent = std::iterator<std::bidirectional_iterator_tag, R>;
// using pointer = typename _parent::pointer;
// using reference = typename _parent::reference;
// explicit iterator_internal(array_iterator ait) : pos(std::move(ait)){};
// iterator_internal(const iterator_internal & it) : pos(it.pos){};
// iterator_internal & operator++() {
// ++pos;
// return *this;
// };
// iterator_internal operator++(int) {
// iterator tmp(*this);
// operator++();
// return tmp;
// };
// iterator_internal & operator--() {
// --pos;
// return *this;
// };
// iterator_internal operator--(int) {
// iterator_internal tmp(*this);
// operator--();
// return tmp;
// };
// bool operator==(const iterator_internal & rhs) { return pos == rhs.pos;
// }; bool operator!=(const iterator_internal & rhs) { return pos !=
// rhs.pos; }; reference operator*() { return *pos; }; pointer operator->()
// const { return pos; };
// private:
// array_iterator pos;
// };
using iterator = typename Array<T>::scalar_iterator;
using const_iterator = typename Array<T>::const_scalar_iterator;
template <typename iterator_internal> class CSRRow {
public:
CSRRow(iterator_internal begin, iterator_internal end)
: begin_(std::move(begin)), end_(std::move(end)) {}
inline auto begin() const { return begin_; }
inline auto end() const { return end_; }
private:
iterator_internal begin_, end_;
};
inline iterator begin(UInt row) { return rows.begin() + rows_offsets(row); };
inline iterator end(UInt row) {
return rows.begin() + rows_offsets(row + 1);
};
inline const_iterator begin(UInt row) const {
return rows.begin() + rows_offsets(row);
};
inline const_iterator end(UInt row) const {
return rows.begin() + rows_offsets(row + 1);
};
private:
template <typename iterator_internal>
decltype(auto) make_row(iterator_internal begin, iterator_internal end) {
return CSRRow<iterator_internal>(std::move(begin), std::move(end));
}
public:
inline decltype(auto) getRow(UInt row) {
return make_row(begin(row), end(row));
}
inline decltype(auto) getRow(UInt row) const {
return make_row(begin(row), end(row));
}
inline iterator rbegin(UInt row) {
return rows.begin() + rows_offsets(row + 1) - 1;
};
inline iterator rend(UInt row) {
return rows.begin() + rows_offsets(row) - 1;
};
inline const Array<UInt> & getRowsOffset() const { return rows_offsets; };
inline const Array<T> & getRows() const { return rows; };
inline Array<T> & getRows() { return rows; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt nb_rows;
/// array of size nb_rows containing the offset where the values are stored in
Array<UInt> rows_offsets;
/// compressed row values, values of row[i] are stored between rows_offsets[i]
/// and rows_offsets[i+1]
Array<T> rows;
};
/* -------------------------------------------------------------------------- */
/* Data CSR */
/* -------------------------------------------------------------------------- */
/**
* Inherits from CSR<UInt> and can contain information such as matrix values
* where the mother class would be a CSR structure for row and cols
*
* @return nb_rows
*/
template <class T> class DataCSR : public CSR<UInt> {
public:
DataCSR(UInt nb_rows = 0) : CSR<UInt>(nb_rows), data(0, 1){};
inline void resizeCols() {
CSR<UInt>::resizeCols();
data.resize(rows_offsets(nb_rows));
}
inline const Array<T> & getData() const { return data; };
private:
Array<T> data;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "aka_csr_inline_impl.hh"
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const CSR & _this)
// {
// _this.printself(stream);
// return stream;
// }
} // namespace akantu
#endif /* AKANTU_AKA_CSR_HH_ */
diff --git a/src/common/aka_element_classes_info_inline_impl.hh b/src/common/aka_element_classes_info_inline_impl.hh
index 3a05abbe8..e5f889756 100644
--- a/src/common/aka_element_classes_info_inline_impl.hh
+++ b/src/common/aka_element_classes_info_inline_impl.hh
@@ -1,52 +1,55 @@
/**
* @file aka_element_classes_info_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 18 2015
- * @date last modification: Wed Jan 10 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Implementation of the streaming fonction for the element classes
* enums
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_
#define AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_
namespace akantu {
AKANTU_ENUM_OUTPUT_STREAM(
ElementType, AKANTU_ALL_ELEMENT_TYPE(_not_defined)(_max_element_type))
AKANTU_ENUM_INPUT_STREAM(ElementType, AKANTU_ALL_ELEMENT_TYPE)
AKANTU_ENUM_OUTPUT_STREAM(InterpolationType, AKANTU_INTERPOLATION_TYPES)
AKANTU_ENUM_INPUT_STREAM(InterpolationType, AKANTU_INTERPOLATION_TYPES)
AKANTU_ENUM_OUTPUT_STREAM(ElementKind, AKANTU_ELEMENT_KIND)
AKANTU_ENUM_INPUT_STREAM(ElementKind, AKANTU_ELEMENT_KIND)
} // namespace akantu
#endif /* AKANTU_AKA_ELEMENT_CLASSES_INFO_INLINE_IMPL_HH_ */
diff --git a/src/common/aka_enum_macros.hh b/src/common/aka_enum_macros.hh
index bee12f1d2..e96bd5046 100644
--- a/src/common/aka_enum_macros.hh
+++ b/src/common/aka_enum_macros.hh
@@ -1,133 +1,137 @@
/**
* @file aka_enum_macros.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Oct 31 2018
+ * @date creation: Mon Nov 05 2018
+ * @date last modification: Tue Sep 29 2020
*
- * @brief A Documented file.
+ * @brief Macros to help declare enums
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <string>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_ENUM_MACROS_HH_
#define AKANTU_AKA_ENUM_MACROS_HH_
#define AKANTU_PP_ENUM(s, data, i, elem) \
BOOST_PP_TUPLE_REM() \
elem BOOST_PP_COMMA_IF(BOOST_PP_NOT_EQUAL(i, BOOST_PP_DEC(data)))
#if (defined(__GNUC__) || defined(__GNUG__))
#define AKA_GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if AKA_GCC_VERSION < 60000
#define AKANTU_ENUM_HASH(type_name) \
namespace std { \
template <> struct hash<::akantu::type_name> { \
using argument_type = ::akantu::type_name; \
size_t operator()(const argument_type & e) const noexcept { \
auto ue = underlying_type_t<argument_type>(e); \
return uh(ue); \
} \
\
private: \
const hash<underlying_type_t<argument_type>> uh{}; \
}; \
}
#else
#define AKANTU_ENUM_HASH(type_name)
#endif // AKA_GCC_VERSION
#endif // GNU
#define AKANTU_PP_CAT(s, data, elem) BOOST_PP_CAT(data, elem)
#define AKANTU_PP_TYPE_TO_STR(s, data, elem) \
({BOOST_PP_CAT(data, elem), BOOST_PP_STRINGIZE(elem)})
#define AKANTU_PP_STR_TO_TYPE(s, data, elem) \
({BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(data, elem)})
#define AKANTU_CLASS_ENUM_DECLARE(type_name, list) \
enum class type_name { \
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_CAT, _, list)) \
};
#define AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, prefix) \
} \
AKANTU_ENUM_HASH(type_name) \
namespace std { \
inline string to_string(const ::akantu::type_name & type) { \
using namespace akantu; \
static unordered_map<::akantu::type_name, string> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_TYPE_TO_STR, prefix, list))}; \
return convert.at(type); \
} \
} \
namespace akantu { \
inline std::ostream & operator<<(std::ostream & stream, \
const type_name & type) { \
stream << std::to_string(type); \
return stream; \
}
#define AKANTU_ENUM_INPUT_STREAM_(type_name, list, prefix) \
inline std::istream & operator>>(std::istream & stream, \
type_name & type) { /* NOLINT */ \
std::string str; \
stream >> str; /* NOLINT */ \
static std::unordered_map<std::string, type_name> convert{ \
BOOST_PP_SEQ_FOR_EACH_I( \
AKANTU_PP_ENUM, BOOST_PP_SEQ_SIZE(list), \
BOOST_PP_SEQ_TRANSFORM(AKANTU_PP_STR_TO_TYPE, prefix, list))}; \
try { \
type = convert.at(str); \
} catch (std::out_of_range &) { \
std::ostringstream values; \
std::for_each(convert.begin(), convert.end(), [&values](auto && pair) { \
static bool first = true; \
if (not first) \
values << ", "; \
values << "\"" << pair.first << "\""; \
first = false; \
}); \
AKANTU_EXCEPTION("The value " << str << " is not a valid " \
<< BOOST_PP_STRINGIZE(type_name) \
<< " valid values are " << values.str()); \
} \
return stream; \
}
#define AKANTU_CLASS_ENUM_OUTPUT_STREAM(type_name, list) \
AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, type_name::_)
#define AKANTU_ENUM_OUTPUT_STREAM(type_name, list) \
AKANTU_ENUM_OUTPUT_STREAM_(type_name, list, )
#define AKANTU_CLASS_ENUM_INPUT_STREAM(type_name, list) \
AKANTU_ENUM_INPUT_STREAM_(type_name, list, type_name::_)
#define AKANTU_ENUM_INPUT_STREAM(type_name, list) \
AKANTU_ENUM_INPUT_STREAM_(type_name, list, )
#endif /* AKANTU_AKA_ENUM_MACROS_HH_ */
diff --git a/src/common/aka_error.cc b/src/common/aka_error.cc
index 9a3767e0c..c0a142fa9 100644
--- a/src/common/aka_error.cc
+++ b/src/common/aka_error.cc
@@ -1,367 +1,370 @@
/**
* @file aka_error.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 06 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Wed Feb 24 2021
*
* @brief handling of errors
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_common.hh"
#include "aka_config.hh"
#include "aka_iterators.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <csignal>
#include <iostream>
#include <vector>
#if (defined(READLINK_COMMAND) || defined(ADDR2LINE_COMMAND)) && \
(!defined(_WIN32))
#include <execinfo.h>
#include <sys/wait.h>
#endif
#include <chrono>
#include <cmath>
#include <cstring>
#include <cxxabi.h>
#include <fstream>
#include <iomanip>
#include <map>
#include <sys/types.h>
#include <unistd.h>
#ifdef AKANTU_USE_MPI
#include <mpi.h>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
// static void printBacktraceAndExit(int) { std::terminate(); }
// /* ------------------------------------------------------------------------ */
// void initSignalHandler() { std::signal(SIGSEGV, &printBacktraceAndExit); }
/* ------------------------------------------------------------------------ */
std::string demangle(const char * symbol) {
int status;
std::string result;
char * demangled_name;
if ((demangled_name = abi::__cxa_demangle(symbol, nullptr, nullptr,
&status)) != nullptr) {
result = demangled_name;
free(demangled_name);
} else {
result = symbol;
}
return result;
}
/* ------------------------------------------------------------------------ */
#if (defined(READLINK_COMMAND) || defined(ADDR2LINK_COMMAND)) && \
(!defined(_WIN32))
std::string exec(const std::string & cmd) {
FILE * pipe = popen(cmd.c_str(), "r");
if (pipe == nullptr) {
return "";
}
char buffer[1024];
std::string result;
while (feof(pipe) == 0) {
if (fgets(buffer, 128, pipe) != nullptr) {
result += buffer;
}
}
result = result.substr(0, result.size() - 1);
pclose(pipe);
return result;
}
#endif
auto getBacktrace() -> std::vector<std::string> {
std::vector<std::string> backtrace_lines;
#if not defined(_WIN32)
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
std::string me;
char buf[1024];
/* The manpage says it won't null terminate. Let's zero the buffer. */
memset(buf, 0, sizeof(buf));
/* Note we use sizeof(buf)-1 since we may need an extra char for NUL. */
if (readlink("/proc/self/exe", buf, sizeof(buf) - 1) != 0) {
me = std::string(buf);
}
std::ifstream inmaps;
inmaps.open("/proc/self/maps");
std::map<std::string, size_t> addr_map;
std::string line;
while (inmaps.good()) {
std::getline(inmaps, line);
std::stringstream sstr(line);
size_t first = line.find('-');
std::stringstream sstra(line.substr(0, first));
size_t addr;
sstra >> std::hex >> addr;
std::string lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
sstr >> lib;
if (not lib.empty() and (addr_map.find(lib) == addr_map.end())) {
addr_map[lib] = addr;
}
}
if (not me.empty()) {
addr_map[me] = 0;
}
#endif
/// \todo for windows this part could be coded using CaptureStackBackTrace
/// and SymFromAddr
const size_t max_depth = 100;
size_t stack_depth;
void * stack_addrs[max_depth];
char ** stack_strings;
size_t i;
stack_depth = backtrace(stack_addrs, max_depth);
stack_strings = backtrace_symbols(stack_addrs, stack_depth);
/// -1 to remove the call to the printBacktrace function
for (i = 1; i < stack_depth; i++) {
std::string bt_line(stack_strings[i]);
size_t first;
size_t second;
if ((first = bt_line.find('(')) != std::string::npos &&
(second = bt_line.find('+')) != std::string::npos) {
std::string location = bt_line.substr(0, first);
#if defined(READLINK_COMMAND)
std::string location_cmd =
std::string(BOOST_PP_STRINGIZE(READLINK_COMMAND)) +
std::string(" -f ") + location;
location = exec(location_cmd);
#endif
std::string call =
demangle(bt_line.substr(first + 1, second - first - 1).c_str());
size_t f = bt_line.find('[');
size_t s = bt_line.find(']');
std::string address = bt_line.substr(f + 1, s - f - 1);
std::stringstream sstra(address);
size_t addr;
sstra >> std::hex >> addr;
std::string trace = location + " [" + call + "]";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
auto it = addr_map.find(location);
if (it != addr_map.end()) {
std::stringstream syscom;
syscom << BOOST_PP_STRINGIZE(ADDR2LINE_COMMAND) << " 0x" << std::hex
<< (addr - it->second) << " -i -e " << location;
std::string line = exec(syscom.str());
trace += " (" + line + ")";
} else {
#endif
std::stringstream sstr_addr;
sstr_addr << std::hex << addr;
trace += " (0x" + sstr_addr.str() + ")";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
}
#endif
backtrace_lines.push_back(trace);
} else {
backtrace_lines.push_back(bt_line);
}
}
free(stack_strings);
#endif
return backtrace_lines;
}
/* ------------------------------------------------------------------------ */
void printBacktrace(const std::vector<std::string> & backtrace) {
auto w = size_t(std::floor(std::log10(double(backtrace.size()))) + 1);
std::cerr << "BACKTRACE : " << backtrace.size() << " stack frames.\n";
for (auto && data : enumerate(backtrace))
std::cerr << " [" << std::setw(w) << (std::get<0>(data) + 1) << "] "
<< std::get<1>(data) << "\n";
std::cerr << "END BACKTRACE" << std::endl;
}
/* ------------------------------------------------------------------------ */
namespace {
void terminate_handler() {
auto eptr = std::current_exception();
auto *t = abi::__cxa_current_exception_type();
auto name = (t != nullptr) ? demangle(t->name()) : std::string("unknown");
try {
if (eptr) {
std::rethrow_exception(eptr);
} else {
printBacktrace();
std::cerr << AKANTU_LOCATION
<< "!! Execution terminated for unknown reasons !!"
<< std::endl;
}
} catch (Exception & e) {
printBacktrace(e.backtrace());
std::cerr << "!! Uncaught akantu::Exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (std::exception & e) {
std::cerr << "!! Uncaught exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (...) {
std::cerr << "!! Something strange of type \"" << name
<< "\" was thrown.... !!" << std::endl;
}
if (debugger.printBacktrace()) {
std::cerr << "Random generator seed: " << RandomGenerator<UInt>::seed()
<< std::endl;
printBacktrace();
}
}
} // namespace
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
Debugger::Debugger() noexcept {
cout = &std::cerr;
level = dblWarning;
parallel_context = "";
file_open = false;
print_backtrace = false;
//initSignalHandler();
std::set_terminate(terminate_handler);
}
/* ------------------------------------------------------------------------ */
Debugger::~Debugger() {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::exit(int status) {
if (status != 0) {
std::terminate();
}
std::exit(0);
}
/*------------------------------------------------------------------------- */
void Debugger::throwException(const std::string & info,
const std::string & file, unsigned int line,
__attribute__((unused)) bool silent,
__attribute__((unused))
const std::string & location,
const std::string & module) const
noexcept(false) {
#if !defined(AKANTU_NDEBUG)
if (not silent) {
printMessage("###", dblWarning, info + " " + location, module);
}
#endif
debug::Exception ex(info, file, line);
ex.setModule(module);
throw ex;
}
/* ------------------------------------------------------------------------ */
void Debugger::printMessage(const std::string & prefix,
const DebugLevel & level,
const std::string & info,
const std::string & module) const {
if (testLevel(level, module)) {
double timestamp =
std::chrono::duration_cast<std::chrono::duration<double, std::micro>>(
std::chrono::system_clock::now().time_since_epoch())
.count();
*(cout) << parallel_context << "{" << (size_t)timestamp << "} " << prefix
<< " " << info << std::endl;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::setDebugLevel(const DebugLevel & level) {
this->level = level;
}
/* ------------------------------------------------------------------------ */
const DebugLevel & Debugger::getDebugLevel() const { return this->level; }
/* ------------------------------------------------------------------------ */
void Debugger::setLogFile(const std::string & filename) {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
auto * fileout = new std::ofstream(filename.c_str());
file_open = true;
cout = fileout;
}
std::ostream & Debugger::getOutputStream() { return *cout; }
/* ------------------------------------------------------------------------ */
void Debugger::setParallelContext(int rank, int size) {
std::stringstream sstr;
UInt pad = std::ceil(std::log10(size));
sstr << "<" << getpid() << ">[R" << std::setfill(' ') << std::right
<< std::setw(pad) << rank << "|S" << size << "] ";
parallel_context = sstr.str();
}
void setDebugLevel(const DebugLevel & level) {
debugger.setDebugLevel(level);
}
const DebugLevel & getDebugLevel() { return debugger.getDebugLevel(); }
/* ------------------------------------------------------------------------ */
void exit(int status) { Debugger::exit(status); }
} // namespace debug
} // namespace akantu
diff --git a/src/common/aka_error.hh b/src/common/aka_error.hh
index e048320f9..ef549d220 100644
--- a/src/common/aka_error.hh
+++ b/src/common/aka_error.hh
@@ -1,419 +1,422 @@
/**
* @file aka_error.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 09 2021
*
* @brief error management and internal exceptions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <set>
#include <sstream>
#include <typeinfo>
#include <utility>
#include <vector>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ERROR_HH_
#define AKANTU_ERROR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
enum DebugLevel {
dbl0 = 0,
dblError = 0,
dblAssert = 0,
dbl1 = 1,
dblException = 1,
dblCritical = 1,
dbl2 = 2,
dblMajor = 2,
dbl3 = 3,
dblCall = 3,
dblSecondary = 3,
dblHead = 3,
dbl4 = 4,
dblWarning = 4,
dbl5 = 5,
dblInfo = 5,
dbl6 = 6,
dblIn = 6,
dblOut = 6,
dbl7 = 7,
dbl8 = 8,
dblTrace = 8,
dbl9 = 9,
dblAccessory = 9,
dbl10 = 10,
dblDebug = 42,
dbl100 = 100,
dblDump = 100,
dblTest = 1337
};
/* -------------------------------------------------------------------------- */
#define AKANTU_LOCATION \
"(" << std::string(__func__) << "(): " << std::string(__FILE__) << ":" \
<< std::to_string(__LINE__) \
<< ")" // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
/* -------------------------------------------------------------------------- */
namespace debug {
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel();
void initSignalHandler();
std::string demangle(const char * symbol);
template <class T> std::string demangle() {
return demangle(typeid(T).name());
}
template <class T> std::string demangle(const T & t) {
return demangle(typeid(t).name());
}
auto exec(const std::string & cmd) -> std::string;
auto getBacktrace() -> std::vector<std::string>;
void
printBacktrace(const std::vector<std::string> & backtrace = getBacktrace());
void exit(int status) __attribute__((noreturn));
/* ------------------------------------------------------------------------ */
/// exception class that can be thrown by akantu
class Exception : public std::exception {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
protected:
explicit Exception(const std::string & info = "") : _info(info) {}
public:
//! full constructor
Exception(const std::string & info, const std::string & file,
unsigned int line)
: _info(info), _file(file), _line(line) {}
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
public:
const char * what() const noexcept override { return _info.c_str(); }
virtual std::string info() const noexcept {
std::stringstream stream;
stream << debug::demangle(typeid(*this).name()) << " : " << _info << " ["
<< _file << ":" << _line << "]";
return stream.str();
}
public:
void setInfo(const std::string & info) { _info = info; }
void setFile(const std::string & file) { _file = file; }
void setLine(unsigned int line) { _line = line; }
void setModule(const std::string & module) { _module = module; }
void setBacktrace(const std::vector<std::string> & backtrace) {
backtrace_ = backtrace;
}
decltype(auto) backtrace() const { return backtrace_; }
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
protected:
/// exception description and additionals
std::string _info;
private:
/// file it is thrown from
std::string _file;
/// line it is thrown from
unsigned int _line{0};
/// module in which exception was raised
std::string _module{"core"};
std::vector<std::string> backtrace_;
};
class CriticalError : public Exception {};
class AssertException : public Exception {};
class NotImplementedException : public Exception {};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Exception & _this) {
stream << _this.what();
return stream;
}
/* --------------------------------------------------------------------------
*/
class Debugger {
public:
Debugger() noexcept;
virtual ~Debugger();
Debugger(const Debugger &) = default;
Debugger & operator=(const Debugger &) = default;
Debugger(Debugger &&) noexcept = default;
Debugger & operator=(Debugger &&) noexcept = default;
static void exit(int status) __attribute__((noreturn));
void throwException(const std::string & info, const std::string & file,
unsigned int line, bool /*silent*/,
const std::string & /*location*/,
const std::string & module) const noexcept(false)
__attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
void throwCustomException(Except ex, const std::string & info,
const std::string & file, unsigned int line,
const std::string & module) const noexcept(false)
__attribute__((noreturn));
/*----------------------------------------------------------------------- */
template <class Except>
void throwCustomException(Except ex, const std::string & file,
unsigned int line,
const std::string & module_) const noexcept(false)
__attribute__((noreturn));
void printMessage(const std::string & prefix, const DebugLevel & level,
const std::string & info,
const std::string & module_) const;
void setOutStream(std::ostream & out) { cout = &out; }
std::ostream & getOutStream() { return *cout; }
public:
void setParallelContext(int rank, int size);
void setDebugLevel(const DebugLevel & level);
const DebugLevel & getDebugLevel() const;
void setLogFile(const std::string & filename);
std::ostream & getOutputStream();
inline bool testLevel(const DebugLevel & level,
const std::string & module = "core") const {
auto level_reached = (this->level >= (level));
auto correct_module =
(level <= dblCritical) or (modules_to_debug.empty()) or
(modules_to_debug.find(module) != modules_to_debug.end());
return level_reached and correct_module;
}
void printBacktrace(bool on_off) { this->print_backtrace = on_off; }
bool printBacktrace() const { return this->print_backtrace; }
void addModuleToDebug(const std::string & id) {
this->modules_to_debug.insert(id);
}
void removeModuleToDebug(const std::string & id) {
auto it = this->modules_to_debug.find(id);
if (it != this->modules_to_debug.end()) {
this->modules_to_debug.erase(it);
}
}
void listModules() {
for (const auto & module_ : modules_to_debug) {
(*cout) << module_ << std::endl;
}
}
private:
std::string parallel_context;
std::ostream * cout;
bool file_open;
DebugLevel level;
bool print_backtrace;
std::set<std::string> modules_to_debug;
};
extern Debugger debugger; // NOLINT
} // namespace debug
/* -------------------------------------------------------------------------- */
#define AKANTU_STRINGIZE_(str) #str
#define AKANTU_STRINGIZE(str) AKANTU_STRINGIZE_(str)
/* -------------------------------------------------------------------------- */
#define AKANTU_DEBUG_MODULE AKANTU_STRINGIZE(AKANTU_MODULE)
/* -------------------------------------------------------------------------- */
#define AKANTU_STRINGSTREAM_IN(_str, _sstr) \
; \
do { \
std::stringstream _dbg_s_info; \
_dbg_s_info << _sstr; /* NOLINT */ \
(_str) = _dbg_s_info.str(); \
} while (false)
/* -------------------------------------------------------------------------- */
#define AKANTU_EXCEPTION(info) AKANTU_EXCEPTION_(info, false)
#define AKANTU_SILENT_EXCEPTION(info) AKANTU_EXCEPTION_(info, true)
#define AKANTU_EXCEPTION_(info, silent) \
do { \
std::stringstream _dbg_str; \
_dbg_str << info; /* NOLINT */ \
std::stringstream _dbg_loc; \
_dbg_loc << AKANTU_LOCATION; \
::akantu::debug::debugger.throwException(_dbg_str.str(), __FILE__, \
__LINE__, silent, _dbg_loc.str(), \
AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION_INFO(ex, info) \
do { \
std::stringstream _dbg_str; \
_dbg_str << info; /* NOLINT */ \
::akantu::debug::debugger.throwCustomException( \
ex, _dbg_str.str(), __FILE__, __LINE__, AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_CUSTOM_EXCEPTION(ex) \
do { \
::akantu::debug::debugger.throwCustomException(ex, __FILE__, __LINE__, \
AKANTU_DEBUG_MODULE); \
} while (false)
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_NDEBUG
#define AKANTU_DEBUG_TEST(level) (false)
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest, AKANTU_DEBUG_MODULE))
#define AKANTU_DEBUG(level, info)
#define AKANTU_DEBUG_(pref, level, info)
#define AKANTU_DEBUG_IN()
#define AKANTU_DEBUG_OUT()
#define AKANTU_DEBUG_INFO(info)
#define AKANTU_DEBUG_WARNING(info)
#define AKANTU_DEBUG_TRACE(info)
#define AKANTU_DEBUG_ASSERT(test, info)
#define AKANTU_ERROR(info) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), info)
/* -------------------------------------------------------------------------- */
#else
#define AKANTU_DEBUG(level, info) AKANTU_DEBUG_(" ", level, info)
#define AKANTU_DEBUG_(pref, level, info) \
do { \
std::string _dbg_str; \
AKANTU_STRINGSTREAM_IN(_dbg_str, \
info << " " << AKANTU_LOCATION); /* NOLINT */ \
::akantu::debug::debugger.printMessage(pref, level, _dbg_str, \
AKANTU_DEBUG_MODULE); \
} while (false)
#define AKANTU_DEBUG_TEST(level) \
(::akantu::debug::debugger.testLevel(level, AKANTU_DEBUG_MODULE))
#define AKANTU_DEBUG_LEVEL_IS_TEST() \
(::akantu::debug::debugger.testLevel(dblTest))
#define AKANTU_DEBUG_IN() \
AKANTU_DEBUG_( \
"==>", ::akantu::dblIn, \
__func__ \
<< "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
// bugprone-lambda-function-name)
#define AKANTU_DEBUG_OUT() \
AKANTU_DEBUG_( \
"<==", ::akantu::dblOut, \
__func__ \
<< "()") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
// bugprone-lambda-function-name)
#define AKANTU_DEBUG_INFO(info) AKANTU_DEBUG_("---", ::akantu::dblInfo, info)
#define AKANTU_DEBUG_WARNING(info) \
AKANTU_DEBUG_("/!\\", ::akantu::dblWarning, info)
#define AKANTU_DEBUG_TRACE(info) AKANTU_DEBUG_(">>>", ::akantu::dblTrace, info)
#define AKANTU_DEBUG_ASSERT(test, info) \
do { \
if (not(test)) \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::AssertException(), \
"assert [" << #test << "] " \
<< info); /* NOLINT */ \
} while (false)
#define AKANTU_ERROR(info) \
do { \
AKANTU_DEBUG_("!!! ", ::akantu::dblError, info); \
AKANTU_CUSTOM_EXCEPTION_INFO(::akantu::debug::CriticalError(), \
info); /* NOLINT */ \
} while (false)
#endif // AKANTU_NDEBUG
#define AKANTU_TO_IMPLEMENT() \
AKANTU_CUSTOM_EXCEPTION_INFO( \
::akantu::debug::NotImplementedException(), \
__func__ \
<< " : not implemented yet !") // NOLINT(cppcoreguidelines-pro-bounds-array-to-pointer-decay,
// bugprone-lambda-function-name)
/* -------------------------------------------------------------------------- */
namespace debug {
/* ------------------------------------------------------------------------ */
template <class Except>
void Debugger::throwCustomException(Except ex, const std::string & info,
const std::string & file,
unsigned int line,
const std::string & module_) const
noexcept(false) {
ex.setInfo(info);
ex.setFile(file);
ex.setLine(line);
ex.setModule(module_);
if (::akantu::debug::debugger.printBacktrace()) {
ex.setBacktrace(::akantu::debug::getBacktrace());
}
throw ex;
}
/* ------------------------------------------------------------------------ */
template <class Except>
void Debugger::throwCustomException(Except ex, const std::string & file,
unsigned int line,
const std::string & module_) const
noexcept(false) {
ex.setFile(file);
ex.setLine(line);
ex.setModule(module_);
if (::akantu::debug::debugger.printBacktrace()) {
ex.setBacktrace(::akantu::debug::getBacktrace());
}
throw ex;
}
} // namespace debug
} // namespace akantu
#endif /* AKANTU_ERROR_HH_ */
diff --git a/src/common/aka_event_handler_manager.hh b/src/common/aka_event_handler_manager.hh
index 33b5f1544..5cd7afee3 100644
--- a/src/common/aka_event_handler_manager.hh
+++ b/src/common/aka_event_handler_manager.hh
@@ -1,126 +1,128 @@
/**
* @file aka_event_handler_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Tue Feb 09 2021
*
* @brief Base of Event Handler classes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_
#define AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <list>
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class EventHandler> class EventHandlerManager {
private:
using priority_value = std::pair<EventHandlerPriority, EventHandler *>;
using priority_list = std::list<priority_value>;
struct KeyComp {
bool operator()(const priority_value & a, const priority_value & b) const {
return (a.first < b.first);
}
bool operator()(const priority_value & a, UInt b) const {
return (a.first < b);
}
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~EventHandlerManager() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a new EventHandler to the Manager. The register object
/// will then be informed about the events the manager observes.
void registerEventHandler(EventHandler & event_handler,
EventHandlerPriority priority = _ehp_highest) {
auto it = this->searchEventHandler(event_handler);
if (it != this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler was already registered (priority: "
<< priority << ")");
}
auto pos =
std::lower_bound(this->event_handlers.begin(),
this->event_handlers.end(), priority, KeyComp());
this->event_handlers.insert(pos, std::make_pair(priority, &event_handler));
}
/// unregister a EventHandler object. This object will not be
/// notified anymore about the events this manager observes.
void unregisterEventHandler(EventHandler & event_handler) {
auto it = this->searchEventHandler(event_handler);
if (it == this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler is not registered");
}
this->event_handlers.erase(it);
}
/// Notify all the registered EventHandlers about the event that just occured.
template <class Event> void sendEvent(const Event & event) {
for (auto & pair : this->event_handlers) {
pair.second->sendEvent(event);
}
}
private:
typename priority_list::iterator searchEventHandler(EventHandler & handler) {
auto it = this->event_handlers.begin();
auto end = this->event_handlers.end();
for (; it != end && it->second != &handler; ++it) {
;
}
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// list of the event handlers
priority_list event_handlers;
};
} // namespace akantu
#endif /* AKANTU_AKA_EVENT_HANDLER_MANAGER_HH_ */
diff --git a/src/common/aka_extern.cc b/src/common/aka_extern.cc
index 975fed33b..cc58e8651 100644
--- a/src/common/aka_extern.cc
+++ b/src/common/aka_extern.cc
@@ -1,96 +1,98 @@
/**
* @file aka_extern.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Oct 27 2020
*
* @brief initialisation of all global variables
* to insure the order of creation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_math.hh"
#include "aka_named_argument.hh"
#include "aka_random_generator.hh"
#include "communication_tag.hh"
#include "cppargparse.hh"
#include "parser.hh"
#include "solid_mechanics_model.hh"
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <limits>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* error.hpp variables */
/* -------------------------------------------------------------------------- */
namespace debug {
/** \todo write function to get this
* values from the environment or a config file
*/
/// standard output for debug messages
std::ostream * _akantu_debug_cout = &std::cerr;
/// standard output for normal messages
std::ostream & _akantu_cout = std::cout;
/// parallel context used in debug messages
std::string _parallel_context;
Debugger debugger;
} // namespace debug
/* -------------------------------------------------------------------------- */
/// Paser for commandline arguments
::cppargparse::ArgumentParser static_argparser;
/// Parser containing the information parsed by the input file given to initFull
Parser static_parser;
bool Parser::permissive_parser = false;
/* -------------------------------------------------------------------------- */
Real Math::tolerance = 1e2 * std::numeric_limits<Real>::epsilon();
/* -------------------------------------------------------------------------- */
const UInt _all_dimensions [[gnu::unused]] = UInt(-1);
/* -------------------------------------------------------------------------- */
const Array<UInt> empty_filter(0, 1, "empty_filter");
/* -------------------------------------------------------------------------- */
template <> long int RandomGenerator<UInt>::_seed = 5489U;
template <> std::default_random_engine RandomGenerator<UInt>::generator(5489U);
/* -------------------------------------------------------------------------- */
int Tag::max_tag = 0;
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/common/aka_factory.hh b/src/common/aka_factory.hh
index 9e8074422..90fe7e603 100644
--- a/src/common/aka_factory.hh
+++ b/src/common/aka_factory.hh
@@ -1,94 +1,97 @@
/**
* @file aka_factory.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 09 2017
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Tue Mar 30 2021
*
* @brief This is a generic factory
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <map>
#include <memory>
#include <string>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_FACTORY_HH_
#define AKANTU_AKA_FACTORY_HH_
namespace akantu {
template <class Base, class T = ID, class... Args> class Factory {
using allocator_t = std::function<std::unique_ptr<Base>(Args...)>;
private:
Factory() = default;
public:
Factory(const Factory &) = delete;
Factory & operator=(const Factory &) = delete;
static Factory & getInstance() {
static Factory instance;
return instance;
}
/* ------------------------------------------------------------------------ */
bool registerAllocator(const T & id, const allocator_t & allocator) {
if (allocators.find(id) != allocators.end()) {
AKANTU_EXCEPTION("The id \"" << id
<< "\" is already registered in the "
<< debug::demangle(typeid(Base).name()) << " factory");
}
allocators[id] = allocator;
return true;
}
template <typename... AArgs>
std::unique_ptr<Base> allocate(const T & id, AArgs &&... args) const {
if (allocators.find(id) == allocators.end()) {
AKANTU_EXCEPTION("The id \"" << id
<< "\" is not registered in the "
<< debug::demangle(typeid(Base).name()) << " factory.");
}
return std::forward<std::unique_ptr<Base>>(
allocators.at(id)(std::forward<AArgs>(args)...));
}
std::vector<T> getPossibleAllocators() {
std::vector<T> keys;
for (auto & e : allocators) {
keys.push_back(e.first);
}
return keys;
}
private:
std::map<T, allocator_t> allocators;
};
} // namespace akantu
#endif /* AKANTU_AKA_FACTORY_HH_ */
diff --git a/src/common/aka_fwd.hh b/src/common/aka_fwd.hh
index dbff6e8a1..fe3a78fdd 100644
--- a/src/common/aka_fwd.hh
+++ b/src/common/aka_fwd.hh
@@ -1,70 +1,73 @@
/**
* @file aka_fwd.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Wed Oct 25 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief File containing forward declarations in akantu.
* This file helps if circular #include would be needed because two classes
* refer both to each other. This file usually does not need any modification.
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FWD_HH_
#define AKANTU_FWD_HH_
namespace cppargparse {
class ArgumentParser;
}
namespace akantu {
// forward declaration
template <int dim, class model_type> struct ContactData;
template <typename T> class Matrix;
template <typename T> class Vector;
template <typename T> class Tensor3;
template <typename T, bool is_scal = aka::is_scalar<T>::value> class Array;
template <typename T, typename SupportType = ElementType>
class ElementTypeMapArray;
template <class T> class SpatialGrid;
// Model element
template <class ModelPolicy> class ModelElement;
extern const Array<UInt> empty_filter;
class Parser;
class ParserSection;
extern Parser static_parser; // NOLINT
extern cppargparse::ArgumentParser static_argparser; // NOLINT
class Mesh;
class SparseMatrix;
} // namespace akantu
#endif /* AKANTU_FWD_HH_ */
diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index 46ce34137..316f49f19 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,530 +1,533 @@
/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Feb 09 2021
*
* @brief Grid that is auto balanced
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_GRID_DYNAMIC_HH_
#define AKANTU_AKA_GRID_DYNAMIC_HH_
namespace akantu {
class Mesh;
template <typename T> class SpatialGrid {
public:
explicit SpatialGrid(UInt dimension)
: dimension(dimension), spacing(dimension), center(dimension),
lower(dimension), upper(dimension), empty_cell() {}
SpatialGrid(UInt dimension, const Vector<Real> & spacing,
const Vector<Real> & center)
: dimension(dimension), spacing(spacing), center(center),
lower(dimension), upper(dimension), empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = -std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() = default;
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
CellID() = default;
explicit CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(
ids.storage(), ids.storage() + ids.size(), id.ids.storage(),
id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const { return !(operator==(id)); }
class neighbor_cells_iterator
: private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end)
: cell_id(cell_id), position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
if (end) {
this->it++;
}
}
neighbor_cells_iterator & operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i) {
;
}
if (i == position.size()) {
++it;
return *this;
}
for (UInt j = 0; j < i; ++j) {
position(j) = -1;
}
position(i)++;
updateIt();
return *this;
}
neighbor_cells_iterator operator++(int) {
neighbor_cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const neighbor_cells_iterator & rhs) const {
return cell_id == rhs.cell_id && it == rhs.it;
};
bool operator!=(const neighbor_cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
for (UInt i = 0; i < position.size(); ++i) {
it = it * 3 + (position(i) + 1);
}
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
// current cell shift
Vector<Int> position;
};
class Neighbors {
public:
explicit Neighbors(const CellID & cell_id) : cell_id(cell_id) {}
decltype(auto) begin() { return neighbor_cells_iterator(cell_id, false); }
decltype(auto) end() { return neighbor_cells_iterator(cell_id, true); }
private:
const CellID & cell_id;
};
decltype(auto) neighbors() { return Neighbors(*this); }
private:
friend class cells_iterator;
Vector<Int> ids;
};
/* ------------------------------------------------------------------------ */
class Cell {
public:
using iterator = typename std::vector<T>::iterator;
using const_iterator = typename std::vector<T>::const_iterator;
Cell() : id(), data() {}
explicit Cell(const CellID & cell_id) : id(cell_id), data() {}
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) {
data.push_back(d);
return *this;
}
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
private:
CellID id;
std::vector<T> data;
};
private:
using cells_container = std::map<CellID, Cell>;
public:
const Cell & getCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second;
}
return empty_cell;
}
decltype(auto) beginCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.begin();
}
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.end();
}
return empty_cell.end();
}
decltype(auto) beginCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.begin();
}
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.end();
}
return empty_cell.end();
}
/* ------------------------------------------------------------------------ */
class cells_iterator
: private std::iterator<std::forward_iterator_tag, CellID> {
public:
explicit cells_iterator(typename std::map<CellID, Cell>::const_iterator it)
: it(it) {}
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int /*unused*/) {
cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const cells_iterator & rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template <class vector_type>
Cell & insert(const T & d, const vector_type & position) {
auto && cell_id = getCellID(position);
auto && it = cells.find(cell_id);
if (it == cells.end()) {
Cell cell(cell_id);
auto & tmp = (cells[cell_id] = cell).add(d);
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
if (posl <= lower(i)) {
lower(i) = posl;
}
if (posu > upper(i)) {
upper(i) = posu;
}
}
return tmp;
}
return it->second.add(d);
}
/* ------------------------------------------------------------------------ */
inline decltype(auto) begin() const {
auto begin = this->cells.begin();
return cells_iterator(begin);
}
inline decltype(auto) end() const {
auto end = this->cells.end();
return cells_iterator(end);
}
template <class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << lower(i);
};
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << upper(i);
};
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << spacing(i);
};
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << center(i);
};
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* --------------------------------------------------------------------------
*/
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(), "The direction asked ("
<< direction
<< ") is out of range "
<< center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
// if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
AKANTU_SET_MACRO(Spacing, spacing, Vector<Real> &);
AKANTU_GET_MACRO(Center, center, const Vector<Real> &);
AKANTU_SET_MACRO(Center, center, Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SpatialGrid<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "mesh.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
ElementType type = _not_defined;
switch (dimension) {
case 1:
type = _segment_2;
break;
case 2:
type = _quadrangle_4;
break;
case 3:
type = _hexahedron_8;
break;
}
MeshAccessor mesh_accessor(mesh);
auto & connectivity = mesh_accessor.getConnectivity(type);
auto & nodes = mesh_accessor.getNodes();
auto & uint_data = mesh.getDataPointer<UInt>("tag_1", type);
Vector<Real> pos(dimension);
UInt global_id = 0;
for (auto & cell_pair : cells) {
UInt cur_node = nodes.size();
UInt cur_elem = connectivity.size();
const CellID & cell_id = cell_pair.first;
for (UInt i = 0; i < dimension; ++i) {
pos(i) = center(i) + cell_id.getID(i) * spacing(i);
}
nodes.push_back(pos);
for (UInt i = 0; i < dimension; ++i) {
pos(i) += spacing(i);
}
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch (dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(0) += spacing(0);
pos(1) -= spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1);
pos(2) -= spacing(2);
nodes.push_back(pos);
pos(1) += spacing(1);
nodes.push_back(pos);
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(1) -= spacing(1);
pos(2) += spacing(2);
nodes.push_back(pos);
pos(0) += spacing(0);
nodes.push_back(pos);
pos(0) -= spacing(0);
pos(1) += spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
++global_id;
}
}
} // namespace akantu
#endif /* AKANTU_AKA_GRID_DYNAMIC_HH_ */
diff --git a/src/common/aka_math.cc b/src/common/aka_math.cc
index 58f554e73..9a997f3cd 100644
--- a/src/common/aka_math.cc
+++ b/src/common/aka_math.cc
@@ -1,269 +1,271 @@
/**
* @file aka_math.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Implementation of the math toolbox
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_math.hh"
#include "aka_array.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace Math {
/* --------------------------------------------------------------------------
*/
void matrix_vector(UInt m, UInt n, const Array<Real> & A,
const Array<Real> & x, Array<Real> & y, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == x.size(),
"The vector A(" << A.getID() << ") and the vector x("
<< x.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(
A.getNbComponent() == m * n,
"The vector A(" << A.getID() << ") has the good number of component.");
AKANTU_DEBUG_ASSERT(x.getNbComponent() == n,
"The vector x("
<< x.getID()
<< ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(y.getNbComponent() == n,
"The vector y("
<< y.getID()
<< ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_x = x.getNbComponent();
y.resize(nb_element);
Real * A_val = A.storage();
Real * x_val = x.storage();
Real * y_val = y.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_vector(m, n, A_val, x_val, y_val, alpha);
A_val += offset_A;
x_val += offset_x;
y_val += offset_x;
}
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == B.size(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(
A.getNbComponent() == m * k,
"The vector A(" << A.getID() << ") has the good number of component.");
AKANTU_DEBUG_ASSERT(B.getNbComponent() == k * n,
"The vector B("
<< B.getID()
<< ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(C.getNbComponent() == m * n,
"The vector C("
<< C.getID()
<< ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrix(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
void matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.size() == B.size(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(
A.getNbComponent() == m * k,
"The vector A(" << A.getID() << ") has the good number of component.");
AKANTU_DEBUG_ASSERT(B.getNbComponent() == k * n,
"The vector B("
<< B.getID()
<< ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(C.getNbComponent() == m * n,
"The vector C("
<< C.getID()
<< ") do not the good number of component.");
UInt nb_element = A.size();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrixt(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* --------------------------------------------------------------------------
*/
void compute_tangents(const Array<Real> & normals, Array<Real> & tangents) {
AKANTU_DEBUG_IN();
if (normals.empty()) {
return;
}
auto spatial_dimension = normals.getNbComponent();
auto tangent_components = spatial_dimension * (spatial_dimension - 1);
if (tangent_components == 0) {
return;
}
AKANTU_DEBUG_ASSERT(
tangent_components == tangents.getNbComponent(),
"Cannot compute the tangents, the storage array for tangents"
<< " does not have the good amount of components.");
auto nb_normals = normals.size();
tangents.resize(nb_normals);
tangents.zero();
/// compute first tangent
for (auto && data : zip(make_view(normals, spatial_dimension),
make_view(tangents, tangent_components))) {
const auto & normal = std::get<0>(data);
auto & tangent = std::get<1>(data);
if (are_float_equal(norm2(normal.storage()), 0.)) {
tangent(0) = 1.;
} else {
normal2(normal.storage(), tangent.storage());
}
}
/// compute second tangent (3D case)
if (spatial_dimension == 3) {
for (auto && data : zip(make_view(normals, spatial_dimension),
make_view(tangents, tangent_components))) {
const auto & normal = std::get<0>(data);
auto & tangent = std::get<1>(data);
normal3(normal.storage(), tangent.storage(),
tangent.storage() + spatial_dimension);
}
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* --------------------------------------------------------------------------
*/
Real reduce(Array<Real> & array) {
UInt nb_values = array.size();
if (nb_values == 0) {
return 0.;
}
UInt nb_values_to_sum = nb_values >> 1;
std::sort(array.begin(), array.end());
// as long as the half is not empty
while (nb_values_to_sum != 0U) {
UInt remaining = (nb_values - 2 * nb_values_to_sum);
if (remaining != 0U) {
array(nb_values - 2) += array(nb_values - 1);
}
// sum to consecutive values and store the sum in the first half
for (UInt i = 0; i < nb_values_to_sum; ++i) {
array(i) = array(2 * i) + array(2 * i + 1);
}
nb_values = nb_values_to_sum;
nb_values_to_sum >>= 1;
}
return array(0);
}
} // namespace Math
} // namespace akantu
diff --git a/src/common/aka_math.hh b/src/common/aka_math.hh
index a1df46c8e..62eb756f4 100644
--- a/src/common/aka_math.hh
+++ b/src/common/aka_math.hh
@@ -1,284 +1,287 @@
/**
* @file aka_math.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Tue Feb 09 2021
*
* @brief mathematical operations
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <utility>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_MATH_H_
#define AKANTU_AKA_MATH_H_
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace Math {
/// tolerance for functions that need one
extern Real tolerance; // NOLINT
/* ------------------------------------------------------------------------ */
/* Matrix algebra */
/* ------------------------------------------------------------------------ */
/// @f$ y = A*x @f$
void matrix_vector(UInt m, UInt n, const Array<Real> & A,
const Array<Real> & x, Array<Real> & y, Real alpha = 1.);
/// @f$ y = A*x @f$
inline void matrix_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
Real alpha = 1.);
/// @f$ y = A^t*x @f$
inline void matrixt_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
Real alpha = 1.);
/// @f$ C = A*B @f$
void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
void matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha = 1.);
/// @f$ C = A*B @f$
inline void matrix_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B @f$
inline void matrixt_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
inline void matrix_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B^t @f$
inline void matrixt_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
template <bool tr_A, bool tr_B>
inline void matMul(UInt m, UInt n, UInt k, Real alpha, Real * A, Real * B,
Real beta, Real * C);
template <bool tr_A>
inline void matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
Real beta, Real * y);
inline void aXplusY(UInt n, Real alpha, Real * x, Real * y);
inline void matrix33_eigenvalues(Real * A, Real * Adiag);
inline void matrix22_eigenvalues(Real * A, Real * Adiag);
template <UInt dim> inline void eigenvalues(Real * A, Real * d);
/// solve @f$ A x = \Lambda x @f$ and return d and V such as @f$ A V[i:] =
/// d[i] V[i:]@f$
template <typename T> void matrixEig(UInt n, T * A, T * d, T * V = nullptr);
/// determinent of a 2x2 matrix
Real det2(const Real * mat);
/// determinent of a 3x3 matrix
Real det3(const Real * mat);
/// determinent of a nxn matrix
template <UInt n> Real det(const Real * mat);
/// determinent of a nxn matrix
template <typename T> T det(UInt n, const T * A);
/// inverse a nxn matrix
template <UInt n> inline void inv(const Real * A, Real * inv);
/// inverse a nxn matrix
template <typename T> inline void inv(UInt n, const T * A, T * inv);
/// inverse a 3x3 matrix
inline void inv3(const Real * mat, Real * inv);
/// inverse a 2x2 matrix
inline void inv2(const Real * mat, Real * inv);
/// solve A x = b using a LU factorization
template <typename T>
inline void solve(UInt n, const T * A, T * x, const T * b);
/// return the double dot product between 2 tensors in 2d
inline Real matrixDoubleDot22(Real * A, Real * B);
/// return the double dot product between 2 tensors in 3d
inline Real matrixDoubleDot33(Real * A, Real * B);
/// extension of the double dot product to two 2nd order tensor in dimension n
inline Real matrixDoubleDot(UInt n, Real * A, Real * B);
/* ------------------------------------------------------------------------ */
/* Array algebra */
/* ------------------------------------------------------------------------ */
/// vector cross product
inline void vectorProduct3(const Real * v1, const Real * v2, Real * res);
/// normalize a vector
inline void normalize2(Real * v);
/// normalize a vector
inline void normalize3(Real * v);
/// return norm of a 2-vector
inline Real norm2(const Real * v);
/// return norm of a 3-vector
inline Real norm3(const Real * v);
/// return norm of a vector
inline Real norm(UInt n, const Real * v);
/// return the dot product between 2 vectors in 2d
inline Real vectorDot2(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors in 3d
inline Real vectorDot3(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors
inline Real vectorDot(Real * v1, Real * v2, UInt n);
/* ------------------------------------------------------------------------ */
/* Geometry */
/* ------------------------------------------------------------------------ */
/// compute normal a normal to a vector
inline void normal2(const Real * vec, Real * normal);
/// compute normal a normal to a vector
inline void normal3(const Real * vec1, const Real * vec2, Real * normal);
/// compute the tangents to an array of normal vectors
void compute_tangents(const Array<Real> & normals, Array<Real> & tangents);
/// distance in 2D between x and y
inline Real distance_2d(const Real * x, const Real * y);
/// distance in 3D between x and y
inline Real distance_3d(const Real * x, const Real * y);
/// radius of the in-circle of a triangle in 2d space
static inline Real triangle_inradius(const Vector<Real> & coord1,
const Vector<Real> & coord2,
const Vector<Real> & coord3);
/// radius of the in-circle of a tetrahedron
inline Real tetrahedron_inradius(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4);
/// volume of a tetrahedron
inline Real tetrahedron_volume(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4);
/// compute the barycenter of n points
inline void barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter);
/// vector between x and y
inline void vector_2d(const Real * x, const Real * y, Real * res);
/// vector pointing from x to y in 3 spatial dimension
inline void vector_3d(const Real * x, const Real * y, Real * res);
/// test if two scalar are equal within a given tolerance
inline bool are_float_equal(Real x, Real y);
/// test if two vectors are equal within a given tolerance
inline bool are_vector_equal(UInt n, Real * x, Real * y);
#ifdef isnan
#error \
"You probably included <math.h> which is incompatible with aka_math please use\
<cmath> or add a \"#undef isnan\" before akantu includes"
#endif
/// test if a real is a NaN
inline bool isnan(Real x);
/// test if the line x and y intersects each other
inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max);
/// test if a is in the range [x_min, x_max]
inline bool is_in_range(Real a, Real x_min, Real x_max);
inline Real getTolerance() { return Math::tolerance; }
inline void setTolerance(Real tol) { Math::tolerance = tol; }
template <UInt p, typename T> inline T pow(T x);
template <class T1, class T2,
std::enable_if_t<std::is_integral<T1>::value and
std::is_integral<T2>::value> * = nullptr>
inline Real kronecker(T1 i, T2 j) {
return static_cast<Real>(i == j);
}
/// reduce all the values of an array, the summation is done in place and the
/// array is modified
Real reduce(Array<Real> & array);
class NewtonRaphson {
public:
NewtonRaphson(Real tolerance, Real max_iteration)
: tolerance(tolerance), max_iteration(max_iteration) {}
template <class Functor> Real solve(const Functor & funct, Real x_0);
private:
Real tolerance;
Real max_iteration;
};
struct NewtonRaphsonFunctor {
explicit NewtonRaphsonFunctor(const std::string & name) : name(name) {}
virtual ~NewtonRaphsonFunctor() = default;
NewtonRaphsonFunctor(const NewtonRaphsonFunctor & other) = default;
NewtonRaphsonFunctor(NewtonRaphsonFunctor && other) noexcept = default;
NewtonRaphsonFunctor &
operator=(const NewtonRaphsonFunctor & other) = default;
NewtonRaphsonFunctor &
operator=(NewtonRaphsonFunctor && other) noexcept = default;
virtual Real f(Real x) const = 0;
virtual Real f_prime(Real x) const = 0;
std::string name;
};
} // namespace Math
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "aka_math_tmpl.hh"
#endif /* AKANTU_AKA_MATH_H_ */
diff --git a/src/common/aka_math_tmpl.hh b/src/common/aka_math_tmpl.hh
index 4b92956b0..50809863a 100644
--- a/src/common/aka_math_tmpl.hh
+++ b/src/common/aka_math_tmpl.hh
@@ -1,838 +1,843 @@
/**
* @file aka_math_tmpl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Dec 11 2020
*
* @brief Implementation of the inline functions of the math toolkit
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_blas_lapack.hh"
#include "aka_math.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <typeinfo>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace Math {
/* ------------------------------------------------------------------------ */
inline void matrix_vector(UInt im, UInt in,
Real * A, // NOLINT(readability-non-const-parameter)
Real * x, // NOLINT(readability-non-const-parameter)
Real * y, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'N';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
std::fill_n(y, im, 0.);
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[i] += A[i + j * im] * x[j];
}
y[i] *= alpha;
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void
matrixt_vector(UInt im, UInt in,
Real * A, // NOLINT(readability-non-const-parameter)
Real * x, // NOLINT(readability-non-const-parameter)
Real * y, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'T';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
std::fill_n(y, in, 0.);
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[j] += A[j * im + i] * x[i];
}
y[i] *= alpha;
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void matrix_matrix(UInt im, UInt in, UInt ik,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B, // NOLINT(readability-non-const-parameter)
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &k, &beta, C,
&m);
#else
std::fill_n(C, im * in, 0.);
for (UInt j = 0; j < in; ++j) {
UInt _jb = j * ik;
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
C[i + _jc] += A[i + _la] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void
matrixt_matrix(UInt im, UInt in, UInt ik,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B, // NOLINT(readability-non-const-parameter)
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &k, &beta, C,
&m);
#else
std::fill_n(C, im * in, 0.);
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
UInt _jb = j * ik;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
C[i + _jc] += A[l + _ia] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void
matrix_matrixt(UInt im, UInt in, UInt ik,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B, // NOLINT(readability-non-const-parameter)
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &n, &beta, C,
&m);
#else
std::fill_n(C, im * in, 0.);
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
UInt _lb = l * in;
C[i + _jc] += A[i + _la] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void
matrixt_matrixt(UInt im, UInt in, UInt ik,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B, // NOLINT(readability-non-const-parameter)
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &n, &beta, C,
&m);
#else
std::fill_n(C, im * in, 0.);
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
UInt _lb = l * in;
C[i + _jc] += A[l + _ia] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* ------------------------------------------------------------------------ */
inline void aXplusY(UInt n, Real alpha,
Real * x, // NOLINT(readability-non-const-parameter)
Real * y) {
#ifdef AKANTU_USE_BLAS
/// y := alpha x + y
int incx = 1, incy = 1;
aka_axpy(&n, &alpha, x, &incx, y, &incy);
#else
for (UInt i = 0; i < n; ++i) {
*(y++) += alpha * *(x++);
}
#endif
}
/* ------------------------------------------------------------------------ */
inline Real vectorDot(Real * v1, // NOLINT(readability-non-const-parameter)
Real * v2, // NOLINT(readability-non-const-parameter)
UInt in) {
#ifdef AKANTU_USE_BLAS
/// d := v1 . v2
int incx = 1, incy = 1, n = in;
Real d = aka_dot(&n, v1, &incx, v2, &incy);
#else
Real d = 0;
for (UInt i = 0; i < in; ++i) {
d += v1[i] * v2[i];
}
#endif
return d;
}
/* ------------------------------------------------------------------------ */
template <bool tr_A, bool tr_B>
inline void matMul(UInt m, UInt n, UInt k, Real alpha,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B, // NOLINT(readability-non-const-parameter)
Real /*beta*/, Real * C) {
if (tr_A) {
if (tr_B) {
matrixt_matrixt(m, n, k, A, B, C, alpha);
} else {
matrixt_matrix(m, n, k, A, B, C, alpha);
}
} else {
if (tr_B) {
matrix_matrixt(m, n, k, A, B, C, alpha);
} else {
matrix_matrix(m, n, k, A, B, C, alpha);
}
}
}
/* ------------------------------------------------------------------------ */
template <bool tr_A>
inline void matVectMul(UInt m, UInt n, Real alpha,
Real * A, // NOLINT(readability-non-const-parameter)
Real * x, // NOLINT(readability-non-const-parameter)
Real /*beta*/, Real * y) {
if (tr_A) {
matrixt_vector(m, n, A, x, y, alpha);
} else {
matrix_vector(m, n, A, x, y, alpha);
}
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void matrixEig(UInt n,
T * A, // NOLINT(readability-non-const-parameter)
T * d, T * V) {
// Matrix A is row major, so the lapack function in fortran will
// process A^t. Asking for the left eigenvectors of A^t will give the
// transposed right eigenvectors of A so in the C++ code the right
// eigenvectors.
char jobvr{'N'};
if (V != nullptr) {
jobvr = 'V'; // compute left eigenvectors
}
char jobvl{'N'}; // compute right eigenvectors
auto * di = new T[n]; // imaginary part of the eigenvalues
int info;
int N = n;
T wkopt;
int lwork = -1;
// query and allocate the optimal workspace
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, &wkopt,
&lwork, &info);
lwork = int(wkopt);
auto * work = new T[lwork];
// solve the eigenproblem
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, nullptr, &N, V, &N, work,
&lwork, &info);
AKANTU_DEBUG_ASSERT(
info == 0,
"Problem computing eigenvalues/vectors. DGEEV exited with the value "
<< info);
delete[] work;
delete[] di; // I hope for you that there was no complex eigenvalues !!!
}
/* ------------------------------------------------------------------------ */
inline void
matrix22_eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
Real * Adiag) {
/// d = determinant of Matrix A
Real d = det2(A);
/// b = trace of Matrix A
Real b = A[0] + A[3];
Real c = std::sqrt(b * b - 4 * d);
Adiag[0] = .5 * (b + c);
Adiag[1] = .5 * (b - c);
}
/* ------------------------------------------------------------------------ */
inline void
matrix33_eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
Real * Adiag) {
matrixEig(3, A, Adiag);
}
/* ------------------------------------------------------------------------ */
template <UInt dim>
inline void eigenvalues(Real * A, // NOLINT(readability-non-const-parameter)
Real * d) {
if (dim == 1) {
d[0] = A[0];
} else if (dim == 2) {
matrix22_eigenvalues(A, d);
}
// else if(dim == 3) { matrix33_eigenvalues(A, d); }
else {
matrixEig(dim, A, d);
}
}
/* ------------------------------------------------------------------------ */
inline Real det2(const Real * mat) {
return mat[0] * mat[3] - mat[1] * mat[2];
}
/* ------------------------------------------------------------------------ */
inline Real det3(const Real * mat) {
return mat[0] * (mat[4] * mat[8] - mat[7] * mat[5]) -
mat[3] * (mat[1] * mat[8] - mat[7] * mat[2]) +
mat[6] * (mat[1] * mat[5] - mat[4] * mat[2]);
}
/* ------------------------------------------------------------------------ */
template <UInt n> inline Real det(const Real * mat) {
if (n == 1) {
return *mat;
}
if (n == 2) {
return det2(mat);
}
if (n == 3) {
return det3(mat);
}
return det(n, mat);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline T det(UInt n, const T * A) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
auto * LU = new T[N * N];
std::copy(A, A + N * N, LU);
// LU factorization of A
aka_getrf(&N, &N, LU, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
// det(A) = det(L) * det(U) = 1 * det(U) = product_i U_{ii}
T det = 1.;
for (int i = 0; i < N; ++i) {
det *= (2 * (ipiv[i] == i) - 1) * LU[i * n + i];
}
delete[] ipiv;
delete[] LU;
return det;
}
/* ------------------------------------------------------------------------ */
inline void normal2(const Real * vec, Real * normal) {
normal[0] = vec[1];
normal[1] = -vec[0];
normalize2(normal);
}
/* ------------------------------------------------------------------------ */
inline void normal3(const Real * vec1, const Real * vec2, Real * normal) {
vectorProduct3(vec1, vec2, normal);
normalize3(normal);
}
/* ------------------------------------------------------------------------ */
inline void normalize2(Real * vec) {
Real norm = norm2(vec);
vec[0] /= norm;
vec[1] /= norm;
}
/* ------------------------------------------------------------------------ */
inline void normalize3(Real * vec) {
Real norm = norm3(vec);
vec[0] /= norm;
vec[1] /= norm;
vec[2] /= norm;
}
/* ------------------------------------------------------------------------ */
inline Real norm2(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1]);
}
/* ------------------------------------------------------------------------ */
inline Real norm3(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2]);
}
/* ------------------------------------------------------------------------ */
inline Real norm(UInt n, const Real * vec) {
Real norm = 0.;
for (UInt i = 0; i < n; ++i) {
norm += vec[i] * vec[i];
}
return sqrt(norm);
}
/* ------------------------------------------------------------------------ */
inline void inv2(const Real * mat, Real * inv) {
Real det_mat = det2(mat);
inv[0] = mat[3] / det_mat;
inv[1] = -mat[1] / det_mat;
inv[2] = -mat[2] / det_mat;
inv[3] = mat[0] / det_mat;
}
/* ------------------------------------------------------------------------ */
inline void inv3(const Real * mat, Real * inv) {
Real det_mat = det3(mat);
inv[0] = (mat[4] * mat[8] - mat[7] * mat[5]) / det_mat;
inv[1] = (mat[2] * mat[7] - mat[8] * mat[1]) / det_mat;
inv[2] = (mat[1] * mat[5] - mat[4] * mat[2]) / det_mat;
inv[3] = (mat[5] * mat[6] - mat[8] * mat[3]) / det_mat;
inv[4] = (mat[0] * mat[8] - mat[6] * mat[2]) / det_mat;
inv[5] = (mat[2] * mat[3] - mat[5] * mat[0]) / det_mat;
inv[6] = (mat[3] * mat[7] - mat[6] * mat[4]) / det_mat;
inv[7] = (mat[1] * mat[6] - mat[7] * mat[0]) / det_mat;
inv[8] = (mat[0] * mat[4] - mat[3] * mat[1]) / det_mat;
}
/* ------------------------------------------------------------------------ */
template <UInt n> inline void inv(const Real * A, Real * Ainv) {
if (n == 1) {
*Ainv = 1. / *A;
} else if (n == 2) {
inv2(A, Ainv);
} else if (n == 3) {
inv3(A, Ainv);
} else {
inv(n, A, Ainv);
}
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void inv(UInt n, const T * A, T * invA) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
int lwork = N * N;
auto * work = new T[lwork];
std::copy(A, A + n * n, invA);
aka_getrf(&N, &N, invA, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
aka_getri(&N, invA, &N, ipiv, work, &lwork, &info);
if (info != 0) {
AKANTU_ERROR("Cannot invert the matrix (info: " << info << " )");
}
delete[] ipiv;
delete[] work;
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void solve(UInt n, const T * A, T * x, const T * b) {
int N = n;
int info;
auto * ipiv = new int[N];
auto * lu_A = new T[N * N];
std::copy(A, A + N * N, lu_A);
aka_getrf(&N, &N, lu_A, &N, ipiv, &info);
if (info > 0) {
AKANTU_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
char trans = 'N';
int nrhs = 1;
std::copy(b, b + N, x);
aka_getrs(&trans, &N, &nrhs, lu_A, &N, ipiv, x, &N, &info);
if (info != 0) {
AKANTU_ERROR("Cannot solve the system (info: " << info << " )");
}
delete[] ipiv;
delete[] lu_A;
}
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
inline Real
matrixDoubleDot22(Real * A, // NOLINT(readability-non-const-parameter)
Real * B // NOLINT(readability-non-const-parameter)
) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3];
return d;
}
/* ------------------------------------------------------------------------ */
inline Real
matrixDoubleDot33(Real * A, // NOLINT(readability-non-const-parameter)
Real * B // NOLINT(readability-non-const-parameter)
) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3] + A[4] * B[4] +
A[5] * B[5] + A[6] * B[6] + A[7] * B[7] + A[8] * B[8];
return d;
}
/* ------------------------------------------------------------------------ */
inline Real
matrixDoubleDot(UInt n,
Real * A, // NOLINT(readability-non-const-parameter)
Real * B // NOLINT(readability-non-const-parameter)
) {
Real d = 0.;
for (UInt i = 0; i < n; ++i) {
for (UInt j = 0; j < n; ++j) {
d += A[i * n + j] * B[i * n + j];
}
}
return d;
}
/* ------------------------------------------------------------------------ */
inline void vectorProduct3(const Real * v1, const Real * v2, Real * res) {
res[0] = v1[1] * v2[2] - v1[2] * v2[1];
res[1] = v1[2] * v2[0] - v1[0] * v2[2];
res[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
/* ------------------------------------------------------------------------ */
inline Real vectorDot2(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1]);
}
/* ------------------------------------------------------------------------ */
inline Real vectorDot3(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
}
/* ------------------------------------------------------------------------ */
inline Real distance_2d(const Real * x, const Real * y) {
return std::sqrt((y[0] - x[0]) * (y[0] - x[0]) +
(y[1] - x[1]) * (y[1] - x[1]));
}
/* ------------------------------------------------------------------------ */
inline Real triangle_inradius(const Vector<Real> & coord1, const Vector<Real> & coord2,
const Vector<Real> & coord3) {
/**
* @f{eqnarray*}{
* r &=& A / s \\
* A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)}
* \\ s &=& \frac{a + b + c}{2}
* @f}
*/
Real a, b, c;
a = coord1.distance(coord2);
b = coord2.distance(coord3);
c = coord1.distance(coord3);
Real s;
s = (a + b + c) * 0.5;
return std::sqrt((s - a) * (s - b) * (s - c) / s);
}
/* ------------------------------------------------------------------------ */
inline Real distance_3d(const Real * x, const Real * y) {
return std::sqrt((y[0] - x[0]) * (y[0] - x[0]) +
(y[1] - x[1]) * (y[1] - x[1]) +
(y[2] - x[2]) * (y[2] - x[2]));
}
/* ------------------------------------------------------------------------ */
inline Real tetrahedron_volume(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4) {
Real xx[9];
xx[0] = coord2[0];
xx[1] = coord2[1];
xx[2] = coord2[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
auto vol = det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol -= det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol += det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord3[0];
xx[7] = coord3[1];
xx[8] = coord3[2];
vol -= det3(xx);
vol /= 6;
return vol;
}
/* ------------------------------------------------------------------------ */
inline Real tetrahedron_inradius(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4) {
auto l12 = distance_3d(coord1, coord2);
auto l13 = distance_3d(coord1, coord3);
auto l14 = distance_3d(coord1, coord4);
auto l23 = distance_3d(coord2, coord3);
auto l24 = distance_3d(coord2, coord4);
auto l34 = distance_3d(coord3, coord4);
auto s1 = (l12 + l23 + l13) * 0.5;
s1 = std::sqrt(s1 * (s1 - l12) * (s1 - l23) * (s1 - l13));
auto s2 = (l12 + l24 + l14) * 0.5;
s2 = std::sqrt(s2 * (s2 - l12) * (s2 - l24) * (s2 - l14));
auto s3 = (l23 + l34 + l24) * 0.5;
s3 = std::sqrt(s3 * (s3 - l23) * (s3 - l34) * (s3 - l24));
auto s4 = (l13 + l34 + l14) * 0.5;
s4 = std::sqrt(s4 * (s4 - l13) * (s4 - l34) * (s4 - l14));
auto volume = tetrahedron_volume(coord1, coord2, coord3, coord4);
return 3 * volume / (s1 + s2 + s3 + s4);
}
/* ------------------------------------------------------------------------ */
inline void barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter) {
std::fill_n(barycenter, spatial_dimension, 0.);
for (UInt n = 0; n < nb_points; ++n) {
UInt offset = n * spatial_dimension;
for (UInt i = 0; i < spatial_dimension; ++i) {
barycenter[i] += coord[offset + i] / (Real)nb_points;
}
}
}
/* ------------------------------------------------------------------------ */
inline void vector_2d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
}
/* ------------------------------------------------------------------------ */
inline void vector_3d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
res[2] = y[2] - x[2];
}
/* ------------------------------------------------------------------------ */
/// Combined absolute and relative tolerance test proposed in
/// Real-time collision detection by C. Ericson (2004)
inline bool are_float_equal(const Real x, const Real y) {
Real abs_max = std::max(std::abs(x), std::abs(y));
abs_max = std::max(abs_max, Real(1.));
return std::abs(x - y) <= (tolerance * abs_max);
}
/* ------------------------------------------------------------------------ */
inline bool isnan(Real x) {
#if defined(__INTEL_COMPILER)
#pragma warning(push)
#pragma warning(disable : 1572)
#endif // defined(__INTEL_COMPILER)
// x = x return false means x = quiet_NaN
return !(x == x);
#if defined(__INTEL_COMPILER)
#pragma warning(pop)
#endif // defined(__INTEL_COMPILER)
}
/* ------------------------------------------------------------------------ */
inline bool are_vector_equal(UInt n, Real * x, Real * y) {
bool test = true;
for (UInt i = 0; i < n; ++i) {
test &= are_float_equal(x[i], y[i]);
}
return test;
}
/* ------------------------------------------------------------------------ */
inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max) {
return not((x_max < y_min) or (x_min > y_max));
}
/* ------------------------------------------------------------------------ */
inline bool is_in_range(Real a, Real x_min, Real x_max) {
return ((a >= x_min) and (a <= x_max));
}
/* ------------------------------------------------------------------------ */
template <UInt p, typename T> inline T pow(T x) {
return (pow<p - 1, T>(x) * x);
}
template <> inline UInt pow<0, UInt>(__attribute__((unused)) UInt x) {
return (1);
}
template <> inline Real pow<0, Real>(__attribute__((unused)) Real x) {
return (1.);
}
/* ------------------------------------------------------------------------ */
template <class Functor>
Real NewtonRaphson::solve(const Functor & funct, Real x_0) {
Real x = x_0;
Real f_x = funct.f(x);
UInt iter = 0;
while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
x -= f_x / funct.f_prime(x);
f_x = funct.f(x);
iter++;
}
AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
"Newton Raphson ("
<< funct.name << ") solve did not converge in "
<< this->max_iteration << " iterations (tolerance: "
<< this->tolerance << ")");
return x;
}
} // namespace Math
} // namespace akantu
diff --git a/src/common/aka_named_argument.hh b/src/common/aka_named_argument.hh
index a00ebdde0..4fa9ba58d 100644
--- a/src/common/aka_named_argument.hh
+++ b/src/common/aka_named_argument.hh
@@ -1,166 +1,169 @@
/**
* @file aka_named_argument.hh
*
- * @author Marco Arena
+ * @author Marco Arena <None>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 16 2017
- * @date last modification: Wed Dec 06 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief tool to use named arguments in functions
*
*
+ * @section LICENSE
+ *
* Public Domain ? https://gist.github.com/ilpropheta/7576dce4c3249df89f85
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_compatibilty_with_cpp_standard.hh"
/* -------------------------------------------------------------------------- */
#include <tuple>
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_NAMED_ARGUMENT_HH_
#define AKANTU_AKA_NAMED_ARGUMENT_HH_
namespace akantu {
namespace named_argument {
struct param_t_trait {};
/* -- Pack utils (proxy version) ------------------------------------------ */
/// Proxy containing [tag, value]
template <typename tag, typename type> struct param_t : param_t_trait {
using _tag = tag;
using _type = type;
template <typename T>
explicit param_t(T && value) // NOLINT
: _value(std::forward<T>(value)) {}
type _value;
};
/*
* Tagged proxy that allows syntax _name = value
* operator=(T&&) returns a param_t instance
**/
template <typename tag> struct param_proxy {
using _tag = tag;
template <typename T> decltype(auto) operator=(T && value) {
return param_t<tag, decltype(value)>{std::forward<T>(value)};
}
};
/* Same as type_at but it's supposed to be used by passing
a pack of param_t (_tag is looked for instead of a
plain type). This and type_at should be refactored.
*/
template <typename T, typename head, typename... tail> struct type_at_p {
enum {
_tmp = (std::is_same<T, typename std::decay_t<head>::_tag>::value)
? 0
: type_at_p<T, tail...>::_pos
};
enum { _pos = _tmp == -1 ? -1 : 1 + _tmp };
};
template <typename T, typename head> struct type_at_p<T, head> {
enum {
_pos =
(std::is_same<T, typename std::decay<head>::type::_tag>::value ? 1
: -1)
};
};
template <typename... Ts> struct type_at {
enum { _pos = -1 };
};
template <typename T, typename head, typename... tail>
struct type_at<T, head, tail...> {
enum { _tmp = type_at_p<T, head, tail...>::_pos };
enum { _pos = _tmp == 1 ? 0 : (_tmp == -1 ? -1 : _tmp - 1) };
};
/* Same as get_at but it's supposed to be used by passing
a pack of param_t (_type is retrieved instead)
This and get_at should be refactored.
*/
template <int pos, int curr> struct get_at {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
static decltype(auto) get(head && /*unused*/, tail &&... t) {
return get_at<pos, curr + 1>::get(std::forward<tail>(t)...);
}
};
template <int pos> struct get_at<pos, pos> {
static_assert(pos >= 0, "Required parameter");
template <typename head, typename... tail>
static decltype(auto) get(head && h, tail &&... /*unused*/) {
return std::forward<decltype(h._value)>(h._value);
}
};
// Optional version
template <int pos, int curr> struct get_optional {
template <typename T, typename... pack>
static decltype(auto) get(T && /*unused*/, pack &&... _pack) {
return get_at<pos, curr>::get(std::forward<pack>(_pack)...);
}
};
template <int curr> struct get_optional<-1, curr> {
template <typename T, typename... pack>
static decltype(auto) get(T && _default, pack &&... /*unused*/) {
return std::forward<T>(_default);
}
};
} // namespace named_argument
// CONVENIENCE MACROS FOR CLASS DESIGNERS ==========
#define TAG_OF_ARGUMENT(_name) p_##_name
#define TAG_OF_ARGUMENT_WNS(_name) TAG_OF_ARGUMENT(_name)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define REQUIRED_NAMED_ARG(_name) \
named_argument::get_at< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(std::forward<pack>(_pack)...)
#define OPTIONAL_NAMED_ARG(_name, _defaultVal) \
named_argument::get_optional< \
named_argument::type_at<TAG_OF_ARGUMENT_WNS(_name), pack...>::_pos, \
0>::get(_defaultVal, std::forward<pack>(_pack)...)
#define DECLARE_NAMED_ARGUMENT(name) \
struct TAG_OF_ARGUMENT(name) {}; \
named_argument::param_proxy<TAG_OF_ARGUMENT_WNS(name)> _##name \
__attribute__((unused))
namespace {
struct use_named_args_t {};
use_named_args_t use_named_args __attribute__((unused));
} // namespace
template <typename T> struct is_named_argument : public std::false_type {};
template <typename... type>
struct is_named_argument<named_argument::param_t<type...>>
: public std::true_type {};
template <typename... pack>
using are_named_argument =
aka::conjunction<is_named_argument<std::decay_t<pack>>...>;
} // namespace akantu
#endif /* AKANTU_AKA_NAMED_ARGUMENT_HH_ */
diff --git a/src/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index f531373c0..eaae6c1bb 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -1,283 +1,285 @@
/**
* @file aka_random_generator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief generic random generator
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <random>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_RANDOM_GENERATOR_HH_
#define AKANTU_AKA_RANDOM_GENERATOR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* List of available distributions */
/* -------------------------------------------------------------------------- */
// clang-format off
#define AKANTU_RANDOM_DISTRIBUTION_TYPES \
((uniform , std::uniform_real_distribution )) \
((exponential , std::exponential_distribution )) \
((gamma , std::gamma_distribution )) \
((weibull , std::weibull_distribution )) \
((extreme_value, std::extreme_value_distribution)) \
((normal , std::normal_distribution )) \
((lognormal , std::lognormal_distribution )) \
((chi_squared , std::chi_squared_distribution )) \
((cauchy , std::cauchy_distribution )) \
((fisher_f , std::fisher_f_distribution )) \
((student_t , std::student_t_distribution ))
// clang-format on
#define AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(elem) BOOST_PP_CAT(_rdt_, elem)
#define AKANTU_RANDOM_DISTRIBUTION_PREFIX(s, data, elem) \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem))
enum RandomDistributionType {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_RANDOM_DISTRIBUTION_PREFIX, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)),
_rdt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Generator */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomGenerator {
/* ------------------------------------------------------------------------ */
private:
static long int _seed; // NOLINT
static std::default_random_engine generator; // NOLINT
/* ------------------------------------------------------------------------ */
public:
inline T operator()() { return generator(); }
/// function to print the contain of the class
void printself(std::ostream & stream, int /* indent */) const {
stream << "RandGenerator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s) {
_seed = s;
generator.seed(_seed);
}
static long int seed() { return _seed; }
static constexpr T min() { return std::default_random_engine::min(); }
static constexpr T max() { return std::default_random_engine::max(); }
};
#if defined(__clang__)
template <typename T> long int RandomGenerator<T>::_seed; // NOLINT
template <typename T> std::default_random_engine RandomGenerator<T>::generator;
#endif
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#undef AKANTU_RANDOM_DISTRIBUTION_PREFIX
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE(r, data, elem) \
case AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)): { \
stream << BOOST_PP_STRINGIZE(AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
RandomDistributionType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
default:
stream << UInt(type) << " not a RandomDistributionType";
break;
}
return stream;
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE
/* -------------------------------------------------------------------------- */
/* Some Helper */
/* -------------------------------------------------------------------------- */
template <typename T, class Distribution> class RandomDistributionTypeHelper {
enum { value = _rdt_not_defined };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE(r, data, elem) \
template <typename T> \
struct RandomDistributionTypeHelper<T, BOOST_PP_TUPLE_ELEM(2, 1, elem) < \
T> > { \
enum { \
value = AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)) \
}; \
\
static void printself(std::ostream & stream) { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)); \
} \
};
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE
/* -------------------------------------------------------------------------- */
template <class T> class RandomDistribution {
public:
virtual ~RandomDistribution() = default;
RandomDistribution() = default;
RandomDistribution(const RandomDistribution & other) = default;
RandomDistribution(RandomDistribution && other) noexcept = default;
RandomDistribution & operator=(const RandomDistribution & other) = default;
RandomDistribution &
operator=(RandomDistribution && other) noexcept = default;
virtual T operator()(RandomGenerator<UInt> & gen) = 0;
virtual std::unique_ptr<RandomDistribution<T>> make_unique() const = 0;
virtual void printself(std::ostream & stream, int = 0) const = 0;
};
template <class T, class Distribution>
class RandomDistributionProxy : public RandomDistribution<T> {
public:
explicit RandomDistributionProxy(Distribution dist)
: distribution(std::move(dist)) {}
T operator()(RandomGenerator<UInt> & gen) override {
return distribution(gen);
}
std::unique_ptr<RandomDistribution<T>> make_unique() const override {
return std::make_unique<RandomDistributionProxy<T, Distribution>>(
distribution);
}
void printself(std::ostream & stream, int /* indent */ = 0) const override {
RandomDistributionTypeHelper<T, Distribution>::printself(stream);
stream << " [ " << distribution << " ]";
}
private:
Distribution distribution;
};
/* -------------------------------------------------------------------------- */
/* RandomParameter */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomParameter {
public:
template <class Distribution>
explicit RandomParameter(T base_value, Distribution dist)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<T, Distribution>::value)),
distribution_proxy(
std::make_unique<RandomDistributionProxy<T, Distribution>>(
std::move(dist))) {}
explicit RandomParameter(T base_value)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<
T, std::uniform_real_distribution<T>>::value)),
distribution_proxy(
std::make_unique<
RandomDistributionProxy<T, std::uniform_real_distribution<T>>>(
std::uniform_real_distribution<T>(0., 0.))) {}
RandomParameter(const RandomParameter & other)
: base_value(other.base_value), type(other.type),
distribution_proxy(other.distribution_proxy->make_unique()) {}
RandomParameter & operator=(const RandomParameter & other) {
distribution_proxy = other.distribution_proxy->make_unique();
base_value = other.base_value;
type = other.type;
return *this;
}
RandomParameter(RandomParameter && other) noexcept = default;
RandomParameter & operator=(RandomParameter && other) noexcept = default;
virtual ~RandomParameter() = default;
inline void setBaseValue(const T & value) { this->base_value = value; }
inline T getBaseValue() const { return this->base_value; }
template <template <typename> class Generator, class iterator>
void setValues(iterator it, iterator end) {
RandomGenerator<UInt> gen;
for (; it != end; ++it) {
*it = this->base_value + (*distribution_proxy)(gen);
}
}
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << base_value;
stream << " + " << *distribution_proxy;
}
private:
/// Value with no random variations
T base_value;
/// Random distribution type
RandomDistributionType type;
/// Proxy to store a std random distribution
std::unique_ptr<RandomDistribution<T>> distribution_proxy;
};
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomDistribution<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomParameter<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_AKA_RANDOM_GENERATOR_HH_ */
diff --git a/src/common/aka_safe_enum.hh b/src/common/aka_safe_enum.hh
index 1705846c8..7bd757357 100644
--- a/src/common/aka_safe_enum.hh
+++ b/src/common/aka_safe_enum.hh
@@ -1,94 +1,96 @@
/**
* @file aka_safe_enum.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Safe enums type (see More C++ Idioms/Type Safe Enum on Wikibooks
* http://en.wikibooks.org/wiki/More_C%2B%2B_Idioms/Type_Safe_Enum)
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_SAFE_ENUM_HH_
#define AKANTU_AKA_SAFE_ENUM_HH_
namespace akantu {
/// Safe enumerated type
template <typename def, typename inner = typename def::type>
class safe_enum : public def {
using type = typename def::type;
public:
constexpr explicit safe_enum(type v = def::_end_) : val(v) {}
constexpr inner underlying() const { return val; }
constexpr bool operator==(const safe_enum & s) const {
return this->val == s.val;
}
constexpr bool operator!=(const safe_enum & s) const {
return this->val != s.val;
}
constexpr bool operator<(const safe_enum & s) const {
return this->val < s.val;
}
constexpr bool operator<=(const safe_enum & s) const {
return this->val <= s.val;
}
constexpr bool operator>(const safe_enum & s) const {
return this->val > s.val;
}
constexpr bool operator>=(const safe_enum & s) const {
return this->val >= s.val;
}
constexpr operator inner() { return val; };
public:
// Works only if enumerations are contiguous.
class const_iterator {
public:
constexpr explicit const_iterator(type v) : it(v) {}
constexpr const_iterator & operator++() {
++it;
return *this;
}
constexpr safe_enum operator*() { return safe_enum(static_cast<type>(it)); }
constexpr bool operator!=(const_iterator const & it) { return it.it != this->it; }
private:
int it;
};
constexpr auto begin() const { return const_iterator(def::_begin_); }
constexpr auto end() const { return const_iterator(def::_end_); }
private:
inner val;
};
} // namespace akantu
#endif /* AKANTU_AKA_SAFE_ENUM_HH_ */
diff --git a/src/common/aka_typelist.hh b/src/common/aka_typelist.hh
deleted file mode 100644
index 15c211272..000000000
--- a/src/common/aka_typelist.hh
+++ /dev/null
@@ -1,154 +0,0 @@
-/**
- * @file aka_typelist.hh
- *
- * @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
- *
- * @date creation: Fri Jan 04 2013
- * @date last modification: Mon Jun 19 2017
- *
- * @brief Objects that support the visitor design pattern
- *
- *
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
- *
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef AKANTU_TYPELIST_HH_
-#define AKANTU_TYPELIST_HH_
-
-#include "aka_common.hh"
-
-namespace akantu {
-
-struct Empty_type {};
-class Null_type {};
-
-template <class T, class U> struct Typelist {
- typedef T Head;
- typedef U Tail;
-};
-
-template <typename T1 = Null_type, typename T2 = Null_type,
- typename T3 = Null_type, typename T4 = Null_type,
- typename T5 = Null_type, typename T6 = Null_type,
- typename T7 = Null_type, typename T8 = Null_type,
- typename T9 = Null_type, typename T10 = Null_type,
- typename T11 = Null_type, typename T12 = Null_type,
- typename T13 = Null_type, typename T14 = Null_type,
- typename T15 = Null_type, typename T16 = Null_type,
- typename T17 = Null_type, typename T18 = Null_type,
- typename T19 = Null_type, typename T20 = Null_type>
-struct MakeTypelist {
-private:
- typedef typename MakeTypelist<T2, T3, T4, T5, T6, T7, T8, T9, T10, T11, T12,
- T13, T14, T15, T16, T17, T18, T19, T20>::Result
- TailResult;
-
-public:
- typedef Typelist<T1, TailResult> Result;
-};
-
-template <> struct MakeTypelist<> { typedef Null_type Result; };
-
-////////////////////////////////////////////////////////////////////////////////
-// class template Length
-// Computes the length of a typelist
-// Invocation (TList is a typelist):
-// Length<TList>::value
-// returns a compile-time constant containing the length of TList, not counting
-// the end terminator (which by convention is Null_type)
-////////////////////////////////////////////////////////////////////////////////
-
-template <class TList> struct Length;
-template <> struct Length<Null_type> {
- enum { value = 0 };
-};
-
-template <class T, class U> struct Length<Typelist<T, U>> {
- enum { value = 1 + Length<U>::value };
-};
-
-////////////////////////////////////////////////////////////////////////////////
-// class template TypeAt
-// Finds the type at a given index in a typelist
-// Invocation (TList is a typelist and index is a compile-time integral
-// constant):
-// TypeAt<TList, index>::Result
-// returns the type in position 'index' in TList
-// If you pass an out-of-bounds index, the result is a compile-time error
-////////////////////////////////////////////////////////////////////////////////
-
-template <class TList, unsigned int index> struct TypeAt;
-
-template <class Head, class Tail> struct TypeAt<Typelist<Head, Tail>, 0> {
- typedef Head Result;
-};
-
-template <class Head, class Tail, unsigned int i>
-struct TypeAt<Typelist<Head, Tail>, i> {
- typedef typename TypeAt<Tail, i - 1>::Result Result;
-};
-
-////////////////////////////////////////////////////////////////////////////////
-// class template Erase
-// Erases the first occurence, if any, of a type in a typelist
-// Invocation (TList is a typelist and T is a type):
-// Erase<TList, T>::Result
-// returns a typelist that is TList without the first occurence of T
-////////////////////////////////////////////////////////////////////////////////
-
-template <class TList, class T> struct Erase;
-
-template <class T> // Specialization 1
-struct Erase<Null_type, T> {
- typedef Null_type Result;
-};
-
-template <class T, class Tail> // Specialization 2
-struct Erase<Typelist<T, Tail>, T> {
- typedef Tail Result;
-};
-
-template <class Head, class Tail, class T> // Specialization 3
-struct Erase<Typelist<Head, Tail>, T> {
- typedef Typelist<Head, typename Erase<Tail, T>::Result> Result;
-};
-
-template <class TList, class T> struct IndexOf;
-
-template <class T> struct IndexOf<Null_type, T> {
- enum { value = -1 };
-};
-
-template <class T, class Tail> struct IndexOf<Typelist<T, Tail>, T> {
- enum { value = 0 };
-};
-
-template <class Head, class Tail, class T>
-struct IndexOf<Typelist<Head, Tail>, T> {
-private:
- enum { temp = IndexOf<Tail, T>::value };
-
-public:
- enum { value = (temp == -1 ? -1 : 1 + temp) };
-};
-
-} // namespace akantu
-
-#endif /* AKANTU_TYPELIST_HH_ */
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index fbd84f695..69a126bc4 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,1556 +1,1558 @@
/**
* @file aka_types.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 17 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief description of the "simple" types
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_math.hh"
/* -------------------------------------------------------------------------- */
#include <initializer_list>
#include <iomanip>
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_TYPES_HH_
#define AKANTU_AKA_TYPES_HH_
namespace akantu {
enum NormType { L_1 = 1, L_2 = 2, L_inf = UInt(-1) };
/**
* DimHelper is a class to generalize the setup of a dim array from 3
* values. This gives a common interface in the TensorStorage class
* independently of its derived inheritance (Vector, Matrix, Tensor3)
* @tparam dim
*/
template <UInt dim> struct DimHelper {
static inline void setDims(UInt m, UInt n, UInt p,
std::array<UInt, dim> & dims);
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<1> {
static inline void setDims(UInt m, UInt /*n*/, UInt /*p*/,
std::array<UInt, 1> & dims) {
dims[0] = m;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<2> {
static inline void setDims(UInt m, UInt n, UInt /*p*/,
std::array<UInt, 2> & dims) {
dims[0] = m;
dims[1] = n;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<3> {
static inline void setDims(UInt m, UInt n, UInt p,
std::array<UInt, 3> & dims) {
dims[0] = m;
dims[1] = n;
dims[2] = p;
}
};
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType> class TensorStorage;
/* -------------------------------------------------------------------------- */
/* Proxy classes */
/* -------------------------------------------------------------------------- */
namespace tensors {
template <class A, class B> struct is_copyable {
enum : bool { value = false };
};
template <class A> struct is_copyable<A, A> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType::proxy> {
enum : bool { value = true };
};
} // namespace tensors
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace types {
namespace details {
template <typename reference_> class vector_iterator {
public:
using difference_type = std::ptrdiff_t;
using value_type = std::decay_t<reference_>;
using pointer = value_type *;
using reference = reference_;
using iterator_category = std::input_iterator_tag;
vector_iterator(pointer ptr) : ptr(ptr) {}
// input iterator ++it
vector_iterator & operator++() {
++ptr;
return *this;
}
// input iterator it++
vector_iterator operator++(int) {
auto cpy = *this;
++ptr;
return cpy;
}
vector_iterator & operator+=(int n) {
ptr += n;
return *this;
}
vector_iterator operator+(int n) {
vector_iterator cpy(*this);
cpy += n;
return cpy;
}
// input iterator it != other_it
bool operator!=(const vector_iterator & other) const {
return ptr != other.ptr;
}
bool operator==(const vector_iterator & other) const {
return ptr == other.ptr;
}
difference_type operator-(const vector_iterator & other) const {
return this->ptr - other.ptr;
}
// input iterator dereference *it
reference operator*() { return *ptr; }
pointer operator->() { return ptr; }
private:
pointer ptr;
};
} // namespace details
} // namespace types
/**
* @class TensorProxy aka_types.hh
* The TensorProxy class is a proxy class to the
* TensorStorage it handles the wrapped case. That is to say if an accessor
* should give access to a Tensor wrapped on some data, like the
* Array<T>::iterator they can return a TensorProxy that will be automatically
* transformed as a TensorStorage wrapped on the same data
* @tparam T stored type
* @tparam ndim order of the tensor
* @tparam _RetType real derived type
*/
template <typename T, UInt ndim, class RetType_>
class TensorProxy : public TensorProxyTrait {
protected:
using RetTypeProxy = typename RetType_::proxy;
constexpr TensorProxy(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->values = data;
}
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
explicit TensorProxy(const Other & other) {
this->values = other.storage();
for (UInt i = 0; i < ndim; ++i) {
this->n[i] = other.size(i);
}
}
public:
using RetType = RetType_;
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
}
inline UInt size() const {
UInt _size = 1;
for (UInt d = 0; d < ndim; ++d) {
_size *= this->n[d];
}
return _size;
}
T * storage() const { return values; }
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
inline TensorProxy & operator=(const Other & other) {
AKANTU_DEBUG_ASSERT(
other.size() == this->size(),
"You are trying to copy two tensors with different sizes");
std::copy_n(other.storage(), this->size(), this->values);
return *this;
}
// template <class Other, typename = std::enable_if_t<
// tensors::is_copyable<TensorProxy, Other>::value>>
// inline TensorProxy & operator=(const Other && other) {
// AKANTU_DEBUG_ASSERT(
// other.size() == this->size(),
// "You are trying to copy two tensors with different sizes");
// memcpy(this->values, other.storage(), this->size() * sizeof(T));
// return *this;
// }
template <typename O> inline RetTypeProxy & operator*=(const O & o) {
RetType(*this) *= o;
return static_cast<RetTypeProxy &>(*this);
}
template <typename O> inline RetTypeProxy & operator/=(const O & o) {
RetType(*this) /= o;
return static_cast<RetTypeProxy &>(*this);
}
protected:
T * values;
std::array<UInt, ndim> n;
};
/* -------------------------------------------------------------------------- */
template <typename T> class VectorProxy : public TensorProxy<T, 1, Vector<T>> {
using parent = TensorProxy<T, 1, Vector<T>>;
using type = Vector<T>;
public:
constexpr VectorProxy(T * data, UInt n) : parent(data, n, 0, 0) {}
template <class Other> explicit VectorProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline VectorProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
// inline VectorProxy<T> & operator=(const VectorProxy && other) {
// parent::operator=(other);
// return *this;
// }
using iterator = types::details::vector_iterator<T &>;
using const_iterator = types::details::vector_iterator<const T &>;
iterator begin() { return iterator(this->storage()); }
iterator end() { return iterator(this->storage() + this->size()); }
const_iterator begin() const { return const_iterator(this->storage()); }
const_iterator end() const {
return const_iterator(this->storage() + this->size());
}
/* ------------------------------------------------------------------------ */
T & operator()(UInt index) { return this->values[index]; };
const T & operator()(UInt index) const { return this->values[index]; };
};
template <typename T> class MatrixProxy : public TensorProxy<T, 2, Matrix<T>> {
using parent = TensorProxy<T, 2, Matrix<T>>;
using type = Matrix<T>;
public:
MatrixProxy(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
template <class Other> explicit MatrixProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline MatrixProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
template <typename T>
class Tensor3Proxy : public TensorProxy<T, 3, Tensor3<T>> {
using parent = TensorProxy<T, 3, Tensor3<T>>;
using type = Tensor3<T>;
public:
Tensor3Proxy(const T * data, UInt m, UInt n, UInt k)
: parent(data, m, n, k) {}
Tensor3Proxy(const Tensor3Proxy & src) : parent(src) {}
Tensor3Proxy(const Tensor3<T> & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline Tensor3Proxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
/* -------------------------------------------------------------------------- */
/* Tensor base class */
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType>
class TensorStorage : public TensorTrait {
public:
using value_type = T;
friend class Array<T>;
protected:
template <class TensorType> void copySize(const TensorType & src) {
for (UInt d = 0; d < ndim; ++d) {
this->n[d] = src.size(d); // NOLINT
}
this->_size = src.size();
}
TensorStorage() = default;
TensorStorage(const TensorProxy<T, ndim, RetType> & proxy) {
this->copySize(proxy);
this->values = proxy.storage();
this->wrapped = true;
}
public:
TensorStorage(const TensorStorage & src) = delete;
TensorStorage(const TensorStorage & src, bool deep_copy) : values(nullptr) {
if (deep_copy) {
this->deepCopy(src);
} else {
this->shallowCopy(src);
}
}
protected:
TensorStorage(UInt m, UInt n, UInt p, const T & def) {
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = new T[this->_size]; // NOLINT
this->set(def);
this->wrapped = false;
}
TensorStorage(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = data;
this->wrapped = true;
}
public:
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void shallowCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped) {
delete[] this->values;
}
this->values = src.storage();
this->wrapped = true;
}
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void deepCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped) {
delete[] this->values;
}
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
this->values = new T[this->_size]; // NOLINT
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
std::copy_n(src.storage(), this->_size, this->values);
this->wrapped = false;
}
virtual ~TensorStorage() {
if (!this->wrapped) {
delete[] this->values;
}
}
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const TensorStorage & other) {
if (this == &other) {
return *this;
}
this->operator=(aka::as_type<RetType>(other));
return *this;
}
// inline TensorStorage & operator=(TensorStorage && other) noexcept {
// std::swap(n, other.n);
// std::swap(_size, other._size);
// std::swap(values, other.values);
// std::swap(wrapped, other.wrapped);
// return *this;
// }
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const RetType & src) {
if (this != &src) {
if (this->wrapped) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
// this test is not sufficient for Tensor of order higher than 1
AKANTU_DEBUG_ASSERT(this->_size == src.size(),
"Tensors of different size ("
<< this->_size << " != " << src.size() << ")");
std::copy_n(src.storage(), this->_size, this->values);
} else {
deepCopy(src);
}
}
return *this;
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator+=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
for (UInt i = 0; i < _size; ++i) {
*(a++) += *(b++);
}
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator-=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
for (UInt i = 0; i < _size; ++i) {
*(a++) -= *(b++);
}
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator+=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i) {
*(a++) += x;
}
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator-=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i) {
*(a++) -= x;
}
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator*=(const T & x) {
T * a = this->storage();
for (UInt i = 0; i < _size; ++i) {
*(a++) *= x;
}
return *(static_cast<RetType *>(this));
}
/* ---------------------------------------------------------------------- */
inline RetType & operator/=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i) {
*(a++) /= x;
}
return *(static_cast<RetType *>(this));
}
/// \f[Y = \alpha X + Y\f]
inline RetType & aXplusY(const TensorStorage & other, const T & alpha = 1.) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
Math::aXplusY(this->_size, alpha, other.storage(), this->storage());
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
T * storage() const { return values; }
UInt size() const { return _size; }
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
};
/* ------------------------------------------------------------------------ */
inline void set(const T & t) { std::fill_n(values, _size, t); };
inline void zero() { this->set(0.); };
template <class TensorType> inline void copy(const TensorType & other) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be copied");
std::copy_n(other.storage(), _size, values);
}
bool isWrapped() const { return this->wrapped; }
protected:
inline void computeSize() {
_size = 1;
for (UInt d = 0; d < ndim; ++d) {
_size *= this->n[d];
}
}
protected:
template <typename R, NormType norm_type> struct NormHelper {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it) {
_norm += std::pow(std::abs(*it), norm_type);
}
return std::pow(_norm, 1. / norm_type);
}
}; // namespace akantu
template <typename R> struct NormHelper<R, L_1> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it) {
_norm += std::abs(*it);
}
return _norm;
}
};
template <typename R> struct NormHelper<R, L_2> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it) {
_norm += *it * *it;
}
return sqrt(_norm);
}
};
template <typename R> struct NormHelper<R, L_inf> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it) {
_norm = std::max(std::abs(*it), _norm);
}
return _norm;
}
};
public:
/*----------------------------------------------------------------------- */
/// "Entrywise" norm norm<L_p> @f[ \|\boldsymbol{T}\|_p = \left(
/// \sum_i^{n[0]}\sum_j^{n[1]}\sum_k^{n[2]} |T_{ijk}|^p \right)^{\frac{1}{p}}
/// @f]
template <NormType norm_type> inline T norm() const {
return NormHelper<T, norm_type>::norm(*this);
}
protected:
std::array<UInt, ndim> n{};
UInt _size{0};
T * values{nullptr};
bool wrapped{false};
};
/* -------------------------------------------------------------------------- */
/* Vector */
/* -------------------------------------------------------------------------- */
template <typename T> class Vector : public TensorStorage<T, 1, Vector<T>> {
using parent = TensorStorage<T, 1, Vector<T>>;
public:
using value_type = typename parent::value_type;
using proxy = VectorProxy<T>;
public:
Vector() : parent() {}
explicit Vector(UInt n, const T & def = T()) : parent(n, 0, 0, def) {}
Vector(T * data, UInt n) : parent(data, n, 0, 0) {}
Vector(const Vector & src, bool deep_copy = true) : parent(src, deep_copy) {}
Vector(const TensorProxy<T, 1, Vector> & src) : parent(src) {}
Vector(std::initializer_list<T> list) : parent(list.size(), 0, 0, T()) {
UInt i = 0;
for (auto val : list) {
operator()(i++) = val;
}
}
public:
using iterator = types::details::vector_iterator<T &>;
using const_iterator = types::details::vector_iterator<const T &>;
iterator begin() { return iterator(this->storage()); }
iterator end() { return iterator(this->storage() + this->size()); }
const_iterator begin() const { return const_iterator(this->storage()); }
const_iterator end() const {
return const_iterator(this->storage() + this->size());
}
public:
~Vector() override = default;
/* ------------------------------------------------------------------------ */
inline Vector & operator=(const Vector & src) {
parent::operator=(src);
return *this;
}
inline Vector & operator=(Vector && src) noexcept = default;
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i) {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline const T & operator()(UInt i) const {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline T & operator[](UInt i) { return this->operator()(i); }
inline const T & operator[](UInt i) const { return this->operator()(i); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(Real x) { return parent::operator*=(x); }
inline Vector<T> & operator/=(Real x) { return parent::operator/=(x); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(const Vector<T> & vect) {
AKANTU_DEBUG_ASSERT(this->_size == vect._size,
"The vectors have non matching sizes");
T * a = this->storage();
T * b = vect.storage();
for (UInt i = 0; i < this->_size; ++i) {
*(a++) *= *(b++);
}
return *this;
}
/* ------------------------------------------------------------------------ */
inline Real dot(const Vector<T> & vect) const {
return Math::vectorDot(this->values, vect.storage(), this->_size);
}
/* ------------------------------------------------------------------------ */
inline Real mean() const {
Real mean = 0;
T * a = this->storage();
for (UInt i = 0; i < this->_size; ++i) {
mean += *(a++);
}
return mean / this->_size;
}
/* ------------------------------------------------------------------------ */
inline Vector & crossProduct(const Vector<T> & v1, const Vector<T> & v2) {
AKANTU_DEBUG_ASSERT(this->size() == 3,
"crossProduct is only defined in 3D (n=" << this->size()
<< ")");
AKANTU_DEBUG_ASSERT(
this->size() == v1.size() && this->size() == v2.size(),
"crossProduct is not a valid operation non matching size vectors");
Math::vectorProduct3(v1.storage(), v2.storage(), this->values);
return *this;
}
inline Vector crossProduct(const Vector<T> & v) {
Vector<T> tmp(this->size());
tmp.crossProduct(*this, v);
return tmp;
}
/* ------------------------------------------------------------------------ */
inline void solve(const Matrix<T> & A, const Vector<T> & b) {
AKANTU_DEBUG_ASSERT(
this->size() == A.rows() && this->_size == A.cols(),
"The size of the solution vector mismatches the size of the matrix");
AKANTU_DEBUG_ASSERT(
this->_size == b._size,
"The rhs vector has a mismatch in size with the matrix");
Math::solve(this->_size, A.storage(), this->values, b.storage());
}
/* ------------------------------------------------------------------------ */
template <bool tr_A>
inline void mul(const Matrix<T> & A, const Vector<T> & x, T alpha = T(1));
/* ------------------------------------------------------------------------ */
inline Real norm() const { return parent::template norm<L_2>(); }
template <NormType nt> inline Real norm() const {
return parent::template norm<nt>();
}
/* ------------------------------------------------------------------------ */
inline Vector<Real> & normalize() {
Real n = norm();
operator/=(n);
return *this;
}
/* ------------------------------------------------------------------------ */
/// norm of (*this - x)
inline Real distance(const Vector<T> & y) const {
Real * vx = this->values;
Real * vy = y.storage();
Real sum_2 = 0;
for (UInt i = 0; i < this->_size; ++i, ++vx, ++vy) { // NOLINT
sum_2 += (*vx - *vy) * (*vx - *vy);
}
return sqrt(sum_2);
}
/* ------------------------------------------------------------------------ */
inline bool equal(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
UInt i = 0;
while (i < this->_size && (std::abs(*(a++) - *(b++)) < tolerance)) {
++i;
}
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
inline short compare(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
if (std::abs(*a - *b) > tolerance) {
return (((*a - *b) > tolerance) ? 1 : -1);
}
}
return 0;
}
/* ------------------------------------------------------------------------ */
inline bool operator==(const Vector<T> & v) const { return equal(v); }
inline bool operator!=(const Vector<T> & v) const { return !operator==(v); }
inline bool operator<(const Vector<T> & v) const { return compare(v) == -1; }
inline bool operator>(const Vector<T> & v) const { return compare(v) == 1; }
template <typename Func, typename Acc>
decltype(auto) accumulate(const Vector<T> & v, Acc && accumulator,
Func && func) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
accumulator = func(*a, *b, std::forward<Acc>(accumulator));
}
return accumulator;
}
inline bool operator<=(const Vector<T> & v) const {
bool res = true;
return accumulate(v, res, [](auto && a, auto && b, auto && accumulator) {
return accumulator & (a <= b);
});
}
inline bool operator>=(const Vector<T> & v) const {
bool res = true;
return accumulate(v, res, [](auto && a, auto && b, auto && accumulator) {
return accumulator & (a >= b);
});
}
/* ------------------------------------------------------------------------ */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << "[";
for (UInt i = 0; i < this->_size; ++i) {
if (i != 0) {
stream << ", ";
}
stream << this->values[i];
}
stream << "]";
}
/* ---------------------------------------------------------------------- */
static inline Vector<T> zeros(UInt n) {
Vector<T> tmp(n);
tmp.set(T());
return tmp;
}
};
using RVector = Vector<Real>;
/* ------------------------------------------------------------------------ */
template <>
inline bool Vector<UInt>::equal(const Vector<UInt> & v,
__attribute__((unused)) Real tolerance) const {
UInt * a = this->storage();
UInt * b = v.storage();
UInt i = 0;
while (i < this->_size && (*(a++) == *(b++))) {
++i;
}
return i == this->_size;
}
/* -------------------------------------------------------------------------- */
namespace types {
namespace details {
template <typename Mat> class column_iterator {
public:
using difference_type = std::ptrdiff_t;
using value_type = decltype(std::declval<Mat>().operator()(0));
using pointer = value_type *;
using reference = value_type &;
using iterator_category = std::input_iterator_tag;
column_iterator(Mat & mat, UInt col) : mat(mat), col(col) {}
decltype(auto) operator*() { return mat(col); }
decltype(auto) operator++() {
++col;
AKANTU_DEBUG_ASSERT(col <= mat.cols(), "The iterator is out of bound");
return *this;
}
decltype(auto) operator++(int) {
auto tmp = *this;
++col;
AKANTU_DEBUG_ASSERT(col <= mat.cols(), "The iterator is out of bound");
return tmp;
}
bool operator!=(const column_iterator & other) const {
return col != other.col;
}
bool operator==(const column_iterator & other) const {
return not operator!=(other);
}
private:
Mat & mat;
UInt col;
};
} // namespace details
} // namespace types
/* ------------------------------------------------------------------------ */
/* Matrix */
/* ------------------------------------------------------------------------ */
template <typename T> class Matrix : public TensorStorage<T, 2, Matrix<T>> {
using parent = TensorStorage<T, 2, Matrix<T>>;
public:
using value_type = typename parent::value_type;
using proxy = MatrixProxy<T>;
public:
Matrix() : parent() {}
Matrix(UInt m, UInt n, const T & def = T()) : parent(m, n, 0, def) {}
Matrix(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
Matrix(const Matrix & src, bool deep_copy = true) : parent(src, deep_copy) {}
Matrix(const MatrixProxy<T> & src) : parent(src) {}
Matrix(std::initializer_list<std::initializer_list<T>> list) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot create a tensor on non trivial types");
std::size_t n = 0;
std::size_t m = list.size();
for (auto row : list) {
n = std::max(n, row.size());
}
DimHelper<2>::setDims(m, n, 0, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(0);
UInt i{0};
UInt j{0};
for (auto & row : list) {
for (auto & val : row) {
at(i, j++) = val;
}
++i;
j = 0;
}
}
~Matrix() override = default;
/* ------------------------------------------------------------------------ */
inline Matrix & operator=(const Matrix & src) {
parent::operator=(src);
return *this;
}
inline Matrix & operator=(Matrix && src) noexcept = default;
public:
/* ---------------------------------------------------------------------- */
UInt rows() const { return this->n[0]; }
UInt cols() const { return this->n[1]; }
/* ---------------------------------------------------------------------- */
inline T & at(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
inline const T & at(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i, UInt j) { return this->at(i, j); }
inline const T & operator()(UInt i, UInt j) const { return this->at(i, j); }
/// give a line vector wrapped on the column i
inline VectorProxy<T> operator()(UInt j) {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
inline VectorProxy<T> operator()(UInt j) const {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
public:
decltype(auto) begin() {
return types::details::column_iterator<Matrix<T>>(*this, 0);
}
decltype(auto) begin() const {
return types::details::column_iterator<const Matrix<T>>(*this, 0);
}
decltype(auto) end() {
return types::details::column_iterator<Matrix<T>>(*this, this->cols());
}
decltype(auto) end() const {
return types::details::column_iterator<const Matrix<T>>(*this,
this->cols());
}
/* ------------------------------------------------------------------------ */
inline void block(const Matrix & block, UInt pos_i, UInt pos_j) {
AKANTU_DEBUG_ASSERT(pos_i + block.rows() <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block.cols() <= cols(),
"The block size or position are not correct");
for (UInt i = 0; i < block.rows(); ++i) {
for (UInt j = 0; j < block.cols(); ++j) {
this->at(i + pos_i, j + pos_j) = block(i, j);
}
}
}
inline Matrix block(UInt pos_i, UInt pos_j, UInt block_rows,
UInt block_cols) const {
AKANTU_DEBUG_ASSERT(pos_i + block_rows <= rows(),
"The block size or position are not correct");
AKANTU_DEBUG_ASSERT(pos_i + block_cols <= cols(),
"The block size or position are not correct");
Matrix block(block_rows, block_cols);
for (UInt i = 0; i < block_rows; ++i) {
for (UInt j = 0; j < block_cols; ++j) {
block(i, j) = this->at(i + pos_i, j + pos_j);
}
}
return block;
}
inline T & operator[](UInt idx) { return *(this->values + idx); };
inline const T & operator[](UInt idx) const { return *(this->values + idx); };
/* ---------------------------------------------------------------------- */
inline Matrix operator*(const Matrix & B) const {
Matrix C(this->rows(), B.cols());
C.mul<false, false>(*this, B);
return C;
}
/* ----------------------------------------------------------------------- */
inline Matrix & operator*=(const T & x) { return parent::operator*=(x); }
inline Matrix & operator*=(const Matrix & B) {
Matrix C(*this);
this->mul<false, false>(C, B);
return *this;
}
/* ---------------------------------------------------------------------- */
template <bool tr_A, bool tr_B>
inline void mul(const Matrix & A, const Matrix & B, T alpha = 1.0) {
UInt k = A.cols();
if (tr_A) {
k = A.rows();
}
#ifndef AKANTU_NDEBUG
if (tr_B) {
AKANTU_DEBUG_ASSERT(k == B.cols(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.rows(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(k == B.rows(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.cols(),
"matrices to multiply have no fit dimensions");
}
if (tr_A) {
AKANTU_DEBUG_ASSERT(this->rows() == A.cols(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(this->rows() == A.rows(),
"matrices to multiply have no fit dimensions");
}
#endif // AKANTU_NDEBUG
Math::matMul<tr_A, tr_B>(this->rows(), this->cols(), k, alpha, A.storage(),
B.storage(), 0., this->storage());
}
/* ---------------------------------------------------------------------- */
inline void outerProduct(const Vector<T> & A, const Vector<T> & B) {
AKANTU_DEBUG_ASSERT(
A.size() == this->rows() && B.size() == this->cols(),
"A and B are not compatible with the size of the matrix");
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
this->values[i + j * this->rows()] += A[i] * B[j];
}
}
}
private:
class EigenSorter {
public:
EigenSorter(const Vector<T> & eigs) : eigs(eigs) {}
bool operator()(const UInt & a, const UInt & b) const {
return (eigs(a) > eigs(b));
}
private:
const Vector<T> & eigs;
};
public:
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues, Matrix<T> & eigenvectors,
bool sort = true) const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eig is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(eigenvalues.size() == this->cols(),
"eigenvalues should be of size " << this->cols()
<< ".");
#ifndef AKANTU_NDEBUG
if (eigenvectors.storage() != nullptr) {
AKANTU_DEBUG_ASSERT((eigenvectors.rows() == eigenvectors.cols()) &&
(eigenvectors.rows() == this->cols()),
"Eigenvectors needs to be a square matrix of size "
<< this->cols() << " x " << this->cols() << ".");
}
#endif
Matrix<T> tmp = *this;
Vector<T> tmp_eigs(eigenvalues.size());
Matrix<T> tmp_eig_vects(eigenvectors.rows(), eigenvectors.cols());
if (tmp_eig_vects.rows() == 0 || tmp_eig_vects.cols() == 0) {
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage());
} else {
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage(),
tmp_eig_vects.storage());
}
if (not sort) {
eigenvalues = tmp_eigs;
eigenvectors = tmp_eig_vects;
return;
}
Vector<UInt> perm(eigenvalues.size());
for (UInt i = 0; i < perm.size(); ++i) {
perm(i) = i;
}
std::sort(perm.storage(), perm.storage() + perm.size(),
EigenSorter(tmp_eigs));
for (UInt i = 0; i < perm.size(); ++i) {
eigenvalues(i) = tmp_eigs(perm(i));
}
if (tmp_eig_vects.rows() != 0 && tmp_eig_vects.cols() != 0) {
for (UInt i = 0; i < perm.size(); ++i) {
for (UInt j = 0; j < eigenvectors.rows(); ++j) {
eigenvectors(j, i) = tmp_eig_vects(j, perm(i));
}
}
}
}
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues) const {
Matrix<T> empty;
eig(eigenvalues, empty);
}
/* ---------------------------------------------------------------------- */
inline void eye(T alpha = 1.) {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eye is not a valid operation on a rectangular matrix");
this->zero();
for (UInt i = 0; i < this->cols(); ++i) {
this->values[i + i * this->rows()] = alpha;
}
}
/* ---------------------------------------------------------------------- */
static inline Matrix<T> eye(UInt m, T alpha = 1.) {
Matrix<T> tmp(m, m);
tmp.eye(alpha);
return tmp;
}
/* ---------------------------------------------------------------------- */
inline T trace() const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"trace is not a valid operation on a rectangular matrix");
T trace = 0.;
for (UInt i = 0; i < this->rows(); ++i) {
trace += this->values[i + i * this->rows()];
}
return trace;
}
/* ---------------------------------------------------------------------- */
inline Matrix transpose() const {
Matrix tmp(this->cols(), this->rows());
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
tmp(j, i) = operator()(i, j);
}
}
return tmp;
}
/* ---------------------------------------------------------------------- */
inline void inverse(const Matrix & A) {
AKANTU_DEBUG_ASSERT(A.cols() == A.rows(),
"inv is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(this->cols() == A.cols(),
"the matrix should have the same size as its inverse");
if (this->cols() == 1) {
*this->values = 1. / *A.storage();
} else if (this->cols() == 2) {
Math::inv2(A.storage(), this->values);
} else if (this->cols() == 3) {
Math::inv3(A.storage(), this->values);
} else {
Math::inv(this->cols(), A.storage(), this->values);
}
}
inline Matrix inverse() {
Matrix inv(this->rows(), this->cols());
inv.inverse(*this);
return inv;
}
/* --------------------------------------------------------------------- */
inline T det() const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"inv is not a valid operation on a rectangular matrix");
if (this->cols() == 1) {
return *(this->values);
}
if (this->cols() == 2) {
return Math::det2(this->values);
}
if (this->cols() == 3) {
return Math::det3(this->values);
}
return Math::det(this->cols(), this->values);
}
/* --------------------------------------------------------------------- */
inline T doubleDot(const Matrix<T> & other) const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"doubleDot is not a valid operation on a rectangular matrix");
if (this->cols() == 1) {
return *(this->values) * *(other.storage());
}
if (this->cols() == 2) {
return Math::matrixDoubleDot22(this->values, other.storage());
}
if (this->cols() == 3) {
return Math::matrixDoubleDot33(this->values, other.storage());
}
AKANTU_ERROR("doubleDot is not defined for other spatial dimensions"
<< " than 1, 2 or 3.");
}
/* ---------------------------------------------------------------------- */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << "[";
for (UInt i = 0; i < this->n[0]; ++i) {
if (i != 0) {
stream << ", ";
}
stream << "[";
for (UInt j = 0; j < this->n[1]; ++j) {
if (j != 0) {
stream << ", ";
}
stream << operator()(i, j);
}
stream << "]";
}
stream << "]";
};
};
/* ------------------------------------------------------------------------ */
template <typename T>
template <bool tr_A>
inline void Vector<T>::mul(const Matrix<T> & A, const Vector<T> & x, T alpha) {
#ifndef AKANTU_NDEBUG
UInt n = x.size();
if (tr_A) {
AKANTU_DEBUG_ASSERT(n == A.rows(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.cols(),
"matrix and vector to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(n == A.cols(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.rows(),
"matrix and vector to multiply have no fit dimensions");
}
#endif
Math::matVectMul<tr_A>(A.rows(), A.cols(), alpha, A.storage(), x.storage(),
0., this->storage());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Matrix<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Vector<T> & _this) {
_this.printself(stream);
return stream;
}
/* ------------------------------------------------------------------------ */
/* Tensor3 */
/* ------------------------------------------------------------------------ */
template <typename T> class Tensor3 : public TensorStorage<T, 3, Tensor3<T>> {
using parent = TensorStorage<T, 3, Tensor3<T>>;
public:
using value_type = typename parent::value_type;
using proxy = Tensor3Proxy<T>;
public:
Tensor3() : parent(){};
Tensor3(UInt m, UInt n, UInt p, const T & def = T()) : parent(m, n, p, def) {}
Tensor3(T * data, UInt m, UInt n, UInt p) : parent(data, m, n, p) {}
Tensor3(const Tensor3 & src, bool deep_copy = true)
: parent(src, deep_copy) {}
Tensor3(const proxy & src) : parent(src) {}
public:
/* ------------------------------------------------------------------------ */
inline Tensor3 & operator=(const Tensor3 & src) {
parent::operator=(src);
return *this;
}
/* ---------------------------------------------------------------------- */
inline T & operator()(UInt i, UInt j, UInt k) {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline const T & operator()(UInt i, UInt j, UInt k) const {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline MatrixProxy<T> operator()(UInt k) {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator()(UInt k) const {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator[](UInt k) {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator[](UInt k) const {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
};
/* -------------------------------------------------------------------------- */
// support operations for the creation of other vectors
/* -------------------------------------------------------------------------- */
template <typename T>
Vector<T> operator*(const T & scalar, const Vector<T> & a) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator/(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r *= b;
return r;
}
template <typename T>
Vector<T> operator+(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r += b;
return r;
}
template <typename T>
Vector<T> operator-(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r -= b;
return r;
}
template <typename T>
Vector<T> operator*(const Matrix<T> & A, const Vector<T> & b) {
Vector<T> r(b.size());
r.template mul<false>(A, b);
return r;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<T> operator*(const T & scalar, const Matrix<T> & a) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator*(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator/(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Matrix<T> operator+(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r += b;
return r;
}
template <typename T>
Matrix<T> operator-(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r -= b;
return r;
}
} // namespace akantu
#include <iterator>
namespace std {
template <typename R>
struct iterator_traits<::akantu::types::details::vector_iterator<R>> {
protected:
using iterator = ::akantu::types::details::vector_iterator<R>;
public:
using iterator_category = typename iterator::iterator_category;
using value_type = typename iterator::value_type;
using difference_type = typename iterator::difference_type;
using pointer = typename iterator::pointer;
using reference = typename iterator::reference;
};
template <typename Mat>
struct iterator_traits<::akantu::types::details::column_iterator<Mat>> {
protected:
using iterator = ::akantu::types::details::column_iterator<Mat>;
public:
using iterator_category = typename iterator::iterator_category;
using value_type = typename iterator::value_type;
using difference_type = typename iterator::difference_type;
using pointer = typename iterator::pointer;
using reference = typename iterator::reference;
};
} // namespace std
#endif /* AKANTU_AKA_TYPES_HH_ */
diff --git a/src/common/aka_visitor.hh b/src/common/aka_visitor.hh
deleted file mode 100644
index f5392d8af..000000000
--- a/src/common/aka_visitor.hh
+++ /dev/null
@@ -1,163 +0,0 @@
-/**
- * @file aka_visitor.hh
- *
- * @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
- *
- * @date creation: Fri Jan 04 2013
- * @date last modification: Mon Jun 19 2017
- *
- * @brief Objects that support the visitor design pattern
- *
- *
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
- *
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef AKANTU_VISITOR_HH_
-#define AKANTU_VISITOR_HH_
-
-#include "aka_typelist.hh"
-
-namespace akantu {
-
-///////////////////////////////////////////////////////////////////////////
-// visitor class template, adapted from the Andrei Alexandrescu's
-// "Modern C++ Design"
-
-enum Visit_type { Mutable, Immutable };
-
-template <class T, typename R = void, Visit_type = Mutable> class StrictVisitor;
-
-template <class T, typename R> class StrictVisitor<T, R, Mutable> {
-public:
- typedef R ReturnType;
- typedef T ParamType;
- virtual ~StrictVisitor() {}
- virtual ReturnType Visit(ParamType &) = 0;
-};
-
-template <class T, typename R> class StrictVisitor<T, R, Immutable> {
-public:
- typedef R ReturnType;
- typedef const T ParamType;
- virtual ~StrictVisitor() {}
- virtual ReturnType Visit(ParamType &) = 0;
-};
-
-/// class template StrictVisitor (specialization)
-
-template <class Head, class Tail, typename R>
-class StrictVisitor<Typelist<Head, Tail>, R, Mutable>
- : public StrictVisitor<Head, R, Mutable>,
- public StrictVisitor<Tail, R, Mutable> {
-public:
- typedef R ReturnType;
- typedef Head ParamType;
- // using StrictVisitor<Head, R>::Visit;
- // using StrictVisitor<Tail, R>::Visit;
-};
-
-template <class Head, typename R>
-class StrictVisitor<Typelist<Head, Null_type>, R, Mutable>
- : public StrictVisitor<Head, R, Mutable> {
-public:
- typedef R ReturnType;
- typedef Head ParamType;
- using StrictVisitor<Head, R, Mutable>::Visit;
-};
-
-template <class Head, class Tail, typename R>
-class StrictVisitor<Typelist<Head, Tail>, R, Immutable>
- : public StrictVisitor<Head, R, Immutable>,
- public StrictVisitor<Tail, R, Immutable> {
-public:
- typedef R ReturnType;
- typedef Head ParamType;
- // using StrictVisitor<Head, R>::Visit;
- // using StrictVisitor<Tail, R>::Visit;
-};
-
-template <class Head, typename R>
-class StrictVisitor<Typelist<Head, Null_type>, R, Immutable>
- : public StrictVisitor<Head, R, Immutable> {
-public:
- typedef R ReturnType;
- typedef Head ParamType;
- using StrictVisitor<Head, R, Immutable>::Visit;
-};
-
-////////////////////////////////////////////////////////////////////////////////
-// class template NonStrictVisitor
-// Implements non-strict visitation (you can implement only part of the Visit
-// functions)
-//
-
-template <class R> struct DefaultFunctor {
- template <class T> R operator()(T &) { return R(); }
-};
-
-template <class T, typename R = void, Visit_type V = Mutable,
- class F = DefaultFunctor<R>>
-class BaseVisitorImpl;
-
-template <class Head, class Tail, typename R, Visit_type V, class F>
-class BaseVisitorImpl<Typelist<Head, Tail>, R, V, F>
- : public StrictVisitor<Head, R, V>, public BaseVisitorImpl<Tail, R, V, F> {
-public:
- typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
- virtual R Visit(ParamType & h) { return F()(h); }
-};
-
-template <class Head, typename R, Visit_type V, class F>
-class BaseVisitorImpl<Typelist<Head, Null_type>, R, V, F>
- : public StrictVisitor<Head, R, V> {
-public:
- typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
- virtual R Visit(ParamType & h) { return F()(h); }
-};
-
-/// Visitor
-template <class R> struct Strict {};
-
-template <typename R, class TList, Visit_type V = Mutable,
- template <class> class FunctorPolicy = DefaultFunctor>
-class Visitor : public BaseVisitorImpl<TList, R, V, FunctorPolicy<R>> {
-public:
- typedef R ReturnType;
-
- template <class Visited> ReturnType GenericVisit(Visited & host) {
- StrictVisitor<Visited, ReturnType, V> & subObj = *this;
- return subObj.Visit(host);
- }
-};
-
-template <typename R, class TList, Visit_type V>
-class Visitor<R, TList, V, Strict> : public StrictVisitor<TList, R, V> {
-public:
- typedef R ReturnType;
-
- template <class Visited> ReturnType GenericVisit(Visited & host) {
- StrictVisitor<Visited, ReturnType, V> & subObj = *this;
- return subObj.Visit(host);
- }
-};
-
-} // namespace akantu
-
-#endif /* AKANTU_VISITOR_HH_ */
diff --git a/src/common/aka_voigthelper.cc b/src/common/aka_voigthelper.cc
index 45e21cdf8..95199c21b 100644
--- a/src/common/aka_voigthelper.cc
+++ b/src/common/aka_voigthelper.cc
@@ -1,67 +1,69 @@
/**
* @file aka_voigthelper.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Voigt indices
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_voigthelper.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* clang-format off */
template <> const UInt VoigtHelper<1>::mat[][1] = {{0}};
template <> const UInt VoigtHelper<2>::mat[][2] = {{0, 2},
{3, 1}};
template <> const UInt VoigtHelper<3>::mat[][3] = {{0, 5, 4},
{8, 1, 3},
{7, 6, 2}};
template <> const UInt VoigtHelper<1>::vec[][2] = {{0, 0}};
template <> const UInt VoigtHelper<2>::vec[][2] = {{0, 0},
{1, 1},
{0, 1},
{1, 0}};
template <> const UInt VoigtHelper<3>::vec[][2] = {{0, 0},
{1, 1},
{2, 2},
{1, 2},
{0, 2},
{0, 1},
{2, 1},
{2, 0},
{1, 0}};
template <> const Real VoigtHelper<1>::factors[] = {1.};
template <> const Real VoigtHelper<2>::factors[] = {1., 1., 2.};
template <> const Real VoigtHelper<3>::factors[] = {1., 1., 1.,
2., 2., 2.};
/* clang-format on */
} // namespace akantu
diff --git a/src/common/aka_voigthelper.hh b/src/common/aka_voigthelper.hh
index 59f19dde2..c0bd499be 100644
--- a/src/common/aka_voigthelper.hh
+++ b/src/common/aka_voigthelper.hh
@@ -1,100 +1,103 @@
/**
* @file aka_voigthelper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Helper file for Voigt notation
* Wikipedia convention: @f[2*\epsilon_{ij} (i!=j) = voigt_\epsilon_{I}@f]
* http://en.wikipedia.org/wiki/Voigt_notation
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKA_VOIGTHELPER_HH_
#define AKA_VOIGTHELPER_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim> class VoigtHelper {
static_assert(dim > 0U, "Cannot be < 1D");
static_assert(dim < 4U, "Cannot be > 3D");
public:
/* ------------------------------------------------------------------------ */
template <class M, class V>
static inline void matrixToVoigt(M && matrix, V && vector);
template <class M> static inline decltype(auto) matrixToVoigt(M && matrix);
template <class M, class V>
static inline void matrixToVoigtWithFactors(M && matrix, V && vector);
template <class M>
static inline decltype(auto) matrixToVoigtWithFactors(M && matrix);
template <class M, class V>
static inline void voigtToMatrix(V && vector, M && matrix);
template <class V> static inline decltype(auto) voigtToMatrix(V && vector);
/* ------------------------------------------------------------------------ */
/// transfer the B matrix to a Voigt notation B matrix
inline static void transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element);
/// transfer the BNL matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
/// transfer the BL2 matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
public:
static constexpr UInt size{(dim * (dim - 1)) / 2 + dim};
// matrix of vector index I as function of tensor indices i,j
static const UInt mat[dim][dim];
// array of matrix indices ij as function of vector index I
static const UInt vec[dim * dim][2];
// factors to multiply the strain by for voigt notation
static const Real factors[size];
};
} // namespace akantu
#include "aka_voigthelper_tmpl.hh"
#endif
diff --git a/src/common/aka_voigthelper_tmpl.hh b/src/common/aka_voigthelper_tmpl.hh
index 9ac5094e1..2ba35a305 100644
--- a/src/common/aka_voigthelper_tmpl.hh
+++ b/src/common/aka_voigthelper_tmpl.hh
@@ -1,241 +1,243 @@
/**
* @file aka_voigthelper_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
- * @date last modification: Wed Dec 06 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of the voight helper
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_voigthelper.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_VOIGTHELPER_TMPL_HH_
#define AKANTU_AKA_VOIGTHELPER_TMPL_HH_
namespace akantu {
template <UInt dim> constexpr UInt VoigtHelper<dim>::size;
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::matrixToVoigt(M && matrix, V && vector) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
vector(I) = matrix(i, j);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M>
inline decltype(auto) VoigtHelper<dim>::matrixToVoigt(M && matrix) {
Vector<Real> vector(size);
matrixToVoigt(std::forward<M>(matrix), vector);
return vector;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::matrixToVoigtWithFactors(M && matrix,
V && vector) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
vector(I) = factors[I] * matrix(i, j);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M>
inline decltype(auto) VoigtHelper<dim>::matrixToVoigtWithFactors(M && matrix) {
Vector<Real> vector(size);
matrixToVoigtWithFactors(std::forward<M>(matrix), vector);
return vector;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class M, class V>
inline void VoigtHelper<dim>::voigtToMatrix(V && vector, M && matrix) {
for (UInt I = 0; I < size; ++I) {
auto i = vec[I][0];
auto j = vec[I][1];
matrix(i, j) = matrix(j, i) = vector(I);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
template <class V>
inline decltype(auto) VoigtHelper<dim>::voigtToMatrix(V && vector) {
Matrix<Real> matrix(dim, dim);
voigtToMatrix(std::forward<V>(vector), matrix);
return matrix;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element) {
Bvoigt.zero();
for (UInt i = 0; i < dim; ++i) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Bvoigt(i, i + n * dim) = B(i, n);
}
}
if (dim == 2) {
/// in 2D, fill the @f$ [\frac{\partial N_i}{\partial x}, \frac{\partial
/// N_i}{\partial y}]@f$ row
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Bvoigt(2, 1 + n * 2) = B(0, n);
Bvoigt(2, 0 + n * 2) = B(1, n);
}
}
if (dim == 3) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Real dndx = B(0, n);
Real dndy = B(1, n);
Real dndz = B(2, n);
/// in 3D, fill the @f$ [0, \frac{\partial N_i}{\partial y},
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(3, 1 + n * 3) = dndz;
Bvoigt(3, 2 + n * 3) = dndy;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x}, 0,
/// \frac{N_i}{\partial z}]@f$ row
Bvoigt(4, 0 + n * 3) = dndz;
Bvoigt(4, 2 + n * 3) = dndx;
/// in 3D, fill the @f$ [\frac{\partial N_i}{\partial x},
/// \frac{N_i}{\partial y}, 0]@f$ row
Bvoigt(5, 0 + n * 3) = dndy;
Bvoigt(5, 1 + n * 3) = dndx;
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void VoigtHelper<dim>::transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.zero();
// see Finite element formulations for large deformation dynamic analysis,
// Bathe et al. IJNME vol 9, 1975, page 364 B_{NL}
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < nb_nodes_per_element; ++m) {
for (UInt n = 0; n < dim; ++n) {
// std::cout << B(n, m) << std::endl;
Bvoigt(i * dim + n, m * dim + i) = B(n, m);
}
}
}
// TODO: Verify the 2D and 1D case
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<1>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.zero();
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
Bvoigt(0, j) = grad_u(0, 0) * B(0, j);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<3>::transferBMatrixToBL2(const Matrix<Real> & dNdX,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.zero();
for (UInt I = 0; I < 3; ++I) {
for (UInt a = 0; a < nb_nodes_per_element; ++a) {
for (UInt i = 0; i < 3; ++i) {
Bvoigt(I, a * 3 + i) = grad_u(i, I) * dNdX(I, a);
}
}
}
for (UInt Iv = 3; Iv < 6; ++Iv) {
for (UInt a = 0; a < nb_nodes_per_element; ++a) {
for (UInt k = 0; k < 3; ++k) {
UInt aux = Iv - 3;
for (UInt m = 0; m < 3; ++m) {
if (m != aux) {
UInt index1 = m;
UInt index2 = 3 - m - aux;
Bvoigt(Iv, a * 3 + k) += grad_u(k, index1) * dNdX(index2, a);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void VoigtHelper<2>::transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element) {
Bvoigt.zero();
for (UInt i = 0; i < 2; ++i) {
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
for (UInt k = 0; k < 2; ++k) {
Bvoigt(i, j * 2 + k) = grad_u(k, i) * B(i, j);
}
}
}
for (UInt j = 0; j < nb_nodes_per_element; ++j) {
for (UInt k = 0; k < 2; ++k) {
for (UInt m = 0; m < 2; ++m) {
UInt index1 = m;
UInt index2 = (2 - 1) - m;
Bvoigt(2, j * 2 + k) += grad_u(k, index1) * B(index2, j);
}
}
}
}
} // namespace akantu
#endif /* AKANTU_AKA_VOIGTHELPER_TMPL_HH_ */
diff --git a/src/common/aka_warning.hh b/src/common/aka_warning.hh
index a8b6cd264..24a0225b9 100644
--- a/src/common/aka_warning.hh
+++ b/src/common/aka_warning.hh
@@ -1,67 +1,69 @@
/**
* @file aka_warning.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Nov 14 2016
- * @date last modification: Fri Dec 02 2016
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Tue Nov 17 2020
*
* @brief file to include to remove some warnings
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/**
AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
AKANTU_WARNING_IGNORE_VARIADIC_MACRO_ARGUMENTS
**/
// --- Intel warnings ----------------------------------------------------------
#if defined(__INTEL_COMPILER)
# if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
# endif
// --- Clang Warnings ----------------------------------------------------------
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
# pragma clang diagnostic push
# if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
# pragma clang diagnostic ignored "-Wunused-parameter"
# endif
# if defined(AKANTU_WARNING_IGNORE_VARIADIC_MACRO_ARGUMENTS)
# pragma clang diagnostic ignored "-Wgnu-zero-variadic-macro-arguments"
# endif
// --- GCC warnings ------------------------------------------------------------
#elif (defined(__GNUC__) || defined(__GNUG__))
# define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
# pragma GCC diagnostic ignored "-Wunused-parameter"
# endif
# if defined(AKANTU_WARNING_IGNORE_VARIADIC_MACRO_ARGUMENTS)
# pragma GCC diagnostic ignored "-Wvariadic-macros"
# pragma GCC diagnostic ignored "-Wpedantic"
# endif
#endif
diff --git a/src/common/aka_warning_restore.hh b/src/common/aka_warning_restore.hh
index 2c0795c91..67ac911c7 100644
--- a/src/common/aka_warning_restore.hh
+++ b/src/common/aka_warning_restore.hh
@@ -1,54 +1,56 @@
/**
* @file aka_warning_restore.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Nov 14 2016
- * @date last modification: Fri Dec 02 2016
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Tue Nov 17 2020
*
* @brief file to include to reactivate the previously deactivatied warnings
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
// --- Intel -------------------------------------------------------------------
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
// --- Clang -------------------------------------------------------------------
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
# pragma clang diagnostic pop
// --- GCC ---------------------------------------------------------------------
#elif defined(__GNUG__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic pop
# else
# if defined(AKANTU_WARNING_IGNORE_UNUSED_PARAMETER)
# pragma GCC diagnostic warning "-Wunused-parameter"
# endif
# if defined(AKANTU_WARNING_IGNORE_VARIADIC_MACRO_ARGUMENTS)
# pragma GCC diagnostic ignored "-Wpedantic"
# endif
# endif
#endif
#undef AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
#undef AKANTU_WARNING_IGNORE_VARIADIC_MACRO_ARGUMENTS
diff --git a/src/fe_engine/cohesive_element.hh b/src/fe_engine/cohesive_element.hh
index 2e7367366..4e473a201 100644
--- a/src/fe_engine/cohesive_element.hh
+++ b/src/fe_engine/cohesive_element.hh
@@ -1,89 +1,91 @@
/**
* @file cohesive_element.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Generates the cohesive element structres (defined in
* element_class.hh)
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COHESIVE_ELEMENT_HH_
#define AKANTU_COHESIVE_ELEMENT_HH_
namespace akantu {
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_4, _gt_cohesive_2d_4,
_itp_lagrange_segment_2, _ek_cohesive, 2,
_git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_6, _gt_cohesive_2d_6,
_itp_lagrange_segment_3, _ek_cohesive, 2,
_git_segment, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_1d_2, _gt_cohesive_1d_2,
_itp_lagrange_point_1, _ek_cohesive, 1,
_git_point, 1);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_6, _gt_cohesive_3d_6,
_itp_lagrange_triangle_3, _ek_cohesive, 3,
_git_triangle, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_12, _gt_cohesive_3d_12,
_itp_lagrange_triangle_6, _ek_cohesive, 3,
_git_triangle, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_8, _gt_cohesive_3d_8,
_itp_lagrange_quadrangle_4, _ek_cohesive,
3, _git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_16, _gt_cohesive_3d_16,
_itp_serendip_quadrangle_8, _ek_cohesive,
3, _git_segment, 3);
template <ElementType> struct CohesiveFacetProperty {
static const ElementType cohesive_type = _not_defined;
};
#define AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(ftype, ctype) \
template <> struct CohesiveFacetProperty<ftype> { \
static const ElementType cohesive_type = ctype; \
}
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_point_1, _cohesive_1d_2);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_2, _cohesive_2d_4);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_3, _cohesive_2d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_3, _cohesive_3d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_6, _cohesive_3d_12);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_4, _cohesive_3d_8);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_8, _cohesive_3d_16);
} // namespace akantu
#endif /* AKANTU_COHESIVE_ELEMENT_HH_ */
diff --git a/src/fe_engine/element.hh b/src/fe_engine/element.hh
index 64891a668..3c5b29168 100644
--- a/src/fe_engine/element.hh
+++ b/src/fe_engine/element.hh
@@ -1,127 +1,129 @@
/**
* @file element.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Jan 23 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Element helper class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_HH_
#define AKANTU_ELEMENT_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element */
/* -------------------------------------------------------------------------- */
class Element {
public:
ElementType type;
UInt element;
GhostType ghost_type;
// ElementKind kind;
// ElementType type{_not_defined};
// UInt element{0};
// GhostType ghost_type{_not_ghost};
// ElementKind kind{_ek_regular};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline ElementKind kind() const;
inline bool operator==(const Element & elem) const {
return std::tie(type, element, ghost_type) ==
std::tie(elem.type, elem.element, elem.ghost_type);
}
inline bool operator!=(const Element & elem) const {
return std::tie(type, element, ghost_type) !=
std::tie(elem.type, elem.element, elem.ghost_type);
}
// inline bool operator==(const Element & elem) const {
// return ((element == elem.element) && (type == elem.type) &&
// (ghost_type == elem.ghost_type) && (kind == elem.kind));
// }
// inline bool operator!=(const Element & elem) const {
// return ((element != elem.element) || (type != elem.type) ||
// (ghost_type != elem.ghost_type) || (kind != elem.kind));
// }
inline bool operator<(const Element & rhs) const;
};
namespace {
const Element ElementNull{_not_defined, UInt(-1), _casper};
// Element{_not_defined, 0, _casper, _ek_not_defined};
} // namespace
/* -------------------------------------------------------------------------- */
inline bool Element::operator<(const Element & rhs) const {
// bool res =
// (rhs == ElementNull) ||
// ((this->kind < rhs.kind) ||
// ((this->kind == rhs.kind) &&
// ((this->ghost_type < rhs.ghost_type) ||
// ((this->ghost_type == rhs.ghost_type) &&
// ((this->type < rhs.type) ||
// ((this->type == rhs.type) && (this->element < rhs.element)))))));
return ((rhs == ElementNull) ||
std::tie(ghost_type, type, element) <
std::tie(rhs.ghost_type, rhs.type, rhs.element));
}
} // namespace akantu
namespace std {
inline string to_string(const akantu::Element & _this) {
if (_this == akantu::ElementNull) {
return "ElementNull";
}
string str = "Element [" + to_string(_this.type) + ", " +
to_string(_this.element) + ", " + to_string(_this.ghost_type) +
"]";
return str;
}
} // namespace std
namespace akantu {
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Element & _this) {
stream << std::to_string(_this);
return stream;
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_HH_ */
diff --git a/src/fe_engine/element_class.hh b/src/fe_engine/element_class.hh
index c38f6f73e..6df433c19 100644
--- a/src/fe_engine/element_class.hh
+++ b/src/fe_engine/element_class.hh
@@ -1,432 +1,436 @@
/**
* @file element_class.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Dec 11 2020
*
* @brief Declaration of the ElementClass main class and the
* Integration and Interpolation elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_HH_
#define AKANTU_ELEMENT_CLASS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/// default element class structure
template <ElementType element_type> struct ElementClassProperty {
static const GeometricalType geometrical_type{_gt_not_defined};
static const InterpolationType interpolation_type{_itp_not_defined};
static const ElementKind element_kind{_ek_regular};
static const UInt spatial_dimension{0};
static const GaussIntegrationType gauss_integration_type{_git_not_defined};
static const UInt polynomial_degree{0};
};
#if !defined(DOXYGEN)
/// Macro to generate the element class structures for different element types
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
#else
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order)
#endif
/* -------------------------------------------------------------------------- */
/* Geometry */
/* -------------------------------------------------------------------------- */
/// Default GeometricalShape structure
template <GeometricalType geometrical_type> struct GeometricalShape {
static const GeometricalShapeType shape{_gst_point};
};
/// Templated GeometricalShape with function contains
template <GeometricalShapeType shape> struct GeometricalShapeContains {
/// Check if the point (vector in 2 and 3D) at natural coordinate coor
template <class vector_type>
static inline bool contains(const vector_type & coord);
};
#if !defined(DOXYGEN)
/// Macro to generate the GeometricalShape structures for different geometrical
/// types
#define AKANTU_DEFINE_SHAPE(geom_type, geom_shape) \
template <> struct GeometricalShape<geom_type> { \
static const GeometricalShapeType shape{geom_shape}; \
}
AKANTU_DEFINE_SHAPE(_gt_hexahedron_20, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_hexahedron_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_15, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_6, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_point, _gst_point);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_4, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_2, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_3, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_10, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_4, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_3, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_6, _gst_triangle);
#endif
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type>
struct GeometricalElementProperty {};
template <ElementType element_type>
struct ElementClassExtraGeometryProperties {};
/* -------------------------------------------------------------------------- */
/// Templated GeometricalElement with function getInradius
template <GeometricalType geometrical_type,
GeometricalShapeType shape =
GeometricalShape<geometrical_type>::shape>
class GeometricalElement {
using geometrical_property = GeometricalElementProperty<geometrical_type>;
public:
/// compute the in-radius: \todo should be renamed for characteristic length
static inline Real getInradius(const Matrix<Real> & /*coord*/) {
AKANTU_TO_IMPLEMENT();
}
/// true if the natural coordinates are in the element
template <class vector_type>
static inline bool contains(const vector_type & coord);
public:
static AKANTU_GET_MACRO_NOT_CONST(SpatialDimension,
geometrical_property::spatial_dimension,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbNodesPerElement,
geometrical_property::nb_nodes_per_element,
UInt);
static inline constexpr auto getNbFacetTypes() {
return geometrical_property::nb_facet_types;
};
static inline UInt getNbFacetsPerElement(UInt t);
static inline UInt getNbFacetsPerElement();
static inline constexpr auto getFacetLocalConnectivityPerElement(UInt t = 0);
};
/* -------------------------------------------------------------------------- */
/* Interpolation */
/* -------------------------------------------------------------------------- */
/// default InterpolationProperty structure
template <InterpolationType interpolation_type> struct InterpolationProperty {};
#if !defined(DOXYGEN)
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim) \
template <> struct InterpolationProperty<itp_type> { \
static constexpr InterpolationKind kind{itp_kind}; \
static constexpr UInt nb_nodes_per_element{nb_nodes}; \
static constexpr UInt natural_space_dimension{ndim}; \
}
#else
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim)
#endif
/* -------------------------------------------------------------------------- */
/// Generic (templated by the enum InterpolationType which specifies the order
/// and the dimension of the interpolation) class handling the elemental
/// interpolation
template <InterpolationType interpolation_type,
InterpolationKind kind =
InterpolationProperty<interpolation_type>::kind>
class InterpolationElement {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
Matrix<Real> & N);
/// compute the shape values for a given point in natural coordinates
template <class vector_type>
static inline void computeShapes(const vector_type & /*unused*/,
vector_type & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
Tensor3<Real> & dnds);
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
template <class vector_type, class matrix_type>
static inline void computeDNDS(const vector_type & /*unused*/,
matrix_type & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/**
* compute @f$ @f$
**/
static inline void computeD2NDS2(const Matrix<Real> & natural_coord,
Tensor3<Real> & d2nds2);
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the
* second variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
template <class vector_type, class matrix_type>
static inline void computeD2NDS2(const vector_type &, matrix_type &) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
/// in the case of spatial_dimension != natural_space_dimension
static inline void computeSpecialJacobian(const Matrix<Real> & /*unused*/,
Real & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate a field given (arbitrary) natural coordinates
static inline void
interpolateOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolation point
static inline void interpolate(const Matrix<Real> & nodal_values,
const Vector<Real> & shapes,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolations points
static inline void interpolate(const Matrix<Real> & nodal_values,
const Matrix<Real> & shapes,
Matrix<Real> & interpolated);
/// compute the gradient of a given field on the given natural coordinates
static inline void
gradientOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & f, Matrix<Real> & gradient);
public:
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(InterpolationProperty<interpolation_type>::nb_nodes_per_element *
InterpolationProperty<interpolation_type>::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension,
InterpolationProperty<interpolation_type>::natural_space_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
};
/* -------------------------------------------------------------------------- */
/* Integration */
/* -------------------------------------------------------------------------- */
template <GaussIntegrationType git_class, UInt nb_points>
struct GaussIntegrationTypeData {
/// quadrature points in natural coordinates
static Real quad_positions[];
/// weights for the Gauss integration
static Real quad_weights[];
};
template <ElementType type,
UInt n = ElementClassProperty<type>::polynomial_degree>
class GaussIntegrationElement {
public:
static UInt getNbQuadraturePoints();
static Matrix<Real> getQuadraturePoints();
static Vector<Real> getWeights();
};
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
template <ElementType element_type,
ElementKind element_kind =
ElementClassProperty<element_type>::element_kind>
class ElementClass
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using element_property = ElementClassProperty<element_type>;
using interpolation_property =
typename interpolation_element::interpolation_property;
public:
/**
* compute @f$ J = \frac{\partial x_j}{\partial s_i} @f$ the variation of real
* coordinates along with variation of natural coordinates on a given point in
* natural coordinates
*/
static inline void computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J);
/**
* compute the Jacobian matrix by computing the variation of real coordinates
* along with variation of natural coordinates on a given set of points in
* natural coordinates
*/
static inline void computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J);
/// compute the jacobians of a serie of natural coordinates
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a set of
/// points
static inline void computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJacobian(const Matrix<Real> & J, Real & jacobians);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv);
/// compute shape derivatives (input is dxds) for a given point
static inline void computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv);
/// compute the normal of a surface defined by the function f
static inline void
computeNormalsOnNaturalCoordinates(const Matrix<Real> & coord,
Matrix<Real> & f, Matrix<Real> & normals);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Vector<Real> & real_coords,
const Matrix<Real> & node_coords,
Vector<Real> & natural_coords,
UInt max_iterations = 100,
Real tolerance = 1e-10);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Matrix<Real> & real_coords,
const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords,
UInt max_iterations = 100,
Real tolerance = 1e-10);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, element_kind, ElementKind);
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
using element_class_extra_geom_property =
ElementClassExtraGeometryProperties<element_type>;
static constexpr auto getP1ElementType() {
return element_class_extra_geom_property::p1_type;
}
static constexpr auto getFacetType(UInt t = 0) {
return element_class_extra_geom_property::facet_type[t];
}
static constexpr auto getFacetTypes();
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "geometrical_element_property.hh"
#include "interpolation_element_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_hexahedron_8_inline_impl.hh"
#include "element_class_pentahedron_6_inline_impl.hh"
/* keep order */
#include "element_class_hexahedron_20_inline_impl.hh"
#include "element_class_pentahedron_15_inline_impl.hh"
#include "element_class_point_1_inline_impl.hh"
#include "element_class_quadrangle_4_inline_impl.hh"
#include "element_class_quadrangle_8_inline_impl.hh"
#include "element_class_segment_2_inline_impl.hh"
#include "element_class_segment_3_inline_impl.hh"
#include "element_class_tetrahedron_10_inline_impl.hh"
#include "element_class_tetrahedron_4_inline_impl.hh"
#include "element_class_triangle_3_inline_impl.hh"
#include "element_class_triangle_6_inline_impl.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "element_class_structural.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#if defined(AKANTU_IGFEM)
#include "element_class_igfem.hh"
#endif
#endif /* AKANTU_ELEMENT_CLASS_HH_ */
diff --git a/src/fe_engine/element_class_structural.hh b/src/fe_engine/element_class_structural.hh
index 76732da6a..72ea08316 100644
--- a/src/fe_engine/element_class_structural.hh
+++ b/src/fe_engine/element_class_structural.hh
@@ -1,274 +1,276 @@
/**
* @file element_class_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Mon Feb 01 2021
*
* @brief Specialization of the element classes for structural elements
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_
#define AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_
namespace akantu {
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY( \
itp_type, itp_geom_type, ndof, nb_stress, nb_dnds_cols) \
template <> struct InterpolationProperty<itp_type> { \
static const InterpolationKind kind{_itk_structural}; \
static const UInt nb_nodes_per_element{ \
InterpolationProperty<itp_geom_type>::nb_nodes_per_element}; \
static const InterpolationType itp_geometry_type{itp_geom_type}; \
static const UInt natural_space_dimension{ \
InterpolationProperty<itp_geom_type>::natural_space_dimension}; \
static const UInt nb_degree_of_freedom{ndof}; \
static const UInt nb_stress_components{nb_stress}; \
static const UInt dnds_columns{nb_dnds_cols}; \
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type>
class InterpolationElement<interpolation_type, _itk_structural> {
public:
using interpolation_property = InterpolationProperty<interpolation_type>;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
const Matrix<Real> & T, Tensor3<Real> & Ns) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> N_T = Ns(i);
Matrix<Real> N(N_T.rows(), N_T.cols());
computeShapes(natural_coord(i), real_coord, N);
N_T.mul<false, false>(N, T);
}
}
/// compute the shape values for a given point in natural coordinates
static inline void computeShapes(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & N);
static inline void computeShapesMass(const Matrix<Real> & natural_coords,
const Matrix<Real> & xs,
const Matrix<Real> & T,
Tensor3<Real> & Ns) {
for (UInt i = 0; i < natural_coords.cols(); ++i) {
Matrix<Real> N_T = Ns(i);
Vector<Real> X = natural_coords(i);
Matrix<Real> N(interpolation_property::nb_degree_of_freedom, N_T.cols());
computeShapes(X, xs, N);
N_T.mul<false, false>(N.block(0, 0, N_T.rows(), N_T.cols()), T);
}
}
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & Js,
const Tensor3<Real> & DNDSs,
const Matrix<Real> & R,
Tensor3<Real> & Bs) {
for (UInt i = 0; i < Js.size(2); ++i) {
Matrix<Real> J = Js(i);
Matrix<Real> DNDS = DNDSs(i);
Matrix<Real> DNDX(DNDS.rows(), DNDS.cols());
auto inv_J = J.inverse();
DNDX.mul<false, false>(inv_J, DNDS);
Matrix<Real> B_R = Bs(i);
Matrix<Real> B(B_R.rows(), B_R.cols());
arrangeInVoigt(DNDX, B);
B_R.mul<false, false>(B, R);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
const Matrix<Real> & real_coord,
Tensor3<Real> & dnds) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> dnds_t = dnds(i);
computeDNDS(natural_coord(i), real_coord, dnds_t);
}
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
static inline void computeDNDS(const Vector<Real> & natural_coord,
const Matrix<Real> & real_coord,
Matrix<Real> & dnds);
/**
* arrange B in Voigt notation from DNDS
*/
static inline void arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
// Default implementation assumes dnds is already in Voigt notation
B.deepCopy(dnds);
}
public:
static inline constexpr auto getNbNodesPerInterpolationElement() {
return interpolation_property::nb_nodes_per_element;
}
static inline constexpr auto getShapeSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getShapeIndependantSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_stress_components;
}
static inline constexpr auto getShapeDerivativesSize() {
return interpolation_property::nb_nodes_per_element *
interpolation_property::nb_degree_of_freedom *
interpolation_property::nb_stress_components;
}
static inline constexpr auto getNaturalSpaceDimension() {
return interpolation_property::natural_space_dimension;
}
static inline constexpr auto getNbDegreeOfFreedom() {
return interpolation_property::nb_degree_of_freedom;
}
static inline constexpr auto getNbStressComponents() {
return interpolation_property::nb_stress_components;
}
};
/// Macro to generate the element class structures for different structural
/// element types
/* -------------------------------------------------------------------------- */
#define AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY( \
elem_type, geom_type, interp_type, parent_el_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementType parent_element_type{parent_el_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
/* ElementClass for structural elements */
/* -------------------------------------------------------------------------- */
template <ElementType element_type>
class ElementClass<element_type, _ek_structural>
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
using geometrical_element =
GeometricalElement<ElementClassProperty<element_type>::geometrical_type>;
using interpolation_element = InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>;
using parent_element =
ElementClass<ElementClassProperty<element_type>::parent_element_type>;
public:
static inline void
computeRotationMatrix(Matrix<Real> & /*R*/, const Matrix<Real> & /*X*/,
const Vector<Real> & /*extra_normal*/) {
AKANTU_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJMat(const Vector<Real> & natural_coords,
const Matrix<Real> & Xs, Matrix<Real> & J) {
Matrix<Real> dnds(Xs.rows(), Xs.cols());
parent_element::computeDNDS(natural_coords, dnds);
J.mul<false, true>(dnds, Xs);
}
static inline void computeJMat(const Matrix<Real> & natural_coords,
const Matrix<Real> & Xs, Tensor3<Real> & Js) {
for (UInt i = 0; i < natural_coords.cols(); ++i) {
// because non-const l-value reference does not bind to r-value
Matrix<Real> J = Js(i);
computeJMat(Vector<Real>(natural_coords(i)), Xs, J);
}
}
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
using itp = typename interpolation_element::interpolation_property;
Tensor3<Real> Js(itp::natural_space_dimension, itp::natural_space_dimension,
natural_coords.cols());
computeJMat(natural_coords, node_coords, Js);
for (UInt i = 0; i < natural_coords.cols(); ++i) {
Matrix<Real> J = Js(i);
jacobians(i) = J.det();
}
}
static inline void computeRotation(const Matrix<Real> & node_coords,
Matrix<Real> & rotation);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, _ek_structural, ElementKind);
static AKANTU_GET_MACRO_NOT_CONST(P1ElementType, _not_defined, ElementType);
static AKANTU_GET_MACRO_NOT_CONST(FacetType, _not_defined, ElementType);
static constexpr auto getFacetType(__attribute__((unused)) UInt t = 0) {
return _not_defined;
}
static constexpr AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static constexpr auto getFacetTypes() {
return ElementClass<_not_defined>::getFacetTypes();
}
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "element_class_hermite_inline_impl.hh"
/* keep order */
#include "element_class_bernoulli_beam_inline_impl.hh"
#include "element_class_kirchhoff_shell_inline_impl.hh"
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_ELEMENT_CLASS_STRUCTURAL_HH_ */
diff --git a/src/fe_engine/element_class_tmpl.hh b/src/fe_engine/element_class_tmpl.hh
index d56817541..03007b1bb 100644
--- a/src/fe_engine/element_class_tmpl.hh
+++ b/src/fe_engine/element_class_tmpl.hh
@@ -1,538 +1,541 @@
/**
* @file element_class_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 29 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Implementation of the inline templated function of the element class
* descriptions
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "gauss_integration_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_TMPL_HH_
#define AKANTU_ELEMENT_CLASS_TMPL_HH_
namespace akantu {
template <ElementType element_type, ElementKind element_kind>
inline constexpr auto
ElementClass<element_type, element_kind>::getFacetTypes() {
return VectorProxy<const ElementType>(
element_class_extra_geom_property::facet_type.data(),
geometrical_element::getNbFacetTypes());
}
/* -------------------------------------------------------------------------- */
/* GeometricalElement */
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline constexpr auto
GeometricalElement<geometrical_type,
shape>::getFacetLocalConnectivityPerElement(UInt t) {
int pos = 0;
for (UInt i = 0; i < t; ++i) {
pos += geometrical_property::nb_facets[i] *
geometrical_property::nb_nodes_per_facet[i];
}
return MatrixProxy<const UInt>(
geometrical_property::facet_connectivity_vect.data() + pos,
geometrical_property::nb_facets[t],
geometrical_property::nb_nodes_per_facet[t]);
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement() {
UInt total_nb_facets = 0;
for (UInt n = 0; n < geometrical_property::nb_facet_types; ++n) {
total_nb_facets += geometrical_property::nb_facets[n];
}
return total_nb_facets;
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement(UInt t) {
return geometrical_property::nb_facets[t];
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
template <class vector_type>
inline bool GeometricalElement<geometrical_type, shape>::contains(
const vector_type & coords) {
return GeometricalShapeContains<shape>::contains(coords);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_point>::contains(const vector_type & coords) {
return (coords(0) < std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_square>::contains(const vector_type & coords) {
bool in = true;
for (UInt i = 0; i < coords.size() && in; ++i) {
in &= ((coords(i) >= -(1. + std::numeric_limits<Real>::epsilon())) &&
(coords(i) <= (1. + std::numeric_limits<Real>::epsilon())));
}
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_triangle>::contains(const vector_type & coords) {
bool in = true;
Real sum = 0;
for (UInt i = 0; (i < coords.size()) && in; ++i) {
in &= ((coords(i) >= -(Math::getTolerance())) &&
(coords(i) <= (1. + Math::getTolerance())));
sum += coords(i);
}
if (in) {
return (in && (sum <= (1. + Math::getTolerance())));
}
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_prism>::contains(const vector_type & coords) {
bool in = ((coords(0) >= -1.) && (coords(0) <= 1.)); // x in segment [-1, 1]
// y and z in triangle
in &= ((coords(1) >= 0) && (coords(1) <= 1.));
in &= ((coords(2) >= 0) && (coords(2) <= 1.));
Real sum = coords(1) + coords(2);
return (in && (sum <= 1));
}
/* -------------------------------------------------------------------------- */
/* InterpolationElement */
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeShapes(
const Matrix<Real> & natural_coord, Matrix<Real> & N) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(N(p));
Vector<Real> ncoord_p(natural_coord(p));
computeShapes(ncoord_p, Np);
}
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeDNDS(
const Matrix<Real> & natural_coord, Tensor3<Real> & dnds) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> dnds_p(dnds(p));
Vector<Real> ncoord_p(natural_coord(p));
computeDNDS(ncoord_p, dnds_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on a point a field for which values are given on the
* node of the element using the shape functions at this interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(
shapes.storage(),
InterpolationProperty<interpolation_type>::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on several points a field for which values are given on the
* node of the element using the shape functions at the interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated values of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Matrix<Real> & shapes,
Matrix<Real> & interpolated) {
UInt nb_points = shapes.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(shapes(p));
Vector<Real> interpolated_p(interpolated(p));
interpolate(nodal_values, Np, interpolated_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate the field on a point given in natural coordinates the field which
* values are given on the node of the element
*
* @param natural_coords natural coordinates of point where to interpolate \xi
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::interpolateOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated) {
Vector<Real> shapes(
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeShapes(natural_coords, shapes);
interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
/// @f$ gradient_{ij} = \frac{\partial f_j}{\partial s_i} = \sum_k
/// \frac{\partial N_k}{\partial s_i}f_{j n_k} @f$
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::gradientOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & f,
Matrix<Real> & gradient) {
Matrix<Real> dnds(
InterpolationProperty<interpolation_type>::natural_space_dimension,
InterpolationProperty<interpolation_type>::nb_nodes_per_element);
computeDNDS(natural_coords, dnds);
gradient.mul<false, true>(f, dnds);
}
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J) {
UInt nb_points = dnds.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> J_p(J(p));
Matrix<Real> dnds_p(dnds(p));
computeJMat(dnds_p, node_coords, J_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J) {
/// @f$ J = dxds = dnds * x @f$
J.mul<false, true>(dnds, node_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
UInt nb_points = natural_coords.cols();
Matrix<Real> dnds(interpolation_property::natural_space_dimension,
interpolation_property::nb_nodes_per_element);
Matrix<Real> J(natural_coords.rows(), node_coords.rows());
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> ncoord_p(natural_coords(p));
interpolation_element::computeDNDS(ncoord_p, dnds);
computeJMat(dnds, node_coords, J);
computeJacobian(J, jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
computeJacobian(J(p), jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeJacobian(const Matrix<Real> & J,
Real & jacobians) {
if (J.rows() == J.cols()) {
jacobians = Math::det<element_property::spatial_dimension>(J.storage());
} else {
interpolation_element::computeSpecialJacobian(J, jacobians);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p(shape_deriv(p));
computeShapeDerivatives(J(p), dnds(p), shape_deriv_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv) {
Matrix<Real> inv_J(J.rows(), J.cols());
Math::inv<element_property::spatial_dimension>(J.storage(), inv_J.storage());
shape_deriv.mul<false, false>(inv_J, dnds);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeNormalsOnNaturalCoordinates(
const Matrix<Real> & coord, Matrix<Real> & f, Matrix<Real> & normals) {
UInt dimension = normals.rows();
UInt nb_points = coord.cols();
AKANTU_DEBUG_ASSERT((dimension - 1) ==
interpolation_property::natural_space_dimension,
"cannot extract a normal because of dimension mismatch "
<< dimension - 1 << " "
<< interpolation_property::natural_space_dimension);
Matrix<Real> J(dimension, interpolation_property::natural_space_dimension);
for (UInt p = 0; p < nb_points; ++p) {
interpolation_element::gradientOnNaturalCoordinates(coord(p), f, J);
if (dimension == 2) {
Math::normal2(J.storage(), normals(p).storage());
}
if (dimension == 3) {
Math::normal3(J(0).storage(), J(1).storage(), normals(p).storage());
}
}
}
/* ------------------------------------------------------------------------- */
/**
* In the non linear cases we need to iterate to find the natural coordinates
*@f$\xi@f$
* provided real coordinates @f$x@f$.
*
* We want to solve: @f$ x- \phi(\xi) = 0@f$ with @f$\phi(\xi) = \sum_I N_I(\xi)
*x_I@f$
* the mapping function which uses the nodal coordinates @f$x_I@f$.
*
* To that end we use the Newton method and the following series:
*
* @f$ \frac{\partial \phi(x_k)}{\partial \xi} \left( \xi_{k+1} - \xi_k \right)
*= x - \phi(x_k)@f$
*
* When we consider elements embedded in a dimension higher than them (2D
*triangle in a 3D space for example)
* @f$ J = \frac{\partial \phi(\xi_k)}{\partial \xi}@f$ is of dimension
*@f$dim_{space} \times dim_{elem}@f$ which
* is not invertible in most cases. Rather we can solve the problem:
*
* @f$ J^T J \left( \xi_{k+1} - \xi_k \right) = J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that
*
* @f$ d\xi = \xi_{k+1} - \xi_k = (J^T J)^{-1} J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that if the series converges we have:
*
* @f$ 0 = J^T \left( \phi(\xi_\infty) - x \right) @f$
*
* And we see that this is ill-posed only if @f$ J^T x = 0@f$ which means that
*the vector provided
* is normal to any tangent which means it is outside of the element itself.
*
* @param real_coords: the real coordinates the natural coordinates are sought
*for
* @param node_coords: the coordinates of the nodes forming the element
* @param natural_coords: output->the sought natural coordinates
* @param spatial_dimension: spatial dimension of the problem
*
**/
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Vector<Real> & real_coords, const Matrix<Real> & node_coords,
Vector<Real> & natural_coords, UInt max_iterations, Real tolerance) {
UInt spatial_dimension = real_coords.size();
UInt dimension = natural_coords.size();
// matrix copy of the real_coords
Matrix<Real> mreal_coords(real_coords.storage(), spatial_dimension, 1);
// initial guess
natural_coords.zero();
// real space coordinates provided by initial guess
Matrix<Real> physical_guess(spatial_dimension, 1);
// objective function f = real_coords - physical_guess
Matrix<Real> f(spatial_dimension, 1);
// J Jacobian matrix computed on the natural_guess
Matrix<Real> J(dimension, spatial_dimension);
// J^t
Matrix<Real> Jt(spatial_dimension, dimension);
// G = J^t * J
Matrix<Real> G(dimension, dimension);
// Ginv = G^{-1}
Matrix<Real> Ginv(dimension, dimension);
// J = Ginv * J^t
Matrix<Real> F(spatial_dimension, dimension);
// dxi = \xi_{k+1} - \xi in the iterative process
Matrix<Real> dxi(dimension, 1);
Matrix<Real> dxit(1, dimension);
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
auto update_f = [&f, &physical_guess, &natural_coords, &node_coords,
&mreal_coords, spatial_dimension]() {
Vector<Real> physical_guess_v(physical_guess.storage(), spatial_dimension);
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute initial objective function value f = real_coords - physical_guess
f = mreal_coords;
f -= physical_guess;
// compute initial error
auto error = f.norm<L_2>();
return error;
};
auto inverse_map_error = update_f();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
UInt iterations{0};
while (tolerance < inverse_map_error and iterations < max_iterations) {
// compute J^t
interpolation_element::gradientOnNaturalCoordinates(natural_coords,
node_coords, Jt);
J = Jt.transpose();
// compute G
G.mul<false, true>(J, J);
// inverse G
Ginv.inverse(G);
// compute F
F.mul<true, false>(J, Ginv);
// compute increment
dxit.mul<true, false>(f, F);
dxi = dxit.transpose();
// update our guess
natural_coords += Vector<Real>(dxi(0));
inverse_map_error = update_f();
iterations++;
}
if(iterations >= max_iterations) {
AKANTU_EXCEPTION("The solver in inverse map did not converge");
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Matrix<Real> & real_coords, const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords, UInt max_iterations, Real tolerance) {
UInt nb_points = real_coords.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> X(real_coords(p));
Vector<Real> ncoord_p(natural_coords(p));
inverseMap(X, node_coords, ncoord_p, max_iterations, tolerance);
}
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_CLASS_TMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
index 98b59a223..b611e910b 100644
--- a/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_bernoulli_beam_inline_impl.hh
@@ -1,233 +1,239 @@
/**
* @file element_class_bernoulli_beam_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Fri Feb 05 2021
*
* @brief Specialization of the element_class class for the type
* _bernoulli_beam_2
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
- *
+ */
+
+
+/**
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
//#include "aka_element_classes_info.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_
#define AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_2,
_itp_lagrange_segment_2, 3,
2, 6);
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_bernoulli_beam_3,
_itp_lagrange_segment_2, 6,
4, 6);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_2,
_gt_segment_2,
_itp_bernoulli_beam_2,
_segment_2, _ek_structural, 2,
_git_segment, 3);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(_bernoulli_beam_3,
_gt_segment_2,
_itp_bernoulli_beam_3,
_segment_2, _ek_structural, 3,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 t1 u2 v2 t2
N = {{L(0), 0 , 0 , L(1), 0 , 0 }, // u
{0 , H(0, 0), H(0, 1), 0 , H(0, 2), H(0, 3)}, // v
{0 , H(1, 0), H(1, 1), 0 , H(1, 2), H(1, 3)}}; // theta
// clang-format on
}
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
Vector<Real> L(2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeShapes(
natural_coords, L);
Matrix<Real> H(2, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
natural_coords, real_coord, H);
// clang-format off
// u1 v1 w1 tx1 ty1 tz1 u2 v2 w2 tx2 ty2 tz2
N = {{L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 , 0 , 0 , 0 }, // u
{0 , H(0, 0), 0 , 0 , 0 , H(0, 1), 0 , H(0, 2), 0 , 0 , 0 , H(0, 3)}, // v
{0 , 0 , H(0, 0), 0 , -H(0, 1), 0 , 0 , 0 , H(0, 2), 0 , -H(0, 3), 0 }, // w
{0 , 0 , 0 , L(0), 0 , 0 , 0 , 0 , 0 , L(1), 0 , 0 }, // thetax
{0 , 0 , H(1, 0), 0 , -H(1, 1), 0 , 0 , 0 , H(1, 2), 0 , -H(1, 3), 0 }, // thetay
{0 , H(1, 0), 0 , 0 , 0 , H(1, 1), 0 , H(1, 2), 0 , 0 , 0 , H(1, 3)}}; // thetaz
// clang-format on
}
/* -------------------------------------------------------------------------- */
#if 0
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeShapesDisplacements(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
}
#endif
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
Matrix<Real> L(1, 2);
InterpolationElement<_itp_lagrange_segment_2, _itk_lagrangian>::computeDNDS(
natural_coords, L);
Matrix<Real> H(1, 4);
InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, H);
// Storing the derivatives in dnds
dnds.block(L, 0, 0);
dnds.block(H, 0, 2);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 t1 u2 v2 t2
B = {{L(0, 0), 0, 0, L(0, 1), 0, 0 },
{0, -H(0, 0), -H(0, 1), 0, -H(0, 2), -H(0, 3)}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & dnds) {
InterpolationElement<_itp_bernoulli_beam_2, _itk_structural>::computeDNDS(
natural_coords, real_coord, dnds);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_bernoulli_beam_3, _itk_structural>::arrangeInVoigt(
const Matrix<Real> & dnds, Matrix<Real> & B) {
auto L = dnds.block(0, 0, 1, 2); // Lagrange shape derivatives
auto H = dnds.block(0, 2, 1, 4); // Hermite shape derivatives
// clang-format off
// u1 v1 w1 x1 y1 z1 u2 v2 w2 x2 y2 z2
B = {{L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 , 0 , 0 , 0 }, // eps
{0 , -H(0, 0), 0 , 0 , 0 , -H(0, 1), 0 , -H(0, 2), 0 , 0 , 0 ,-H(0, 3)}, // chi strong axis
{0 , 0 , -H(0, 0), 0 , H(0, 1) , 0 , 0 , 0 , -H(0, 2) , 0 , H(0, 3) , 0 }, // chi weak axis
{0 , 0 , 0 , L(0, 0), 0 , 0 , 0 , 0 , 0 , L(0, 1), 0 , 0 }}; // chi torsion
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_2>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & /*n*/) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto cs = (x2 - x1);
cs.normalize();
auto c = cs(0);
auto s = cs(1);
// clang-format off
/// Definition of the rotation matrix
R = {{ c, s, 0.},
{-s, c, 0.},
{ 0., 0., 1.}};
// clang-format on
}
/* -------------------------------------------------------------------------- */
template <>
inline void ElementClass<_bernoulli_beam_3>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & n) {
Vector<Real> x2 = X(1); // X2
Vector<Real> x1 = X(0); // X1
auto dim = X.rows();
auto x = (x2 - x1);
x.normalize();
auto x_n = x.crossProduct(n);
Matrix<Real> Pe = {{1., 0., 0.}, {0., -1., 0.}, {0., 0., 1.}};
Matrix<Real> Pg(dim, dim);
Pg(0) = x;
Pg(1) = x_n;
Pg(2) = n;
Pe *= Pg.inverse();
R.zero();
/// Definition of the rotation matrix
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
R(i + dim, j + dim) = R(i, j) = Pe(i, j);
}
}
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_CLASS_BERNOULLI_BEAM_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh b/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
index 77ad5d0ff..f744254cb 100644
--- a/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_hermite_inline_impl.hh
@@ -1,176 +1,181 @@
/**
* @file element_class_hermite_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 10 2017
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Tue Feb 09 2021
*
* @brief Specialization of the element_class class for the type
* _hermite
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
--x-----q1----|----q2-----x---> x
-1 0 1
@endverbatim
*
* @f[
* \begin{array}{ll}
* M_1(\xi) &= 1/4(\xi^{3}/-3\xi+2)\\
* M_2(\xi) &= -1/4(\xi^{3}-3\xi-2)
* \end{array}
*
* \begin{array}{ll}
* L_1(\xi) &= 1/4(\xi^{3}-\xi^{2}-\xi+1)\\
* L_2(\xi) &= 1/4(\xi^{3}+\xi^{2}-\xi-1)
* \end{array}
*
* \begin{array}{ll}
* M'_1(\xi) &= 3/4(\xi^{2}-1)\\
* M'_2(\xi) &= -3/4(\xi^{2}-1)
* \end{array}
*
* \begin{array}{ll}
* L'_1(\xi) &= 1/4(3\xi^{2}-2\xi-1)\\
* L'_2(\xi) &= 1/4(3\xi^{2}+2\xi-1)
* \end{array}
*@f]
*
*
*@f[
* \begin{array}{ll}
* N'_1(\xi) &= -1/2\\
* N'_2(\xi) &= 1/2
* \end{array}]
*
* \begin{array}{ll}
* -M''_1(\xi) &= -3\xi/2\\
* -M''_2(\xi) &= 3\xi/2\\
* \end{array}
*
* \begin{array}{ll}
* -L''_1(\xi) &= -1/2a(3\xi/a-1)\\
* -L''_2(\xi) &= -1/2a(3\xi/a+1)
* \end{array}
*@f]
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_
#define AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(_itp_hermite_2,
_itp_lagrange_segment_2, 2,
1, 4);
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
inline Real computeLength(const Matrix<Real> & real_coord) {
Vector<Real> x1 = real_coord(0);
Vector<Real> x2 = real_coord(1);
return x1.distance(x2);
}
inline void computeShapes(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & N) {
/// natural coordinate
Real xi = natural_coords(0);
auto xi2 = xi * xi;
auto xi3 = xi * xi * xi;
// Cubic Hermite splines interpolating displacement
auto M1 = 1. / 4. * (2. - 3. * xi + xi3);
auto M2 = 1. / 4. * (2. + 3. * xi - xi3);
auto L1 = a / 4. * (1 - xi - xi2 + xi3);
auto L2 = a / 4. * (-1 - xi + xi2 + xi3);;
#if 1 // Version where we also interpolate the rotations
// Derivatives (with respect to x) of previous functions interpolating
// rotations
auto M1_ = 3. / (4. * a) * (xi2 - 1);
auto M2_ = 3. / (4. * a) * (1 - xi2);
auto L1_ = 1 / 4. * (3 * xi2 - 2 * xi - 1);
auto L2_ = 1 / 4. * (3 * xi2 + 2 * xi - 1);
// clang-format off
// v1 t1 v2 t2
N = {{M1 , L1 , M2 , L2}, // displacement interpolation
{M1_, L1_, M2_, L2_}}; // rotation interpolation
// clang-format on
#else // Version where we only interpolate displacements
// clang-format off
// v1 t1 v2 t2
N = {{M1, L1, M2, L2}};
// clang-format on
#endif
}
/* ---------------------------------------------------------------------- */
inline void computeDNDS(const Vector<Real> & natural_coords, Real a,
Matrix<Real> & B) {
// natural coordinate
Real xi = natural_coords(0);
// Derivatives with respect to xi for rotations
auto M1 = 3. / 2. * xi;
auto M2 = 3. / 2. * (-xi);
auto L1 = 1. * a / 2. * (3 * xi - 1);
auto L2 = 1. * a / 2. * (3 * xi + 1);
// v1 t1 v2 t2
B = {{M1, L1, M2, L2}}; // computing curvature : {chi} = [B]{d}
B /= a; // to account for first order deriv w/r to x
}
} // namespace details
} // namespace
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_hermite_2, _itk_structural>::computeShapes(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & N) {
auto L = details::computeLength(real_coord);
details::computeShapes(natural_coords, L / 2, N);
}
/* -------------------------------------------------------------------------- */
template <>
inline void InterpolationElement<_itp_hermite_2, _itk_structural>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coord,
Matrix<Real> & B) {
auto L = details::computeLength(real_coord);
details::computeDNDS(natural_coords, L / 2, B);
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_CLASS_HERMITE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.hh b/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.hh
index ab5a52808..fd6f06b11 100644
--- a/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_hexahedron_20_inline_impl.hh
@@ -1,224 +1,231 @@
/**
* @file element_class_hexahedron_20_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sacha Laffely <sacha.laffely@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Scantamburlo <damien.scantamburlo@epfl.ch>
*
* @date creation: Tue Mar 31 2015
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Feb 07 2020
*
* @brief Specialization of the element_class class for the type _hexahedron_20
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
-terms of the GNU Lesser General Public License as published by the Free
-Software Foundation, either version 3 of the License, or (at your option) any
-later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-details.
- *
- * You should have received a copy of the GNU Lesser General Public License
-along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\y
\z /
| /
7-----|18--------6
/| | / /|
/ | | / / |
19 | | / 17 |
/ 15 | / / 14
/ | | / / |
4-------16---/---5 |
| | +----|------------\x
| 3-------10-|-----2
| / | /
12 / 13 /
| 11 | 9
| / | /
|/ |/
0--------8-------1
x y z
* N0 -1 -1 -1
* N1 1 -1 -1
* N2 1 1 -1
* N3 -1 1 -1
* N4 -1 -1 1
* N5 1 -1 1
* N6 1 1 1
* N7 -1 1 1
* N8 0 -1 -1
* N9 1 0 -1
* N10 0 1 -1
* N11 -1 0 -1
* N12 -1 -1 0
* N13 1 -1 0
* N14 1 1 0
* N15 -1 1 0
* N16 0 -1 1
* N17 1 0 1
* N18 0 1 1
* N19 -1 0 1
* \endverbatim
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_hexahedron_20, _gt_hexahedron_20,
_itp_serendip_hexahedron_20, _ek_regular,
3, _git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_serendip_hexahedron_20>::computeShapes(
const vector_type & c, vector_type & N) {
// Shape function , Natural coordinates
N(0) =
0.125 * (1 - c(0)) * (1 - c(1)) * (1 - c(2)) * (-2 - c(0) - c(1) - c(2));
N(1) =
0.125 * (1 + c(0)) * (1 - c(1)) * (1 - c(2)) * (-2 + c(0) - c(1) - c(2));
N(2) =
0.125 * (1 + c(0)) * (1 + c(1)) * (1 - c(2)) * (-2 + c(0) + c(1) - c(2));
N(3) =
0.125 * (1 - c(0)) * (1 + c(1)) * (1 - c(2)) * (-2 - c(0) + c(1) - c(2));
N(4) =
0.125 * (1 - c(0)) * (1 - c(1)) * (1 + c(2)) * (-2 - c(0) - c(1) + c(2));
N(5) =
0.125 * (1 + c(0)) * (1 - c(1)) * (1 + c(2)) * (-2 + c(0) - c(1) + c(2));
N(6) =
0.125 * (1 + c(0)) * (1 + c(1)) * (1 + c(2)) * (-2 + c(0) + c(1) + c(2));
N(7) =
0.125 * (1 - c(0)) * (1 + c(1)) * (1 + c(2)) * (-2 - c(0) + c(1) + c(2));
N(8) = 0.25 * (1 - c(0) * c(0)) * (1 - c(1)) * (1 - c(2));
N(9) = 0.25 * (1 - c(1) * c(1)) * (1 + c(0)) * (1 - c(2));
N(10) = 0.25 * (1 - c(0) * c(0)) * (1 + c(1)) * (1 - c(2));
N(11) = 0.25 * (1 - c(1) * c(1)) * (1 - c(0)) * (1 - c(2));
N(12) = 0.25 * (1 - c(2) * c(2)) * (1 - c(0)) * (1 - c(1));
N(13) = 0.25 * (1 - c(2) * c(2)) * (1 + c(0)) * (1 - c(1));
N(14) = 0.25 * (1 - c(2) * c(2)) * (1 + c(0)) * (1 + c(1));
N(15) = 0.25 * (1 - c(2) * c(2)) * (1 - c(0)) * (1 + c(1));
N(16) = 0.25 * (1 - c(0) * c(0)) * (1 - c(1)) * (1 + c(2));
N(17) = 0.25 * (1 - c(1) * c(1)) * (1 + c(0)) * (1 + c(2));
N(18) = 0.25 * (1 - c(0) * c(0)) * (1 + c(1)) * (1 + c(2));
N(19) = 0.25 * (1 - c(1) * c(1)) * (1 - c(0)) * (1 + c(2));
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_serendip_hexahedron_20>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
// derivatives
// ddx
dnds(0, 0) =
0.25 * (c(0) + 0.5 * (c(1) + c(2) + 1)) * (c(1) - 1) * (c(2) - 1);
dnds(0, 1) =
0.25 * (c(0) - 0.5 * (c(1) + c(2) + 1)) * (c(1) - 1) * (c(2) - 1);
dnds(0, 2) =
-0.25 * (c(0) + 0.5 * (c(1) - c(2) - 1)) * (c(1) + 1) * (c(2) - 1);
dnds(0, 3) =
-0.25 * (c(0) - 0.5 * (c(1) - c(2) - 1)) * (c(1) + 1) * (c(2) - 1);
dnds(0, 4) =
-0.25 * (c(0) + 0.5 * (c(1) - c(2) + 1)) * (c(1) - 1) * (c(2) + 1);
dnds(0, 5) =
-0.25 * (c(0) - 0.5 * (c(1) - c(2) + 1)) * (c(1) - 1) * (c(2) + 1);
dnds(0, 6) =
0.25 * (c(0) + 0.5 * (c(1) + c(2) - 1)) * (c(1) + 1) * (c(2) + 1);
dnds(0, 7) =
0.25 * (c(0) - 0.5 * (c(1) + c(2) - 1)) * (c(1) + 1) * (c(2) + 1);
dnds(0, 8) = -0.5 * c(0) * (c(1) - 1) * (c(2) - 1);
dnds(0, 9) = 0.25 * (c(1) * c(1) - 1) * (c(2) - 1);
dnds(0, 10) = 0.5 * c(0) * (c(1) + 1) * (c(2) - 1);
dnds(0, 11) = -0.25 * (c(1) * c(1) - 1) * (c(2) - 1);
dnds(0, 12) = -0.25 * (c(2) * c(2) - 1) * (c(1) - 1);
dnds(0, 13) = 0.25 * (c(1) - 1) * (c(2) * c(2) - 1);
dnds(0, 14) = -0.25 * (c(1) + 1) * (c(2) * c(2) - 1);
dnds(0, 15) = 0.25 * (c(1) + 1) * (c(2) * c(2) - 1);
dnds(0, 16) = 0.5 * c(0) * (c(1) - 1) * (c(2) + 1);
dnds(0, 17) = -0.25 * (c(2) + 1) * (c(1) * c(1) - 1);
dnds(0, 18) = -0.5 * c(0) * (c(1) + 1) * (c(2) + 1);
dnds(0, 19) = 0.25 * (c(2) + 1) * (c(1) * c(1) - 1);
// ddy
dnds(1, 0) =
0.25 * (c(1) + 0.5 * (c(0) + c(2) + 1)) * (c(0) - 1) * (c(2) - 1);
dnds(1, 1) =
-0.25 * (c(1) - 0.5 * (c(0) - c(2) - 1)) * (c(0) + 1) * (c(2) - 1);
dnds(1, 2) =
-0.25 * (c(1) + 0.5 * (c(0) - c(2) - 1)) * (c(0) + 1) * (c(2) - 1);
dnds(1, 3) =
0.25 * (c(1) - 0.5 * (c(0) + c(2) + 1)) * (c(0) - 1) * (c(2) - 1);
dnds(1, 4) =
-0.25 * (c(1) + 0.5 * (c(0) - c(2) + 1)) * (c(0) - 1) * (c(2) + 1);
dnds(1, 5) =
0.25 * (c(1) - 0.5 * (c(0) + c(2) - 1)) * (c(0) + 1) * (c(2) + 1);
dnds(1, 6) =
0.25 * (c(1) + 0.5 * (c(0) + c(2) - 1)) * (c(0) + 1) * (c(2) + 1);
dnds(1, 7) =
-0.25 * (c(1) - 0.5 * (c(0) - c(2) + 1)) * (c(0) - 1) * (c(2) + 1);
dnds(1, 8) = -0.25 * (c(0) * c(0) - 1) * (c(2) - 1);
dnds(1, 9) = 0.5 * c(1) * (c(0) + 1) * (c(2) - 1);
dnds(1, 10) = 0.25 * (c(0) * c(0) - 1) * (c(2) - 1);
dnds(1, 11) = -0.5 * c(1) * (c(0) - 1) * (c(2) - 1);
dnds(1, 12) = -0.25 * (c(2) * c(2) - 1) * (c(0) - 1);
dnds(1, 13) = 0.25 * (c(0) + 1) * (c(2) * c(2) - 1);
dnds(1, 14) = -0.25 * (c(0) + 1) * (c(2) * c(2) - 1);
dnds(1, 15) = 0.25 * (c(0) - 1) * (c(2) * c(2) - 1);
dnds(1, 16) = 0.25 * (c(2) + 1) * (c(0) * c(0) - 1);
dnds(1, 17) = -0.5 * c(1) * (c(0) + 1) * (c(2) + 1);
dnds(1, 18) = -0.25 * (c(2) + 1) * (c(0) * c(0) - 1);
dnds(1, 19) = 0.5 * c(1) * (c(0) - 1) * (c(2) + 1);
// ddz
dnds(2, 0) =
0.25 * (c(2) + 0.5 * (c(0) + c(1) + 1)) * (c(0) - 1) * (c(1) - 1);
dnds(2, 1) =
-0.25 * (c(2) - 0.5 * (c(0) - c(1) - 1)) * (c(0) + 1) * (c(1) - 1);
dnds(2, 2) =
0.25 * (c(2) - 0.5 * (c(0) + c(1) - 1)) * (c(0) + 1) * (c(1) + 1);
dnds(2, 3) =
-0.25 * (c(2) + 0.5 * (c(0) - c(1) + 1)) * (c(0) - 1) * (c(1) + 1);
dnds(2, 4) =
0.25 * (c(2) - 0.5 * (c(0) + c(1) + 1)) * (c(0) - 1) * (c(1) - 1);
dnds(2, 5) =
-0.25 * (c(2) + 0.5 * (c(0) - c(1) - 1)) * (c(0) + 1) * (c(1) - 1);
dnds(2, 6) =
0.25 * (c(2) + 0.5 * (c(0) + c(1) - 1)) * (c(0) + 1) * (c(1) + 1);
dnds(2, 7) =
-0.25 * (c(2) - 0.5 * (c(0) - c(1) + 1)) * (c(0) - 1) * (c(1) + 1);
dnds(2, 8) = -0.25 * (c(0) * c(0) - 1) * (c(1) - 1);
dnds(2, 9) = 0.25 * (c(1) * c(1) - 1) * (c(0) + 1);
dnds(2, 10) = 0.25 * (c(0) * c(0) - 1) * (c(1) + 1);
dnds(2, 11) = -0.25 * (c(1) * c(1) - 1) * (c(0) - 1);
dnds(2, 12) = -0.5 * c(2) * (c(1) - 1) * (c(0) - 1);
dnds(2, 13) = 0.5 * c(2) * (c(0) + 1) * (c(1) - 1);
dnds(2, 14) = -0.5 * c(2) * (c(0) + 1) * (c(1) + 1);
dnds(2, 15) = 0.5 * c(2) * (c(0) - 1) * (c(1) + 1);
dnds(2, 16) = 0.25 * (c(1) - 1) * (c(0) * c(0) - 1);
dnds(2, 17) = -0.25 * (c(0) + 1) * (c(1) * c(1) - 1);
dnds(2, 18) = -0.25 * (c(1) + 1) * (c(0) * c(0) - 1);
dnds(2, 19) = 0.25 * (c(0) - 1) * (c(1) * c(1) - 1);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_hexahedron_20>::getInradius(const Matrix<Real> & coord) {
return GeometricalElement<_gt_hexahedron_8>::getInradius(coord) * 0.5;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.hh b/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.hh
index d1dfaef27..1ed0e2a36 100644
--- a/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_hexahedron_8_inline_impl.hh
@@ -1,247 +1,253 @@
/**
* @file element_class_hexahedron_8_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
* @date creation: Mon Mar 14 2011
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Feb 07 2020
*
* @brief Specialization of the element_class class for the type _hexahedron_8
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\zeta
^
(-1,1,1) | (1,1,1)
7---|------6
/| | /|
/ | | / |
(-1,-1,1) 4----------5 | (1,-1,1)
| | | | |
| | | | |
| | +---|-------> \xi
| | / | |
(-1,1,-1) | 3-/-----|--2 (1,1,-1)
| / / | /
|/ / |/
0-/--------1
(-1,-1,-1) / (1,-1,-1)
/
\eta
@endverbatim
*
* \f[
* \begin{array}{llll}
* N1 = (1 - \xi) (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \xi} = - (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi) (1 - \zeta) / 8
* & \frac{\partial N1}{\partial \zeta} = - (1 - \xi) (1 - \eta) / 8 \\
* N2 = (1 + \xi) (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \xi} = (1 - \eta) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi) (1 - \zeta) / 8
* & \frac{\partial N2}{\partial \zeta} = - (1 + \xi) (1 - \eta) / 8 \\
* N3 = (1 + \xi) (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \xi} = (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \eta} = (1 + \xi) (1 - \zeta) / 8
* & \frac{\partial N3}{\partial \zeta} = - (1 + \xi) (1 + \eta) / 8 \\
* N4 = (1 - \xi) (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \xi} = - (1 + \eta) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \eta} = (1 - \xi) (1 - \zeta) / 8
* & \frac{\partial N4}{\partial \zeta} = - (1 - \xi) (1 + \eta) / 8 \\
* N5 = (1 - \xi) (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \xi} = - (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \eta} = - (1 - \xi) (1 + \zeta) / 8
* & \frac{\partial N5}{\partial \zeta} = (1 - \xi) (1 - \eta) / 8 \\
* N6 = (1 + \xi) (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \xi} = (1 - \eta) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \eta} = - (1 + \xi) (1 + \zeta) / 8
* & \frac{\partial N6}{\partial \zeta} = (1 + \xi) (1 - \eta) / 8 \\
* N7 = (1 + \xi) (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \xi} = (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \eta} = (1 + \xi) (1 + \zeta) / 8
* & \frac{\partial N7}{\partial \zeta} = (1 + \xi) (1 + \eta) / 8 \\
* N8 = (1 - \xi) (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \xi} = - (1 + \eta) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \eta} = (1 - \xi) (1 + \zeta) / 8
* & \frac{\partial N8}{\partial \zeta} = (1 - \xi) (1 + \eta) / 8 \\
* \end{array}
* \f]
*
* @f{eqnarray*}{
* \xi_{q0} &=& -1/\sqrt{3} \qquad \eta_{q0} = -1/\sqrt{3} \qquad \zeta_{q0} =
-1/\sqrt{3} \\
* \xi_{q1} &=& 1/\sqrt{3} \qquad \eta_{q1} = -1/\sqrt{3} \qquad \zeta_{q1} =
-1/\sqrt{3} \\
* \xi_{q2} &=& 1/\sqrt{3} \qquad \eta_{q2} = 1/\sqrt{3} \qquad \zeta_{q2} =
-1/\sqrt{3} \\
* \xi_{q3} &=& -1/\sqrt{3} \qquad \eta_{q3} = 1/\sqrt{3} \qquad \zeta_{q3} =
-1/\sqrt{3} \\
* \xi_{q4} &=& -1/\sqrt{3} \qquad \eta_{q4} = -1/\sqrt{3} \qquad \zeta_{q4} =
1/\sqrt{3} \\
* \xi_{q5} &=& 1/\sqrt{3} \qquad \eta_{q5} = -1/\sqrt{3} \qquad \zeta_{q5} =
1/\sqrt{3} \\
* \xi_{q6} &=& 1/\sqrt{3} \qquad \eta_{q6} = 1/\sqrt{3} \qquad \zeta_{q6} =
1/\sqrt{3} \\
* \xi_{q7} &=& -1/\sqrt{3} \qquad \eta_{q7} = 1/\sqrt{3} \qquad \zeta_{q7} =
1/\sqrt{3} \\
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_hexahedron_8, _gt_hexahedron_8,
_itp_lagrange_hexahedron_8, _ek_regular, 3,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_hexahedron_8>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
N(0) = .125 * (1 - c(0)) * (1 - c(1)) * (1 - c(2)); /// N1(q_0)
N(1) = .125 * (1 + c(0)) * (1 - c(1)) * (1 - c(2)); /// N2(q_0)
N(2) = .125 * (1 + c(0)) * (1 + c(1)) * (1 - c(2)); /// N3(q_0)
N(3) = .125 * (1 - c(0)) * (1 + c(1)) * (1 - c(2)); /// N4(q_0)
N(4) = .125 * (1 - c(0)) * (1 - c(1)) * (1 + c(2)); /// N5(q_0)
N(5) = .125 * (1 + c(0)) * (1 - c(1)) * (1 + c(2)); /// N6(q_0)
N(6) = .125 * (1 + c(0)) * (1 + c(1)) * (1 + c(2)); /// N7(q_0)
N(7) = .125 * (1 - c(0)) * (1 + c(1)) * (1 + c(2)); /// N8(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_hexahedron_8>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial
* N4}{\partial \xi}
* & \frac{\partial N5}{\partial \xi} & \frac{\partial
* N6}{\partial \xi}
* & \frac{\partial N7}{\partial \xi} & \frac{\partial
* N8}{\partial \xi}\\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial
* N4}{\partial \eta}
* & \frac{\partial N5}{\partial \eta} & \frac{\partial
* N6}{\partial \eta}
* & \frac{\partial N7}{\partial \eta} & \frac{\partial
* N8}{\partial \eta}\\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial
* N4}{\partial \zeta}
* & \frac{\partial N5}{\partial \zeta} & \frac{\partial
* N6}{\partial \zeta}
* & \frac{\partial N7}{\partial \zeta} & \frac{\partial
* N8}{\partial \zeta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -.125 * (1 - c(1)) * (1 - c(2));
dnds(0, 1) = .125 * (1 - c(1)) * (1 - c(2));
dnds(0, 2) = .125 * (1 + c(1)) * (1 - c(2));
dnds(0, 3) = -.125 * (1 + c(1)) * (1 - c(2));
dnds(0, 4) = -.125 * (1 - c(1)) * (1 + c(2));
;
dnds(0, 5) = .125 * (1 - c(1)) * (1 + c(2));
;
dnds(0, 6) = .125 * (1 + c(1)) * (1 + c(2));
;
dnds(0, 7) = -.125 * (1 + c(1)) * (1 + c(2));
;
dnds(1, 0) = -.125 * (1 - c(0)) * (1 - c(2));
;
dnds(1, 1) = -.125 * (1 + c(0)) * (1 - c(2));
;
dnds(1, 2) = .125 * (1 + c(0)) * (1 - c(2));
;
dnds(1, 3) = .125 * (1 - c(0)) * (1 - c(2));
;
dnds(1, 4) = -.125 * (1 - c(0)) * (1 + c(2));
;
dnds(1, 5) = -.125 * (1 + c(0)) * (1 + c(2));
;
dnds(1, 6) = .125 * (1 + c(0)) * (1 + c(2));
;
dnds(1, 7) = .125 * (1 - c(0)) * (1 + c(2));
;
dnds(2, 0) = -.125 * (1 - c(0)) * (1 - c(1));
;
dnds(2, 1) = -.125 * (1 + c(0)) * (1 - c(1));
;
dnds(2, 2) = -.125 * (1 + c(0)) * (1 + c(1));
;
dnds(2, 3) = -.125 * (1 - c(0)) * (1 + c(1));
;
dnds(2, 4) = .125 * (1 - c(0)) * (1 - c(1));
;
dnds(2, 5) = .125 * (1 + c(0)) * (1 - c(1));
;
dnds(2, 6) = .125 * (1 + c(0)) * (1 + c(1));
;
dnds(2, 7) = .125 * (1 - c(0)) * (1 + c(1));
;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_hexahedron_8>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
Real e = u0.distance(u4);
Real f = u1.distance(u5);
Real g = u2.distance(u6);
Real h = u3.distance(u7);
Real i = u4.distance(u5);
Real j = u5.distance(u6);
Real k = u6.distance(u7);
Real l = u7.distance(u4);
Real p = std::min({a, b, c, d, e, f, g, h, i, j, k, l});
return p;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
index 2b5ce778f..520b6f31d 100644
--- a/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_kirchhoff_shell_inline_impl.hh
@@ -1,223 +1,226 @@
/**
* @file element_class_kirchhoff_shell_inline_impl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 04 2014
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Element class Kirchhoff Shell
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_
#define AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_STRUCTURAL_INTERPOLATION_TYPE_PROPERTY(
_itp_discrete_kirchhoff_triangle_18, _itp_lagrange_triangle_3, 6, 6, 21);
AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY(
_discrete_kirchhoff_triangle_18, _gt_triangle_3,
_itp_discrete_kirchhoff_triangle_18, _triangle_3, _ek_structural, 3,
_git_triangle, 2);
/* -------------------------------------------------------------------------- */
namespace detail {
inline void computeBasisChangeMatrix(Matrix<Real> & P,
const Matrix<Real> & X) {
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
Vector<Real> a1 = X2 - X1;
Vector<Real> a2 = X3 - X1;
a1.normalize();
Vector<Real> e3 = a1.crossProduct(a2);
e3.normalize();
Vector<Real> e2 = e3.crossProduct(a1);
P(0) = a1;
P(1) = e2;
P(2) = e3;
P = P.transpose();
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <>
inline void
ElementClass<_discrete_kirchhoff_triangle_18>::computeRotationMatrix(
Matrix<Real> & R, const Matrix<Real> & X, const Vector<Real> & /*n*/) {
auto dim = X.rows();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, X);
R.zero();
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
R(i + dim, j + dim) = R(i, j) = P(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeShapes(
const Vector<Real> & /*natural_coords*/,
const Matrix<Real> & /*real_coord*/, Matrix<Real> & /*N*/) {}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18>::computeDNDS(
const Vector<Real> & natural_coords, const Matrix<Real> & real_coordinates,
Matrix<Real> & B) {
auto dim = real_coordinates.cols();
Matrix<Real> P(dim, dim);
detail::computeBasisChangeMatrix(P, real_coordinates);
auto X = P * real_coordinates;
Vector<Real> X1 = X(0);
Vector<Real> X2 = X(1);
Vector<Real> X3 = X(2);
std::array<Vector<Real>, 3> A = {X2 - X1, X3 - X2, X1 - X3};
std::array<Real, 3> L;
std::array<Real, 3> C;
std::array<Real, 3> S;
// Setting all last coordinates to 0
std::for_each(A.begin(), A.end(), [](auto & a) { a(2) = 0; });
// Computing lengths
std::transform(A.begin(), A.end(), L.begin(),
[](auto & a) { return a.template norm<L_2>(); });
// Computing cosines
std::transform(A.begin(), A.end(), L.begin(), C.begin(),
[](auto & a, auto & l) { return a(0) / l; });
// Computing sines
std::transform(A.begin(), A.end(), L.begin(), S.begin(),
[](auto & a, auto & l) { return a(1) / l; });
// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
// Derivative of quadratic interpolation functions
Matrix<Real> dP = {{4 * (1 - 2 * xi - eta), 4 * eta, -4 * eta},
{-4 * xi, 4 * xi, 4 * (1 - xi - 2 * eta)}};
Matrix<Real> dNx1 = {
{3. / 2 * (dP(0, 0) * C[0] / L[0] - dP(0, 2) * C[2] / L[2]),
3. / 2 * (dP(0, 1) * C[1] / L[1] - dP(0, 0) * C[0] / L[0]),
3. / 2 * (dP(0, 2) * C[2] / L[2] - dP(0, 1) * C[1] / L[1])},
{3. / 2 * (dP(1, 0) * C[0] / L[0] - dP(1, 2) * C[2] / L[2]),
3. / 2 * (dP(1, 1) * C[1] / L[1] - dP(1, 0) * C[0] / L[0]),
3. / 2 * (dP(1, 2) * C[2] / L[2] - dP(1, 1) * C[1] / L[1])}};
Matrix<Real> dNx2 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * C[0] * C[0] + dP(0, 2) * C[2] * C[2]),
1 - 3. / 4 * (dP(0, 1) * C[1] * C[1] + dP(0, 0) * C[0] * C[0]),
- 3. / 4 * (dP(0, 2) * C[2] * C[2] + dP(0, 1) * C[1] * C[1])},
{-1 - 3. / 4 * (dP(1, 0) * C[0] * C[0] + dP(1, 2) * C[2] * C[2]),
- 3. / 4 * (dP(1, 1) * C[1] * C[1] + dP(1, 0) * C[0] * C[0]),
1 - 3. / 4 * (dP(1, 2) * C[2] * C[2] + dP(1, 1) * C[1] * C[1])}};
// clang-format on
Matrix<Real> dNx3 = {
{-3. / 4 * (dP(0, 0) * C[0] * S[0] + dP(0, 2) * C[2] * S[2]),
-3. / 4 * (dP(0, 1) * C[1] * S[1] + dP(0, 0) * C[0] * S[0]),
-3. / 4 * (dP(0, 2) * C[2] * S[2] + dP(0, 1) * C[1] * S[1])},
{-3. / 4 * (dP(1, 0) * C[0] * S[0] + dP(1, 2) * C[2] * S[2]),
-3. / 4 * (dP(1, 1) * C[1] * S[1] + dP(1, 0) * C[0] * S[0]),
-3. / 4 * (dP(1, 2) * C[2] * S[2] + dP(1, 1) * C[1] * S[1])}};
Matrix<Real> dNy1 = {
{3. / 2 * (dP(0, 0) * S[0] / L[0] - dP(0, 2) * S[2] / L[2]),
3. / 2 * (dP(0, 1) * S[1] / L[1] - dP(0, 0) * S[0] / L[0]),
3. / 2 * (dP(0, 2) * S[2] / L[2] - dP(0, 1) * S[1] / L[1])},
{3. / 2 * (dP(1, 0) * S[0] / L[0] - dP(1, 2) * S[2] / L[2]),
3. / 2 * (dP(1, 1) * S[1] / L[1] - dP(1, 0) * S[0] / L[0]),
3. / 2 * (dP(1, 2) * S[2] / L[2] - dP(1, 1) * S[1] / L[1])}};
const Matrix<Real> & dNy2 = dNx3;
Matrix<Real> dNy3 = {
// clang-format off
{-1 - 3. / 4 * (dP(0, 0) * S[0] * S[0] + dP(0, 2) * S[2] * S[2]),
1 - 3. / 4 * (dP(0, 1) * S[1] * S[1] + dP(0, 0) * S[0] * S[0]),
- 3. / 4 * (dP(0, 2) * S[2] * S[2] + dP(0, 1) * S[1] * S[1])},
{-1 - 3. / 4 * (dP(1, 0) * S[0] * S[0] + dP(1, 2) * S[2] * S[2]),
- 3. / 4 * (dP(1, 1) * S[1] * S[1] + dP(1, 0) * S[0] * S[0]),
1 - 3. / 4 * (dP(1, 2) * S[2] * S[2] + dP(1, 1) * S[1] * S[1])}};
// clang-format on
// Derivative of linear (membrane mode) functions
Matrix<Real> dNm(2, 3);
InterpolationElement<_itp_lagrange_triangle_3, _itk_lagrangian>::computeDNDS(
natural_coords, dNm);
UInt i = 0;
for (const Matrix<Real> & mat : {dNm, dNx1, dNx2, dNx3, dNy1, dNy2, dNy3}) {
B.block(mat, 0, i);
i += mat.cols();
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_discrete_kirchhoff_triangle_18,
_itk_structural>::arrangeInVoigt(const Matrix<Real> & dnds,
Matrix<Real> & B) {
Matrix<Real> dNm(2, 3);
Matrix<Real> dNx1(2, 3);
Matrix<Real> dNx2(2, 3);
Matrix<Real> dNx3(2, 3);
Matrix<Real> dNy1(2, 3);
Matrix<Real> dNy2(2, 3);
Matrix<Real> dNy3(2, 3);
UInt i = 0;
for (Matrix<Real> * mat : {&dNm, &dNx1, &dNx2, &dNx3, &dNy1, &dNy2, &dNy3}) {
*mat = dnds.block(0, i, 2, 3);
i += mat->cols();
}
for (UInt i = 0; i < 3; ++i) {
// clang-format off
Matrix<Real> Bm = {{dNm(0, i), 0, 0, 0, 0, 0},
{0, dNm(1, i), 0, 0, 0, 0},
{dNm(1, i), dNm(0, i), 0, 0, 0, 0}};
Matrix<Real> Bf = {{0, 0, dNx1(0, i), -dNx3(0, i), dNx2(0, i), 0},
{0, 0, dNy1(1, i), -dNy3(1, i), dNy2(1, i), 0},
{0, 0, dNx1(1, i) + dNy1(0, i), -dNx3(1, i) - dNy3(0, i), dNx2(1, i) + dNy2(0, i), 0}};
// clang-format on
B.block(Bm, 0, i * 6);
B.block(Bf, 3, i * 6);
}
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_CLASS_KIRCHHOFF_SHELL_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.hh b/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.hh
index a280e6d15..e02d0ae16 100644
--- a/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_pentahedron_15_inline_impl.hh
@@ -1,178 +1,184 @@
/**
* @file element_class_pentahedron_15_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sacha Laffely <sacha.laffely@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Scantamburlo <damien.scantamburlo@epfl.ch>
*
* @date creation: Tue Mar 31 2015
- * @date last modification: Thu Dec 28 2017
+ * @date last modification: Fri Feb 07 2020
*
* @brief Specialization of the element_class class for the type
* _pentahedron_15
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
-Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
-terms of the GNU Lesser General Public License as published by the Free
-Software Foundation, either version 3 of the License, or (at your option) any
-later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-details.
- *
- * You should have received a copy of the GNU Lesser General Public License
-along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* \verbatim
z
^
|
|
| 1
| /|\
|/ | \
10 7 6
/ | \
/ | \
4 2--8--0
| \ / /
| \11 /
13 12 9---------->y
| / \ /
|/ \ /
5--14--3
/
/
/
v
x
\endverbatim
x y z
* N0 -1 1 0
* N1 -1 0 1
* N2 -1 0 0
* N3 1 1 0
* N4 1 0 1
* N5 1 0 0
* N6 -1 0.5 0.5
* N7 -1 0 0.5
* N8 -1 0.5 0
* N9 0 1 0
* N10 0 0 1
* N11 0 0 0
* N12 1 0.5 0.5
* N13 1 0 0.5
* N14 1 0.5 0
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_pentahedron_15, _gt_pentahedron_15,
_itp_lagrange_pentahedron_15, _ek_regular,
3, _git_pentahedron, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_15>::computeShapes(
const vector_type & c, vector_type & N) {
auto & x = c(0);
auto & y = c(1);
auto & z = c(2);
// Shape Functions, Natural coordinates
N(0) = 0.5 * y * (1 - x) * (2 * y - 2 - x);
N(1) = 0.5 * z * (1 - x) * (2 * z - 2 - x);
N(2) = 0.5 * (x - 1) * (1 - y - z) * (x + 2 * y + 2 * z);
N(3) = 0.5 * y * (1 + x) * (2 * y - 2 + x);
N(4) = 0.5 * z * (1 + x) * (2 * z - 2 + x);
N(5) = 0.5 * (-x - 1) * (1 - y - z) * (-x + 2 * y + 2 * z);
N(6) = 2.0 * y * z * (1 - x);
N(7) = 2.0 * z * (1 - y - z) * (1 - x);
N(8) = 2.0 * y * (1 - x) * (1 - y - z);
N(9) = y * (1 - x * x);
N(10) = z * (1 - x * x);
N(11) = (1 - y - z) * (1 - x * x);
N(12) = 2.0 * y * z * (1 + x);
N(13) = 2.0 * z * (1 - y - z) * (1 + x);
N(14) = 2.0 * y * (1 - y - z) * (1 + x);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_15>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
auto & x = c(0);
auto & y = c(1);
auto & z = c(2);
// ddx
dnds(0, 0) = 0.5 * y * (2 * x - 2 * y + 1);
dnds(0, 1) = 0.5 * z * (2 * x - 2 * z + 1);
dnds(0, 2) = -0.5 * (2 * x + 2 * y + 2 * z - 1) * (y + z - 1);
dnds(0, 3) = 0.5 * y * (2 * x + 2 * y - 1);
dnds(0, 4) = 0.5 * z * (2 * x + 2 * z - 1);
dnds(0, 5) = -0.5 * (y + z - 1) * (2 * x - 2 * y - 2 * z + 1);
dnds(0, 6) = -2.0 * y * z;
dnds(0, 7) = 2.0 * z * (y + z - 1);
dnds(0, 8) = 2.0 * y * (y + z - 1);
dnds(0, 9) = -2.0 * x * y;
dnds(0, 10) = -2.0 * x * z;
dnds(0, 11) = 2.0 * x * (y + z - 1);
dnds(0, 12) = 2.0 * y * z;
dnds(0, 13) = -2.0 * z * (y + z - 1);
dnds(0, 14) = -2.0 * y * (y + z - 1);
// ddy
dnds(1, 0) = -0.5 * (x - 1) * (4 * y - x - 2);
dnds(1, 1) = 0.0;
dnds(1, 2) = -0.5 * (x - 1) * (4 * y + x + 2 * (2 * z - 1));
dnds(1, 3) = 0.5 * (x + 1) * (4 * y + x - 2);
dnds(1, 4) = 0.0;
dnds(1, 5) = 0.5 * (x + 1) * (4 * y - x + 2 * (2 * z - 1));
dnds(1, 6) = -2.0 * (x - 1) * z;
dnds(1, 7) = 2.0 * z * (x - 1);
dnds(1, 8) = 2.0 * (2 * y + z - 1) * (x - 1);
dnds(1, 9) = -(x * x - 1);
dnds(1, 10) = 0.0;
dnds(1, 11) = (x * x - 1);
dnds(1, 12) = 2.0 * z * (x + 1);
dnds(1, 13) = -2.0 * z * (x + 1);
dnds(1, 14) = -2.0 * (2 * y + z - 1) * (x + 1);
// ddz
dnds(2, 0) = 0.0;
dnds(2, 1) = -0.5 * (x - 1) * (4 * z - x - 2);
dnds(2, 2) = -0.5 * (x - 1) * (4 * z + x + 2 * (2 * y - 1));
dnds(2, 3) = 0.0;
dnds(2, 4) = 0.5 * (x + 1) * (4 * z + x - 2);
dnds(2, 5) = 0.5 * (x + 1) * (4 * z - x + 2 * (2 * y - 1));
dnds(2, 6) = -2.0 * (x - 1) * y;
dnds(2, 7) = 2.0 * (x - 1) * (2 * z + y - 1);
dnds(2, 8) = 2.0 * y * (x - 1);
dnds(2, 9) = 0.0;
dnds(2, 10) = -(x * x - 1);
dnds(2, 11) = (x * x - 1);
dnds(2, 12) = 2.0 * (x + 1) * y;
dnds(2, 13) = -2.0 * (x + 1) * (2 * z + y - 1);
dnds(2, 14) = -2.0 * (x + 1) * y;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real GeometricalElement<_gt_pentahedron_15>::getInradius(
const Matrix<Real> & coord) {
return GeometricalElement<_gt_pentahedron_6>::getInradius(coord) * 0.5;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
index 7183b1f64..5c0122b5f 100644
--- a/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_pentahedron_6_inline_impl.hh
@@ -1,161 +1,168 @@
/**
* @file element_class_pentahedron_6_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Mar 14 2011
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Specialization of the element_class class for the type _pentahedron_6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- * PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
- *
+ */
+
+/**
* @verbatim
/z
|
|
| 1
| /|\
|/ | \
/ | \
/ | \
/ | \
4 2-----0
| \ / /
| \/ /
| \ /----------/y
| / \ /
|/ \ /
5---.--3
/
/
/
\x
x y z
* N0 -1 1 0
* N1 -1 0 1
* N2 -1 0 0
* N3 1 1 0
* N4 1 0 1
* N5 1 0 0
\endverbatim
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_pentahedron_6, _gt_pentahedron_6,
_itp_lagrange_pentahedron_6, _ek_regular,
3, _git_pentahedron, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
N(0) = 0.5 * c(1) * (1 - c(0)); // N1(q)
N(1) = 0.5 * c(2) * (1 - c(0)); // N2(q)
N(2) = 0.5 * (1 - c(1) - c(2)) * (1 - c(0)); // N3(q)
N(3) = 0.5 * c(1) * (1 + c(0)); // N4(q)
N(4) = 0.5 * c(2) * (1 + c(0)); // N5(q)
N(5) = 0.5 * (1 - c(1) - c(2)) * (1 + c(0)); // N6(q)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_pentahedron_6>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
dnds(0, 0) = -0.5 * c(1);
dnds(0, 1) = -0.5 * c(2);
dnds(0, 2) = -0.5 * (1 - c(1) - c(2));
dnds(0, 3) = 0.5 * c(1);
dnds(0, 4) = 0.5 * c(2);
dnds(0, 5) = 0.5 * (1 - c(1) - c(2));
dnds(1, 0) = 0.5 * (1 - c(0));
dnds(1, 1) = 0.0;
dnds(1, 2) = -0.5 * (1 - c(0));
dnds(1, 3) = 0.5 * (1 + c(0));
dnds(1, 4) = 0.0;
dnds(1, 5) = -0.5 * (1 + c(0));
dnds(2, 0) = 0.0;
dnds(2, 1) = 0.5 * (1 - c(0));
dnds(2, 2) = -0.5 * (1 - c(0));
dnds(2, 3) = 0.0;
dnds(2, 4) = 0.5 * (1 + c(0));
dnds(2, 5) = -0.5 * (1 + c(0));
}
/* -------------------------------------------------------------------------- */
// I have to duplicate this code since the Real * coords do not know their size
// in the Math module.
// If later we use eigen or Vector to implement this function
// there should be only one function in akantu::Math
// -> this is temporary for the release deadline which was so extended
inline Real triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3) {
/**
* @f{eqnarray*}{
* r &=& A / s \\
* A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)} \\
* s &=& \frac{a + b + c}{2}
* @f}
*/
auto a = Math::distance_3d(coord1, coord2);
auto b = Math::distance_3d(coord2, coord3);
auto c = Math::distance_3d(coord1, coord3);
auto s = (a + b + c) * 0.5;
return std::sqrt((s - a) * (s - b) * (s - c) / s);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_pentahedron_6>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
auto inradius_triangle_1 =
triangle_inradius(u0.storage(), u1.storage(), u2.storage());
auto inradius_triangle_2 =
triangle_inradius(u3.storage(), u4.storage(), u5.storage());
auto d1 = u3.distance(u0) * 0.5;
auto d2 = u5.distance(u2) * 0.5;
auto d3 = u4.distance(u1) * 0.5;
auto p =
2. * std::min({inradius_triangle_1, inradius_triangle_2, d1, d2, d3});
return p;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_point_1_inline_impl.hh b/src/fe_engine/element_classes/element_class_point_1_inline_impl.hh
index d9dd55e2a..188dacccd 100644
--- a/src/fe_engine/element_classes/element_class_point_1_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_point_1_inline_impl.hh
@@ -1,79 +1,86 @@
/**
* @file element_class_point_1_inline_impl.hh
*
+ * @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Feb 28 2020
*
* @brief Specialization of the element_class class for the type _point_1
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
x
(0)
@endverbatim
*
* @f{eqnarray*}{
* N1 &=& 1
* @f}
*
* @f{eqnarray*}{
* q_0 &=& 0
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_point_1, _gt_point, _itp_lagrange_point_1,
_ek_regular, 0, _git_point, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_point_1>::computeShapes(
__attribute__((unused)) const vector_type & natural_coords,
vector_type & N) {
N(0) = 1; /// N1(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_point_1>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
__attribute__((unused)) matrix_type & dnds) {}
/* -------------------------------------------------------------------------- */
template <>
inline void InterpolationElement<_itp_lagrange_point_1>::computeSpecialJacobian(
__attribute__((unused)) const Matrix<Real> & J, Real & jac) {
jac = 0.;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_point>::getInradius(__attribute__((unused))
const Matrix<Real> & coord) {
return 0.;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh b/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh
index bc4ebb244..b64037202 100644
--- a/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_quadrangle_4_inline_impl.hh
@@ -1,173 +1,179 @@
/**
* @file element_class_quadrangle_4_inline_impl.hh
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Specialization of the element_class class for the type _quadrangle_4
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\eta
^
(-1,1) | (1,1)
x---------x
| | |
| | |
--|---------|-----> \xi
| | |
| | |
x---------x
(-1,-1) | (1,-1)
@endverbatim
*
* @f[
* \begin{array}{lll}
* N1 = (1 - \xi) (1 - \eta) / 4
* & \frac{\partial N1}{\partial \xi} = - (1 - \eta) / 4
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi) / 4 \\
* N2 = (1 + \xi) (1 - \eta) / 4 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta) / 4
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi) / 4 \\
* N3 = (1 + \xi) (1 + \eta) / 4 \\
* & \frac{\partial N3}{\partial \xi} = (1 + \eta) / 4
* & \frac{\partial N3}{\partial \eta} = (1 + \xi) / 4 \\
* N4 = (1 - \xi) (1 + \eta) / 4
* & \frac{\partial N4}{\partial \xi} = - (1 + \eta) / 4
* & \frac{\partial N4}{\partial \eta} = (1 - \xi) / 4 \\
* \end{array}
* @f]
*
* @f{eqnarray*}{
* \xi_{q0} &=& 0 \qquad \eta_{q0} = 0
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_quadrangle_4, _gt_quadrangle_4,
_itp_lagrange_quadrangle_4, _ek_regular, 2,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_quadrangle_4>::computeShapes(
const vector_type & c, vector_type & N) {
N(0) = 1. / 4. * (1. - c(0)) * (1. - c(1)); /// N1(q_0)
N(1) = 1. / 4. * (1. + c(0)) * (1. - c(1)); /// N2(q_0)
N(2) = 1. / 4. * (1. + c(0)) * (1. + c(1)); /// N3(q_0)
N(3) = 1. / 4. * (1. - c(0)) * (1. + c(1)); /// N4(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_quadrangle_4>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial
* N4}{\partial \xi}\\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial
* N4}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1. / 4. * (1. - c(1));
dnds(0, 1) = 1. / 4. * (1. - c(1));
dnds(0, 2) = 1. / 4. * (1. + c(1));
dnds(0, 3) = -1. / 4. * (1. + c(1));
dnds(1, 0) = -1. / 4. * (1. - c(0));
dnds(1, 1) = -1. / 4. * (1. + c(0));
dnds(1, 2) = 1. / 4. * (1. + c(0));
dnds(1, 3) = 1. / 4. * (1. - c(0));
}
/* -------------------------------------------------------------------------- */
template<>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_quadrangle_4>::computeD2NDS2(
const vector_type & /*c*/, matrix_type & d2nds2) {
d2nds2.zero();
d2nds2(1, 0) = 1./4.;
d2nds2(1, 1) = -1./4.;
d2nds2(1, 2) = 1./4.;
d2nds2(1, 3) = -1./4.;
d2nds2(2, 0) = 1./4.;
d2nds2(2, 1) = -1./4.;
d2nds2(2, 2) = 1./4.;
d2nds2(2, 3) = -1./4.;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_quadrangle_4>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_quadrangle_4>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Real a = u0.distance(u1);
Real b = u1.distance(u2);
Real c = u2.distance(u3);
Real d = u3.distance(u0);
// Real septimetre = (a + b + c + d) / 2.;
// Real p = Math::distance_2d(coord + 0, coord + 4);
// Real q = Math::distance_2d(coord + 2, coord + 6);
// Real area = sqrt(4*(p*p * q*q) - (a*a + b*b + c*c + d*d)*(a*a + c*c - b*b -
// d*d)) / 4.;
// Real h = sqrt(area); // to get a length
// Real h = area / septimetre; // formula of inradius for circumscritable
// quadrelateral
Real h = std::min({a, b, c, d});
return h;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
index 28b5e9459..cb6f34429 100644
--- a/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_quadrangle_8_inline_impl.hh
@@ -1,184 +1,189 @@
/**
* @file element_class_quadrangle_8_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 18 2011
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Specialization of the ElementClass for the _quadrangle_8
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\eta
^
|
(-1,1) (0,1) (1,1)
x-------x-------x
| | |
| | |
| | |
(-1,0)| | |(1,0)
----x---------------X-----> \xi
| | |
| | |
| | |
| | |
x-------x-------x
(-1,-1) (0,-1) (1,-1)
|
@endverbatim
*
* @f[
* \begin{array}{lll}
* N1 = (1 - \xi) (1 - \eta)(- 1 - \xi - \eta) / 4
* & \frac{\partial N1}{\partial \xi} = (1 - \eta)(2 \xi + \eta) / 4
* & \frac{\partial N1}{\partial \eta} = (1 - \xi)(\xi + 2 \eta) / 4 \\
* N2 = (1 + \xi) (1 - \eta)(- 1 + \xi - \eta) / 4 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta)(2 \xi - \eta) / 4
* & \frac{\partial N2}{\partial \eta} = - (1 + \xi)(\xi - 2 \eta) / 4 \\
* N3 = (1 + \xi) (1 + \eta)(- 1 + \xi + \eta) / 4 \\
* & \frac{\partial N3}{\partial \xi} = (1 + \eta)(2 \xi + \eta) / 4
* & \frac{\partial N3}{\partial \eta} = (1 + \xi)(\xi + 2 \eta) / 4 \\
* N4 = (1 - \xi) (1 + \eta)(- 1 - \xi + \eta) / 4
* & \frac{\partial N4}{\partial \xi} = (1 + \eta)(2 \xi - \eta) / 4
* & \frac{\partial N4}{\partial \eta} = - (1 - \xi)(\xi - 2 \eta) / 4 \\
* N5 = (1 - \xi^2) (1 - \eta) / 2
* & \frac{\partial N1}{\partial \xi} = - \xi (1 - \eta)
* & \frac{\partial N1}{\partial \eta} = - (1 - \xi^2) / 2 \\
* N6 = (1 + \xi) (1 - \eta^2) / 2 \\
* & \frac{\partial N2}{\partial \xi} = (1 - \eta^2) / 2
* & \frac{\partial N2}{\partial \eta} = - \eta (1 + \xi) \\
* N7 = (1 - \xi^2) (1 + \eta) / 2 \\
* & \frac{\partial N3}{\partial \xi} = - \xi (1 + \eta)
* & \frac{\partial N3}{\partial \eta} = (1 - \xi^2) / 2 \\
* N8 = (1 - \xi) (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \xi} = - (1 - \eta^2) / 2
* & \frac{\partial N4}{\partial \eta} = - \eta (1 - \xi) \\
* \end{array}
* @f]
*
* @f{eqnarray*}{
* \xi_{q0} &=& 0 \qquad \eta_{q0} = 0
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_quadrangle_8, _gt_quadrangle_8,
_itp_serendip_quadrangle_8, _ek_regular, 2,
_git_segment, 3);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeShapes(
const vector_type & c, vector_type & N) {
/// Natural coordinates
const Real xi = c(0);
const Real eta = c(1);
N(0) = .25 * (1 - xi) * (1 - eta) * (-1 - xi - eta);
N(1) = .25 * (1 + xi) * (1 - eta) * (-1 + xi - eta);
N(2) = .25 * (1 + xi) * (1 + eta) * (-1 + xi + eta);
N(3) = .25 * (1 - xi) * (1 + eta) * (-1 - xi + eta);
N(4) = .5 * (1 - xi * xi) * (1 - eta);
N(5) = .5 * (1 + xi) * (1 - eta * eta);
N(6) = .5 * (1 - xi * xi) * (1 + eta);
N(7) = .5 * (1 - xi) * (1 - eta * eta);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_serendip_quadrangle_8>::computeDNDS(
const vector_type & c, matrix_type & dnds) {
const Real xi = c(0);
const Real eta = c(1);
/// dN/dxi
dnds(0, 0) = .25 * (1 - eta) * (2 * xi + eta);
dnds(0, 1) = .25 * (1 - eta) * (2 * xi - eta);
dnds(0, 2) = .25 * (1 + eta) * (2 * xi + eta);
dnds(0, 3) = .25 * (1 + eta) * (2 * xi - eta);
dnds(0, 4) = -xi * (1 - eta);
dnds(0, 5) = .5 * (1 - eta * eta);
dnds(0, 6) = -xi * (1 + eta);
dnds(0, 7) = -.5 * (1 - eta * eta);
/// dN/deta
dnds(1, 0) = .25 * (1 - xi) * (2 * eta + xi);
dnds(1, 1) = .25 * (1 + xi) * (2 * eta - xi);
dnds(1, 2) = .25 * (1 + xi) * (2 * eta + xi);
dnds(1, 3) = .25 * (1 - xi) * (2 * eta - xi);
dnds(1, 4) = -.5 * (1 - xi * xi);
dnds(1, 5) = -eta * (1 + xi);
dnds(1, 6) = .5 * (1 - xi * xi);
dnds(1, 7) = -eta * (1 - xi);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_quadrangle_8>::getInradius(const Matrix<Real> & coord) {
Vector<Real> u0 = coord(0);
Vector<Real> u1 = coord(1);
Vector<Real> u2 = coord(2);
Vector<Real> u3 = coord(3);
Vector<Real> u4 = coord(4);
Vector<Real> u5 = coord(5);
Vector<Real> u6 = coord(6);
Vector<Real> u7 = coord(7);
auto a = u0.distance(u4);
auto b = u4.distance(u1);
auto h = std::min(a, b);
a = u1.distance(u5);
b = u5.distance(u2);
h = std::min(h, std::min(a, b));
a = u2.distance(u6);
b = u6.distance(u3);
h = std::min(h, std::min(a, b));
a = u3.distance(u7);
b = u7.distance(u0);
h = std::min(h, std::min(a, b));
return h;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_serendip_quadrangle_8>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_segment_2_inline_impl.hh b/src/fe_engine/element_classes/element_class_segment_2_inline_impl.hh
index 327c12940..9f0d2252e 100644
--- a/src/fe_engine/element_classes/element_class_segment_2_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_segment_2_inline_impl.hh
@@ -1,116 +1,123 @@
/**
* @file element_class_segment_2_inline_impl.hh
*
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Specialization of the element_class class for the type _segment_2
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
q
--x--------|--------x---> x
-1 0 1
@endverbatim
*
* @f{eqnarray*}{
* w_1(x) &=& 1/2(1 - x) \\
* w_2(x) &=& 1/2(1 + x)
* @f}
*
* @f{eqnarray*}{
* x_{q} &=& 0
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_segment_2, _gt_segment_2,
_itp_lagrange_segment_2, _ek_regular, 1,
_git_segment, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_segment_2>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// natural coordinate
Real c = natural_coords(0);
/// shape functions
N(0) = 0.5 * (1 - c);
N(1) = 0.5 * (1 + c);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_segment_2>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/// dN1/de
dnds(0, 0) = -.5;
/// dN2/de
dnds(0, 1) = .5;
}
/* -------------------------------------------------------------------------- */
template<>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_segment_2>::computeD2NDS2(
const vector_type & /*natural_coords*/, matrix_type & d2nds2) {
d2nds2.zero();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_segment_2>::computeSpecialJacobian(
const Matrix<Real> & dxds, Real & jac) {
jac = dxds.norm<L_2>();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_segment_2>::getInradius(const Matrix<Real> & coord) {
Vector<Real> a(coord(0));
Vector<Real> b(coord(1));
return a.distance(b);
}
// /* --------------------------------------------------------------------------
// */
// template<> inline bool ElementClass<_segment_2>::contains(const Vector<Real>
// & natural_coords) {
// if (natural_coords(0) < -1.) return false;
// if (natural_coords(0) > 1.) return false;
// return true;
// }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_segment_3_inline_impl.hh b/src/fe_engine/element_classes/element_class_segment_3_inline_impl.hh
index b08d4ab56..42e13e196 100644
--- a/src/fe_engine/element_classes/element_class_segment_3_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_segment_3_inline_impl.hh
@@ -1,106 +1,111 @@
/**
* @file element_class_segment_3_inline_impl.hh
*
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Specialization of the element_class class for the type _segment_3
*
- * \section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
-1 0 1
-----x---------x---------x-----> x
1 3 2
@endverbatim
*
*
* @f[
* \begin{array}{lll}
* x_{1} = -1 & x_{2} = 1 & x_{3} = 0
* \end{array}
* @f]
*
* @f[
* \begin{array}{ll}
* w_1(x) = \frac{x}{2}(x - 1) & w'_1(x) = x - \frac{1}{2}\\
* w_2(x) = \frac{x}{2}(x + 1) & w'_2(x) = x + \frac{1}{2}\\
* w_3(x) = 1-x^2 & w'_3(x) = -2x
* \end{array}
* @f]
*
* @f[
* \begin{array}{ll}
* x_{q1} = -1/\sqrt{3} & x_{q2} = 1/\sqrt{3}
* \end{array}
* @f]
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_segment_3, _gt_segment_3,
_itp_lagrange_segment_3, _ek_regular, 1,
_git_segment, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_segment_3>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
Real c = natural_coords(0);
N(0) = (c - 1) * c / 2;
N(1) = (c + 1) * c / 2;
N(2) = 1 - c * c;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_segment_3>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
Real c = natural_coords(0);
dnds(0, 0) = c - .5;
dnds(0, 1) = c + .5;
dnds(0, 2) = -2 * c;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_segment_3>::computeSpecialJacobian(
const Matrix<Real> & dxds, Real & jac) {
jac = Math::norm2(dxds.storage());
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_segment_3>::getInradius(const Matrix<Real> & coord) {
Real dist1 = std::abs(coord(0, 0) - coord(0, 1));
Real dist2 = std::abs(coord(0, 1) - coord(0, 2));
return std::min(dist1, dist2);
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.hh b/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.hh
index bc302c0bc..aa2dd82c4 100644
--- a/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_tetrahedron_10_inline_impl.hh
@@ -1,277 +1,284 @@
/**
* @file element_class_tetrahedron_10_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Feb 07 2020
*
* @brief Specialization of the element_class class for the type
* _tetrahedron_10
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\zeta
^
|
(0,0,1)
x
|` .
| ` .
| ` .
| ` . (0,0.5,0.5)
| ` x.
| q4 o ` . \eta
| ` . -,
(0,0,0.5) x ` x (0.5,0,0.5) -
| ` x-(0,1,0)
| q3 o` - '
| (0,0.5,0) - ` '
| x- ` x (0.5,0.5,0)
| q1 o - o q2` '
| - ` '
| - ` '
x---------------x--------------` x-----> \xi
(0,0,0) (0.5,0,0) (1,0,0)
@endverbatim
*
*
* @f[
* \begin{array}{lll}
* \xi_{0} = 0 & \eta_{0} = 0 & \zeta_{0} = 0 \\
* \xi_{1} = 1 & \eta_{1} = 0 & \zeta_{1} = 0 \\
* \xi_{2} = 0 & \eta_{2} = 1 & \zeta_{2} = 0 \\
* \xi_{3} = 0 & \eta_{3} = 0 & \zeta_{3} = 1 \\
* \xi_{4} = 1/2 & \eta_{4} = 0 & \zeta_{4} = 0 \\
* \xi_{5} = 1/2 & \eta_{5} = 1/2 & \zeta_{5} = 0 \\
* \xi_{6} = 0 & \eta_{6} = 1/2 & \zeta_{6} = 0 \\
* \xi_{7} = 0 & \eta_{7} = 0 & \zeta_{7} = 1/2 \\
* \xi_{8} = 1/2 & \eta_{8} = 0 & \zeta_{8} = 1/2 \\
* \xi_{9} = 0 & \eta_{9} = 1/2 & \zeta_{9} = 1/2
* \end{array}
* @f]
*
* @f[
* \begin{array}{llll}
* N1 = (1 - \xi - \eta - \zeta) (1 - 2 \xi - 2 \eta - 2 \zeta)
* & \frac{\partial N1}{\partial \xi} = 4 \xi + 4 \eta + 4 \zeta -
3
* & \frac{\partial N1}{\partial \eta} = 4 \xi + 4 \eta + 4 \zeta -
3
* & \frac{\partial N1}{\partial \zeta} = 4 \xi + 4 \eta + 4 \zeta -
3 \\
* N2 = \xi (2 \xi - 1)
* & \frac{\partial N2}{\partial \xi} = 4 \xi - 1
* & \frac{\partial N2}{\partial \eta} = 0
* & \frac{\partial N2}{\partial \zeta} = 0 \\
* N3 = \eta (2 \eta - 1)
* & \frac{\partial N3}{\partial \xi} = 0
* & \frac{\partial N3}{\partial \eta} = 4 \eta - 1
* & \frac{\partial N3}{\partial \zeta} = 0 \\
* N4 = \zeta (2 \zeta - 1)
* & \frac{\partial N4}{\partial \xi} = 0
* & \frac{\partial N4}{\partial \eta} = 0
* & \frac{\partial N4}{\partial \zeta} = 4 \zeta - 1 \\
* N5 = 4 \xi (1 - \xi - \eta - \zeta)
* & \frac{\partial N5}{\partial \xi} = 4 - 8 \xi - 4 \eta - 4
\zeta
* & \frac{\partial N5}{\partial \eta} = -4 \xi
* & \frac{\partial N5}{\partial \zeta} = -4 \xi \\
* N6 = 4 \xi \eta
* & \frac{\partial N6}{\partial \xi} = 4 \eta
* & \frac{\partial N6}{\partial \eta} = 4 \xi
* & \frac{\partial N6}{\partial \zeta} = 0 \\
* N7 = 4 \eta (1 - \xi - \eta - \zeta)
* & \frac{\partial N7}{\partial \xi} = -4 \eta
* & \frac{\partial N7}{\partial \eta} = 4 - 4 \xi - 8 \eta - 4
\zeta
* & \frac{\partial N7}{\partial \zeta} = -4 \eta \\
* N8 = 4 \zeta (1 - \xi - \eta - \zeta)
* & \frac{\partial N8}{\partial \xi} = -4 \zeta
* & \frac{\partial N8}{\partial \eta} = -4 \zeta
* & \frac{\partial N8}{\partial \zeta} = 4 - 4 \xi - 4 \eta - 8
\zeta \\
* N9 = 4 \zeta \xi
* & \frac{\partial N9}{\partial \xi} = 4 \zeta
* & \frac{\partial N9}{\partial \eta} = 0
* & \frac{\partial N9}{\partial \zeta} = 4 \xi \\
* N10 = 4 \eta \zeta
* & \frac{\partial N10}{\partial \xi} = 0
* & \frac{\partial N10}{\partial \eta} = 4 \zeta
* & \frac{\partial N10}{\partial \zeta} = 4 \eta \\
* \end{array}
* @f]
*
* @f[
* a = \frac{5 - \sqrt{5}}{20}\\
* b = \frac{5 + 3 \sqrt{5}}{20}
* \begin{array}{lll}
* \xi_{q_0} = a & \eta_{q_0} = a & \zeta_{q_0} = a \\
* \xi_{q_1} = b & \eta_{q_1} = a & \zeta_{q_1} = a \\
* \xi_{q_2} = a & \eta_{q_2} = b & \zeta_{q_2} = a \\
* \xi_{q_3} = a & \eta_{q_3} = a & \zeta_{q_3} = b
* \end{array}
* @f]
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_tetrahedron_10, _gt_tetrahedron_10,
_itp_lagrange_tetrahedron_10, _ek_regular,
3, _git_tetrahedron, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_10>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
Real zeta = natural_coords(2);
Real sum = xi + eta + zeta;
Real c0 = 1 - sum;
Real c1 = 1 - 2 * sum;
Real c2 = 2 * xi - 1;
Real c3 = 2 * eta - 1;
Real c4 = 2 * zeta - 1;
/// Shape functions
N(0) = c0 * c1;
N(1) = xi * c2;
N(2) = eta * c3;
N(3) = zeta * c4;
N(4) = 4 * xi * c0;
N(5) = 4 * xi * eta;
N(6) = 4 * eta * c0;
N(7) = 4 * zeta * c0;
N(8) = 4 * xi * zeta;
N(9) = 4 * eta * zeta;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_10>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
/**
* \f[
* dnds = \left(
* \begin{array}{cccccccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial N4}{\partial
* \xi}
* & \frac{\partial N5}{\partial \xi} & \frac{\partial N6}{\partial
* \xi}
* & \frac{\partial N7}{\partial \xi} & \frac{\partial N8}{\partial
* \xi}
* & \frac{\partial N9}{\partial \xi} & \frac{\partial
* N10}{\partial \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial N4}{\partial
* \eta}
* & \frac{\partial N5}{\partial \eta} & \frac{\partial N6}{\partial
* \eta}
* & \frac{\partial N7}{\partial \eta} & \frac{\partial N8}{\partial
* \eta}
* & \frac{\partial N9}{\partial \eta} & \frac{\partial
* N10}{\partial \eta} \\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial N4}{\partial
* \zeta}
* & \frac{\partial N5}{\partial \zeta} & \frac{\partial N6}{\partial
* \zeta}
* & \frac{\partial N7}{\partial \zeta} & \frac{\partial N8}{\partial
* \zeta}
* & \frac{\partial N9}{\partial \zeta} & \frac{\partial
* N10}{\partial \zeta}
* \end{array}
* \right)
* \f]
*/
/// Natural coordinates
Real xi = natural_coords(0);
Real eta = natural_coords(1);
Real zeta = natural_coords(2);
Real sum = xi + eta + zeta;
/// \frac{\partial N_i}{\partial \xi}
dnds(0, 0) = 4 * sum - 3;
dnds(0, 1) = 4 * xi - 1;
dnds(0, 2) = 0;
dnds(0, 3) = 0;
dnds(0, 4) = 4 * (1 - sum - xi);
dnds(0, 5) = 4 * eta;
dnds(0, 6) = -4 * eta;
dnds(0, 7) = -4 * zeta;
dnds(0, 8) = 4 * zeta;
dnds(0, 9) = 0;
/// \frac{\partial N_i}{\partial \eta}
dnds(1, 0) = 4 * sum - 3;
dnds(1, 1) = 0;
dnds(1, 2) = 4 * eta - 1;
dnds(1, 3) = 0;
dnds(1, 4) = -4 * xi;
dnds(1, 5) = 4 * xi;
dnds(1, 6) = 4 * (1 - sum - eta);
dnds(1, 7) = -4 * zeta;
dnds(1, 8) = 0;
dnds(1, 9) = 4 * zeta;
/// \frac{\partial N_i}{\partial \zeta}
dnds(2, 0) = 4 * sum - 3;
dnds(2, 1) = 0;
dnds(2, 2) = 0;
dnds(2, 3) = 4 * zeta - 1;
dnds(2, 4) = -4 * xi;
dnds(2, 5) = 0;
dnds(2, 6) = -4 * eta;
dnds(2, 7) = 4 * (1 - sum - zeta);
dnds(2, 8) = 4 * xi;
dnds(2, 9) = 4 * eta;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real GeometricalElement<_gt_tetrahedron_10>::getInradius(
const Matrix<Real> & coord) {
// Only take the four corner tetrahedra
UInt tetrahedra[4][4] = {
{0, 4, 6, 7}, {4, 1, 5, 8}, {6, 5, 2, 9}, {7, 8, 9, 3}};
Real inradius = std::numeric_limits<Real>::max();
for (UInt t = 0; t < 4; t++) {
Real ir = Math::tetrahedron_inradius(
coord(tetrahedra[t][0]).storage(), coord(tetrahedra[t][1]).storage(),
coord(tetrahedra[t][2]).storage(), coord(tetrahedra[t][3]).storage());
inradius = std::min(ir, inradius);
}
return 2. * inradius;
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.hh b/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.hh
index 3027939c4..8daebbd39 100644
--- a/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_tetrahedron_4_inline_impl.hh
@@ -1,138 +1,143 @@
/**
* @file element_class_tetrahedron_4_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Wed Jun 17 2020
*
* @brief Specialization of the element_class class for the type _tetrahedron_4
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\eta
^
|
x (0,0,1,0)
|`
| ` ° \zeta
| ` ° -
| ` x (0,0,0,1)
| q.` - '
| -` '
| - ` '
| - ` '
x------------------x-----> \xi
(1,0,0,0) (0,1,0,0)
@endverbatim
*
* @f{eqnarray*}{
* N1 &=& 1 - \xi - \eta - \zeta \\
* N2 &=& \xi \\
* N3 &=& \eta \\
* N4 &=& \zeta
* @f}
*
* @f[
* \xi_{q0} = 1/4 \qquad \eta_{q0} = 1/4 \qquad \zeta_{q0} = 1/4
* @f]
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_tetrahedron_4, _gt_tetrahedron_4,
_itp_lagrange_tetrahedron_4, _ek_regular,
3, _git_tetrahedron, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_4>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
Real c0 = 1 - natural_coords(0) - natural_coords(1) -
natural_coords(2); /// @f$ c0 = 1 - \xi - \eta - \zeta @f$
Real c1 = natural_coords(1); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(2); /// @f$ c2 = \eta @f$
Real c3 = natural_coords(0); /// @f$ c3 = \zeta @f$
N(0) = c0;
N(1) = c1;
N(2) = c2;
N(3) = c3;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_tetrahedron_4>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi}
* & \frac{\partial N3}{\partial \xi} & \frac{\partial N4}{\partial
* \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta}
* & \frac{\partial N3}{\partial \eta} & \frac{\partial N4}{\partial
* \eta} \\
* \frac{\partial N1}{\partial \zeta} & \frac{\partial N2}{\partial
* \zeta}
* & \frac{\partial N3}{\partial \zeta} & \frac{\partial N4}{\partial
* \zeta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1.;
dnds(1, 0) = -1.;
dnds(2, 0) = -1.;
dnds(0, 1) = 0.;
dnds(1, 1) = 1.;
dnds(2, 1) = 0.;
dnds(0, 2) = 0.;
dnds(1, 2) = 0.;
dnds(2, 2) = 1.;
dnds(0, 3) = 1.;
dnds(1, 3) = 0.;
dnds(2, 3) = 0.;
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_tetrahedron_4>::getInradius(const Matrix<Real> & coord) {
return 2. * Math::tetrahedron_inradius(coord(0).storage(), coord(1).storage(),
coord(2).storage(),
coord(3).storage());
}
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.hh b/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.hh
index f8d2c1597..32ae9db2b 100644
--- a/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_triangle_3_inline_impl.hh
@@ -1,141 +1,148 @@
/**
* @file element_class_triangle_3_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Specialization of the element_class class for the type _triangle_3
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\eta
^
|
x (0,0,1)
|`
| `
| q `
| ° `
x--------x-----> \xi
(1,0,0) (0,1,0)
@endverbatim
*
* @f{eqnarray*}{
* N1 &=& 1 - \xi - \eta \\
* N2 &=& \xi \\
* N3 &=& \eta
* @f}
*
* @f{eqnarray*}{
* \xi_{q0} &=& 1/3 \qquad \eta_{q0} = 1/3
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_triangle_3, _gt_triangle_3,
_itp_lagrange_triangle_3, _ek_regular, 2,
_git_triangle, 1);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_triangle_3>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
N(0) = c0; /// N1(q_0)
N(1) = c1; /// N2(q_0)
N(2) = c2; /// N3(q_0)
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_triangle_3>::computeDNDS(
__attribute__((unused)) const vector_type & natural_coords,
matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi} & \frac{\partial N2}{\partial
* \xi} & \frac{\partial N3}{\partial \xi} \\
* \frac{\partial N1}{\partial \eta} & \frac{\partial N2}{\partial
* \eta} & \frac{\partial N3}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
dnds(0, 0) = -1.;
dnds(0, 1) = 1.;
dnds(0, 2) = 0.;
dnds(1, 0) = -1.;
dnds(1, 1) = 0.;
dnds(1, 2) = 1.;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_triangle_3>::computeD2NDS2(
const vector_type & /*natural_coords*/, matrix_type & d2nds2) {
d2nds2.zero();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_triangle_3>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_triangle_3>::getInradius(const Matrix<Real> & coord) {
return 2. * Math::triangle_inradius(coord(0), coord(1), coord(2));
}
/* -------------------------------------------------------------------------- */
// template<> inline bool ElementClass<_triangle_3>::contains(const Vector<Real>
// & natural_coords) {
// if (natural_coords[0] < 0.) return false;
// if (natural_coords[0] > 1.) return false;
// if (natural_coords[1] < 0.) return false;
// if (natural_coords[1] > 1.) return false;
// if (natural_coords[0]+natural_coords[1] > 1.) return false;
// return true;
// }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.hh b/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.hh
index 770b51aad..db4245376 100644
--- a/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.hh
+++ b/src/fe_engine/element_classes/element_class_triangle_6_inline_impl.hh
@@ -1,199 +1,206 @@
/**
* @file element_class_triangle_6_inline_impl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 16 2010
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Fri Feb 28 2020
*
* @brief Specialization of the element_class class for the type _triangle_6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- terms of the GNU Lesser General Public License as published by the Free
- Software Foundation, either version 3 of the License, or (at your option) any
- later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
- PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
+ */
+
+/**
* @verbatim
\eta
^
|
x 2
| `
| `
| . `
| q2 `
5 x x 4
| `
| `
| .q0 q1. `
| `
x---------x---------x-----> \xi
0 3 1
@endverbatim
*
*
* @f[
* \begin{array}{ll}
* \xi_{0} = 0 & \eta_{0} = 0 \\
* \xi_{1} = 1 & \eta_{1} = 0 \\
* \xi_{2} = 0 & \eta_{2} = 1 \\
* \xi_{3} = 1/2 & \eta_{3} = 0 \\
* \xi_{4} = 1/2 & \eta_{4} = 1/2 \\
* \xi_{5} = 0 & \eta_{5} = 1/2
* \end{array}
* @f]
*
* @f[
* \begin{array}{lll}
* N1 = -(1 - \xi - \eta) (1 - 2 (1 - \xi - \eta))
* & \frac{\partial N1}{\partial \xi} = 1 - 4(1 - \xi - \eta)
* & \frac{\partial N1}{\partial \eta} = 1 - 4(1 - \xi - \eta) \\
* N2 = - \xi (1 - 2 \xi)
* & \frac{\partial N2}{\partial \xi} = - 1 + 4 \xi
* & \frac{\partial N2}{\partial \eta} = 0 \\
* N3 = - \eta (1 - 2 \eta)
* & \frac{\partial N3}{\partial \xi} = 0
* & \frac{\partial N3}{\partial \eta} = - 1 + 4 \eta \\
* N4 = 4 \xi (1 - \xi - \eta)
* & \frac{\partial N4}{\partial \xi} = 4 (1 - 2 \xi - \eta)
* & \frac{\partial N4}{\partial \eta} = - 4 \xi \\
* N5 = 4 \xi \eta
* & \frac{\partial N5}{\partial \xi} = 4 \eta
* & \frac{\partial N5}{\partial \eta} = 4 \xi \\
* N6 = 4 \eta (1 - \xi - \eta)
* & \frac{\partial N6}{\partial \xi} = - 4 \eta
* & \frac{\partial N6}{\partial \eta} = 4 (1 - \xi - 2 \eta)
* \end{array}
* @f]
*
* @f{eqnarray*}{
* \xi_{q0} &=& 1/6 \qquad \eta_{q0} = 1/6 \\
* \xi_{q1} &=& 2/3 \qquad \eta_{q1} = 1/6 \\
* \xi_{q2} &=& 1/6 \qquad \eta_{q2} = 2/3
* @f}
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_triangle_6, _gt_triangle_6,
_itp_lagrange_triangle_6, _ek_regular, 2,
_git_triangle, 2);
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline void InterpolationElement<_itp_lagrange_triangle_6>::computeShapes(
const vector_type & natural_coords, vector_type & N) {
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
N(0) = c0 * (2 * c0 - 1.);
N(1) = c1 * (2 * c1 - 1.);
N(2) = c2 * (2 * c2 - 1.);
N(3) = 4 * c0 * c1;
N(4) = 4 * c1 * c2;
N(5) = 4 * c2 * c0;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type, class matrix_type>
inline void InterpolationElement<_itp_lagrange_triangle_6>::computeDNDS(
const vector_type & natural_coords, matrix_type & dnds) {
/**
* @f[
* dnds = \left(
* \begin{array}{cccccc}
* \frac{\partial N1}{\partial \xi}
* & \frac{\partial N2}{\partial \xi}
* & \frac{\partial N3}{\partial \xi}
* & \frac{\partial N4}{\partial \xi}
* & \frac{\partial N5}{\partial \xi}
* & \frac{\partial N6}{\partial \xi} \\
*
* \frac{\partial N1}{\partial \eta}
* & \frac{\partial N2}{\partial \eta}
* & \frac{\partial N3}{\partial \eta}
* & \frac{\partial N4}{\partial \eta}
* & \frac{\partial N5}{\partial \eta}
* & \frac{\partial N6}{\partial \eta}
* \end{array}
* \right)
* @f]
*/
/// Natural coordinates
Real c0 =
1 - natural_coords(0) - natural_coords(1); /// @f$ c0 = 1 - \xi - \eta @f$
Real c1 = natural_coords(0); /// @f$ c1 = \xi @f$
Real c2 = natural_coords(1); /// @f$ c2 = \eta @f$
dnds(0, 0) = 1 - 4 * c0;
dnds(0, 1) = 4 * c1 - 1.;
dnds(0, 2) = 0.;
dnds(0, 3) = 4 * (c0 - c1);
dnds(0, 4) = 4 * c2;
dnds(0, 5) = -4 * c2;
dnds(1, 0) = 1 - 4 * c0;
dnds(1, 1) = 0.;
dnds(1, 2) = 4 * c2 - 1.;
dnds(1, 3) = -4 * c1;
dnds(1, 4) = 4 * c1;
dnds(1, 5) = 4 * (c0 - c2);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
InterpolationElement<_itp_lagrange_triangle_6>::computeSpecialJacobian(
const Matrix<Real> & J, Real & jac) {
Vector<Real> vprod(J.cols());
Matrix<Real> Jt(J.transpose(), true);
vprod.crossProduct(Jt(0), Jt(1));
jac = vprod.norm();
}
/* -------------------------------------------------------------------------- */
template <>
inline Real
GeometricalElement<_gt_triangle_6>::getInradius(const Matrix<Real> & coord) {
UInt triangles[4][3] = {{0, 3, 5}, {3, 1, 4}, {3, 4, 5}, {5, 4, 2}};
Real inradius = std::numeric_limits<Real>::max();
for (UInt t = 0; t < 4; t++) {
auto ir = Math::triangle_inradius(coord(triangles[t][0]),
coord(triangles[t][1]),
coord(triangles[t][2]));
inradius = std::min(ir, inradius);
}
return 2. * inradius;
}
/* -------------------------------------------------------------------------- */
// template<> inline bool ElementClass<_triangle_6>::contains(const Vector<Real>
// & natural_coords) {
// return ElementClass<_triangle_3>::contains(natural_coords);
// }
} // namespace akantu
diff --git a/src/fe_engine/element_type_conversion.hh b/src/fe_engine/element_type_conversion.hh
index fc9f7da43..8b3e817ad 100644
--- a/src/fe_engine/element_type_conversion.hh
+++ b/src/fe_engine/element_type_conversion.hh
@@ -1,57 +1,59 @@
/**
* @file element_type_conversion.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Aug 11 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief conversion between different types
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_TYPE_CONVERSION_HH_
#define AKANTU_ELEMENT_TYPE_CONVERSION_HH_
namespace akantu {
template <class InType, class OutType>
OutType convertType(InType /*unused*/) {
return OutType();
}
template <>
inline InterpolationType
convertType<ElementType, InterpolationType>(ElementType type) {
InterpolationType itp_type = _itp_not_defined;
#define GET_ITP(type) itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_ITP);
#undef GET_ITP
return itp_type;
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_TYPE_CONVERSION_HH_ */
diff --git a/src/fe_engine/fe_engine.cc b/src/fe_engine/fe_engine.cc
index cb50656b5..cb8ed6117 100644
--- a/src/fe_engine/fe_engine.cc
+++ b/src/fe_engine/fe_engine.cc
@@ -1,89 +1,91 @@
/**
* @file fe_engine.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Fri Feb 28 2020
*
* @brief Implementation of the FEEngine class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FEEngine::FEEngine(Mesh & mesh, UInt element_dimension, const ID & id)
: mesh(mesh),
normals_on_integration_points("normals_on_quad_points", id) {
AKANTU_DEBUG_IN();
this->element_dimension = (element_dimension != _all_dimensions)
? element_dimension
: mesh.getSpatialDimension();
this->mesh.registerEventHandler(*this, _ehp_fe_engine);
init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::init() {}
/* -------------------------------------------------------------------------- */
FEEngine::~FEEngine() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
typename FEEngine::ElementTypesIteratorHelper
FEEngine::elementTypes(UInt dim, GhostType ghost_type, ElementKind kind) const {
return this->getIntegratorInterface().getJacobians().elementTypes(
dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
void FEEngine::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "FEEngine [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + element dimension : " << element_dimension
<< std::endl;
stream << space << " + mesh [" << std::endl;
mesh.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/fe_engine.hh b/src/fe_engine/fe_engine.hh
index 201a1aac7..7a1739b8c 100644
--- a/src/fe_engine/fe_engine.hh
+++ b/src/fe_engine/fe_engine.hh
@@ -1,378 +1,385 @@
/**
* @file fe_engine.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri May 14 2021
*
* @brief FEM class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FE_ENGINE_HH_
#define AKANTU_FE_ENGINE_HH_
namespace akantu {
class Mesh;
class Integrator;
class ShapeFunctions;
class DOFManager;
class Element;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* The generic FEEngine class derived in a FEEngineTemplate class
* containing the
* shape functions and the integration method
*/
class FEEngine : public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FEEngine(Mesh & mesh, UInt element_dimension = _all_dimensions,
const ID & id = "fem");
~FEEngine() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
virtual void
initShapeFunctions(GhostType ghost_type = _not_ghost) = 0;
/// extract the nodal values and store them per element
template <typename T>
static void extractNodalToElementField(
const Mesh & mesh, const Array<T> & nodal_f, Array<T> & elemental_f,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/// filter a field
template <typename T>
static void
filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
Array<T> & filtered_f, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
virtual void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate a scalar value f on all elements of type "type"
virtual Real
integrate(const Array<Real> & f, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate f for all integration points of type "type" but don't sum over
/// all integration points
virtual void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate one element scalar value on all elements of type "type"
virtual Real integrate(const Vector<Real> & f, ElementType type,
UInt index,
GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* compatibility with old FEEngine fashion */
/* ------------------------------------------------------------------------ */
/// get the number of integration points
virtual UInt
getNbIntegrationPoints(ElementType type,
GhostType ghost_type = _not_ghost) const = 0;
/// get the precomputed shapes
const virtual Array<Real> &
getShapes(ElementType type, GhostType ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get the derivatives of shapes
const virtual Array<Real> &
getShapesDerivatives(ElementType type,
GhostType ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get integration points
const virtual Matrix<Real> &
getIntegrationPoints(ElementType type,
GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// Compute the gradient nablauq on the integration points of an element type
/// from nodal values u
virtual void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
UInt nb_degree_of_freedom, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of an element type
/// -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of many element
/// types -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// pre multiplies a tensor by the shapes derivaties
virtual void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left and right multiplies a tensor by the shapes derivaties
virtual void
computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left multiples a vector by the shape functions
virtual void
computeNtb(const Array<Real> & bs, Array<Real> & Ntbs,
ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// left and right multiplies a tensor by the shapes
virtual void
computeNtbN(const Array<Real> & bs, Array<Real> & NtbNs,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Compute the interpolation point position in the global coordinates for
/// many element types
virtual void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & integration_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// Compute the interpolation point position in the global coordinates for an
/// element type
virtual void computeIntegrationPointsCoordinates(
Array<Real> & integration_points_coordinates, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
virtual void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & integration_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> &
integration_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate on a phyiscal point inside an element
virtual void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const = 0;
/// compute the shape on a provided point
virtual void
computeShapes(const Vector<Real> & real_coords, UInt elem,
ElementType type, Vector<Real> & shapes,
GhostType ghost_type = _not_ghost) const = 0;
/// compute the shape derivatives on a provided point
virtual void
computeShapeDerivatives(const Vector<Real> & real_coords, UInt element,
ElementType type,
Matrix<Real> & shape_derivatives,
GhostType ghost_type = _not_ghost) const = 0;
/// assembles the lumped version of @f[ \int N^t rho N @f]
virtual void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type = _not_ghost) const = 0;
/// assembles the matrix @f[ \int N^t rho N @f]
virtual void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
GhostType ghost_type = _not_ghost) = 0;
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const Array<Real> & /*field*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const Array<Real> & /*field*/, Array<Real> & /*normal*/,
ElementType /*type*/,
GhostType /*ghost_type*/ = _not_ghost) const {
AKANTU_TO_IMPLEMENT();
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/// initialise the class
void init();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/// get the dimension of the element handeled by this fe_engine object
AKANTU_GET_MACRO(ElementDimension, element_dimension, UInt);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO(Mesh, mesh, const Mesh &);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO_NOT_CONST(Mesh, mesh, Mesh &);
/// get the in-radius of an element
static inline Real getElementInradius(const Matrix<Real> & coord,
ElementType type);
+ inline Real getElementInradius(const Element & element) const;
+
/// get the normals on integration points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NormalsOnIntegrationPoints,
normals_on_integration_points, Real);
/// get cohesive element type for a given facet type
static inline ElementType
getCohesiveElementType(ElementType type_facet);
/// get igfem element type for a given regular type
static inline Vector<ElementType>
getIGFEMElementTypes(ElementType type);
/// get the interpolation element associated to an element type
static inline InterpolationType
getInterpolationType(ElementType el_type);
/// get the shape function class (probably useless: see getShapeFunction in
/// fe_engine_template.hh)
virtual const ShapeFunctions & getShapeFunctionsInterface() const = 0;
/// get the integrator class (probably useless: see getIntegrator in
/// fe_engine_template.hh)
virtual const Integrator & getIntegratorInterface() const = 0;
AKANTU_GET_MACRO(ID, id, ID);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// spatial dimension of the problem
UInt element_dimension;
/// the mesh on which all computation are made
Mesh & mesh;
/// normals at integration points
ElementTypeMapArray<Real> normals_on_integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const FEEngine & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "fe_engine_inline_impl.hh"
#include "fe_engine_template.hh"
#endif /* AKANTU_FE_ENGINE_HH_ */
diff --git a/src/fe_engine/fe_engine_inline_impl.hh b/src/fe_engine/fe_engine_inline_impl.hh
index 87968ecaf..763c4ba1e 100644
--- a/src/fe_engine/fe_engine_inline_impl.hh
+++ b/src/fe_engine/fe_engine_inline_impl.hh
@@ -1,190 +1,208 @@
/**
* @file fe_engine_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Implementation of the inline functions of the FEEngine Class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FE_ENGINE_INLINE_IMPL_HH_
#define AKANTU_FE_ENGINE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real FEEngine::getElementInradius(const Matrix<Real> & coord,
ElementType type) {
Real inradius = 0;
#define GET_INRADIUS(type) inradius = ElementClass<type>::getInradius(coord);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_INRADIUS);
#undef GET_INRADIUS
return inradius;
}
+/* -------------------------------------------------------------------------- */
+inline Real FEEngine::getElementInradius(const Element & element) const {
+ auto spatial_dimension = mesh.getSpatialDimension();
+ auto positions = make_view(mesh.getNodes(), spatial_dimension).begin();
+ auto connectivity = mesh.getConnectivities().get(element);
+
+ Matrix<Real> coords(spatial_dimension, connectivity.size());
+
+ for(auto && data : zip(connectivity, coords)) {
+ std::get<1>(data) = positions[std::get<0>(data)];
+ }
+
+ return getElementInradius(coords, element.type);
+}
+
+
/* -------------------------------------------------------------------------- */
inline InterpolationType FEEngine::getInterpolationType(ElementType type) {
return convertType<ElementType, InterpolationType>(type);
}
/* -------------------------------------------------------------------------- */
/// @todo rewrite this function in order to get the cohesive element
/// type directly from the facet
#if defined(AKANTU_COHESIVE_ELEMENT)
inline ElementType FEEngine::getCohesiveElementType(ElementType type) {
ElementType ctype;
#define GET_COHESIVE_TYPE(type) \
ctype = CohesiveFacetProperty<type>::cohesive_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_COHESIVE_TYPE);
#undef GET_COHESIVE_TYPE
return ctype;
}
#else
inline ElementType FEEngine::getCohesiveElementType(__attribute__((unused))
ElementType type_facet) {
return _not_defined;
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
} // akantu
#include "igfem_helper.hh"
namespace akantu {
inline Vector<ElementType> FEEngine::getIGFEMElementTypes(ElementType type) {
#define GET_IGFEM_ELEMENT_TYPES(type) \
return IGFEMHelper::getIGFEMElementTypes<type>();
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(GET_IGFEM_ELEMENT_TYPES);
#undef GET_IGFEM_ELEMENT_TYPES
}
#endif
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::extractNodalToElementField(const Mesh & mesh,
const Array<T> & nodal_f,
Array<T> & elemental_f,
ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
T * nodal_f_val = nodal_f.storage();
T * f_val = elemental_f.storage();
UInt * el_conn;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter) {
el_conn = conn_val + filter_elements(el) * nb_nodes_per_element;
} else {
el_conn = conn_val + el * nb_nodes_per_element;
}
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = *(el_conn + n);
std::copy(nodal_f_val + node * nb_degree_of_freedom,
nodal_f_val + (node + 1) * nb_degree_of_freedom, f_val);
f_val += nb_degree_of_freedom;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
Array<T> & filtered_f, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
filtered_f.resize(0);
return;
}
UInt nb_degree_of_freedom = elem_f.getNbComponent();
UInt nb_data_per_element = elem_f.size() / nb_element;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
filtered_f.resize(nb_element * nb_data_per_element);
T * elem_f_val = elem_f.storage();
T * f_val = filtered_f.storage();
UInt el_offset;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter) {
el_offset = filter_elements(el);
} else {
el_offset = el;
}
std::copy(elem_f_val +
el_offset * nb_data_per_element * nb_degree_of_freedom,
elem_f_val +
(el_offset + 1) * nb_data_per_element * nb_degree_of_freedom,
f_val);
f_val += nb_degree_of_freedom * nb_data_per_element;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_FE_ENGINE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/fe_engine_template.hh b/src/fe_engine/fe_engine_template.hh
index fa51a0442..68c288f61 100644
--- a/src/fe_engine/fe_engine_template.hh
+++ b/src/fe_engine/fe_engine_template.hh
@@ -1,426 +1,431 @@
/**
* @file fe_engine_template.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri May 14 2021
*
* @brief templated class that calls integration and shape objects
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FE_ENGINE_TEMPLATE_HH_
#define AKANTU_FE_ENGINE_TEMPLATE_HH_
namespace akantu {
class DOFManager;
namespace fe_engine {
namespace details {
template <ElementKind> struct AssembleLumpedTemplateHelper;
template <ElementKind> struct AssembleFieldMatrixHelper;
} // namespace details
} // namespace fe_engine
template <ElementKind, typename> struct AssembleFieldMatrixStructHelper;
struct DefaultIntegrationOrderFunctor {
template <ElementType type> static inline constexpr int getOrder() {
return ElementClassProperty<type>::polynomial_degree;
}
};
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind = _ek_regular,
class IntegrationOrderFunctor = DefaultIntegrationOrderFunctor>
class FEEngineTemplate : public FEEngine {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using Integ = I<kind, IntegrationOrderFunctor>;
using Shape = S<kind>;
FEEngineTemplate(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "fem");
~FEEngineTemplate() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
void initShapeFunctions(GhostType ghost_type = _not_ghost) override;
void initShapeFunctions(const Array<Real> & nodes,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate a scalar value on all elements of type "type"
Real
integrate(const Array<Real> & f, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate one element scalar value on all elements of type "type"
Real integrate(const Vector<Real> & f, ElementType type, UInt index,
GhostType ghost_type = _not_ghost) const override;
/// integrate partially around an integration point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate on a phyiscal point inside an element
void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const override;
/// get the number of integration points
UInt getNbIntegrationPoints(ElementType type,
GhostType ghost_type = _not_ghost) const override;
/// get shapes precomputed
const Array<Real> & getShapes(ElementType type,
GhostType ghost_type = _not_ghost,
UInt id = 0) const override;
/// get the derivatives of shapes
const Array<Real> & getShapesDerivatives(ElementType type,
GhostType ghost_type = _not_ghost,
UInt id = 0) const override;
/// get integration points
const inline Matrix<Real> &
getIntegrationPoints(ElementType type,
GhostType ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// compute the gradient of a nodal field on the integration points
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points given a
/// by_element_type
void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// pre multiplies a tensor by the shapes derivaties
void
computeBtD(const Array<Real> & Ds, Array<Real> & BtDs, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left and right multiplies a tensor by the shapes derivaties
void computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left multiples a vector by the shape functions
void
computeNtb(const Array<Real> & bs, Array<Real> & Ntbs, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// left and right multiplies a tensor by the shapes
void computeNtbN(
const Array<Real> & bs, Array<Real> & NtbNs, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const override;
/// compute the position of integration points given by an element_type_map
/// from nodes position
inline void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements =
nullptr) const override;
/// compute the position of integration points from nodes position
inline void computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, ElementType type,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
inline void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter =
nullptr) const override;
/// find natural coords from real coords provided an element
void inverseMap(const Vector<Real> & real_coords, UInt element,
ElementType type, Vector<Real> & natural_coords,
GhostType ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
inline bool contains(const Vector<Real> & real_coords, UInt element,
ElementType type,
GhostType ghost_type = _not_ghost) const;
/// compute the shape on a provided point
inline void computeShapes(const Vector<Real> & real_coords, UInt element,
ElementType type, Vector<Real> & shapes,
GhostType ghost_type = _not_ghost) const override;
/// compute the shape derivatives on a provided point
inline void
computeShapeDerivatives(const Vector<Real> & real_coords, UInt element,
ElementType type, Matrix<Real> & shape_derivatives,
GhostType ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
void
computeNormalsOnIntegrationPoints(GhostType ghost_type = _not_ghost) override;
void
computeNormalsOnIntegrationPoints(const Array<Real> & field,
GhostType ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field, Array<Real> & normal, ElementType type,
GhostType ghost_type = _not_ghost) const override;
template <ElementType type>
void computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
GhostType ghost_type) const;
private:
// To avoid a weird full specialization of a method in a non specalized class
void computeNormalsOnIntegrationPointsPoint1(const Array<Real> & /*unused*/,
Array<Real> & normal,
GhostType ghost_type) const;
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type) const override;
/// assemble a field as a matrix (ex. rho to mass matrix)
void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type) const override;
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
// template <class Functor>
// void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
// const ID & dof_id, DOFManager & dof_manager,
// ElementType type,
// GhostType ghost_type) const;
// /// assemble a field as a matrix (ex. rho to mass matrix)
// template <class Functor>
// void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
// const ID & dof_id, DOFManager & dof_manager,
// ElementType type,
// GhostType ghost_type) const;
// #ifdef AKANTU_STRUCTURAL_MECHANICS
// /// assemble a field as a matrix (ex. rho to mass matrix)
// void assembleFieldMatrix(const Array<Real> & field_1,
// UInt nb_degree_of_freedom, SparseMatrix & M,
// Array<Real> * n,
// ElementTypeMapArray<Real> & rotation_mat,
// ElementType type,
// GhostType ghost_type = _not_ghost)
// const;
// /// compute shapes function in a matrix for structural elements
// void
// computeShapesMatrix(ElementType type, UInt nb_degree_of_freedom,
// UInt nb_nodes_per_element, Array<Real> * n, UInt id,
// UInt degree_to_interpolate, UInt degree_interpolated,
// const bool sign,
// GhostType ghost_type = _not_ghost) const
// override;
// #endif
private:
friend struct fe_engine::details::AssembleLumpedTemplateHelper<kind>;
friend struct fe_engine::details::AssembleFieldMatrixHelper<kind>;
friend struct AssembleFieldMatrixStructHelper<kind, void>;
/// templated function to compute the scaling to assemble a lumped matrix
template <ElementType type>
void assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const;
/// @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j
/// dV = \int \rho \varphi_i dV @f$
template <ElementType type>
void assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const;
/// @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
template <ElementType type>
void assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
GhostType ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <ElementType type>
void assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
template <ElementType type>
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused)) GhostType ghost_type) const;
#endif
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
void onElementsAdded(const Array<Element> & /*new_elements*/,
const NewElementsEvent & /*unused*/) override;
void onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const RemovedElementsEvent & /*unused*/) override;
void onElementsChanged(const Array<Element> & /*unused*/,
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the shape class (probably useless: see getShapeFunction)
const ShapeFunctions & getShapeFunctionsInterface() const override {
return shape_functions;
};
/// get the shape class
const Shape & getShapeFunctions() const { return shape_functions; };
/// get the integrator class (probably useless: see getIntegrator)
const Integrator & getIntegratorInterface() const override {
return integrator;
};
/// get the integrator class
const Integ & getIntegrator() const { return integrator; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Integ integrator;
Shape shape_functions;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "fe_engine_template_tmpl.hh"
#include "fe_engine_template_tmpl_field.hh"
/* -------------------------------------------------------------------------- */
/* Shape Linked specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "fe_engine_template_tmpl_struct.hh"
#endif
/* -------------------------------------------------------------------------- */
/* Shape IGFEM specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
#include "fe_engine_template_tmpl_igfem.hh"
#endif
#endif /* AKANTU_FE_ENGINE_TEMPLATE_HH_ */
diff --git a/src/fe_engine/fe_engine_template_cohesive.cc b/src/fe_engine/fe_engine_template_cohesive.cc
index ab5c78b34..617ff433b 100644
--- a/src/fe_engine/fe_engine_template_cohesive.cc
+++ b/src/fe_engine/fe_engine_template_cohesive.cc
@@ -1,135 +1,137 @@
/**
* @file fe_engine_template_cohesive.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 31 2012
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Specialization of the FEEngineTemplate for cohesive element
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* compatibility functions */
/* -------------------------------------------------------------------------- */
template <>
Real FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = 0.;
#define INTEGRATE(type) \
integral = integrator.integrate<type>(f, ghost_type, filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) const {
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.size() == nb_element,
"The vector intf(" << intf.getID()
<< ") has not the good size.");
#endif
#define INTEGRATE(type) \
integrator.integrate<type>(f, intf, nb_degree_of_freedom, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
gradientOnIntegrationPoints(
const Array<Real> & /* u */, Array<Real> & /* nablauq */,
UInt /* nb_degree_of_freedom */, ElementType /* type */,
GhostType /* ghost_type */,
const Array<UInt> & /* filter_elements */) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl.hh b/src/fe_engine/fe_engine_template_tmpl.hh
index dead0cf5d..a7feec5b0 100644
--- a/src/fe_engine/fe_engine_template_tmpl.hh
+++ b/src/fe_engine/fe_engine_template_tmpl.hh
@@ -1,1444 +1,1449 @@
/**
* @file fe_engine_template_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri May 14 2021
*
* @brief Template implementation of FEEngineTemplate
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager.hh"
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::FEEngineTemplate(
Mesh & mesh, UInt spatial_dimension, const ID & id)
: FEEngine(mesh, spatial_dimension, id),
integrator(mesh, spatial_dimension, id),
shape_functions(mesh, spatial_dimension, id) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::~FEEngineTemplate() =
default;
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GradientOnIntegrationPointsHelper {
template <class S>
static void call(const S & /*unused*/, Mesh & /*unused*/,
const Array<Real> & /*unused*/, Array<Real> & /*unused*/,
const UInt /*unused*/, ElementType /*unused*/,
GhostType /*unused*/, const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_GRADIENT(type) \
if (element_dimension == ElementClass<type>::getSpatialDimension()) \
shape_functions.template gradientOnIntegrationPoints<type>( \
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GradientOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, Mesh & mesh, \
const Array<Real> & u, Array<Real> & nablauq, \
const UInt nb_degree_of_freedom, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
UInt element_dimension = mesh.getSpatialDimension(type); \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_GRADIENT, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_GRADIENT_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER
#undef COMPUTE_GRADIENT
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
#ifndef AKANTU_NDEBUG
UInt element_dimension = mesh.getSpatialDimension(type);
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(
nablauq.getNbComponent() == nb_degree_of_freedom * element_dimension,
"The vector nablauq(" << nablauq.getID()
<< ") has not the good number of component.");
// AKANTU_DEBUG_ASSERT(nablauq.size() == nb_element * nb_points,
// "The vector nablauq(" << nablauq.getID()
// << ") has not the good size.");
#endif
nablauq.resize(nb_element * nb_points);
fe_engine::details::GradientOnIntegrationPointsHelper<kind>::call(
shape_functions, mesh, u, nablauq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
GhostType ghost_type) {
initShapeFunctions(mesh.getNodes(), ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
integrator.initIntegrator(nodes, type, ghost_type);
const auto & control_points = getIntegrationPoints(type, ghost_type);
shape_functions.initShapeFunctions(nodes, control_points, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateHelper {};
#define INTEGRATE(type) \
integrator.template integrate<type>(f, intf, nb_degree_of_freedom, \
ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_HELPER(kind) \
template <> struct IntegrateHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
#ifndef AKANTU_NDEBUG
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element);
fe_engine::details::IntegrateHelper<kind>::call(integrator, f, intf,
nb_degree_of_freedom, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarHelper {};
#define INTEGRATE(type) \
integral = \
integrator.template integrate<type>(f, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER(kind) \
template <> struct IntegrateScalarHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Array<Real> & f, \
ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
Real integral = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return integral; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
UInt nb_quadrature_points = getNbIntegrationPoints(type, ghost_type);
AKANTU_DEBUG_ASSERT(
f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << ") has not the good size. (" << f.size()
<< "!=" << nb_quadrature_points * nb_element << ")");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = fe_engine::details::IntegrateScalarHelper<kind>::call(
integrator, f, type, ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarOnOneElementHelper {};
#define INTEGRATE(type) \
res = integrator.template integrate<type>(f, index, ghost_type);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER(kind) \
template <> struct IntegrateScalarOnOneElementHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Vector<Real> & f, \
ElementType type, UInt index, GhostType ghost_type) { \
Real res = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return res; \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & f, ElementType type, UInt index,
GhostType ghost_type) const {
Real res = fe_engine::details::IntegrateScalarOnOneElementHelper<kind>::call(
integrator, f, type, index, ghost_type);
return res;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateOnIntegrationPointsHelper {};
#define INTEGRATE(type) \
integrator.template integrateOnIntegrationPoints<type>( \
f, intf, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct IntegrateOnIntegrationPointsHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
UInt nb_quadrature_points = getNbIntegrationPoints(type);
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element * nb_quadrature_points);
fe_engine::details::IntegrateOnIntegrationPointsHelper<kind>::call(
integrator, f, intf, nb_degree_of_freedom, type, ghost_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateOnIntegrationPointsHelper {
template <class S>
static void call(const S & /*unused*/, const Array<Real> & /*unused*/,
Array<Real> & /*unused*/, const UInt /*unused*/,
ElementType /*unused*/, GhostType /*unused*/,
const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolateOnIntegrationPoints<type>( \
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct InterpolateOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & u, \
Array<Real> & uq, const UInt nb_degree_of_freedom, \
ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(const Array<Real> & u, Array<Real> & uq,
const UInt nb_degree_of_freedom,
ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
#ifndef AKANTU_NDEBUG
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(uq.getNbComponent() == nb_degree_of_freedom,
"The vector uq("
<< uq.getID()
<< ") has not the good number of component.");
#endif
uq.resize(nb_element * nb_points);
fe_engine::details::InterpolateOnIntegrationPointsHelper<kind>::call(
shape_functions, u, uq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) const {
AKANTU_DEBUG_IN();
const Array<UInt> * filter = nullptr;
for (auto ghost_type : ghost_types) {
for (auto && type : uq.elementTypes(_all_dimensions, ghost_type, kind)) {
UInt nb_quad_per_element = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = 0;
if (filter_elements != nullptr) {
filter = &((*filter_elements)(type, ghost_type));
nb_element = filter->size();
} else {
filter = &empty_filter;
nb_element = mesh.getNbElement(type, ghost_type);
}
UInt nb_tot_quad = nb_quad_per_element * nb_element;
Array<Real> & quad = uq(type, ghost_type);
quad.resize(nb_tot_quad);
interpolateOnIntegrationPoints(u, quad, quad.getNbComponent(), type,
ghost_type, *filter);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDHelper {};
#define COMPUTE_BTD(type) \
shape_functions.template computeBtD<type>(Ds, BtDs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER(kind) \
template <> struct ComputeBtDHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
Array<Real> & BtDs, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTD, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtD_HELPER
#undef COMPUTE_BTD
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDHelper<kind>::call(
shape_functions, Ds, BtDs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeBtDBHelper {};
#define COMPUTE_BTDB(type) \
shape_functions.template computeBtDB<type>(Ds, BtDBs, order_d, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER(kind) \
template <> struct ComputeBtDBHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & Ds, \
Array<Real> & BtDBs, UInt order_d, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_BTDB, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_BtDB_HELPER
#undef COMPUTE_BTDB
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeBtDBHelper<kind>::call(
shape_functions, Ds, BtDBs, order_d, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNtbNHelper {};
#define COMPUTE_NtbN(type) \
shape_functions.template computeNtbN<type>(bs, NtbNs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_NtbN_HELPER(kind) \
template <> struct ComputeNtbNHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & bs, \
Array<Real> & NtbNs, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_NtbN, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_NtbN_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_NtbN_HELPER
#undef COMPUTE_NtbN
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeNtbN(
const Array<Real> & bs, Array<Real> & NtbNs, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeNtbNHelper<kind>::call(
shape_functions, bs, NtbNs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNtbHelper {};
#define COMPUTE_Ntb(type) \
shape_functions.template computeNtb<type>(bs, Ntbs, ghost_type, \
filter_elements);
#define AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER(kind) \
template <> struct ComputeNtbHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & bs, \
Array<Real> & Ntbs, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_Ntb, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER)
#undef AKANTU_SPECIALIZE_COMPUTE_Ntb_HELPER
#undef COMPUTE_Ntb
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeNtb(
const Array<Real> & bs, Array<Real> & Ntbs, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
fe_engine::details::ComputeNtbHelper<kind>::call(
shape_functions, bs, Ntbs, type, ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, spatial_dimension, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_for_interpolation", getID());
quadrature_points_coordinates.initialize(*this,
_nb_component = spatial_dimension);
computeIntegrationPointsCoordinates(quadrature_points_coordinates,
element_filter);
shape_functions.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, quadrature_points_coordinates,
element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
ElementTypeMapArray<Real> interpolation_points_coordinates_matrices(
"interpolation_points_coordinates_matrices", id);
ElementTypeMapArray<Real> quad_points_coordinates_inv_matrices(
"quad_points_coordinates_inv_matrices", id);
initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, element_filter);
interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
shape_functions.interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateHelper {
template <class S>
static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
UInt /*unused*/, const Matrix<Real> & /*unused*/,
Vector<Real> & /*unused*/, ElementType /*unused*/,
GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolate<type>( \
real_coords, element, nodal_values, interpolated, ghost_type);
#define AKANTU_SPECIALIZE_INTERPOLATE_HELPER(kind) \
template <> struct InterpolateHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const Matrix<Real> & nodal_values, \
Vector<Real> & interpolated, ElementType type, \
GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INTERPOLATE_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE)
#undef AKANTU_SPECIALIZE_INTERPOLATE_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::interpolate(
const Vector<Real> & real_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated, const Element & element) const {
AKANTU_DEBUG_IN();
fe_engine::details::InterpolateHelper<kind>::call(
shape_functions, real_coords, element.element, nodal_values, interpolated,
element.type, element.ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(GhostType ghost_type) {
AKANTU_DEBUG_IN();
computeNormalsOnIntegrationPoints(mesh.getNodes(), ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
// Real * coord = mesh.getNodes().storage();
UInt spatial_dimension = mesh.getSpatialDimension();
// allocate the normal arrays
normals_on_integration_points.initialize(
*this, _nb_component = spatial_dimension,
_spatial_dimension = element_dimension, _ghost_type = ghost_type,
_element_kind = kind);
// loop over the type to build the normals
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
auto & normals_on_quad = normals_on_integration_points(type, ghost_type);
computeNormalsOnIntegrationPoints(field, normals_on_quad, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNormalsOnIntegrationPoints {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
const Array<Real> & /*unused*/, Array<Real> & /*unused*/,
ElementType /*unused*/, GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_NORMALS_ON_INTEGRATION_POINTS(type) \
fem.template computeNormalsOnIntegrationPoints<type>(field, normal, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS(kind) \
template <> struct ComputeNormalsOnIntegrationPoints<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Array<Real> & field, Array<Real> & normal, \
ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_NORMALS_ON_INTEGRATION_POINTS, \
kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS,
AKANTU_FE_ENGINE_LIST_COMPUTE_NORMALS_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS
#undef COMPUTE_NORMALS_ON_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal, ElementType type,
GhostType ghost_type) const {
fe_engine::details::ComputeNormalsOnIntegrationPoints<kind>::call(
*this, field, normal, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
if (type == _point_1) {
computeNormalsOnIntegrationPointsPoint1(field, normal, ghost_type);
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
Array<Real> f_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, field, f_el, type, ghost_type);
const Matrix<Real> & quads =
integrator.template getIntegrationPoints<type>(ghost_type);
Array<Real>::matrix_iterator f_it =
f_el.begin(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem) {
ElementClass<type>::computeNormalsOnNaturalCoordinates(quads, *f_it,
*normals_on_quad);
++normals_on_quad;
++f_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct InverseMapHelper {
template <class S>
static void call(const S & /*shape_functions*/,
const Vector<Real> & /*real_coords*/, UInt /*element*/,
ElementType /*type*/, Vector<Real> & /*natural_coords*/,
GhostType /*ghost_type*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define INVERSE_MAP(type) \
shape_functions.template inverseMap<type>(real_coords, element, \
natural_coords, ghost_type);
#define AKANTU_SPECIALIZE_INVERSE_MAP_HELPER(kind) \
template <> struct InverseMapHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
ElementType type, Vector<Real> & natural_coords, \
GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INVERSE_MAP, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INVERSE_MAP_HELPER,
AKANTU_FE_ENGINE_LIST_INVERSE_MAP)
#undef AKANTU_SPECIALIZE_INVERSE_MAP_HELPER
#undef INVERSE_MAP
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::inverseMap(
const Vector<Real> & real_coords, UInt element, ElementType type,
Vector<Real> & natural_coords, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
InverseMapHelper<kind>::call(shape_functions, real_coords, element, type,
natural_coords, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ContainsHelper {
template <class S>
static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
UInt /*unused*/, ElementType /*unused*/,
GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define CONTAINS(type) \
contain = shape_functions.template contains<type>(real_coords, element, \
ghost_type);
#define AKANTU_SPECIALIZE_CONTAINS_HELPER(kind) \
template <> struct ContainsHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static bool call(const S<k> & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
ElementType type, GhostType ghost_type) { \
bool contain = false; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(CONTAINS, kind); \
return contain; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_CONTAINS_HELPER,
AKANTU_FE_ENGINE_LIST_CONTAINS)
#undef AKANTU_SPECIALIZE_CONTAINS_HELPER
#undef CONTAINS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline bool FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::contains(
const Vector<Real> & real_coords, UInt element, ElementType type,
GhostType ghost_type) const {
return fe_engine::details::ContainsHelper<kind>::call(
shape_functions, real_coords, element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapesHelper {
template <class S>
static void call(const S & /*unused*/, const Vector<Real> & /*unused*/,
UInt /*unused*/, const ElementType /*unused*/,
Vector<Real> & /*unused*/, GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPES(type) \
shape_functions.template computeShapes<type>(real_coords, element, shapes, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER(kind) \
template <> struct ComputeShapesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Vector<Real> & shapes, \
GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER
#undef COMPUTE_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapes(
const Vector<Real> & real_coords, UInt element, ElementType type,
Vector<Real> & shapes, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapesHelper<kind>::call(
shape_functions, real_coords, element, type, shapes, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapeDerivativesHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt element,
__attribute__((unused)) const ElementType type,
__attribute__((unused)) Matrix<Real> & shape_derivatives,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPE_DERIVATIVES(type) \
Matrix<Real> coords_mat(real_coords.storage(), shape_derivatives.rows(), 1); \
Tensor3<Real> shapesd_tensor(shape_derivatives.storage(), \
shape_derivatives.rows(), \
shape_derivatives.cols(), 1); \
shape_functions.template computeShapeDerivatives<type>( \
coords_mat, element, shapesd_tensor, ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER(kind) \
template <> struct ComputeShapeDerivativesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Matrix<Real> & shape_derivatives, \
GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPE_DERIVATIVES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER
#undef COMPUTE_SHAPE_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapeDerivatives(
const Vector<Real> & real_coords, UInt element, ElementType type,
Matrix<Real> & shape_derivatives, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapeDerivativesHelper<kind>::call(
shape_functions, real_coords, element, type, shape_derivatives,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetNbIntegrationPointsHelper {};
#define GET_NB_INTEGRATION_POINTS(type) \
nb_quad_points = integrator.template getNbIntegrationPoints<type>(ghost_type);
#define AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetNbIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static UInt call(const I<k, IOF> & integrator, const ElementType type, \
GhostType ghost_type) { \
UInt nb_quad_points = 0; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_NB_INTEGRATION_POINTS, kind); \
return nb_quad_points; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER
#undef GET_NB_INTEGRATION
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline UInt
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
ElementType type, GhostType ghost_type) const {
return fe_engine::details::GetNbIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesHelper {};
#define GET_SHAPES(type) ret = &(shape_functions.getShapes(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_HELPER(kind) \
template <> struct GetShapesHelper<kind> { \
template <class S> \
static const Array<Real> & call(const S & shape_functions, \
const ElementType type, \
GhostType ghost_type) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_SHAPES_HELPER)
#undef AKANTU_SPECIALIZE_GET_SHAPES_HELPER
#undef GET_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapes(
ElementType type, GhostType ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesHelper<kind>::call(shape_functions, type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesDerivativesHelper {
template <template <ElementKind> class S, ElementKind k>
static const Array<Real> & call(const S<k> & /*unused*/,
ElementType /*unused*/,
GhostType /*unused*/, UInt /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define GET_SHAPES_DERIVATIVES(type) \
ret = &(shape_functions.getShapesDerivatives(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER(kind) \
template <> struct GetShapesDerivativesHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static const Array<Real> & \
call(const S<k> & shape_functions, const ElementType type, \
GhostType ghost_type, __attribute__((unused)) UInt id) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES_DERIVATIVES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_GET_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_GET_SHAPE_DERIVATIVES_HELPER
#undef GET_SHAPES_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapesDerivatives(
ElementType type, GhostType ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesDerivativesHelper<kind>::call(
shape_functions, type, ghost_type, id);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetIntegrationPointsHelper {};
#define GET_INTEGRATION_POINTS(type) \
ret = &(integrator.template getIntegrationPoints<type>(ghost_type));
#define AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static const Matrix<Real> & call(const I<k, IOF> & integrator, \
const ElementType type, \
GhostType ghost_type) { \
const Matrix<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_INTEGRATION_POINTS, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER
#undef GET_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Matrix<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getIntegrationPoints(
ElementType type, GhostType ghost_type) const {
return fe_engine::details::GetIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::printself(
std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "FEEngineTemplate [" << std::endl;
stream << space << " + parent [" << std::endl;
FEEngine::printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + shape functions [" << std::endl;
shape_functions.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + integrator [" << std::endl;
integrator.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements, const NewElementsEvent & /*unused*/) {
integrator.onElementsAdded(new_elements);
shape_functions.onElementsAdded(new_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsRemoved(
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const RemovedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsChanged(
const Array<Element> & /*unused*/, const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPointsPoint1(const Array<Real> & /*unused*/,
Array<Real> & normal,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == 1,
"Mesh dimension must be 1 to compute normals on points!");
const auto type = _point_1;
auto spatial_dimension = mesh.getSpatialDimension();
// UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_points = getNbIntegrationPoints(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
auto nb_element = connectivity.size();
normal.resize(nb_element * nb_points);
auto normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
const auto & segments = mesh.getElementToSubelement(type, ghost_type);
const auto & coords = mesh.getNodes();
const Mesh * mesh_segment;
if (mesh.isMeshFacets()) {
mesh_segment = &(mesh.getMeshParent());
} else {
mesh_segment = &mesh;
}
for (UInt elem = 0; elem < nb_element; ++elem) {
UInt nb_segment = segments(elem).size();
AKANTU_DEBUG_ASSERT(
nb_segment > 0,
"Impossible to compute a normal on a point connected to 0 segments");
Real normal_value = 1;
if (nb_segment == 1) {
auto point = connectivity(elem);
const auto segment = segments(elem)[0];
const auto & segment_connectivity =
mesh_segment->getConnectivity(segment.type, segment.ghost_type);
Vector<UInt> segment_points = segment_connectivity.begin(
Mesh::getNbNodesPerElement(segment.type))[segment.element];
Real difference;
if (segment_points(0) == point) {
difference = coords(elem) - coords(segment_points(1));
} else {
difference = coords(elem) - coords(segment_points(0));
}
normal_value = difference / std::abs(difference);
}
for (UInt n(0); n < nb_points; ++n) {
(*normals_on_quad)(0, n) = normal_value;
}
++normals_on_quad;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl_field.hh b/src/fe_engine/fe_engine_template_tmpl_field.hh
index 59bca0a79..83abf6100 100644
--- a/src/fe_engine/fe_engine_template_tmpl_field.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_field.hh
@@ -1,505 +1,507 @@
/**
* @file fe_engine_template_tmpl_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
- * @date last modification: Thu Dec 07 2017
+ * @date last modification: Sat Mar 13 2021
*
* @brief implementation of the assemble field s functions
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_
#define AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Matrix lumping functions */
/* -------------------------------------------------------------------------- */
namespace fe_engine {
namespace details {
namespace {
template <class Functor>
void fillField(const Functor & field_funct, Array<Real> & field,
UInt nb_element, UInt nb_integration_points,
ElementType type, GhostType ghost_type) {
UInt nb_degree_of_freedom = field.getNbComponent();
field.resize(nb_integration_points * nb_element);
auto field_it = field.begin_reinterpret(
nb_degree_of_freedom, nb_integration_points, nb_element);
Element el{type, 0, ghost_type};
for (; el.element < nb_element; ++el.element, ++field_it) {
field_funct(*field_it, el);
}
}
} // namespace
} // namespace details
} // namespace fe_engine
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleLumpedTemplateHelper {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
const std::function<void(Matrix<Real> &,
const Element &)> & /*unused*/,
const ID & /*unused*/, const ID & /*unused*/,
DOFManager & /*unused*/, ElementType /*unused*/,
GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define ASSEMBLE_LUMPED(type) \
fem.template assembleFieldLumped<type>(field_funct, lumped, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_HELPER(kind) \
template <> struct AssembleLumpedTemplateHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void \
call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const std::function<void(Matrix<Real> &, const Element &)> & \
field_funct, \
const ID & lumped, const ID & dof_id, DOFManager & dof_manager, \
ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_LUMPED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_ASSEMBLE_HELPER,
AKANTU_FE_ENGINE_LIST_ASSEMBLE_FIELDS)
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER_LIST_KIND
#undef ASSEMBLE_LUMPED
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleLumpedTemplateHelper<kind>::call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldLumped(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_integration_points = this->getNbIntegrationPoints(type);
Array<Real> field(0, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
nb_integration_points, type, ghost_type);
switch (type) {
case _triangle_6:
case _quadrangle_8:
case _tetrahedron_10:
case _hexahedron_20:
case _pentahedron_15:
this->template assembleLumpedDiagonalScaling<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
break;
default:
this->template assembleLumpedRowSum<type>(field, matrix_id, dof_id,
dof_manager, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = field.getNbComponent();
auto * field_times_shapes =
new Array<Real>(0, shapes_size * nb_degree_of_freedom);
shape_functions.template computeNtb<type>(field, *field_times_shapes,
ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
auto * int_field_times_shapes = new Array<Real>(
nb_element, shapes_size * nb_degree_of_freedom, "inte_rho_x_shapes");
integrator.template integrate<type>(
*field_times_shapes, *int_field_times_shapes,
nb_degree_of_freedom * shapes_size, ghost_type, empty_filter);
delete field_times_shapes;
dof_manager.assembleElementalArrayToLumpedMatrix(
dof_id, *int_field_times_shapes, matrix_id, type, ghost_type);
delete int_field_times_shapes;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
ElementType type_p1 = ElementClass<type>::getP1ElementType();
UInt nb_nodes_per_element_p1 = Mesh::getNbNodesPerElement(type_p1);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = field.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
Vector<Real> nodal_factor(nb_nodes_per_element);
#define ASSIGN_WEIGHT_TO_NODES(corner, mid) \
{ \
for (UInt n = 0; n < nb_nodes_per_element_p1; n++) \
nodal_factor(n) = corner; \
for (UInt n = nb_nodes_per_element_p1; n < nb_nodes_per_element; n++) \
nodal_factor(n) = mid; \
}
if (type == _triangle_6)
ASSIGN_WEIGHT_TO_NODES(1. / 12., 1. / 4.);
if (type == _tetrahedron_10)
ASSIGN_WEIGHT_TO_NODES(1. / 32., 7. / 48.);
if (type == _quadrangle_8)
ASSIGN_WEIGHT_TO_NODES(
3. / 76.,
16. / 76.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3 gauss points;
* coeff. are (1./36., 8./36.) for 2x2 gauss points */
if (type == _hexahedron_20)
ASSIGN_WEIGHT_TO_NODES(
7. / 248., 16. / 248.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3x3 gauss
* points; coeff. are (1./40.,
* 1./15.) for 2x2x2 gauss points */
if (type == _pentahedron_15) {
// coefficients derived by scaling the diagonal terms of the corresponding
// consistent mass computed with 8 gauss points;
for (UInt n = 0; n < nb_nodes_per_element_p1; n++) {
nodal_factor(n) = 51. / 2358.;
}
Real mid_triangle = 192. / 2358.;
Real mid_quadrangle = 300. / 2358.;
nodal_factor(6) = mid_triangle;
nodal_factor(7) = mid_triangle;
nodal_factor(8) = mid_triangle;
nodal_factor(9) = mid_quadrangle;
nodal_factor(10) = mid_quadrangle;
nodal_factor(11) = mid_quadrangle;
nodal_factor(12) = mid_triangle;
nodal_factor(13) = mid_triangle;
nodal_factor(14) = mid_triangle;
}
if (nb_element == 0) {
AKANTU_DEBUG_OUT();
return;
}
#undef ASSIGN_WEIGHT_TO_NODES
/// compute @f$ \int \rho dV = \rho V @f$ for each element
auto int_field = std::make_unique<Array<Real>>(
field.size(), nb_degree_of_freedom, "inte_rho_x");
integrator.template integrate<type>(field, *int_field, nb_degree_of_freedom,
ghost_type, empty_filter);
/// distribute the mass of the element to the nodes
auto lumped_per_node = std::make_unique<Array<Real>>(
nb_element, nb_degree_of_freedom * nb_nodes_per_element, "mass_per_node");
auto int_field_it = int_field->begin(nb_degree_of_freedom);
auto lumped_per_node_it =
lumped_per_node->begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Vector<Real> l = (*lumped_per_node_it)(n);
l = *int_field_it;
l *= nodal_factor(n);
}
++int_field_it;
++lumped_per_node_it;
}
dof_manager.assembleElementalArrayToLumpedMatrix(dof_id, *lumped_per_node,
matrix_id, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct AssembleFieldMatrixHelper {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & /*unused*/,
const std::function<void(Matrix<Real> &,
const Element &)> & /*unused*/,
const ID & /*unused*/, const ID & /*unused*/,
DOFManager & /*unused*/, ElementType /*unused*/,
GhostType /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_funct, matrix_id, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER(kind) \
template <> struct AssembleFieldMatrixHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void \
call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const std::function<void(Matrix<Real> &, const Element &)> & \
field_funct, \
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager, \
ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER,
AKANTU_FE_ENGINE_LIST_ASSEMBLE_FIELDS)
#undef AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER
#undef ASSEMBLE_MATRIX
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
ElementType type, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::AssembleFieldMatrixHelper<kind>::template call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ShapesForMassHelper {
template <ElementType type, class ShapeFunctions>
static auto getShapes(ShapeFunctions & shape_functions,
const Matrix<Real> & integration_points,
const Array<Real> & nodes,
UInt & nb_degree_of_freedom, UInt nb_element,
GhostType ghost_type) {
UInt shapes_size = ElementClass<type>::getShapeSize();
Array<Real> shapes(0, shapes_size);
shape_functions.template computeShapesOnIntegrationPoints<type>(
nodes, integration_points, shapes, ghost_type);
UInt nb_integration_points = integration_points.cols();
UInt vect_size = nb_integration_points * nb_element;
UInt lmat_size = nb_degree_of_freedom * shapes_size;
// Extending the shape functions
/// \todo move this in the shape functions as Voigt format shapes to
/// have the code in common with the structural elements
auto shapes_voigt = std::make_unique<Array<Real>>(
vect_size, lmat_size * nb_degree_of_freedom, 0.);
auto mshapes_it = shapes_voigt->begin(nb_degree_of_freedom, lmat_size);
auto shapes_it = shapes.begin(shapes_size);
for (UInt q = 0; q < vect_size; ++q, ++mshapes_it, ++shapes_it) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
for (UInt s = 0; s < shapes_size; ++s) {
(*mshapes_it)(d, s * nb_degree_of_freedom + d) = (*shapes_it)(s);
}
}
}
return shapes_voigt;
}
};
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <> struct ShapesForMassHelper<_ek_structural> {
template <ElementType type, class ShapeFunctions>
static auto getShapes(ShapeFunctions & shape_functions,
const Matrix<Real> & integration_points,
const Array<Real> & nodes,
UInt & nb_degree_of_freedom, UInt /*nb_element*/,
GhostType ghost_type) {
auto nb_unknown = ElementClass<type>::getNbStressComponents();
auto nb_degree_of_freedom_ = ElementClass<type>::getNbDegreeOfFreedom();
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
auto shapes = std::make_unique<Array<Real>>(
0, nb_unknown * nb_nodes_per_element * nb_degree_of_freedom_);
nb_degree_of_freedom = nb_unknown;
shape_functions.template computeShapesMassOnIntegrationPoints<type>(
nodes, integration_points, *shapes, ghost_type);
return shapes;
}
};
#endif
} // namespace details
} // namespace fe_engine
//
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const std::function<void(Matrix<Real> &, const Element &)> & field_funct,
const ID & matrix_id, const ID & dof_id, DOFManager & dof_manager,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
// \int N * N so degree 2 * degree of N
const UInt polynomial_degree =
2 * ElementClassProperty<type>::polynomial_degree;
// getting the integration points
Matrix<Real> integration_points =
integrator.template getIntegrationPoints<type, polynomial_degree>();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
// getting the shapes on the integration points
auto shapes_voigt =
fe_engine::details::ShapesForMassHelper<kind>::template getShapes<type>(
shape_functions, integration_points, mesh.getNodes(),
nb_degree_of_freedom, nb_element, ghost_type);
auto vect_size = shapes_voigt->size();
// getting the value to assemble on the integration points
Array<Real> field(vect_size, nb_degree_of_freedom);
fe_engine::details::fillField(field_funct, field, nb_element,
integration_points.cols(), type, ghost_type);
auto lmat_size = shapes_voigt->getNbComponent() / nb_degree_of_freedom;
// computing \rho * N
Array<Real> local_mat(vect_size, lmat_size * lmat_size);
auto N_it = shapes_voigt->begin(nb_degree_of_freedom, lmat_size);
auto lmat_it = local_mat.begin(lmat_size, lmat_size);
auto field_it = field.begin_reinterpret(nb_degree_of_freedom, field.size());
for (UInt q = 0; q < vect_size; ++q, ++lmat_it, ++N_it, ++field_it) {
const auto & rho = *field_it;
const auto & N = *N_it;
auto & mat = *lmat_it;
Matrix<Real> Nt = N.transpose();
for (UInt d = 0; d < Nt.cols(); ++d) {
Nt(d) *= rho(d);
}
mat.template mul<false, false>(Nt, N);
}
// integrate the elemental values
Array<Real> int_field_times_shapes(nb_element, lmat_size * lmat_size,
"inte_rho_x_shapes");
this->integrator.template integrate<type, polynomial_degree>(
local_mat, int_field_times_shapes, lmat_size * lmat_size, ghost_type);
// assemble the elemental values to the matrix
dof_manager.assembleElementalMatricesToMatrix(
matrix_id, dof_id, int_field_times_shapes, type, ghost_type);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_FE_ENGINE_TEMPLATE_TMPL_FIELD_HH_ */
diff --git a/src/fe_engine/fe_engine_template_tmpl_struct.hh b/src/fe_engine/fe_engine_template_tmpl_struct.hh
index c0fe600ee..d6d80f772 100644
--- a/src/fe_engine/fe_engine_template_tmpl_struct.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_struct.hh
@@ -1,101 +1,103 @@
/**
* @file fe_engine_template_tmpl_struct.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Template implementation of FEEngineTemplate for Structural Element
* Kinds
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_structural.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementKind kind, typename = void>
struct AssembleFieldMatrixStructHelper {};
template <ElementKind kind>
struct AssembleFieldMatrixStructHelper<
kind, typename std::enable_if<kind == _ek_structural>::type> {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> & fem,
const Array<Real> & field_1, UInt nb_degree_of_freedom,
SparseMatrix & M, Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat, ElementType type,
GhostType ghost_type) {
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_1, nb_degree_of_freedom, M, n, \
rotation_mat, ghost_type)
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, _ek_structural);
#undef ASSEMBLE_MATRIX
}
};
// template <template <ElementKind, class> class I, template <ElementKind> class
// S,
// ElementKind kind, class IntegrationOrderFunctor>
// inline void
// FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
// const Array<Real> & field_1, UInt nb_degree_of_freedom, SparseMatrix & M,
// Array<Real> * n, ElementTypeMapArray<Real> & rotation_mat,
// ElementType type, GhostType ghost_type) const {
// AKANTU_DEBUG_IN();
// AssembleFieldMatrixStructHelper<kind>::template call(
// *this, field_1, nb_degree_of_freedom, M, n, rotation_mat, type,
// ghost_type);
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ template <template <ElementKind, class> class I, template <ElementKind>
// class S,
// ElementKind kind, class IntegrationOrderFunctor>
// inline void
// FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapesMatrix(
// ElementType, UInt, UInt, Array<Real> *, UInt, UInt, UInt,
// const bool, GhostType) const {
// AKANTU_TO_IMPLEMENT();
// }
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const Array<Real> & /*unused*/, UInt /*unused*/, SparseMatrix & /*unused*/,
Array<Real> * /*unused*/, ElementTypeMapArray<Real> & /*unused*/,
GhostType /*unused*/) const {
AKANTU_TO_IMPLEMENT();
}
} // namespace akantu
diff --git a/src/fe_engine/gauss_integration.cc b/src/fe_engine/gauss_integration.cc
index 5dc923640..422114a5b 100644
--- a/src/fe_engine/gauss_integration.cc
+++ b/src/fe_engine/gauss_integration.cc
@@ -1,237 +1,239 @@
/**
* @file gauss_integration.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Fri Mar 16 2018
*
* @brief Definition of the integration constants, some of the value are taken
* from r3.01.01 doc from Code Aster
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_class.hh"
using std::sqrt;
namespace akantu {
/* clang-format off */
/* -------------------------------------------------------------------------- */
/* Points */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_positions[] = {0};
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_weights[] = {1.};
/* -------------------------------------------------------------------------- */
/* Segments */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_positions[] = {0.};
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_weights[] = {2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_positions[] = {-1./sqrt(3.), 1./sqrt(3.)};
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_weights[] = {1., 1.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_positions[] = {-sqrt(3./5.), 0., sqrt(3./5.)};
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_weights[] = {5./9., 8./9., 5./9.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_positions[] = {-sqrt((3. + 2.*sqrt(6./5.))/7.),
-sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. + 2.*sqrt(6./5.))/7.)};
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_weights[] = {(18. - sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. - sqrt(30.))/36.};
/* -------------------------------------------------------------------------- */
/* Triangles */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_positions[] = {1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_weights[] = {1./2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_positions[] = {1./6., 1./6.,
2./3., 1./6.,
1./6., 2./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_weights[] = {1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_positions[] = {1./5., 1./5.,
3./5., 1./5.,
1./5., 3./5.,
1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_weights[] = {25./(24.*4.), 25./(24.*4.), 25./(24.*4.), -27/(24.*4.)};
/* -------------------------------------------------------------------------- */
/// Found those one in the TrigGaussRuleInfo from mathematica and matched them to the code aster values
/// http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.AppI.d/AFEM.AppI.pdf
static const Real tri_6_a = (8. - std::sqrt(10.) + std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_b = (8. - std::sqrt(10.) - std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_w1 = (620. - std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
static const Real tri_6_w2 = (620. + std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_positions[] = {tri_6_b, tri_6_b,
1. - 2. * tri_6_b, tri_6_b,
tri_6_b, 1. - 2. * tri_6_b,
tri_6_a, 1. - 2. * tri_6_a,
tri_6_a, tri_6_a,
1. - 2. * tri_6_a, tri_6_a};
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_weights[] = {tri_6_w1, tri_6_w1, tri_6_w1,
tri_6_w2, tri_6_w2, tri_6_w2};
/* -------------------------------------------------------------------------- */
static const Real tri_7_a = (6. + std::sqrt(15.)) / 21.;
static const Real tri_7_b = (6. - std::sqrt(15.)) / 21.;
static const Real tri_7_w1 = (155. + std::sqrt(15.))/2400.;
static const Real tri_7_w2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_positions[] = { 1./3., 1./3.,
tri_7_a, tri_7_a,
1. - 2.*tri_7_a, tri_7_a,
tri_7_a, 1. - 2.*tri_7_a,
tri_7_b, tri_7_b,
1. - 2.*tri_7_b, tri_7_b,
tri_7_b, 1. - 2.*tri_7_b};
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_weights[] = {9./80.,
tri_7_w1, tri_7_w1, tri_7_w1,
tri_7_w2, tri_7_w2, tri_7_w2};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Tetrahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_positions[] = {1./4., 1./4., 1./4.};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_weights[] = {1./6.};
/* -------------------------------------------------------------------------- */
static const Real tet_4_a = (5. - std::sqrt(5.))/20.;
static const Real tet_4_b = (5. + 3.*std::sqrt(5.))/20.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_positions[] = {tet_4_a, tet_4_a, tet_4_a,
tet_4_b, tet_4_a, tet_4_a,
tet_4_a, tet_4_b, tet_4_a,
tet_4_a, tet_4_a, tet_4_b};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_weights[] = {1./24., 1./24., 1./24., 1./24.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_positions[] = {1./4., 1./4., 1./4.,
1./6., 1./6., 1./6.,
1./6., 1./6., 1./2.,
1./6., 1./2., 1./6.,
1./2., 1./6., 1./6.,};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_weights[] = {-2./15., 3./40.,
3./40., 3./40.,
3./40.};
/* -------------------------------------------------------------------------- */
static const Real tet_15_a = (7. + std::sqrt(15.))/34.;
static const Real tet_15_b = (13. - 3. * std::sqrt(15.))/34.;
static const Real tet_15_c = (7. - std::sqrt(15.))/34.;
static const Real tet_15_d = (13. + 3. * std::sqrt(15.))/34.;
static const Real tet_15_e = (5. - std::sqrt(15.))/20.;
static const Real tet_15_f = (5. + std::sqrt(15.))/20.;
static const Real tet_15_w1 = (2665. - 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w2 = (2665. + 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w3 = 5./567.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_positions[] = {1./4., 1./4., 1./4.,
tet_15_a, tet_15_a, tet_15_a,
tet_15_a, tet_15_a, tet_15_b,
tet_15_a, tet_15_b, tet_15_a,
tet_15_b, tet_15_a, tet_15_a,
tet_15_c, tet_15_c, tet_15_c,
tet_15_c, tet_15_c, tet_15_d,
tet_15_c, tet_15_d, tet_15_c,
tet_15_d, tet_15_c, tet_15_c,
tet_15_e, tet_15_e, tet_15_f,
tet_15_e, tet_15_f, tet_15_e,
tet_15_f, tet_15_e, tet_15_e,
tet_15_e, tet_15_f, tet_15_f,
tet_15_f, tet_15_e, tet_15_f,
tet_15_f, tet_15_f, tet_15_e};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_weights[] = {8./405.,
tet_15_w1, tet_15_w1, tet_15_w1, tet_15_w1,
tet_15_w2, tet_15_w2, tet_15_w2, tet_15_w2,
tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3};
/* -------------------------------------------------------------------------- */
/* Pentahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_positions[] = {-1./sqrt(3.), 0.5, 0.5,
-1./sqrt(3.), 0. , 0.5,
-1./sqrt(3.), 0.5, 0.,
1./sqrt(3.), 0.5, 0.5,
1./sqrt(3.), 0. , 0.5,
1./sqrt(3.), 0.5 ,0.};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_weights[] = {1./6., 1./6., 1./6.,
1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_positions[] = {-sqrt(3.)/3., 1./3., 1./3.,
-sqrt(3.)/3., 0.6, 0.2,
-sqrt(3.)/3., 0.2, 0.6,
-sqrt(3.)/3., 0.2, 0.2,
sqrt(3.)/3., 1./3., 1./3.,
sqrt(3.)/3., 0.6, 0.2,
sqrt(3.)/3., 0.2, 0.6,
sqrt(3.)/3., 0.2, 0.2};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_weights[] = {-27./96., 25./96., 25./96., 25./96.,
-27./96., 25./96., 25./96., 25./96.};
/* -------------------------------------------------------------------------- */
static const Real pent_21_x = std::sqrt(3./5.);
static const Real pent_21_a = (6. + std::sqrt(15.)) / 21.;
static const Real pent_21_b = (6. - std::sqrt(15.)) / 21.;
static const Real pent_21_w1_1 = 5./9.;
static const Real pent_21_w2_1 = 8./9.;
static const Real pent_21_w1_2 = (155. + std::sqrt(15.))/2400.;
static const Real pent_21_w2_2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_positions[] = {- pent_21_x, 1./3., 1./3.,
- pent_21_x, pent_21_a, pent_21_a,
- pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
- pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
- pent_21_x, pent_21_b, pent_21_b,
- pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
- pent_21_x, pent_21_b, 1. - 2.*pent_21_b,
0., 1./3., 1./3.,
0., pent_21_a, pent_21_a,
0., 1. - 2.*pent_21_a, pent_21_a,
0., pent_21_a, 1. - 2.*pent_21_a,
0., pent_21_b, pent_21_b,
0., 1. - 2.*pent_21_b, pent_21_b,
0., pent_21_b, 1. - 2.*pent_21_b,
pent_21_x, 1./3., 1./3.,
pent_21_x, pent_21_a, pent_21_a,
pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
pent_21_x, pent_21_b, pent_21_b,
pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
pent_21_x, pent_21_b, 1. - 2.*pent_21_b};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_weights[] = {pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2,
pent_21_w2_1 * 9. / 80.,
pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2,
pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2,
pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2};
} // akantu
diff --git a/src/fe_engine/gauss_integration_tmpl.hh b/src/fe_engine/gauss_integration_tmpl.hh
index 5145e2bca..a759333eb 100644
--- a/src/fe_engine/gauss_integration_tmpl.hh
+++ b/src/fe_engine/gauss_integration_tmpl.hh
@@ -1,278 +1,280 @@
/**
* @file gauss_integration_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 10 2016
- * @date last modification: Wed Nov 29 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief implementation of the gauss integration helpers
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GAUSS_INTEGRATION_TMPL_HH_
#define AKANTU_GAUSS_INTEGRATION_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* GaussIntegrationElement */
/* -------------------------------------------------------------------------- */
namespace _aka_gauss_helpers {
template <GaussIntegrationType type, UInt n>
struct GaussIntegrationNbPoints {
static const UInt nb_points = 0;
};
#if !defined(DOXYGEN)
template <UInt n> struct GaussIntegrationNbPoints<_git_not_defined, n> {
static const UInt nb_points = 0;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_point, n> {
static const UInt nb_points = 1;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_segment, n> {
static const UInt nb_points = (n + 1) / 2 + (bool((n + 1) % 2) ? 1 : 0);
};
#define DECLARE_GAUSS_NB_POINTS(type, order, points) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt nb_points = points; \
}
#define DECLARE_GAUSS_NB_POINTS_PENT(type, order, xo, yo) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt x_order = xo; \
static const UInt yz_order = yo; \
static const UInt nb_points = 1; \
}
DECLARE_GAUSS_NB_POINTS(_git_triangle, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 2, 3);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 3, 4);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 4, 6);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 5, 7);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 2, 4);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 3, 5);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 4, 15);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 5, 15);
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 1, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 2, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 3, 3,
3); // order 3 in x, order 3 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 4, 5,
5); // order 5 in x, order 5 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 5, 5,
5); // order 5 in x, order 5 in y and z
template <GaussIntegrationType type, UInt n, UInt on = n,
bool end_recurse = false>
struct GaussIntegrationNbPointsHelper {
static const UInt pnp = GaussIntegrationNbPoints<type, n>::nb_points;
static const UInt order = n;
static const UInt nb_points = pnp;
};
template <GaussIntegrationType type, UInt n, UInt on>
struct GaussIntegrationNbPointsHelper<type, n, on, true> {
static const UInt nb_points = 0;
};
#endif
/* ------------------------------------------------------------------------ */
/* Generic helper */
/* ------------------------------------------------------------------------ */
template <GaussIntegrationType type, UInt dimension, UInt n>
struct GaussIntegrationTypeDataHelper {
using git_np = GaussIntegrationNbPoints<type, n>;
using git_data = GaussIntegrationTypeData<type, git_np::nb_points>;
static UInt getNbQuadraturePoints() { return git_np::nb_points; }
static Matrix<Real> getQuadraturePoints() {
return Matrix<Real>(git_data::quad_positions, dimension,
git_np::nb_points);
}
static Vector<Real> getWeights() {
return Vector<Real>(git_data::quad_weights, git_np::nb_points);
}
};
#if !defined(DOXYGEN)
/* ------------------------------------------------------------------------ */
/* helper for _segment _quadrangle _hexahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_segment, dimension, dp> {
using git_np = GaussIntegrationNbPoints<_git_segment, dp>;
using git_data = GaussIntegrationTypeData<_git_segment, git_np::nb_points>;
static UInt getNbQuadraturePoints() {
return Math::pow<dimension>(git_np::nb_points);
}
static Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Vector<Real> pos(git_data::quad_positions, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads(d, rq) = pos(n % nquad);
}
offset *= nquad;
}
return quads;
}
static Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Vector<Real> quads_weights(tot_nquad, 1.);
Vector<Real> weights(git_data::quad_weights, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads_weights(rq) *= weights(n % nquad);
}
offset *= nquad;
}
return quads_weights;
}
};
/* ------------------------------------------------------------------------ */
/* helper for _pentahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_pentahedron, dimension, dp> {
using git_info = GaussIntegrationNbPoints<_git_pentahedron, dp>;
using git_np_seg =
GaussIntegrationNbPoints<_git_segment, git_info::x_order>;
using git_np_tri =
GaussIntegrationNbPoints<_git_triangle, git_info::yz_order>;
using git_data_seg =
GaussIntegrationTypeData<_git_segment, git_np_seg::nb_points>;
using git_data_tri =
GaussIntegrationTypeData<_git_triangle, git_np_tri::nb_points>;
static UInt getNbQuadraturePoints() {
return git_np_seg::nb_points * git_np_tri::nb_points;
}
static Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Matrix<Real> pos_seg_w(git_data_seg::quad_positions, 1, nquad_seg);
Matrix<Real> pos_tri_w(git_data_tri::quad_positions, 2, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
Vector<Real> pos_seg = pos_seg_w(ns);
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
Vector<Real> pos_tri = pos_tri_w(nt);
Vector<Real> quad = quads(q);
quad(_x) = pos_seg(_x);
quad(_y) = pos_tri(_x);
quad(_z) = pos_tri(_y);
}
}
return quads;
}
static Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Vector<Real> quads_weights(tot_nquad);
Vector<Real> weight_seg(git_data_seg::quad_weights, nquad_seg);
Vector<Real> weight_tri(git_data_tri::quad_weights, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
quads_weights(q) = weight_seg(ns) * weight_tri(nt);
}
}
return quads_weights;
}
};
#endif
} // namespace _aka_gauss_helpers
template <ElementType element_type, UInt n>
Matrix<Real>
GaussIntegrationElement<element_type, n>::getQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Matrix<Real> tmp(data_helper::getQuadraturePoints());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
Vector<Real> GaussIntegrationElement<element_type, n>::getWeights() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
Vector<Real> tmp(data_helper::getWeights());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
UInt GaussIntegrationElement<element_type, n>::getNbQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
using interpolation_property = InterpolationProperty<itp_type>;
using data_helper = _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n>;
return data_helper::getNbQuadraturePoints();
}
} // namespace akantu
#endif /* AKANTU_GAUSS_INTEGRATION_TMPL_HH_ */
diff --git a/src/fe_engine/geometrical_element_property.cc b/src/fe_engine/geometrical_element_property.cc
index 447050bb8..07807498b 100644
--- a/src/fe_engine/geometrical_element_property.cc
+++ b/src/fe_engine/geometrical_element_property.cc
@@ -1,61 +1,63 @@
/**
* @file geometrical_element_property.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 29 2017
- * @date last modification: Thu Nov 30 2017
+ * @date last modification: Thu Feb 20 2020
*
- * @brief A Documented file.
+ * @brief Specialization of the geometrical types
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_INSTANTIATE_TYPES(r, data, type) \
constexpr std::array<UInt, ElementClass<type>::getNbFacetTypes()> \
GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>::nb_facets; \
constexpr std::array<UInt, ElementClass<type>::getNbFacetTypes()> \
GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>::nb_nodes_per_facet; \
constexpr std::array< \
UInt, detail::sizeFacetConnectivity<GeometricalElementProperty< \
ElementClassProperty<type>::geometrical_type>>()> \
GeometricalElementProperty<ElementClassProperty< \
type>::geometrical_type>::facet_connectivity_vect; \
constexpr std::array<ElementType, ElementClass<type>::getNbFacetTypes()> \
ElementClassExtraGeometryProperties<type>::facet_type;
BOOST_PP_SEQ_FOR_EACH(AKANTU_INSTANTIATE_TYPES, _,
(_not_defined)AKANTU_ek_regular_ELEMENT_TYPE)
#if defined(AKANTU_COHESIVE_ELEMENT)
BOOST_PP_SEQ_FOR_EACH(AKANTU_INSTANTIATE_TYPES, _,
AKANTU_ek_cohesive_ELEMENT_TYPE)
#endif
} // namespace akantu
diff --git a/src/fe_engine/geometrical_element_property.hh b/src/fe_engine/geometrical_element_property.hh
index 836b5bb3d..a2b7c09dc 100644
--- a/src/fe_engine/geometrical_element_property.hh
+++ b/src/fe_engine/geometrical_element_property.hh
@@ -1,477 +1,481 @@
/**
* @file geometrical_element_property.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 29 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Specialization of the geometrical types
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace detail {
template <typename properties> constexpr size_t sizeFacetConnectivity() {
size_t s = 0;
for (size_t n = 0; n < properties::nb_facet_types; ++n) {
s += properties::nb_facets[n] * properties::nb_nodes_per_facet[n];
}
return s == 0 ? 1 : s;
}
} // namespace detail
#if !defined(DOXYGEN)
template <> struct GeometricalElementProperty<_gt_not_defined> {
static constexpr UInt spatial_dimension{0};
static constexpr UInt nb_nodes_per_element{0};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{0}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{0}};
static constexpr std::array<UInt, 1> facet_connectivity_vect{{0}};
};
template <> struct GeometricalElementProperty<_gt_point> {
static constexpr UInt spatial_dimension{0};
static constexpr UInt nb_nodes_per_element{1};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{1}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
static constexpr std::array<UInt, 1> facet_connectivity_vect{{0}};
};
template <> struct GeometricalElementProperty<_gt_segment_2> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{2};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
};
template <> struct GeometricalElementProperty<_gt_segment_3> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{3};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
// clang-format off
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_triangle_3> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{3};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 6> facet_connectivity_vect{{
0, 1, 2,
1, 2, 0}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_triangle_6> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 9> facet_connectivity_vect{{
0, 1, 2,
1, 2, 0,
3, 4, 5}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_tetrahedron_4> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 12> facet_connectivity_vect{{
0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_tetrahedron_10> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{10};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6}};
// clang-format off
static constexpr std::array<UInt, 6*4> facet_connectivity_vect{{
0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3,
6, 5, 6, 4,
5, 9, 7, 8,
4, 8, 9, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_quadrangle_4> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 2*4> facet_connectivity_vect{{
0, 1, 2, 3,
1, 2, 3, 0}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_quadrangle_8> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{4}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 4*3> facet_connectivity_vect{{
0, 1, 2, 3,
1, 2, 3, 0,
4, 5, 6, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_hexahedron_8> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{6}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{4}};
// clang-format off
static constexpr std::array<UInt, 4*6> facet_connectivity_vect{{
0, 0, 1, 2, 3, 4,
3, 1, 2, 3, 0, 5,
2, 5, 6, 7, 4, 6,
1, 4, 5, 6, 7, 7}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_hexahedron_20> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{20};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{6}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{8}};
// clang-format off
static constexpr std::array<UInt, 8*6> facet_connectivity_vect{{
0, 1, 2, 3, 0, 4,
1, 2, 3, 0, 3, 5,
5, 6, 7, 4, 2, 6,
4, 5, 6, 7, 1, 7,
8, 9, 10, 11, 11, 16,
13, 14, 15, 12, 10, 17,
16, 17, 18, 19, 9, 18,
12, 13, 14, 15, 8, 19}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_pentahedron_6> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{2};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2, 3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3, 4}};
// clang-format off
static constexpr std::array<UInt, 3*2 + 4*3> facet_connectivity_vect{{
// first type
0, 3,
2, 4,
1, 5,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4}};
// clang-format on
};
template <> struct GeometricalElementProperty<_gt_pentahedron_15> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{15};
static constexpr UInt nb_facet_types{2};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2, 3}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6, 8}};
// clang-format off
static constexpr std::array<UInt, 6*2 + 8*3> facet_connectivity_vect{{
// first type
0, 3,
2, 4,
1, 5,
8, 12,
7, 13,
6, 14,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4,
6, 9, 7,
10, 14, 11,
12, 11, 13,
9, 8, 10}};
// clang-format on
};
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_2d_4> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{4};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{2}};
// clang-format off
static constexpr std::array<UInt, 2 * 2> facet_connectivity_vect{{
0, 2,
1, 3}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_2d_6> {
static constexpr UInt spatial_dimension{2};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 3*2> facet_connectivity_vect{{
0, 3,
1, 4,
2, 5}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_1d_2> {
static constexpr UInt spatial_dimension{1};
static constexpr UInt nb_nodes_per_element{2};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{1}};
// clang-format off
static constexpr std::array<UInt, 2> facet_connectivity_vect{{0, 1}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_3d_6> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{6};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{3}};
// clang-format off
static constexpr std::array<UInt, 3*2> facet_connectivity_vect{{
0, 3,
1, 4,
2, 5}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_3d_12> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{12};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{6}};
// clang-format off
static constexpr std::array<UInt, 6*2> facet_connectivity_vect{{
0, 6,
1, 7,
2, 8,
3, 9,
4, 10,
5, 11}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_3d_8> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{8};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{4}};
// clang-format off
static constexpr std::array<UInt, 4*2> facet_connectivity_vect{{
0, 4,
1, 5,
2, 6,
3, 7}};
// clang-format on
};
/* -------------------------------------------------------------------------- */
template <> struct GeometricalElementProperty<_gt_cohesive_3d_16> {
static constexpr UInt spatial_dimension{3};
static constexpr UInt nb_nodes_per_element{16};
static constexpr UInt nb_facet_types{1};
static constexpr std::array<UInt, nb_facet_types> nb_facets{{2}};
static constexpr std::array<UInt, nb_facet_types> nb_nodes_per_facet{{8}};
// clang-format off
static constexpr std::array<UInt, 8*2> facet_connectivity_vect{{
0, 8,
1, 9,
2, 10,
3, 11,
4, 12,
5, 13,
6, 14,
7, 15}};
// clang-format on
};
#endif // AKANTU_COHESIVE_ELEMENT
/* -------------------------------------------------------------------------- */
template <> struct ElementClassExtraGeometryProperties<_not_defined> {
static constexpr ElementType p1_type{_not_defined};
static constexpr std::array<ElementType, 1> facet_type{{_not_defined}};
};
template <> struct ElementClassExtraGeometryProperties<_point_1> {
static constexpr ElementType p1_type{_point_1};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_segment_2> {
static constexpr ElementType p1_type{_segment_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_segment_3> {
static constexpr ElementType p1_type{_segment_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_triangle_3> {
static constexpr ElementType p1_type{_triangle_3};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_triangle_6> {
static constexpr ElementType p1_type{_triangle_3};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_tetrahedron_4> {
static constexpr ElementType p1_type{_tetrahedron_4};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_3}};
};
template <> struct ElementClassExtraGeometryProperties<_tetrahedron_10> {
static constexpr ElementType p1_type{_tetrahedron_4};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_6}};
};
template <> struct ElementClassExtraGeometryProperties<_quadrangle_4> {
static constexpr ElementType p1_type{_quadrangle_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_quadrangle_8> {
static constexpr ElementType p1_type{_quadrangle_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_hexahedron_8> {
static constexpr ElementType p1_type{_hexahedron_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_hexahedron_20> {
static constexpr ElementType p1_type{_hexahedron_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_8}};
};
template <> struct ElementClassExtraGeometryProperties<_pentahedron_6> {
static constexpr ElementType p1_type{_pentahedron_6};
static constexpr std::array<ElementType, 2> facet_type{
{_triangle_3, _quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_pentahedron_15> {
static constexpr ElementType p1_type{_pentahedron_6};
static constexpr std::array<ElementType, 2> facet_type{
{_triangle_6, _quadrangle_8}};
};
#if defined(AKANTU_COHESIVE_ELEMENT)
template <> struct ElementClassExtraGeometryProperties<_cohesive_2d_4> {
static constexpr ElementType p1_type{_cohesive_2d_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_2}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_2d_6> {
static constexpr ElementType p1_type{_cohesive_2d_4};
static constexpr std::array<ElementType, 1> facet_type{{_segment_3}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_1d_2> {
static constexpr ElementType p1_type{_cohesive_1d_2};
static constexpr std::array<ElementType, 1> facet_type{{_point_1}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_6> {
static constexpr ElementType p1_type{_cohesive_3d_6};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_3}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_12> {
static constexpr ElementType p1_type{_cohesive_3d_6};
static constexpr std::array<ElementType, 1> facet_type{{_triangle_6}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_8> {
static constexpr ElementType p1_type{_cohesive_3d_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_4}};
};
template <> struct ElementClassExtraGeometryProperties<_cohesive_3d_16> {
static constexpr ElementType p1_type{_cohesive_3d_8};
static constexpr std::array<ElementType, 1> facet_type{{_quadrangle_8}};
};
#endif // AKANTU_COHESIVE_ELEMENT
#endif // !defined(DOXYGEN)
} // namespace akantu
diff --git a/src/fe_engine/integration_point.hh b/src/fe_engine/integration_point.hh
index 4e8037213..cefbfc1ba 100644
--- a/src/fe_engine/integration_point.hh
+++ b/src/fe_engine/integration_point.hh
@@ -1,170 +1,172 @@
/**
* @file integration_point.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jun 17 2015
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief definition of the class IntegrationPoint
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_types.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_QUADRATURE_POINT_H
#define AKANTU_QUADRATURE_POINT_H
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class IntegrationPoint;
extern const IntegrationPoint IntegrationPointNull;
/* -------------------------------------------------------------------------- */
class IntegrationPoint : public Element {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using position_type = Vector<Real>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationPoint(const Element & element, UInt num_point = 0,
UInt nb_quad_per_element = 0)
: Element(element), num_point(num_point),
global_num(element.element * nb_quad_per_element + num_point),
position(nullptr, 0){};
IntegrationPoint(ElementType type = _not_defined, UInt element = 0,
UInt num_point = 0, GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
position(nullptr, 0){};
IntegrationPoint(UInt element, UInt num_point, UInt global_num,
const position_type & position, ElementType type,
GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
global_num(global_num), position(nullptr, 0) {
this->position.shallowCopy(position);
};
IntegrationPoint(const IntegrationPoint & quad)
: Element(quad), num_point(quad.num_point), global_num(quad.global_num),
position(nullptr, 0) {
position.shallowCopy(quad.position);
};
virtual ~IntegrationPoint() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline bool operator==(const IntegrationPoint & quad) const {
return Element::operator==(quad) && this->num_point == quad.num_point;
}
inline bool operator!=(const IntegrationPoint & quad) const {
return Element::operator!=(quad) || (num_point != quad.num_point) ||
(global_num != quad.global_num);
}
bool operator<(const IntegrationPoint & rhs) const {
bool res = Element::operator<(rhs) ||
(Element::operator==(rhs) && this->num_point < rhs.num_point);
return res;
}
inline IntegrationPoint & operator=(const IntegrationPoint & q) {
if (this != &q) {
element = q.element;
type = q.type;
ghost_type = q.ghost_type;
num_point = q.num_point;
global_num = q.global_num;
position.shallowCopy(q.position);
}
return *this;
}
/// get the position of the integration point
AKANTU_GET_MACRO(Position, position, const position_type &);
/// set the position of the integration point
void setPosition(const position_type & position) {
this->position.shallowCopy(position);
}
/// deep copy of the position of the integration point
void copyPosition(const position_type & position) {
this->position.deepCopy(position);
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << space << "IntegrationPoint [";
stream << *static_cast<const Element *>(this);
stream << ", " << num_point << "(" << global_num << ")"
<< "]";
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// number of quadrature point in the element
UInt num_point;
/// global number of the quadrature point
UInt global_num{0};
// TODO might be temporary: however this class should be tought maybe...
std::string material_id;
private:
/// position of the quadrature point
position_type position;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationPoint & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_QUADRATURE_POINT_H */
diff --git a/src/fe_engine/integrator.hh b/src/fe_engine/integrator.hh
index 6acc7aaf1..c034272a0 100644
--- a/src/fe_engine/integrator.hh
+++ b/src/fe_engine/integrator.hh
@@ -1,136 +1,138 @@
/**
* @file integrator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief interface for integrator classes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_INTEGRATOR_HH_
#define AKANTU_INTEGRATOR_HH_
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Integrator(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "integrator")
: mesh(mesh), _spatial_dimension(spatial_dimension),
jacobians("jacobians", id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
virtual ~Integrator() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty method
template <ElementType type>
inline void precomputeJacobiansOnQuadraturePoints(__attribute__((unused))
GhostType ghost_type) {}
/// empty method
void integrateOnElement(const Array<Real> & /*f*/, Real * /*intf*/,
UInt /*nb_degree_of_freedom*/,
const Element & /*elem*/,
GhostType /*ghost_type*/) const {};
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << space << "Integrator [" << std::endl;
jacobians.printself(stream, indent + 1);
stream << space << "]" << std::endl;
};
/* ------------------------------------------------------------------------ */
public:
virtual void onElementsAdded(const Array<Element> & /*unused*/) {}
virtual void
onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & new_numbering) {
jacobians.onElementsRemoved(new_numbering);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// access to the jacobians
Array<Real> & getJacobians(ElementType type,
GhostType ghost_type = _not_ghost) {
return jacobians(type, ghost_type);
};
/// access to the jacobians const
const Array<Real> & getJacobians(ElementType type,
GhostType ghost_type = _not_ghost) const {
return jacobians(type, ghost_type);
};
AKANTU_GET_MACRO(Jacobians, jacobians, const ElementTypeMapArray<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// mesh associated to the integrator
const Mesh & mesh;
// spatial dimension of the elements to consider
UInt _spatial_dimension;
/// jacobians for all elements
ElementTypeMapArray<Real> jacobians;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "integrator_inline_impl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Integrator & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_INTEGRATOR_HH_ */
diff --git a/src/fe_engine/integrator_gauss.hh b/src/fe_engine/integrator_gauss.hh
index 8897fe963..ec7dabd37 100644
--- a/src/fe_engine/integrator_gauss.hh
+++ b/src/fe_engine/integrator_gauss.hh
@@ -1,203 +1,205 @@
/**
* @file integrator_gauss.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Gauss integration facilities
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTEGRATOR_GAUSS_HH_
#define AKANTU_INTEGRATOR_GAUSS_HH_
namespace akantu {
namespace integrator {
namespace details {
template <ElementKind> struct GaussIntegratorComputeJacobiansHelper;
} // namespace details
} // namespace integrator
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss : public Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegratorGauss(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "integrator_gauss");
~IntegratorGauss() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initIntegrator(const Array<Real> & nodes, ElementType type,
GhostType ghost_type);
template <ElementType type>
inline void initIntegrator(const Array<Real> & nodes,
GhostType ghost_type);
/// integrate f on the element "elem" of type "type"
template <ElementType type>
inline void integrateOnElement(const Array<Real> & f, Real * intf,
UInt nb_degree_of_freedom, UInt elem,
GhostType ghost_type) const;
/// integrate f for all elements of type "type"
template <ElementType type>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate scalar field in_f
template <ElementType type, UInt polynomial_degree>
Real integrate(const Array<Real> & in_f,
GhostType ghost_type = _not_ghost) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
Real integrate(const Vector<Real> & in_f, UInt index,
GhostType ghost_type) const;
/// integrate scalar field in_f
template <ElementType type>
Real integrate(const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate a field without using the pre-computed values
template <ElementType type, UInt polynomial_degree>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, GhostType ghost_type) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// return a matrix with quadrature points natural coordinates
template <ElementType type>
const Matrix<Real> & getIntegrationPoints(GhostType ghost_type) const;
/// return number of quadrature points
template <ElementType type>
UInt getNbIntegrationPoints(GhostType ghost_type) const;
template <ElementType type, UInt n> Matrix<Real> getIntegrationPoints() const;
template <ElementType type, UInt n>
Vector<Real> getIntegrationWeights() const;
protected:
friend struct integrator::details::GaussIntegratorComputeJacobiansHelper<
kind>;
template <ElementType type>
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
GhostType ghost_type);
// multiply the jacobians by the integration weights and stores the results in
// jacobians
template <ElementType type, UInt polynomial_degree>
void multiplyJacobiansByWeights(
Array<Real> & jacobians,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
void computeQuadraturePoints(GhostType ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
void checkJacobians(GhostType ghost_type) const;
/// internal integrate partially around a quadrature point (@f$ intf_q = f_q *
/// J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const;
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const Array<Real> & jacobians,
UInt nb_element) const;
public:
/// compute the jacobians on quad points for a given element
template <ElementType type>
void computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & quad,
Vector<Real> & jacobians) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
template <ElementType type>
void onElementsAddedByType(const Array<UInt> & new_elements,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// integrate the field f with the jacobian jac -> inte
inline void integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const;
private:
/// ElementTypeMap of the quadrature points
ElementTypeMap<Matrix<Real>> quadrature_points;
};
} // namespace akantu
#include "integrator_gauss_inline_impl.hh"
#endif /* AKANTU_INTEGRATOR_GAUSS_HH_ */
diff --git a/src/fe_engine/integrator_gauss_inline_impl.hh b/src/fe_engine/integrator_gauss_inline_impl.hh
index cd4c13a56..e743f55a9 100644
--- a/src/fe_engine/integrator_gauss_inline_impl.hh
+++ b/src/fe_engine/integrator_gauss_inline_impl.hh
@@ -1,763 +1,765 @@
/**
* @file integrator_gauss_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Oct 27 2020
*
* @brief inline function of gauss integrator
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
struct IntegratorGaussException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrateOnElement(
const Array<Real> & f, Real * intf, UInt nb_degree_of_freedom,
const UInt elem, GhostType ghost_type) const {
Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = ElementClass<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f do not have the good number of component.");
Real * f_val = f.storage() + elem * f.getNbComponent();
Real * jac_val = jac_loc.storage() + elem * nb_quadrature_points;
integrate(f_val, jac_val, intf, nb_degree_of_freedom, nb_quadrature_points);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & in_f, UInt index, GhostType ghost_type) const {
const Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points =
GaussIntegrationElement<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(in_f.size() == nb_quadrature_points,
"The vector f do not have nb_quadrature_points entries.");
Real * jac_val = jac_loc.storage() + index * nb_quadrature_points;
Real intf;
integrate(in_f.storage(), jac_val, &intf, 1, nb_quadrature_points);
return intf;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
Real * f, Real * jac, Real * inte, UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const {
std::fill_n(inte, nb_degree_of_freedom, 0.);
Real * cjac = jac;
for (UInt q = 0; q < nb_quadrature_points; ++q) {
for (UInt dof = 0; dof < nb_degree_of_freedom; ++dof) {
inte[dof] += *f * *cjac;
++f;
}
++cjac;
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline const Matrix<Real> &
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints(
GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline UInt
IntegratorGauss<kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
GhostType ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type).cols();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Matrix<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints() const {
return GaussIntegrationElement<type,
polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Vector<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationWeights() const {
return GaussIntegrationElement<type, polynomial_degree>::getWeights();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::computeQuadraturePoints(
GhostType ghost_type) {
Matrix<Real> & quads = quadrature_points(type, ghost_type);
const UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
quads =
GaussIntegrationElement<type, polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & quad,
Vector<Real> & jacobians) const {
// jacobian
ElementClass<type>::computeJacobian(quad, node_coords, jacobians);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
IntegratorGauss<kind, IntegrationOrderFunctor>::IntegratorGauss(
const Mesh & mesh, UInt spatial_dimension, const ID & id)
: Integrator(mesh, spatial_dimension, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::checkJacobians(
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->quadrature_points(type, ghost_type).cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
Real * jacobians_val = jacobians(type, ghost_type).storage();
for (UInt i = 0; i < nb_element * nb_quadrature_points;
++i, ++jacobians_val) {
if (*jacobians_val < 0) {
AKANTU_CUSTOM_EXCEPTION_INFO(debug::IntegratorGaussException{},
"Negative jacobian computed,"
<< " possible problem in the element "
"node ordering (Quadrature Point "
<< i % nb_quadrature_points << ":"
<< i / nb_quadrature_points << ":"
<< type << ":" << ghost_type << ")");
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
const Matrix<Real> & x = *x_it;
if (filter_elements != empty_filter) {
jacobians_it = jacobians_begin + filter_elements(elem);
}
Vector<Real> & J = *jacobians_it;
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <>
template <ElementType type>
void IntegratorGauss<_ek_structural, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
const UInt spatial_dimension = mesh.getSpatialDimension();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt nb_quadrature_points = quad_points.cols();
const UInt nb_dofs = ElementClass<type>::getNbDegreeOfFreedom();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
auto jacobians_begin = jacobians_it;
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
nb_element = x_el.size();
const bool has_extra_normal =
mesh.hasData<Real>("extra_normal", type, ghost_type);
Array<Real>::const_vector_iterator extra_normal;
Array<Real>::const_vector_iterator extra_normal_begin;
if (has_extra_normal) {
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
extra_normal_begin = extra_normal;
}
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
if (filter_elements != empty_filter) {
jacobians_it = jacobians_begin + filter_elements(elem);
extra_normal = extra_normal_begin + filter_elements(elem);
}
const Matrix<Real> & X = *x_it;
Vector<Real> & J = *jacobians_it;
Matrix<Real> R(nb_dofs, nb_dofs);
if (has_extra_normal) {
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
} else {
ElementClass<type>::computeRotationMatrix(R, X, Vector<Real>(X.rows()));
}
// Extracting relevant lines
auto x = (R.block(0, 0, spatial_dimension, spatial_dimension) * X)
.block(0, 0, ElementClass<type>::getNaturalSpaceDimension(),
ElementClass<type>::getNbNodesPerElement());
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
if (filter_elements == empty_filter) {
++jacobians_it;
++extra_normal;
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
template <>
template <ElementType type>
void IntegratorGauss<_ek_cohesive, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
auto jacobians_begin =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
auto x_it = x_el.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_nodes_per_subelement = nb_nodes_per_element / 2;
Matrix<Real> x(spatial_dimension, nb_nodes_per_subelement);
nb_element = x_el.size();
UInt l_el = 0;
auto compute = [&](const auto & el) {
Vector<Real> J(jacobians_begin[el]);
Matrix<Real> X(x_it[l_el]);
++l_el;
for (UInt n = 0; n < nb_nodes_per_subelement; ++n) {
Vector<Real>(x(n)) =
(Vector<Real>(X(n)) + Vector<Real>(X(n + nb_nodes_per_subelement))) /
2.;
}
if (type == _cohesive_1d_2) {
J(0) = 1;
} else {
this->computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
}
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & jacobians_tmp = jacobians.alloc(0, 1, type, ghost_type);
this->computeJacobiansOnIntegrationPoints<type>(
nodes, quadrature_points(type, ghost_type), jacobians_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::multiplyJacobiansByWeights(
Array<Real> & jacobians, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points =
GaussIntegrationElement<type, polynomial_degree>::getNbQuadraturePoints();
Vector<Real> weights =
GaussIntegrationElement<type, polynomial_degree>::getWeights();
auto && view = make_view(jacobians, nb_quadrature_points);
if (filter_elements != empty_filter) {
auto J_it = view.begin();
for (auto el : filter_elements) {
Vector<Real> J(J_it[el]);
J *= weights;
}
} else {
for (auto & J : make_view(jacobians, nb_quadrature_points)) {
J *= weights;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const Array<Real> & jacobians, UInt nb_element) const {
AKANTU_DEBUG_IN();
intf.resize(nb_element);
if (nb_element == 0) {
return;
}
UInt nb_points = jacobians.size() / nb_element;
Array<Real>::const_matrix_iterator J_it;
Array<Real>::matrix_iterator inte_it;
Array<Real>::const_matrix_iterator f_it;
f_it = in_f.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
inte_it = intf.begin_reinterpret(nb_degree_of_freedom, 1, nb_element);
J_it = jacobians.begin_reinterpret(nb_points, 1, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Matrix<Real> & f = *f_it;
const Matrix<Real> & J = *J_it;
Matrix<Real> & inte_f = *inte_it;
inte_f.mul<false, false>(f, J);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
auto * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrate(in_f, intf, nb_degree_of_freedom, *filtered_J, nb_element);
delete filtered_J;
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrate(in_f, intf, nb_degree_of_freedom, jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
Matrix<Real> quads = this->getIntegrationPoints<type, polynomial_degree>();
Array<Real> jacobians;
this->computeJacobiansOnIntegrationPoints<type>(mesh.getNodes(), quads,
jacobians, ghost_type);
this->multiplyJacobiansByWeights<type, polynomial_degree>(jacobians);
this->integrate(in_f, intf, nb_degree_of_freedom, jacobians,
mesh.getNbElement(type, ghost_type));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, GhostType ghost_type) const {
AKANTU_DEBUG_IN();
Array<Real> intfv(0, 1);
integrate<type, polynomial_degree>(in_f, intfv, 1, ghost_type);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
Array<Real> intfv(0, 1);
integrate<type>(in_f, intfv, 1, ghost_type, filter_elements);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const {
AKANTU_DEBUG_IN();
UInt nb_points = jacobians.size() / nb_element;
intf.resize(nb_element * nb_points);
auto J_it = jacobians.begin();
auto f_it = in_f.begin(nb_degree_of_freedom);
auto inte_it = intf.begin(nb_degree_of_freedom);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Real & J = *J_it;
const Vector<Real> & f = *f_it;
Vector<Real> & inte_f = *inte_it;
inte_f = f;
inte_f *= J;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = this->jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.size();
auto * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
*filtered_J, nb_element);
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::onElementsAddedByType(
const Array<UInt> & elements, GhostType ghost_type) {
const auto & nodes = mesh.getNodes();
if (not quadrature_points.exists(type, ghost_type)) {
computeQuadraturePoints<type>(ghost_type);
}
if (not jacobians.exists(type, ghost_type)) {
jacobians.alloc(0, 1, type, ghost_type);
}
this->computeJacobiansOnIntegrationPoints(
nodes, quadrature_points(type, ghost_type), jacobians(type, ghost_type),
type, ghost_type, elements);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type), elements);
}
/* -------------------------------------------------------------------------- */
namespace integrator {
namespace details {
template <ElementKind kind> struct IntegratorOnElementsAddedHelper {};
#define ON_ELEMENT_ADDED(type) \
integrator.template onElementsAddedByType<type>(elements, ghost_type);
#define AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER(kind) \
template <> struct IntegratorOnElementsAddedHelper<kind> { \
template <class I> \
static void call(I & integrator, const Array<UInt> & elements, \
ElementType type, GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ON_ELEMENT_ADDED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER)
#undef AKANTU_SPECIALIZE_ON_ELEMENT_ADDED_HELPER
#undef ON_ELEMENT_ADDED
} // namespace details
} // namespace integrator
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements) {
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
if (mesh.getSpatialDimension(type) != _spatial_dimension) {
continue;
}
if (mesh.getKind(type) != kind) {
continue;
}
integrator::details::IntegratorOnElementsAddedHelper<kind>::call(
*this, elements_range.getElements(), type, ghost_type);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, GhostType ghost_type) {
computeQuadraturePoints<type>(ghost_type);
precomputeJacobiansOnQuadraturePoints<type>(nodes, ghost_type);
checkJacobians<type>(ghost_type);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type));
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorInitHelper {};
#define INIT_INTEGRATOR(type) \
_int.template initIntegrator<type>(nodes, ghost_type)
#define AKANTU_GAUSS_INTERGRATOR_INIT_HELPER(kind) \
template <> struct GaussIntegratorInitHelper<kind> { \
template <ElementKind k, class IOF> \
static void call(IntegratorGauss<k, IOF> & _int, \
const Array<Real> & nodes, ElementType type, \
GhostType ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INIT_INTEGRATOR, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_INIT_HELPER)
#undef AKANTU_GAUSS_INTERGRATOR_INIT_HELPER
#undef INIT_INTEGRATOR
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, ElementType type, GhostType ghost_type) {
integrator::details::GaussIntegratorInitHelper<kind>::call(*this, nodes, type,
ghost_type);
}
namespace integrator {
namespace details {
template <ElementKind kind> struct GaussIntegratorComputeJacobiansHelper {};
#define AKANTU_COMPUTE_JACOBIANS(type) \
_int.template computeJacobiansOnIntegrationPoints<type>( \
nodes, quad_points, jacobians, ghost_type, filter_elements);
#define AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS(kind) \
template <> struct GaussIntegratorComputeJacobiansHelper<kind> { \
template <ElementKind k, class IOF> \
static void \
call(const IntegratorGauss<k, IOF> & _int, const Array<Real> & nodes, \
const Matrix<Real> & quad_points, Array<Real> & jacobians, \
ElementType type, GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_JACOBIANS, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS)
#undef AKANTU_GAUSS_INTERGRATOR_COMPUTE_JACOBIANS
#undef AKANTU_COMPUTE_JACOBIANS
} // namespace details
} // namespace integrator
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
integrator::details::GaussIntegratorComputeJacobiansHelper<kind>::call(
*this, nodes, quad_points, jacobians, type, ghost_type, filter_elements);
}
} // namespace akantu
diff --git a/src/fe_engine/interpolation_element_tmpl.hh b/src/fe_engine/interpolation_element_tmpl.hh
index 74bf1d54b..13ce075a3 100644
--- a/src/fe_engine/interpolation_element_tmpl.hh
+++ b/src/fe_engine/interpolation_element_tmpl.hh
@@ -1,72 +1,74 @@
/**
* @file interpolation_element_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 06 2013
- * @date last modification: Wed Nov 29 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief interpolation property description
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_
#define AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Regular Elements */
/* -------------------------------------------------------------------------- */
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_not_defined, _itk_not_defined, 0,
0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_point_1,
_itk_lagrangian, 1, 0);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_2,
_itk_lagrangian, 2, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_segment_3,
_itk_lagrangian, 3, 1);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_3,
_itk_lagrangian, 3, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_triangle_6,
_itk_lagrangian, 6, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_4,
_itk_lagrangian, 4, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_tetrahedron_10,
_itk_lagrangian, 10, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_quadrangle_4,
_itk_lagrangian, 4, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_quadrangle_8,
_itk_lagrangian, 8, 2);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_hexahedron_8,
_itk_lagrangian, 8, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_serendip_hexahedron_20,
_itk_lagrangian, 20, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_6,
_itk_lagrangian, 6, 3);
AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(_itp_lagrange_pentahedron_15,
_itk_lagrangian, 15, 3);
} // namespace akantu
#endif /* AKANTU_INTERPOLATION_ELEMENT_TMPL_HH_ */
diff --git a/src/fe_engine/shape_cohesive.hh b/src/fe_engine/shape_cohesive.hh
index 21818137c..e5dab2beb 100644
--- a/src/fe_engine/shape_cohesive.hh
+++ b/src/fe_engine/shape_cohesive.hh
@@ -1,188 +1,191 @@
/**
* @file shape_cohesive.hh
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri May 14 2021
*
* @brief shape functions for cohesive elements description
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_COHESIVE_HH_
#define AKANTU_SHAPE_COHESIVE_HH_
namespace akantu {
struct CohesiveReduceFunctionMean {
inline Real operator()(Real u_plus, Real u_minus) {
return .5 * (u_plus + u_minus);
}
};
struct CohesiveReduceFunctionOpening {
inline Real operator()(Real u_plus, Real u_minus) {
return (u_plus - u_minus);
}
};
template <> class ShapeLagrange<_ek_cohesive> : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_cohesive");
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
ElementType type, GhostType ghost_type);
/// extract the nodal values and store them per element
template <ElementType type, class ReduceFunction>
void extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type, class ReduceFunction>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
interpolateOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/// compute the gradient of u on the integration points in the natural
/// coordinates
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
variationOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/* ------------------------------------------------------------------------ */
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
UInt /*order_d*/, GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/// multiply a field by shape functions
template <ElementType type>
void
computeNtb(const Array<Real> & /*bs*/, Array<Real> & /*Ntbs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/ = empty_filter) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeNtbN(const Array<Real> & /*bs*/, Array<Real> & /*NtbNs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/// compute the gradient of u on the integration points
template <ElementType type, class ReduceFunction>
void variationOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the normals to the field u on integration points
template <ElementType type, class ReduceFunction>
void computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
};
/// standard output stream operator
template <class ShapeFunction>
inline std::ostream & operator<<(std::ostream & stream,
const ShapeCohesive<ShapeFunction> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_cohesive_inline_impl.hh"
#endif /* AKANTU_SHAPE_COHESIVE_HH_ */
diff --git a/src/fe_engine/shape_cohesive_inline_impl.hh b/src/fe_engine/shape_cohesive_inline_impl.hh
index ce49829b1..b4ad63c0f 100644
--- a/src/fe_engine/shape_cohesive_inline_impl.hh
+++ b/src/fe_engine/shape_cohesive_inline_impl.hh
@@ -1,331 +1,333 @@
/**
* @file shape_cohesive_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 03 2012
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief ShapeCohesive inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_
#define AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline ShapeLagrange<_ek_cohesive>::ShapeLagrange(const Mesh & mesh,
UInt spatial_dimension,
const ID & id)
: ShapeLagrangeBase(mesh, spatial_dimension, _ek_cohesive, id) {}
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
/* -------------------------------------------------------------------------- */
inline void ShapeLagrange<_ek_cohesive>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
ElementType type, GhostType ghost_type) {
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & /*unused*/, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
UInt spatial_dimension = ElementClass<type>::getNaturalSpaceDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Real * shapesd_val = shape_derivatives.storage();
auto compute = [&](const auto & el) {
auto ptr = shapesd_val + el * nb_points * size_of_shapesd;
Tensor3<Real> B(ptr, spatial_dimension, nb_nodes_per_element, nb_points);
ElementClass<type>::computeDNDS(integration_points, B);
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
ShapeLagrange<_ek_cohesive>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrange<_ek_cohesive>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_itp_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
const auto & conn_array = this->mesh.getConnectivity(type, ghost_type);
auto conn = conn_array.begin(conn_array.getNbComponent() / 2, 2);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
elemental_f.resize(nb_element);
Array<Real>::matrix_iterator u_it =
elemental_f.begin(nb_degree_of_freedom, nb_nodes_per_itp_element);
ReduceFunction reduce_function;
auto compute = [&](const auto & el) {
Matrix<Real> & u = *u_it;
Matrix<UInt> el_conn(conn[el]);
// compute the average/difference of the nodal field loaded from cohesive
// element
for (UInt n = 0; n < el_conn.rows(); ++n) {
UInt node_plus = el_conn(n, 0);
UInt node_minus = el_conn(n, 1);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
Real u_plus = nodal_f(node_plus, d);
Real u_minus = nodal_f(node_minus, d);
u(d, n) = reduce_function(u_plus, u_minus);
}
}
++u_it;
};
for_each_element(nb_element, filter_elements, compute);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(this->shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes(itp_type, ghost_type), filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::variationOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
this->shapes_derivatives.exists(itp_type, ghost_type),
"No shapes for the type "
<< this->shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
this->extractNodalToElementField<type, ReduceFunction>(in_u, u_el, ghost_type,
filter_elements);
this->template gradientElementalFieldOnIntegrationPoints<type>(
u_el, nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type, class ReduceFunction>
void ShapeLagrange<_ek_cohesive>::computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_points = this->integration_points(type, ghost_type).cols();
UInt spatial_dimension = this->mesh.getSpatialDimension();
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
normals_u.resize(nb_points * nb_element);
Array<Real> tangents_u(0, (spatial_dimension * (spatial_dimension - 1)));
if (spatial_dimension > 1) {
tangents_u.resize(nb_element * nb_points);
this->template variationOnIntegrationPoints<type, ReduceFunction>(
u, tangents_u, spatial_dimension, ghost_type, filter_elements);
}
Real * tangent = tangents_u.storage();
if (spatial_dimension == 3) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Math::vectorProduct3(tangent, tangent + spatial_dimension,
normal.storage());
normal /= normal.norm();
tangent += spatial_dimension * 2;
}
} else if (spatial_dimension == 2) {
for (auto & normal : make_view(normals_u, spatial_dimension)) {
Vector<Real> a1(tangent, spatial_dimension);
normal(0) = -a1(1);
normal(1) = a1(0);
normal.normalize();
tangent += spatial_dimension;
}
} else if (spatial_dimension == 1) {
const auto facet_type = Mesh::getFacetType(type);
const auto & mesh_facets = mesh.getMeshFacets();
const auto & facets = mesh_facets.getSubelementToElement(type, ghost_type);
const auto & segments =
mesh_facets.getElementToSubelement(facet_type, ghost_type);
Real values[2];
for (auto el : arange(nb_element)) {
if (filter_elements != empty_filter) {
el = filter_elements(el);
}
for (UInt p = 0; p < 2; ++p) {
Element facet = facets(el, p);
Element segment = segments(facet.element)[0];
Vector<Real> barycenter(values + p, 1);
mesh.getBarycenter(segment, barycenter);
}
Real difference = values[0] - values[1];
AKANTU_DEBUG_ASSERT(difference != 0.,
"Error in normal computation for cohesive elements");
normals_u(el) = difference / std::abs(difference);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_SHAPE_COHESIVE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_functions.cc b/src/fe_engine/shape_functions.cc
index 80f0d33f2..b09fcafc6 100644
--- a/src/fe_engine/shape_functions.cc
+++ b/src/fe_engine/shape_functions.cc
@@ -1,241 +1,243 @@
/**
* @file shape_functions.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Tue Feb 09 2021
*
* @brief implementation of th shape functions interface
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ShapeFunctions::ShapeFunctions(const Mesh & mesh, UInt spatial_dimension,
const ID & id)
: shapes("shapes_generic", id),
shapes_derivatives("shapes_derivatives_generic", id),
mesh(mesh), _spatial_dimension(spatial_dimension) {}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void
ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
GhostType ghost_type, const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_element_filter;
if (element_filter == empty_filter) {
nb_element_filter = nb_element;
} else {
nb_element_filter = element_filter.size();
}
auto nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
auto nb_interpolation_points_per_elem =
interpolation_points_coordinates.size() / nb_element;
AKANTU_DEBUG_ASSERT(interpolation_points_coordinates.size() % nb_element == 0,
"Number of interpolation points should be a multiple of "
"total number of elements");
if (not quad_points_coordinates_inv_matrices.exists(type, ghost_type)) {
quad_points_coordinates_inv_matrices.alloc(
nb_element_filter, nb_quad_per_element * nb_quad_per_element, type,
ghost_type);
} else {
quad_points_coordinates_inv_matrices(type, ghost_type)
.resize(nb_element_filter);
}
if (!interpolation_points_coordinates_matrices.exists(type, ghost_type)) {
interpolation_points_coordinates_matrices.alloc(
nb_element_filter,
nb_interpolation_points_per_elem * nb_quad_per_element, type,
ghost_type);
} else {
interpolation_points_coordinates_matrices(type, ghost_type)
.resize(nb_element_filter);
}
Array<Real> & quad_inv_mat =
quad_points_coordinates_inv_matrices(type, ghost_type);
Array<Real> & interp_points_mat =
interpolation_points_coordinates_matrices(type, ghost_type);
Matrix<Real> quad_coord_matrix(nb_quad_per_element, nb_quad_per_element);
Array<Real>::const_matrix_iterator quad_coords_it =
quadrature_points_coordinates.begin_reinterpret(
spatial_dimension, nb_quad_per_element, nb_element_filter);
Array<Real>::const_matrix_iterator points_coords_begin =
interpolation_points_coordinates.begin_reinterpret(
spatial_dimension, nb_interpolation_points_per_elem, nb_element);
Array<Real>::matrix_iterator inv_quad_coord_it =
quad_inv_mat.begin(nb_quad_per_element, nb_quad_per_element);
Array<Real>::matrix_iterator int_points_mat_it = interp_points_mat.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
/// loop over the elements of the current material and element type
for (UInt el = 0; el < nb_element_filter;
++el, ++inv_quad_coord_it, ++int_points_mat_it, ++quad_coords_it) {
/// matrix containing the quadrature points coordinates
const Matrix<Real> & quad_coords = *quad_coords_it;
/// matrix to store the matrix inversion result
Matrix<Real> & inv_quad_coord_matrix = *inv_quad_coord_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(quad_coords,
quad_coord_matrix);
/// invert the interpolation matrix
inv_quad_coord_matrix.inverse(quad_coord_matrix);
/// matrix containing the interpolation points coordinates
const Matrix<Real> & points_coords =
points_coords_begin[element_filter(el)];
/// matrix to store the interpolation points coordinates
/// compatible with these functions
Matrix<Real> & inv_points_coord_matrix = *int_points_mat_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(points_coords,
inv_points_coord_matrix);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
for (auto ghost_type : ghost_types) {
auto types_iterable = mesh.elementTypes(spatial_dimension, ghost_type);
if (element_filter != nullptr) {
types_iterable =
element_filter->elementTypes(spatial_dimension, ghost_type);
}
for (auto type : types_iterable) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
continue;
}
const Array<UInt> * elem_filter;
if (element_filter != nullptr) {
elem_filter = &((*element_filter)(type, ghost_type));
} else {
elem_filter = &(empty_filter);
}
#define AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS(type) \
this->initElementalFieldInterpolationFromIntegrationPoints<type>( \
interpolation_points_coordinates(type, ghost_type), \
interpolation_points_coordinates_matrices, \
quad_points_coordinates_inv_matrices, \
quadrature_points_coordinates(type, ghost_type), ghost_type, \
*elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS);
#undef AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
auto types_iterable = mesh.elementTypes(spatial_dimension, ghost_type);
if (element_filter != nullptr) {
types_iterable =
element_filter->elementTypes(spatial_dimension, ghost_type);
}
for (auto type : types_iterable) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
continue;
}
const Array<UInt> * elem_filter;
if (element_filter != nullptr) {
elem_filter = &((*element_filter)(type, ghost_type));
} else {
elem_filter = &(empty_filter);
}
#define AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS(type) \
interpolateElementalFieldFromIntegrationPoints<type>( \
field(type, ghost_type), \
interpolation_points_coordinates_matrices(type, ghost_type), \
quad_points_coordinates_inv_matrices(type, ghost_type), result, \
ghost_type, *elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS);
#undef AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/shape_functions.hh b/src/fe_engine/shape_functions.hh
index 96b5f4d07..b4ce221c1 100644
--- a/src/fe_engine/shape_functions.hh
+++ b/src/fe_engine/shape_functions.hh
@@ -1,214 +1,216 @@
/**
* @file shape_functions.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief shape function class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_FUNCTIONS_HH_
#define AKANTU_SHAPE_FUNCTIONS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeFunctions(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape");
virtual ~ShapeFunctions() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << space << "Shapes [" << std::endl;
integration_points.printself(stream, indent + 1);
// shapes.printself(stream, indent + 1);
// shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/// set the integration points for a given element
template <ElementType type>
void setIntegrationPointsByType(const Matrix<Real> & integration_points,
GhostType ghost_type);
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const;
protected:
/// interpolate nodal values stored by element on the integration points
template <ElementType type>
void interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, GhostType ghost_type,
const Array<Real> & shapes,
const Array<UInt> & filter_elements = empty_filter) const;
/// gradient of nodal values stored by element on the control points
template <ElementType type>
void gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
GhostType ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const;
protected:
/// By element versions of non-templated eponym methods
template <ElementType type>
inline void interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const Array<UInt> & element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
template <ElementType type>
inline void initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
GhostType ghost_type, const Array<UInt> & element_filter) const;
/// build matrix for the interpolation of field form integration points
template <ElementType type>
inline void buildElementalFieldInterpolationMatrix(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order =
ElementClassProperty<type>::polynomial_degree) const;
/// build the so called interpolation matrix (first collumn is 1, then the
/// other collumns are the traansposed coordinates)
static inline void buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order);
public:
virtual void onElementsAdded(const Array<Element> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
virtual void onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the size of the shapes returned by the element class
static inline UInt getShapeSize(ElementType type);
/// get the size of the shapes derivatives returned by the element class
static inline UInt getShapeDerivativesSize(ElementType type);
inline const Matrix<Real> &
getIntegrationPoints(ElementType type,
GhostType ghost_type) const {
return integration_points(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> &
getShapes(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get a the shapes derivatives vector
inline const Array<Real> &
getShapesDerivatives(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// shape functions for all elements
ElementTypeMapArray<Real, InterpolationType> shapes;
/// shape functions derivatives for all elements
ElementTypeMapArray<Real, InterpolationType> shapes_derivatives;
/// associated mesh
const Mesh & mesh;
// spatial dimension of the elements to consider
UInt _spatial_dimension;
/// shape functions for all elements
ElementTypeMap<Matrix<Real>> integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ShapeFunctions & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_functions_inline_impl.hh"
#endif /* AKANTU_SHAPE_FUNCTIONS_HH_ */
diff --git a/src/fe_engine/shape_functions_inline_impl.hh b/src/fe_engine/shape_functions_inline_impl.hh
index 14f870227..5c8a09164 100644
--- a/src/fe_engine/shape_functions_inline_impl.hh
+++ b/src/fe_engine/shape_functions_inline_impl.hh
@@ -1,414 +1,416 @@
/**
* @file shape_functions_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 27 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Sat Dec 19 2020
*
* @brief ShapeFunctions inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_
#define AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
ShapeFunctions::getShapes(ElementType el_type,
GhostType ghost_type) const {
return shapes(FEEngine::getInterpolationType(el_type), ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> &
ShapeFunctions::getShapesDerivatives(ElementType el_type,
GhostType ghost_type) const {
return shapes_derivatives(FEEngine::getInterpolationType(el_type),
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeSize(ElementType type) {
AKANTU_DEBUG_IN();
UInt shape_size = 0;
#define GET_SHAPE_SIZE(type) shape_size = ElementClass<type>::getShapeSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_SIZE); // ,
#undef GET_SHAPE_SIZE
AKANTU_DEBUG_OUT();
return shape_size;
}
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeDerivativesSize(ElementType type) {
AKANTU_DEBUG_IN();
UInt shape_derivatives_size = 0;
#define GET_SHAPE_DERIVATIVES_SIZE(type) \
shape_derivatives_size = ElementClass<type>::getShapeDerivativesSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_DERIVATIVES_SIZE); // ,
#undef GET_SHAPE_DERIVATIVES_SIZE
AKANTU_DEBUG_OUT();
return shape_derivatives_size;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::setIntegrationPointsByType(const Matrix<Real> & points,
GhostType ghost_type) {
if (not this->integration_points.exists(type, ghost_type)) {
this->integration_points(type, ghost_type).shallowCopy(points);
}
}
/* -------------------------------------------------------------------------- */
inline void
ShapeFunctions::buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order) {
switch (integration_order) {
case 1: {
for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
}
break;
}
case 2: {
UInt nb_quadrature_points = coordMatrix.cols();
for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
for (UInt j = 1; j < nb_quadrature_points; ++j) {
coordMatrix(i, j) = coordinates(j - 1, i);
}
}
break;
}
default: {
AKANTU_TO_IMPLEMENT();
break;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix(
const Matrix<Real> & /*unused*/, Matrix<Real> & /*unused*/,
UInt /*unused*/) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_2>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_3>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_3>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_6>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_4>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_10>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/**
* @todo Write a more efficient interpolation for quadrangles by
* dropping unnecessary quadrature points
*
*/
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_4>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_4>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_8>(
const Matrix<Real> & /*unused*/ coordinates,
Matrix<Real> & /*unused*/ coordMatrix,
UInt /*unused*/ integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_8>::polynomial_degree) {
AKANTU_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
// UInt j = 0;
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
// for (UInt e = 0; e <= 2; ++e) {
// for (UInt n = 0; n <= 2; ++n) {
// coordMatrix(i, j) = std::pow(x, e) * std::pow(y, n);
// ++j;
// }
// }
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, GhostType ghost_type,
const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
auto nb_element = this->mesh.getNbElement(type, ghost_type);
auto nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
auto nb_interpolation_points_per_elem =
interpolation_points_coordinates_matrices.getNbComponent() /
nb_quad_per_element;
if (not result.exists(type, ghost_type)) {
result.alloc(nb_element * nb_interpolation_points_per_elem,
field.getNbComponent(), type, ghost_type);
}
if (element_filter != empty_filter) {
nb_element = element_filter.size();
}
Matrix<Real> coefficients(nb_quad_per_element, field.getNbComponent());
auto & result_vec = result(type, ghost_type);
auto field_it = field.begin_reinterpret(field.getNbComponent(),
nb_quad_per_element, nb_element);
auto interpolation_points_coordinates_it =
interpolation_points_coordinates_matrices.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
auto result_begin = result_vec.begin_reinterpret(
field.getNbComponent(), nb_interpolation_points_per_elem,
result_vec.size() / nb_interpolation_points_per_elem);
auto inv_quad_coord_it = quad_points_coordinates_inv_matrices.begin(
nb_quad_per_element, nb_quad_per_element);
/// loop over the elements of the current filter and element type
for (UInt el = 0; el < nb_element; ++el, ++field_it, ++inv_quad_coord_it,
++interpolation_points_coordinates_it) {
/**
* matrix containing the inversion of the quadrature points'
* coordinates
*/
const auto & inv_quad_coord_matrix = *inv_quad_coord_it;
/**
* multiply it by the field values over quadrature points to get
* the interpolation coefficients
*/
coefficients.mul<false, true>(inv_quad_coord_matrix, *field_it);
/// matrix containing the points' coordinates
const auto & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the
/// result
Matrix<Real> res(result_begin[element_filter(el)]);
res.mul<true, true>(coefficients, coord);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, GhostType ghost_type,
const Array<Real> & shapes, const Array<UInt> & filter_elements) const {
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getShapeSize();
auto nb_points = shapes.size() / mesh.getNbElement(type, ghost_type);
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
Array<Real>::const_matrix_iterator N_it;
Array<Real> * filtered_N = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_N = new Array<Real>(0, shapes.getNbComponent());
FEEngine::filterElementalData(mesh, shapes, *filtered_N, type, ghost_type,
filter_elements);
N_it = filtered_N->begin_reinterpret(nb_nodes_per_element, nb_points,
nb_element);
} else {
N_it =
shapes.begin_reinterpret(nb_nodes_per_element, nb_points, nb_element);
}
uq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto inter_u_it =
uq.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++N_it, ++u_it, ++inter_u_it) {
const auto & u = *u_it;
const auto & N = *N_it;
auto & inter_u = *inter_u_it;
inter_u.template mul<false, false>(u, N);
}
delete filtered_N;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
GhostType ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
auto nb_points = integration_points(type, ghost_type).cols();
auto element_dimension = ElementClass<type>::getNaturalSpaceDimension();
auto nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
auto nb_element = mesh.getNbElement(type, ghost_type);
Array<Real>::const_matrix_iterator B_it;
Array<Real> * filtered_B = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filtered_B = new Array<Real>(0, shapes_derivatives.getNbComponent());
FEEngine::filterElementalData(mesh, shapes_derivatives, *filtered_B, type,
ghost_type, filter_elements);
B_it = filtered_B->begin(element_dimension, nb_nodes_per_element);
} else {
B_it = shapes_derivatives.begin(element_dimension, nb_nodes_per_element);
}
out_nablauq.resize(nb_element * nb_points);
auto u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
auto nabla_u_it = out_nablauq.begin(nb_degree_of_freedom, element_dimension);
for (UInt el = 0; el < nb_element; ++el, ++u_it) {
const auto & u = *u_it;
for (UInt q = 0; q < nb_points; ++q, ++B_it, ++nabla_u_it) {
const auto & B = *B_it;
auto & nabla_u = *nabla_u_it;
nabla_u.template mul<false, true>(u, B);
}
}
delete filtered_B;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_SHAPE_FUNCTIONS_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_lagrange.hh b/src/fe_engine/shape_lagrange.hh
index 23cd96a4b..81f4a47c9 100644
--- a/src/fe_engine/shape_lagrange.hh
+++ b/src/fe_engine/shape_lagrange.hh
@@ -1,176 +1,180 @@
/**
* @file shape_lagrange.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri May 14 2021
*
* @brief lagrangian shape functions class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_LAGRANGE_HH_
#define AKANTU_SHAPE_LAGRANGE_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Shape> class ShapeCohesive;
class ShapeIGFEM;
template <ElementKind kind> class ShapeLagrange : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_lagrange");
~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialization function for structural elements not yet implemented
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
ElementType type,
GhostType ghost_type);
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, ElementType type,
GhostType ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void
precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & real_coords, UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
GhostType ghost_type) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void computeBtD(const Array<Real> & Ds, Array<Real> & BtDs,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
template <ElementType type>
void computeBtDB(const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// multiply a field by shape functions @f$ fts_{ij} = f_i * \varphi_j @f$
template <ElementType type>
void computeNtb(const Array<Real> & bs, Array<Real> & Ntbs,
GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void computeNtbN(const Array<Real> & bs, Array<Real> & NtbNs,
GhostType ghost_type,
const Array<UInt> & filter_elements) const;
/// find natural coords from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords,
GhostType ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
template <ElementType type>
bool contains(const Vector<Real> & real_coords, UInt elem,
GhostType ghost_type) const;
/// compute the shape on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & real_coords, UInt elem,
Vector<Real> & shapes, GhostType ghost_type) const;
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & real_coords, UInt elem,
Tensor3<Real> & shapes,
GhostType ghost_type) const;
protected:
/// compute the shape derivatives on integration points for a given element
template <ElementType type>
inline void
computeShapeDerivativesOnCPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_inline_impl.hh"
#endif /* AKANTU_SHAPE_LAGRANGE_HH_ */
diff --git a/src/fe_engine/shape_lagrange_base.cc b/src/fe_engine/shape_lagrange_base.cc
index 9ba9ec3e7..c30cd5d1f 100644
--- a/src/fe_engine/shape_lagrange_base.cc
+++ b/src/fe_engine/shape_lagrange_base.cc
@@ -1,171 +1,174 @@
/**
* @file shape_lagrange_base.cc
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Dec 09 2020
*
- * @brief common par for the shape lagrange
+ * @brief common part for the shape lagrange
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
ShapeLagrangeBase::ShapeLagrangeBase(const Mesh & mesh, UInt spatial_dimension,
ElementKind kind, const ID & id)
: ShapeFunctions(mesh, spatial_dimension, id), _kind(kind) {}
/* -------------------------------------------------------------------------- */
ShapeLagrangeBase::~ShapeLagrangeBase() = default;
/* -------------------------------------------------------------------------- */
#define AKANTU_COMPUTE_SHAPES(type) \
_this.template computeShapesOnIntegrationPoints<type>( \
nodes, integration_points, shapes, ghost_type, filter_elements)
namespace shape_lagrange {
namespace details {
template <ElementKind kind> struct Helper {
template <class S>
static void call(const S & /*unused*/, const Array<Real> & /*unused*/,
const Matrix<Real> & /*unused*/,
Array<Real> & /*unused*/, ElementType /*unused*/,
GhostType /*unused*/,
const Array<UInt> & /*unused*/) {
AKANTU_TO_IMPLEMENT();
}
};
#if !defined(DOXYGEN)
#define AKANTU_COMPUTE_SHAPES_KIND(kind) \
template <> struct Helper<kind> { \
template <class S> \
static void call(const S & _this, const Array<Real> & nodes, \
const Matrix<Real> & integration_points, \
Array<Real> & shapes, ElementType type, \
GhostType ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_COMPUTE_SHAPES_KIND,
AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE)
} // namespace details
} // namespace shape_lagrange
#endif
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, ElementType type,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
auto kind = Mesh::getKind(type);
#define AKANTU_COMPUTE_SHAPES_KIND_SWITCH(kind) \
shape_lagrange::details::Helper<kind>::call( \
*this, nodes, integration_points, shapes, type, ghost_type, \
filter_elements);
AKANTU_BOOST_LIST_SWITCH(
AKANTU_COMPUTE_SHAPES_KIND_SWITCH,
BOOST_PP_LIST_TO_SEQ(AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE), kind);
#undef AKANTU_COMPUTE_SHAPES
#undef AKANTU_COMPUTE_SHAPES_KIND
#undef AKANTU_COMPUTE_SHAPES_KIND_SWITCH
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsAdded(const Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
const auto & nodes = mesh.getNodes();
for (auto elements_range : MeshElementsByTypes(new_elements)) {
auto type = elements_range.getType();
auto ghost_type = elements_range.getGhostType();
if (mesh.getSpatialDimension(type) != _spatial_dimension) {
continue;
}
if (mesh.getKind(type) != _kind) {
continue;
}
const auto & elements = elements_range.getElements();
auto itp_type = FEEngine::getInterpolationType(type);
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
const auto & natural_coords = integration_points(type, ghost_type);
computeShapesOnIntegrationPoints(nodes, natural_coords,
shapes(itp_type, ghost_type), type,
ghost_type, elements);
if (_spatial_dimension != mesh.getSpatialDimension()) {
continue;
}
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
computeShapeDerivativesOnIntegrationPoints(
nodes, natural_coords, shapes_derivatives(itp_type, ghost_type), type,
ghost_type, elements);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::onElementsRemoved(
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & new_numbering) {
this->shapes.onElementsRemoved(new_numbering);
this->shapes_derivatives.onElementsRemoved(new_numbering);
}
/* -------------------------------------------------------------------------- */
void ShapeLagrangeBase::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Shapes Lagrange [" << std::endl;
ShapeFunctions::printself(stream, indent + 1);
shapes.printself(stream, indent + 1);
shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/fe_engine/shape_lagrange_base.hh b/src/fe_engine/shape_lagrange_base.hh
index a033026c4..2770dfe4f 100644
--- a/src/fe_engine/shape_lagrange_base.hh
+++ b/src/fe_engine/shape_lagrange_base.hh
@@ -1,88 +1,90 @@
/**
* @file shape_lagrange_base.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Base class for the shape lagrange
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_LAGRANGE_BASE_HH_
#define AKANTU_SHAPE_LAGRANGE_BASE_HH_
namespace akantu {
class ShapeLagrangeBase : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrangeBase(const Mesh & mesh, UInt spatial_dimension, ElementKind kind,
const ID & id = "shape_lagrange");
~ShapeLagrangeBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the shape functions for given interpolation points
virtual void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
virtual void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
void
onElementsRemoved(const Array<Element> & elements,
const ElementTypeMapArray<UInt> & new_numbering) override;
protected:
/// The kind to consider
ElementKind _kind;
};
} // namespace akantu
#include "shape_lagrange_base_inline_impl.hh"
#endif /* AKANTU_SHAPE_LAGRANGE_BASE_HH_ */
diff --git a/src/fe_engine/shape_lagrange_base_inline_impl.hh b/src/fe_engine/shape_lagrange_base_inline_impl.hh
index d809c5fd1..e799f8280 100644
--- a/src/fe_engine/shape_lagrange_base_inline_impl.hh
+++ b/src/fe_engine/shape_lagrange_base_inline_impl.hh
@@ -1,85 +1,87 @@
/**
* @file shape_lagrange_base_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 09 2017
- * @date last modification: Wed Oct 11 2017
+ * @date last modification: Tue Sep 29 2020
*
- * @brief A Documented file.
+ * @brief common part for the shape lagrange
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_
#define AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeLagrangeBase::computeShapesOnIntegrationPoints(
const Array<Real> & /*unused*/, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
shapes.resize(nb_element * nb_points);
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), nb_points,
nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
for (UInt elem = 0; elem < nb_element; ++elem) {
if (filter_elements != empty_filter) {
shapes_it = shapes_begin + filter_elements(elem);
}
Matrix<Real> & N = *shapes_it;
ElementClass<type>::computeShapes(integration_points, N);
if (filter_elements == empty_filter) {
++shapes_it;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_SHAPE_LAGRANGE_BASE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_lagrange_inline_impl.hh b/src/fe_engine/shape_lagrange_inline_impl.hh
index 0cd7ee9c4..c25921523 100644
--- a/src/fe_engine/shape_lagrange_inline_impl.hh
+++ b/src/fe_engine/shape_lagrange_inline_impl.hh
@@ -1,579 +1,582 @@
/**
* @file shape_lagrange_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 27 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri May 14 2021
*
* @brief ShapeLagrange inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "aka_voigthelper.hh"
#include "fe_engine.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_
#define AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
if (ElementClass<type>::getNaturalSpaceDimension() == \
mesh.getSpatialDimension() || \
kind != _ek_regular) \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <ElementKind kind>
inline void ShapeLagrange<kind>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
ElementType type, GhostType ghost_type) {
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
inline void ShapeLagrange<kind>::computeShapeDerivativesOnCPointsByElement(
const Matrix<Real> & node_coords, const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const {
AKANTU_DEBUG_IN();
// compute dnds
Tensor3<Real> dnds(node_coords.rows(), node_coords.cols(),
natural_coords.cols());
ElementClass<type>::computeDNDS(natural_coords, dnds);
// compute jacobian
Tensor3<Real> J(node_coords.rows(), natural_coords.rows(),
natural_coords.cols());
ElementClass<type>::computeJMat(dnds, node_coords, J);
// compute dndx
ElementClass<type>::computeShapeDerivatives(J, dnds, shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::inverseMap(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & natural_coords,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
ElementClass<type>::inverseMap(real_coords, nodes_coord, natural_coords);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
bool ShapeLagrange<kind>::contains(const Vector<Real> & real_coords, UInt elem,
GhostType ghost_type) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
return ElementClass<type>::contains(natural_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolate(const Vector<Real> & real_coords,
UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
GhostType ghost_type) const {
UInt nb_shapes = ElementClass<type>::getShapeSize();
Vector<Real> shapes(nb_shapes);
computeShapes<type>(real_coords, elem, shapes, ghost_type);
ElementClass<type>::interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapes(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & shapes,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
ElementClass<type>::computeShapes(natural_coords, shapes);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivatives(
const Matrix<Real> & real_coords, UInt elem, Tensor3<Real> & shapesd,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_points = real_coords.cols();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == shapesd.size(0) &&
nb_nodes_per_element == shapesd.size(1),
"Shape size doesn't match");
AKANTU_DEBUG_ASSERT(nb_points == shapesd.size(2),
"Number of points doesn't match shapes size");
Matrix<Real> natural_coords(spatial_dimension, nb_points);
// Creates the matrix of natural coordinates
for (UInt i = 0; i < nb_points; i++) {
Vector<Real> real_point = real_coords(i);
Vector<Real> natural_point = natural_coords(i);
inverseMap<type>(real_point, elem, natural_point, ghost_type);
}
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
computeShapeDerivativesOnCPointsByElement<type>(nodes_coord, natural_coords,
shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
ShapeLagrange<kind>::ShapeLagrange(const Mesh & mesh, UInt spatial_dimension,
const ID & id)
: ShapeLagrangeBase(mesh, spatial_dimension, kind, id) {}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type,
filter_elements);
Real * shapesd_val = shape_derivatives.storage();
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
if (filter_elements != empty_filter) {
shapesd_val = shape_derivatives.storage() +
filter_elements(elem) * size_of_shapesd * nb_points;
}
Matrix<Real> & X = *x_it;
Tensor3<Real> B(shapesd_val, spatial_dimension, nb_nodes_per_element,
nb_points);
computeShapeDerivativesOnCPointsByElement<type>(X, integration_points, B);
if (filter_elements == empty_filter) {
shapesd_val += size_of_shapesd * nb_points;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, ElementType type, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
#define AKANTU_COMPUTE_SHAPES(type) \
computeShapeDerivativesOnIntegrationPoints<type>( \
nodes, integration_points, shape_derivatives, ghost_type, \
filter_elements);
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(AKANTU_COMPUTE_SHAPES);
#undef AKANTU_COMPUTE_SHAPES
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< shapes.printType(itp_type, ghost_type));
this->interpolateOnIntegrationPoints<type>(in_u, out_uq, nb_degree_of_freedom,
shapes(itp_type, ghost_type),
ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
shapes_derivatives.exists(itp_type, ghost_type),
"No shapes derivatives for the type "
<< shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->gradientElementalFieldOnIntegrationPoints<type>(
u_el, out_nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
auto spatial_dimension = mesh.getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view =
make_view(shapes_derivatives, spatial_dimension, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_derivatives_filtered, spatial_dimension,
nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values :
zip(range(B_it, B_end),
make_view(Ds, Ds.getNbComponent() / spatial_dimension,
spatial_dimension),
make_view(BtDs, BtDs.getNbComponent() / nb_nodes_per_element,
nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
// transposed due to the storage layout of B
Bt_D.template mul<false, false>(D, B);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeBtDB(
const Array<Real> & Ds, Array<Real> & BtDBs, UInt order_d,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
constexpr auto dim = ElementClass<type>::getSpatialDimension();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, dim, nb_nodes_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, dim, nb_nodes_per_element);
B_it = view.begin();
B_end = view.end();
}
if (order_d == 4) {
UInt tangent_size = VoigtHelper<dim>::size;
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, tangent_size, tangent_size),
make_view(BtDBs, dim * nb_nodes_per_element,
dim * nb_nodes_per_element))) {
const auto & Bfull = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(Bfull, B,
nb_nodes_per_element);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
} else if (order_d == 2) {
Matrix<Real> Bt_D(nb_nodes_per_element, dim);
for (auto && values :
zip(range(B_it, B_end), make_view(Ds, dim, dim),
make_view(BtDBs, nb_nodes_per_element, nb_nodes_per_element))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D_B = std::get<2>(values);
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
}
}
template <>
template <>
inline void ShapeLagrange<_ek_regular>::computeBtDB<_point_1>(
const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/, UInt /*order_d*/,
GhostType /*ghost_type*/, const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeNtbN(
const Array<Real> & bs, Array<Real> & NtbNs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto size_of_shapes = ElementClass<type>::getShapeSize();
auto nb_degree_of_freedom = bs.getNbComponent();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> shapes_filtered(0, size_of_shapes);
auto && view = make_view(shapes(itp_type, ghost_type), 1, size_of_shapes);
auto N_it = view.begin();
auto N_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes(itp_type, ghost_type),
shapes_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_filtered, 1, size_of_shapes);
N_it = view.begin();
N_end = view.end();
}
Matrix<Real> Nt_b(nb_nodes_per_element, nb_degree_of_freedom);
for (auto && values :
zip(range(N_it, N_end), make_view(bs, nb_degree_of_freedom, 1),
make_view(NtbNs, nb_nodes_per_element, nb_nodes_per_element))) {
const auto & N = std::get<0>(values);
const auto & b = std::get<1>(values);
auto & Nt_b_N = std::get<2>(values);
Nt_b.template mul<true, false>(N, b);
Nt_b_N.template mul<false, false>(Nt_b, N);
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeNtb(
const Array<Real> & bs, Array<Real> & Ntbs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
Ntbs.resize(bs.size());
auto size_of_shapes = ElementClass<type>::getShapeSize();
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto nb_degree_of_freedom = bs.getNbComponent();
Array<Real> shapes_filtered(0, size_of_shapes);
auto && view = make_view(shapes(itp_type, ghost_type), 1, size_of_shapes);
auto N_it = view.begin();
auto N_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes(itp_type, ghost_type),
shapes_filtered, type, ghost_type,
filter_elements);
auto && view = make_view(shapes_filtered, 1, size_of_shapes);
N_it = view.begin();
N_end = view.end();
}
for (auto && values :
zip(make_view(bs, nb_degree_of_freedom, 1), range(N_it, N_end),
make_view(Ntbs, nb_degree_of_freedom, size_of_shapes))) {
const auto & b = std::get<0>(values);
const auto & N = std::get<1>(values);
auto & Ntb = std::get<2>(values);
Ntb.template mul<false, false>(b, N);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_SHAPE_LAGRANGE_INLINE_IMPL_HH_ */
diff --git a/src/fe_engine/shape_structural.cc b/src/fe_engine/shape_structural.cc
index 16d6d9ca0..698854eae 100644
--- a/src/fe_engine/shape_structural.cc
+++ b/src/fe_engine/shape_structural.cc
@@ -1,52 +1,54 @@
/**
* @file shape_structural.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Thu Dec 21 2017
+ * @date last modification: Tue Aug 27 2019
*
* @brief ShapeStructural implementation
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_structural.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
ShapeStructural<_ek_structural>::ShapeStructural(Mesh & mesh,
UInt spatial_dimension,
const ID & id)
: ShapeFunctions(mesh, spatial_dimension, id),
rotation_matrices("rotation_matrices", id) {}
/* -------------------------------------------------------------------------- */
template <> ShapeStructural<_ek_structural>::~ShapeStructural() = default;
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/fe_engine/shape_structural.hh b/src/fe_engine/shape_structural.hh
index 763f96619..e2668d85e 100644
--- a/src/fe_engine/shape_structural.hh
+++ b/src/fe_engine/shape_structural.hh
@@ -1,199 +1,201 @@
/**
* @file shape_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri May 14 2021
*
* @brief shape class for element with different set of shapes functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_STRUCTURAL_HH_
#define AKANTU_SHAPE_STRUCTURAL_HH_
namespace akantu {
template <ElementKind kind> class ShapeStructural : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// Ctors/Dtors should be explicitely implemented for _ek_structural
public:
ShapeStructural(Mesh & mesh, UInt spatial_dimension,
const ID & id = "shape_structural");
~ShapeStructural() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override {
std::string space(indent, AKANTU_INDENT);
stream << space << "ShapesStructural [" << std::endl;
rotation_matrices.printself(stream, indent + 1);
ShapeFunctions::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
private:
template <ElementType type>
void computeShapesOnIntegrationPointsInternal(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter,
bool mass = false) const;
public:
/// compute shape functions on given integration points
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const {
this->template computeShapesOnIntegrationPointsInternal<type>(
nodes, integration_points, shapes, ghost_type, filter_elements, false);
}
template <ElementType type>
void computeShapesMassOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements = empty_filter) const {
this->template computeShapesOnIntegrationPointsInternal<type>(
nodes, integration_points, shapes, ghost_type, filter_elements, true);
}
/// initialization function for structural elements
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
ElementType type, GhostType ghost_type);
/// precompute the rotation matrices for the elements dofs
template <ElementType type>
void precomputeRotationMatrices(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_dof,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_dof,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
const Matrix<Real> & /*nodal_values*/,
Vector<Real> & /*interpolated*/,
GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shapes on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & /*real_coords*/, UInt /*elem*/,
Vector<Real> & /*shapes*/,
GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & /*real_coords*/,
UInt /*elem*/, Tensor3<Real> & /*shapes*/,
GhostType /*ghost_type*/) const {
AKANTU_TO_IMPLEMENT();
}
/// get the rotations vector
inline const Array<Real> &
getRotations(ElementType el_type, __attribute__((unused))
GhostType ghost_type = _not_ghost) const {
return rotation_matrices(el_type);
}
/* ------------------------------------------------------------------------ */
template <ElementType type>
void computeBtD(const Array<Real> & /*Ds*/, Array<Real> & /*BtDs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeBtDB(const Array<Real> & /*Ds*/, Array<Real> & /*BtDBs*/,
UInt /*order_d*/, GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
template <ElementType type>
void computeNtbN(const Array<Real> & /*bs*/, Array<Real> & /*NtbNs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/) const {
AKANTU_TO_IMPLEMENT();
}
/// multiply a field by shape functions
template <ElementType type>
void
computeNtb(const Array<Real> & /*bs*/, Array<Real> & /*Ntbs*/,
GhostType /*ghost_type*/,
const Array<UInt> & /*filter_elements*/ = empty_filter) const {
AKANTU_TO_IMPLEMENT();
}
protected:
ElementTypeMapArray<Real> rotation_matrices;
};
} // namespace akantu
#include "shape_structural_inline_impl.hh"
#endif /* AKANTU_SHAPE_STRUCTURAL_HH_ */
diff --git a/src/fe_engine/shape_structural_inline_impl.hh b/src/fe_engine/shape_structural_inline_impl.hh
index 820898908..6005cb75a 100644
--- a/src/fe_engine/shape_structural_inline_impl.hh
+++ b/src/fe_engine/shape_structural_inline_impl.hh
@@ -1,509 +1,511 @@
/**
* @file shape_structural_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 11 2017
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Mon Feb 01 2021
*
* @brief ShapeStructural inline implementation
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "shape_structural.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_
#define AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_
namespace akantu {
namespace {
/// Extract nodal coordinates per elements
template <ElementType type>
std::unique_ptr<Array<Real>> getNodesPerElement(const Mesh & mesh,
const Array<Real> & nodes,
GhostType ghost_type) {
const auto dim = ElementClass<type>::getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nodes_per_element =
std::make_unique<Array<Real>>(0, dim * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, *nodes_per_element, type,
ghost_type);
return nodes_per_element;
}
} // namespace
template <ElementKind kind>
inline void ShapeStructural<kind>::initShapeFunctions(
const Array<Real> & /* unused */, const Matrix<Real> & /* unused */,
ElementType /* unused */, GhostType /* unused */) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeRotationMatrices<type>(nodes, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <>
inline void ShapeStructural<_ek_structural>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
ElementType type, GhostType ghost_type) {
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::computeShapesOnIntegrationPointsInternal(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements, bool mass) const {
auto nb_points = integration_points.cols();
auto nb_element = mesh.getConnectivity(type, ghost_type).size();
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
shapes.resize(nb_element * nb_points);
auto nb_dofs = ElementClass<type>::getNbDegreeOfFreedom();
auto nb_rows = nb_dofs;
if (mass) {
nb_rows = ElementClass<type>::getNbStressComponents();
}
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = nb_rows * nb_dofs * nb_nodes_per_element;
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
auto shapes_it = shapes.begin_reinterpret(
nb_rows, ElementClass<type>::getNbNodesPerInterpolationElement() * nb_dofs,
nb_points, nb_element);
auto shapes_begin = shapes_it;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
}
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
auto nodes_it = nodes_per_element->begin(mesh.getSpatialDimension(),
Mesh::getNbNodesPerElement(type));
auto nodes_begin = nodes_it;
auto rot_matrix_it =
make_view(rotation_matrices(type, ghost_type), nb_dofs, nb_dofs).begin();
auto rot_matrix_begin = rot_matrix_it;
for (UInt elem = 0; elem < nb_element; ++elem) {
if (filter_elements != empty_filter) {
shapes_it = shapes_begin + filter_elements(elem);
nodes_it = nodes_begin + filter_elements(elem);
rot_matrix_it = rot_matrix_begin + filter_elements(elem);
}
Tensor3<Real> & N = *shapes_it;
auto & real_coord = *nodes_it;
auto & RDOFs = *rot_matrix_it;
Matrix<Real> T(N.size(1), N.size(1), 0);
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
T.block(RDOFs, i * RDOFs.rows(), i * RDOFs.rows());
}
if (not mass) {
ElementClass<type>::computeShapes(integration_points, real_coord, T, N);
} else {
ElementClass<type>::computeShapesMass(integration_points, real_coord, T,
N);
}
if (filter_elements == empty_filter) {
++shapes_it;
++nodes_it;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeRotationMatrices(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto spatial_dimension = mesh.getSpatialDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
if (not this->rotation_matrices.exists(type, ghost_type)) {
this->rotation_matrices.alloc(0, nb_dof * nb_dof, type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
rot_matrices.resize(nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
bool has_extra_normal = mesh.hasData<Real>("extra_normal", type, ghost_type);
Array<Real>::const_vector_iterator extra_normal;
if (has_extra_normal) {
extra_normal = mesh.getData<Real>("extra_normal", type, ghost_type)
.begin(spatial_dimension);
}
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & R = std::get<1>(tuple);
if (has_extra_normal) {
ElementClass<type>::computeRotationMatrix(R, X, *extra_normal);
++extra_normal;
} else {
ElementClass<type>::computeRotationMatrix(
R, X, Vector<Real>(spatial_dimension));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_points = integration_points(type, ghost_type).cols();
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto dim = ElementClass<type>::getSpatialDimension();
const auto spatial_dimension = mesh.getSpatialDimension();
const auto natural_spatial_dimension =
ElementClass<type>::getNaturalSpaceDimension();
auto itp_type = FEEngine::getInterpolationType(type);
if (not shapes.exists(itp_type, ghost_type)) {
auto size_of_shapes = this->getShapeSize(type);
this->shapes.alloc(0, size_of_shapes, itp_type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
auto & shapes_ = this->shapes(itp_type, ghost_type);
shapes_.resize(nb_element * nb_points);
auto nodes_per_element = getNodesPerElement<type>(mesh, nodes, ghost_type);
for (auto && tuple :
zip(make_view(shapes_, nb_dof, nb_dof * nb_nodes_per_element, nb_points),
make_view(*nodes_per_element, dim, nb_nodes_per_element),
make_view(rot_matrices, nb_dof, nb_dof))) {
auto & N = std::get<0>(tuple);
auto & X = std::get<1>(tuple);
auto & RDOFs = std::get<2>(tuple);
Matrix<Real> T(N.size(1), N.size(1), 0);
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
T.block(RDOFs, i * RDOFs.rows(), i * RDOFs.rows());
}
auto R = RDOFs.block(0, 0, spatial_dimension, spatial_dimension);
// Rotate to local basis
auto x =
(R * X).block(0, 0, natural_spatial_dimension, nb_nodes_per_element);
ElementClass<type>::computeShapes(natural_coords, x, T, N);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & natural_coords = integration_points(type, ghost_type);
const auto spatial_dimension = mesh.getSpatialDimension();
const auto natural_spatial_dimension =
ElementClass<type>::getNaturalSpaceDimension();
const auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto nb_points = natural_coords.cols();
const auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
const auto nb_element = mesh.getNbElement(type, ghost_type);
const auto nb_stress_components = ElementClass<type>::getNbStressComponents();
auto itp_type = FEEngine::getInterpolationType(type);
if (not this->shapes_derivatives.exists(itp_type, ghost_type)) {
auto size_of_shapesd = this->getShapeDerivativesSize(type);
this->shapes_derivatives.alloc(0, size_of_shapesd, itp_type, ghost_type);
}
auto & rot_matrices = this->rotation_matrices(type, ghost_type);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
auto & shapesd = this->shapes_derivatives(itp_type, ghost_type);
shapesd.resize(nb_element * nb_points);
for (auto && tuple :
zip(make_view(x_el, spatial_dimension, nb_nodes_per_element),
make_view(shapesd, nb_stress_components,
nb_nodes_per_element * nb_dof, nb_points),
make_view(rot_matrices, nb_dof, nb_dof))) {
// compute shape derivatives
auto & X = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & RDOFs = std::get<2>(tuple);
Tensor3<Real> dnds(natural_spatial_dimension,
ElementClass<type>::interpolation_property::dnds_columns,
B.size(2));
ElementClass<type>::computeDNDS(natural_coords, X, dnds);
Tensor3<Real> J(natural_spatial_dimension, natural_spatial_dimension,
natural_coords.cols());
// Computing the coordinates of the element in the natural space
auto R = RDOFs.block(0, 0, spatial_dimension, spatial_dimension);
Matrix<Real> T(B.size(1), B.size(1), 0);
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
T.block(RDOFs, i * RDOFs.rows(), i * RDOFs.rows());
}
// Rotate to local basis
auto x =
(R * X).block(0, 0, natural_spatial_dimension, nb_nodes_per_element);
ElementClass<type>::computeJMat(natural_coords, x, J);
ElementClass<type>::computeShapeDerivatives(J, dnds, T, B);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_dof,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(out_uq.getNbComponent() == nb_dof,
"The output array shape is not correct");
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapes_ = shapes(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_uq.resize(nb_quad_points);
auto out_it = out_uq.begin_reinterpret(nb_dof, 1, nb_quad_points_per_element,
u_el.size());
auto shapes_it =
shapes_.begin_reinterpret(nb_dof, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & uq = *out_it;
const auto & u = *u_it;
auto N = Tensor3<Real>(shapes_it[el]);
for (auto && q : arange(uq.size(2))) {
auto uq_q = Matrix<Real>(uq(q));
auto u_q = Matrix<Real>(u(q));
auto N_q = Matrix<Real>(N(q));
uq_q.mul<false, false>(N_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeStructural<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq, UInt nb_dof,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
auto itp_type = FEEngine::getInterpolationType(type);
const auto & shapesd = shapes_derivatives(itp_type, ghost_type);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto element_dimension = ElementClass<type>::getSpatialDimension();
auto nb_quad_points_per_element = integration_points(type, ghost_type).cols();
auto nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement();
Array<Real> u_el(0, nb_nodes_per_element * nb_dof);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
auto nb_quad_points = nb_quad_points_per_element * u_el.size();
out_nablauq.resize(nb_quad_points);
auto out_it = out_nablauq.begin_reinterpret(
element_dimension, 1, nb_quad_points_per_element, u_el.size());
auto shapesd_it = shapesd.begin_reinterpret(
element_dimension, nb_dof * nb_nodes_per_element,
nb_quad_points_per_element, nb_element);
auto u_it = u_el.begin_reinterpret(nb_dof * nb_nodes_per_element, 1,
nb_quad_points_per_element, u_el.size());
for_each_element(nb_element, filter_elements, [&](auto && el) {
auto & nablau = *out_it;
const auto & u = *u_it;
auto B = Tensor3<Real>(shapesd_it[el]);
for (auto && q : arange(nablau.size(2))) {
auto nablau_q = Matrix<Real>(nablau(q));
auto u_q = Matrix<Real>(u(q));
auto B_q = Matrix<Real>(B(q));
nablau_q.mul<false, false>(B_q, u_q);
}
++out_it;
++u_it;
});
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeBtD(
const Array<Real> & Ds, Array<Real> & BtDs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto nb_stress = ElementClass<type>::getNbStressComponents();
auto nb_dof_per_element = ElementClass<type>::getNbDegreeOfFreedom() *
mesh.getNbNodesPerElement(type);
const auto & shapes_derivatives =
this->shapes_derivatives(itp_type, ghost_type);
Array<Real> shapes_derivatives_filtered(0,
shapes_derivatives.getNbComponent());
auto && view = make_view(shapes_derivatives, nb_stress, nb_dof_per_element);
auto B_it = view.begin();
auto B_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes_derivatives,
shapes_derivatives_filtered, type, ghost_type,
filter_elements);
auto && view =
make_view(shapes_derivatives_filtered, nb_stress, nb_dof_per_element);
B_it = view.begin();
B_end = view.end();
}
for (auto && values : zip(range(B_it, B_end), make_view(Ds, nb_stress),
make_view(BtDs, BtDs.getNbComponent()))) {
const auto & B = std::get<0>(values);
const auto & D = std::get<1>(values);
auto & Bt_D = std::get<2>(values);
Bt_D.template mul<true>(B, D);
}
}
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
void ShapeStructural<_ek_structural>::computeNtb(
const Array<Real> & bs, Array<Real> & Ntbs, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
auto itp_type = ElementClassProperty<type>::interpolation_type;
auto nb_dof = ElementClass<type>::getNbDegreeOfFreedom();
auto nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const auto & shapes = this->shapes(itp_type, ghost_type);
Array<Real> shapes_filtered(0, shapes.getNbComponent());
auto && view = make_view(shapes, nb_dof, nb_dof * nb_nodes_per_element);
auto N_it = view.begin();
auto N_end = view.end();
if (filter_elements != empty_filter) {
FEEngine::filterElementalData(this->mesh, shapes, shapes_filtered, type,
ghost_type, filter_elements);
auto && view =
make_view(shapes_filtered, nb_dof, nb_dof * nb_nodes_per_element);
N_it = view.begin();
N_end = view.end();
}
for (auto && values : zip(range(N_it, N_end), make_view(bs, nb_dof),
make_view(Ntbs, nb_dof * nb_nodes_per_element))) {
const auto & N = std::get<0>(values);
const auto & b = std::get<1>(values);
auto & Nt_b = std::get<2>(values);
Nt_b.template mul<true>(N, b);
}
}
} // namespace akantu
#endif /* AKANTU_SHAPE_STRUCTURAL_INLINE_IMPL_HH_ */
diff --git a/src/geometry/aabb_primitives/aabb_primitive.cc b/src/geometry/aabb_primitives/aabb_primitive.cc
index 69a432fff..55a0c1e37 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.cc
+++ b/src/geometry/aabb_primitives/aabb_primitive.cc
@@ -1,48 +1,50 @@
/**
* @file aabb_primitive.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Mar 16 2018
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aabb_primitive.hh"
namespace akantu {
Triangle_primitive::Point Triangle_primitive::reference_point() const {
return primitive.vertex(0);
}
Line_arc_primitive::Point Line_arc_primitive::reference_point() const {
Real x = to_double(primitive.source().x());
Real y = to_double(primitive.source().y());
Real z = to_double(primitive.source().z());
return cgal::Spherical::Point_3(x, y, z);
}
} // namespace akantu
diff --git a/src/geometry/aabb_primitives/aabb_primitive.hh b/src/geometry/aabb_primitives/aabb_primitive.hh
index 52ddf363b..576bb71cb 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.hh
+++ b/src/geometry/aabb_primitives/aabb_primitive.hh
@@ -1,88 +1,90 @@
/**
* @file aabb_primitive.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Mar 13 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Tue Sep 29 2020
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AABB_PRIMITIVE_HH_
#define AKANTU_AABB_PRIMITIVE_HH_
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/**
* This macro defines a class that is used in the CGAL AABB tree algorithm.
* All the `typedef`s and methods are required by the AABB module.
*
* The member variables are
* - the id of the element associated to the primitive
* - the geometric primitive of the element
*
* @param name the name of the primitive type
* @param kernel the name of the kernel used
*/
#define AKANTU_AABB_CLASS(name, kernel) \
class name##_primitive { \
using Iterator = std::list<name<kernel>>::iterator; /* NOLINT */ \
\
public: \
using Id = UInt; \
using Point = kernel::Point_3; \
using Datum = kernel::name##_3; \
\
public: \
name##_primitive() = default; \
name##_primitive(Iterator it) : meshId(it->id()), primitive(*it) {} \
\
public: \
const Datum & datum() const { return primitive; } \
Point reference_point() const; \
const Id & id() const { return meshId; } \
\
protected: \
Id meshId{0}; \
name<kernel> primitive; /* NOLINT */ \
}
// If the primitive is supported by CGAL::intersection() then the
// implementation process is really easy with this macro
AKANTU_AABB_CLASS(Triangle, cgal::Cartesian);
AKANTU_AABB_CLASS(Line_arc, cgal::Spherical);
#undef AKANTU_AABB_CLASS
} // namespace akantu
#endif // AKANTU_AABB_PRIMITIVE_HH_
diff --git a/src/geometry/aabb_primitives/line_arc.hh b/src/geometry/aabb_primitives/line_arc.hh
index a6d1e86ad..21661d917 100644
--- a/src/geometry/aabb_primitives/line_arc.hh
+++ b/src/geometry/aabb_primitives/line_arc.hh
@@ -1,73 +1,76 @@
/**
* @file line_arc.hh
*
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Segment classe (geometry) for AABB CGAL algos
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_LINE_ARC_HH_
#define AKANTU_LINE_ARC_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Line_arc : public CGAL::Line_arc_3<K> {
public:
/// Default constructor
Line_arc() : CGAL::Line_arc_3<K>() {}
/// Copy constructor
Line_arc(const Line_arc & other)
: CGAL::Line_arc_3<K>(other), mesh_id(other.mesh_id),
seg_id(other.seg_id) {}
/// Construct from 3 points
// "CGAL-4.5/doc_html/Circular_kernel_3/classCGAL_1_1Line__arc__3.html"
Line_arc(const CGAL::Line_3<K> & l, const CGAL::Circular_arc_point_3<K> & a,
const CGAL::Circular_arc_point_3<K> & b)
: CGAL::Line_arc_3<K>(l, a, b) {}
public:
UInt id() const { return mesh_id; }
UInt segId() const { return seg_id; }
void setId(UInt newId) { mesh_id = newId; }
void setSegId(UInt newId) { seg_id = newId; }
protected:
/// Id of the element represented by the primitive
UInt mesh_id{0};
/// Id of the segment represented by the primitive
UInt seg_id{0};
};
} // namespace akantu
#endif // AKANTU_LINE_ARC_HH_
diff --git a/src/geometry/aabb_primitives/tetrahedron.hh b/src/geometry/aabb_primitives/tetrahedron.hh
index fee6663bb..72f07025d 100644
--- a/src/geometry/aabb_primitives/tetrahedron.hh
+++ b/src/geometry/aabb_primitives/tetrahedron.hh
@@ -1,69 +1,71 @@
/**
* @file tetrahedron.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Tetrahedron classe (geometry) for AABB CGAL algos
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TETRAHEDRON_HH_
#define AKANTU_TETRAHEDRON_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Tetrahedron_3 primitive
template <typename K> class Tetrahedron : public CGAL::Tetrahedron_3<K> {
public:
/// Default constructor
Tetrahedron() : CGAL::Tetrahedron_3<K>() {}
/// Copy constructor
Tetrahedron(const Tetrahedron & other)
: CGAL::Tetrahedron_3<K>(other), meshId(other.meshId) {}
/// Construct from 4 points
Tetrahedron(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c, const CGAL::Point_3<K> & d)
: CGAL::Tetrahedron_3<K>(a, b, c, d) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId{0};
};
} // namespace akantu
#endif
diff --git a/src/geometry/aabb_primitives/triangle.hh b/src/geometry/aabb_primitives/triangle.hh
index 11a670902..abcb60af6 100644
--- a/src/geometry/aabb_primitives/triangle.hh
+++ b/src/geometry/aabb_primitives/triangle.hh
@@ -1,74 +1,76 @@
/**
* @file triangle.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Tue Sep 29 2020
*
* @brief Triangle classe (geometry) for AABB CGAL algos
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TRIANGLE_HH_
#define AKANTU_TRIANGLE_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template <typename K> class Triangle : public CGAL::Triangle_3<K> {
using parent = CGAL::Triangle_3<K>;
public:
/// Default constructor
Triangle() = default;
/// Copy constructor
Triangle(const Triangle & other) = default;
Triangle(Triangle && other) noexcept = default;
Triangle & operator=(const Triangle & other) = default;
Triangle & operator=(Triangle && other) noexcept = default;
/// Construct from 3 points
Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c)
: parent(a, b, c) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId{0};
};
} // namespace akantu
#endif // AKANTU_TRIANGLE_HH_
diff --git a/src/geometry/geom_helper_functions.hh b/src/geometry/geom_helper_functions.hh
index 747e85b5d..d4689b388 100644
--- a/src/geometry/geom_helper_functions.hh
+++ b/src/geometry/geom_helper_functions.hh
@@ -1,113 +1,115 @@
/**
* @file geom_helper_functions.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Helper functions for the computational geometry algorithms
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GEOM_HELPER_FUNCTIONS_HH_
#define AKANTU_GEOM_HELPER_FUNCTIONS_HH_
#include "aka_common.hh"
#include "aka_math.hh"
#include "tree_type_helper.hh"
#include "mesh_geom_common.hh"
namespace akantu {
/// Fuzzy compare of two points
template <class Point>
inline bool comparePoints(const Point & a, const Point & b) {
return Math::are_float_equal(a.x(), b.x()) &&
Math::are_float_equal(a.y(), b.y()) &&
Math::are_float_equal(a.z(), b.z());
}
template <>
inline bool comparePoints(const cgal::Spherical::Circular_arc_point_3 & a,
const cgal::Spherical::Circular_arc_point_3 & b) {
return Math::are_float_equal(CGAL::to_double(a.x()),
CGAL::to_double(b.x())) &&
Math::are_float_equal(CGAL::to_double(a.y()),
CGAL::to_double(b.y())) &&
Math::are_float_equal(CGAL::to_double(a.z()), CGAL::to_double(b.z()));
}
/// Fuzzy compare of two segments
template <class K>
inline bool compareSegments(const CGAL::Segment_3<K> & a,
const CGAL::Segment_3<K> & b) {
return (comparePoints(a.source(), b.source()) &&
comparePoints(a.target(), b.target())) ||
(comparePoints(a.source(), b.target()) &&
comparePoints(a.target(), b.source()));
}
/// Compare segment pairs
inline bool
compareSegmentPairs(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
return compareSegments(a.first, b.first);
}
/// Pair ordering operator based on first member
struct segmentPairsLess {
inline bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & a,
const std::pair<cgal::Cartesian::Segment_3, UInt> & b) {
return static_cast<bool>(
CGAL::compare_lexicographically(a.first.min(), b.first.min())) or
static_cast<bool>(
CGAL::compare_lexicographically(a.first.max(), b.first.max()));
}
};
/* -------------------------------------------------------------------------- */
/* Predicates */
/* -------------------------------------------------------------------------- */
/// Predicate used to determine if two segments are equal
class IsSameSegment {
public:
IsSameSegment(const cgal::Cartesian::Segment_3 & segment)
: segment(segment) {}
bool
operator()(const std::pair<cgal::Cartesian::Segment_3, UInt> & test_pair) {
return compareSegments(segment, test_pair.first);
}
protected:
const cgal::Cartesian::Segment_3 segment;
};
} // namespace akantu
#endif // AKANTU_GEOM_HELPER_FUNCTIONS_HH_
diff --git a/src/geometry/mesh_abstract_intersector.hh b/src/geometry/mesh_abstract_intersector.hh
index ddde893b9..580a229f1 100644
--- a/src/geometry/mesh_abstract_intersector.hh
+++ b/src/geometry/mesh_abstract_intersector.hh
@@ -1,120 +1,122 @@
/**
* @file mesh_abstract_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Sat Apr 02 2016
*
* @brief Abstract class for intersection computations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
#define AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <class Query> class MeshAbstractIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshAbstractIntersector(Mesh & mesh);
/// Destructor
~MeshAbstractIntersector() override = default;
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the new_node_per_elem array
AKANTU_GET_MACRO(NewNodePerElem, *new_node_per_elem, const Array<UInt> &);
/// get the intersection_points array
AKANTU_GET_MACRO(IntersectionPoints, intersection_points,
const Array<Real> *);
/// get the nb_seg_by_el UInt
AKANTU_GET_MACRO(NbSegByEl, nb_seg_by_el, UInt);
/**
* @brief Compute the intersection with a query object
*
* This function needs to be implemented for every subclass. It computes the
* intersections
* with the tree of primitives and creates the data for the user.
*
* @param query the CGAL primitive of the query object
*/
virtual void computeIntersectionQuery(const Query & query) = 0;
/// Compute intersection points between the mesh primitives (segments) and a
/// query (surface in 3D or a curve in 2D), double intersection points for the
/// same primitives are not considered. A maximum intersection node per
/// element is set : 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const Query & query,
UInt nb_old_nodes) = 0;
/// Compute intersection between the mesh and a list of queries
virtual void
computeIntersectionQueryList(const std::list<Query> & query_list);
/// Compute intersection points between the mesh and a list of queries
virtual void
computeMeshQueryListIntersectionPoint(const std::list<Query> & query_list,
UInt nb_old_nodes);
/// Compute whatever result is needed from the user (should be move to the
/// appropriate specific classe for genericity)
virtual void
buildResultFromQueryList(const std::list<Query> & query_list) = 0;
protected:
/// new node per element (column 0: number of new nodes, then odd is the
/// intersection node number and even the ID of the intersected segment)
Array<UInt> * new_node_per_elem{nullptr};
/// intersection output: new intersection points
/// (computeMeshQueryListIntersectionPoint)
Array<Real> * intersection_points{nullptr};
/// number of segment in a considered element of the templated type of element
/// specialized intersector
const UInt nb_seg_by_el{0};
};
} // namespace akantu
#include "mesh_abstract_intersector_tmpl.hh"
#endif // AKANTU_MESH_ABSTRACT_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_abstract_intersector_tmpl.hh b/src/geometry/mesh_abstract_intersector_tmpl.hh
index 2ff419809..536d3f778 100644
--- a/src/geometry/mesh_abstract_intersector_tmpl.hh
+++ b/src/geometry/mesh_abstract_intersector_tmpl.hh
@@ -1,78 +1,80 @@
/**
* @file mesh_abstract_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Sat Jan 23 2016
*
* @brief General class for intersection computations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
#define AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
namespace akantu {
template <class Query>
MeshAbstractIntersector<Query>::MeshAbstractIntersector(Mesh & mesh)
: MeshGeomAbstract(mesh) {}
template <class Query>
void MeshAbstractIntersector<Query>::computeIntersectionQueryList(
const std::list<Query> & query_list) {
AKANTU_DEBUG_IN();
auto query_it = query_list.begin();
auto query_end = query_list.end();
for (; query_it != query_end; ++query_it) {
computeIntersectionQuery(*query_it);
}
AKANTU_DEBUG_OUT();
}
template <class Query>
void MeshAbstractIntersector<Query>::computeMeshQueryListIntersectionPoint(
const std::list<Query> & query_list, UInt nb_old_nodes) {
AKANTU_DEBUG_IN();
auto query_it = query_list.begin();
auto query_end = query_list.end();
for (; query_it != query_end; ++query_it) {
computeMeshQueryIntersectionPoint(*query_it, nb_old_nodes);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif // AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_geom_abstract.hh b/src/geometry/mesh_geom_abstract.hh
index 53eb49232..1c90c911b 100644
--- a/src/geometry/mesh_geom_abstract.hh
+++ b/src/geometry/mesh_geom_abstract.hh
@@ -1,62 +1,64 @@
/**
* @file mesh_geom_abstract.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 04 2013
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Sat Jan 23 2016
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GEOM_ABSTRACT_HH_
#define AKANTU_MESH_GEOM_ABSTRACT_HH_
#include "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/// Abstract class for mesh geometry operations
class MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomAbstract(Mesh & mesh) : mesh(mesh){};
virtual ~MeshGeomAbstract() = default;
public:
/// Construct geometric data for computational geometry algorithms
virtual void constructData(GhostType ghost_type = _not_ghost) = 0;
protected:
/// Mesh used to construct the primitives
Mesh & mesh;
};
} // namespace akantu
#endif // AKANTU_MESH_GEOM_ABSTRACT_HH_
diff --git a/src/geometry/mesh_geom_common.hh b/src/geometry/mesh_geom_common.hh
index 9fb22f1fc..309bf3645 100644
--- a/src/geometry/mesh_geom_common.hh
+++ b/src/geometry/mesh_geom_common.hh
@@ -1,56 +1,60 @@
/**
* @file mesh_geom_common.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Common file for MeshGeom module
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_MESH_GEOM_COMMON_HH_
#define AKANTU_MESH_GEOM_COMMON_HH_
#include "aka_common.hh"
+/* -------------------------------------------------------------------------- */
#include <CGAL/MP_Float.h>
#include <CGAL/Quotient.h>
-
+/* -------------------------------------------------------------------------- */
#include <CGAL/Algebraic_kernel_for_spheres_2_3.h>
#include <CGAL/Cartesian.h>
#include <CGAL/Simple_cartesian.h>
#include <CGAL/Spherical_kernel_3.h>
+/* -------------------------------------------------------------------------- */
namespace akantu {
namespace cgal {
using Cartesian = CGAL::Simple_cartesian<Real>;
using Spherical = CGAL::Spherical_kernel_3<
CGAL::Simple_cartesian<CGAL::Quotient<CGAL::MP_Float>>,
CGAL::Algebraic_kernel_for_spheres_2_3<CGAL::Quotient<CGAL::MP_Float>>>;
} // namespace cgal
} // namespace akantu
#endif // AKANTU_MESH_GEOM_COMMON_HH_
diff --git a/src/geometry/mesh_geom_factory.hh b/src/geometry/mesh_geom_factory.hh
index fadde2bdf..7ae2c4d99 100644
--- a/src/geometry/mesh_geom_factory.hh
+++ b/src/geometry/mesh_geom_factory.hh
@@ -1,104 +1,107 @@
/**
* @file mesh_geom_factory.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Tue Sep 08 2020
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#include "geom_helper_functions.hh"
#include "mesh.hh"
#include "mesh_geom_abstract.hh"
#include "tree_type_helper.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GEOM_FACTORY_HH_
#define AKANTU_MESH_GEOM_FACTORY_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to construct AABB tree for intersection computations
*
* This class constructs a CGAL AABB tree of one type of element in a mesh
* for fast intersection computations.
*/
template <UInt dim, ElementType el_type, class Primitive, class Kernel>
class MeshGeomFactory : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomFactory(Mesh & mesh);
/// Desctructor
~MeshGeomFactory() override;
using TreeTypeHelper_ = TreeTypeHelper<Primitive, Kernel>;
using TreeType = typename TreeTypeHelper_::tree;
using ContainerType = typename TreeTypeHelper_::container_type;
public:
/// Construct AABB tree for fast intersection computing
void constructData(GhostType ghost_type = _not_ghost) override;
/**
* @brief Construct a primitive and add it to a list of primitives
*
* This function needs to be specialized for every type that is wished to be
* supported.
* @param node_coordinates coordinates of the nodes making up the element
* @param id element number
* @param list the primitive list (not used inside MeshGeomFactory)
*/
inline void addPrimitive(const Matrix<Real> & /*node_coordinates*/,
UInt /*id*/, ContainerType & /*list*/);
inline void addPrimitive(const Matrix<Real> & node_coordinates, UInt id);
/// Getter for the AABB tree
auto getTree() const -> const TreeType & { return *data_tree; }
/// Getter for primitive list
auto getPrimitiveList() const -> const ContainerType & {
return primitive_list;
}
protected:
/// AABB data tree
TreeType * data_tree{nullptr};
/// Primitive list
ContainerType primitive_list;
};
} // namespace akantu
#include "mesh_geom_factory_tmpl.hh"
#endif // AKANTU_MESH_GEOM_FACTORY_HH_
diff --git a/src/geometry/mesh_geom_factory_tmpl.hh b/src/geometry/mesh_geom_factory_tmpl.hh
index 1382d168f..3ef885d1d 100644
--- a/src/geometry/mesh_geom_factory_tmpl.hh
+++ b/src/geometry/mesh_geom_factory_tmpl.hh
@@ -1,242 +1,245 @@
/**
* @file mesh_geom_factory_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Tue Sep 08 2020
*
* @brief Class for constructing the CGAL primitives of a mesh
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_geom_common.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
#define AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::MeshGeomFactory(Mesh & mesh)
: MeshGeomAbstract(mesh) {}
/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::~MeshGeomFactory() {
delete data_tree;
}
/* -------------------------------------------------------------------------- */
/**
* This function loops over the elements of `type` in the mesh and creates the
* AABB tree of geometrical primitves (`data_tree`).
*/
template <UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::constructData(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
primitive_list.clear();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
const Array<Real> & nodes = mesh.getNodes();
UInt el_index = 0;
auto it = connectivity.begin(nb_nodes_per_element);
auto end = connectivity.end(nb_nodes_per_element);
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
// This loop builds the list of primitives
for (; it != end; ++it, ++el_index) {
const Vector<UInt> & el_connectivity = *it;
for (UInt i = 0; i < nb_nodes_per_element; i++) {
for (UInt j = 0; j < dim; j++) {
node_coordinates(j, i) = nodes(el_connectivity(i), j);
}
}
// the unique elemental id assigned to the primitive is the
// linearized element index over ghost type
addPrimitive(node_coordinates, el_index);
}
delete data_tree;
// This condition allows the use of the mesh geom module
// even if types are not compatible with AABB tree algorithm
if (TreeTypeHelper_::is_valid) {
data_tree = new TreeType(primitive_list.begin(), primitive_list.end());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
enum class GeometricalType {
_triangle,
_tetrahedron,
};
template <ElementType element_type> struct GeometricalTypeHelper {};
template <> struct GeometricalTypeHelper<_triangle_3> {
static const GeometricalType type{GeometricalType::_triangle};
};
template <> struct GeometricalTypeHelper<_triangle_6> {
static const GeometricalType type{GeometricalType::_triangle};
};
template <> struct GeometricalTypeHelper<_tetrahedron_4> {
static const GeometricalType type{GeometricalType::_triangle};
};
#if defined(AKANTU_IGFEM)
template <> struct GeometricalTypeHelper<_igfem_triangle_4> {
static const GeometricalType type{GeometricalType::_triangle};
};
template <> struct GeometricalTypeHelper<_igfem_triangle_5> {
static const GeometricalType type{GeometricalType::_triangle};
};
#endif
template <details::GeometricalType geom_type, class Primitive, class Kernel>
struct AddPrimitiveHelper {};
template <class Primitive>
struct AddPrimitiveHelper<GeometricalType::_triangle, Primitive,
cgal::Cartesian> {
using TreeTypeHelper_ = TreeTypeHelper<Primitive, cgal::Cartesian>;
using ContainerType = typename TreeTypeHelper_::container_type;
static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
ContainerType & list) {
using Point = typename TreeTypeHelper_::point_type;
Point a(node_coordinates(0, 0), node_coordinates(1, 0), 0.);
Point b(node_coordinates(0, 1), node_coordinates(1, 1), 0.);
Point c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
Triangle<cgal::Cartesian> t(a, b, c);
t.setId(id);
list.push_back(t);
}
};
template <class Primitive>
struct AddPrimitiveHelper<GeometricalType::_triangle, Primitive,
cgal::Spherical> {
using TreeTypeHelper_ = TreeTypeHelper<Primitive, cgal::Spherical>;
using ContainerType = typename TreeTypeHelper_::container_type;
static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
ContainerType & list) {
using Point = typename TreeTypeHelper_::point_type;
Point a(node_coordinates(0, 0), node_coordinates(1, 0), 0.);
Point b(node_coordinates(0, 1), node_coordinates(1, 1), 0.);
Point c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
using Line = CGAL::Line_3<cgal::Spherical>;
Line l1(a, b);
Line l2(b, c);
Line l3(c, a);
using Arc = Line_arc<cgal::Spherical>;
Arc s1(l1, a, b);
Arc s2(l2, b, c);
Arc s3(l3, c, a);
s1.setId(id);
s1.setSegId(0);
s2.setId(id);
s2.setSegId(1);
s3.setId(id);
s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
};
template <class Primitive>
struct AddPrimitiveHelper<GeometricalType::_tetrahedron, Primitive,
cgal::Cartesian> {
using TreeTypeHelper_ = TreeTypeHelper<Primitive, cgal::Cartesian>;
using ContainerType = typename TreeTypeHelper_::container_type;
static void addPrimitive(const Matrix<Real> & node_coordinates, UInt id,
ContainerType & list) {
using Point = typename TreeTypeHelper_::point_type;
Point a(node_coordinates(0, 0), node_coordinates(1, 0),
node_coordinates(2, 0));
Point b(node_coordinates(0, 1), node_coordinates(1, 1),
node_coordinates(2, 1));
Point c(node_coordinates(0, 2), node_coordinates(1, 2),
node_coordinates(2, 2));
Point d(node_coordinates(0, 3), node_coordinates(1, 3),
node_coordinates(2, 3));
Triangle<cgal::Cartesian> t1(a, b, c);
Triangle<cgal::Cartesian> t2(b, c, d);
Triangle<cgal::Cartesian> t3(c, d, a);
Triangle<cgal::Cartesian> t4(d, a, b);
t1.setId(id);
t2.setId(id);
t3.setId(id);
t4.setId(id);
list.push_back(t1);
list.push_back(t2);
list.push_back(t3);
list.push_back(t4);
}
};
} // namespace details
} // namespace
/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(
const Matrix<Real> & node_coordinates, UInt id, ContainerType & list) {
details::AddPrimitiveHelper<details::GeometricalTypeHelper<type>::type,
Primitive, Kernel>::addPrimitive(node_coordinates,
id, list);
}
/* -------------------------------------------------------------------------- */
template <UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(
const Matrix<Real> & node_coordinates, UInt id) {
this->addPrimitive(node_coordinates, id, this->primitive_list);
}
} // namespace akantu
#endif // AKANTU_MESH_GEOM_FACTORY_TMPL_HH_
diff --git a/src/geometry/mesh_geom_intersector.hh b/src/geometry/mesh_geom_intersector.hh
index a39f65b87..760576441 100644
--- a/src/geometry/mesh_geom_intersector.hh
+++ b/src/geometry/mesh_geom_intersector.hh
@@ -1,73 +1,75 @@
/**
* @file mesh_geom_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Sat Jan 23 2016
*
* @brief General class for intersection computations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GEOM_INTERSECTOR_HH_
#define AKANTU_MESH_GEOM_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output
* data
*/
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
class MeshGeomIntersector : public MeshAbstractIntersector<Query> {
public:
/// Construct from mesh
explicit MeshGeomIntersector(Mesh & mesh);
/// Destructor
~MeshGeomIntersector() override = default;
public:
/// Construct the primitive tree object
void constructData(GhostType ghost_type = _not_ghost) override;
protected:
/// Factory object containing the primitive tree
MeshGeomFactory<dim, type, Primitive, Kernel> factory;
};
} // namespace akantu
#include "mesh_geom_intersector_tmpl.hh"
#endif // AKANTU_MESH_GEOM_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_geom_intersector_tmpl.hh b/src/geometry/mesh_geom_intersector_tmpl.hh
index 88b0ed78b..8cd6d487b 100644
--- a/src/geometry/mesh_geom_intersector_tmpl.hh
+++ b/src/geometry/mesh_geom_intersector_tmpl.hh
@@ -1,58 +1,60 @@
/**
* @file mesh_geom_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Apr 29 2015
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Sat Jan 23 2016
*
* @brief General class for intersection computations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
#define AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::MeshGeomIntersector(
Mesh & mesh)
: MeshAbstractIntersector<Query>(mesh), factory(mesh) {}
template <UInt dim, ElementType type, class Primitive, class Query,
class Kernel>
void MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::constructData(
GhostType ghost_type) {
this->intersection_points->resize(0);
factory.constructData(ghost_type);
}
} // namespace akantu
#endif // AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_segment_intersector.hh b/src/geometry/mesh_segment_intersector.hh
index 4d3cc5110..8e36a1e82 100644
--- a/src/geometry/mesh_segment_intersector.hh
+++ b/src/geometry/mesh_segment_intersector.hh
@@ -1,108 +1,110 @@
/**
* @file mesh_segment_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Computation of mesh intersection with segments
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
#define AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSegmentIntersector
: public MeshGeomIntersector<dim, type, Triangle<cgal::Cartesian>,
cgal::Cartesian::Segment_3, cgal::Cartesian> {
using K = cgal::Cartesian;
/// Parent class type
using parent_type =
MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K>;
/// Result of intersection function type
using result_type =
typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type;
/// Pair of segments and element id
using pair_type = std::pair<K::Segment_3, UInt>;
public:
/// Construct from mesh
explicit MeshSegmentIntersector(Mesh & mesh, Mesh & result_mesh);
/// Destructor
~MeshSegmentIntersector() override = default;
public:
/**
* @brief Computes the intersection of the mesh with a segment
*
* @param query the segment to compute the intersections with the mesh
*/
void computeIntersectionQuery(const K::Segment_3 & query) override;
/// Compute intersection points between the mesh and a query
void computeMeshQueryIntersectionPoint(const K::Segment_3 & query,
UInt nb_old_nodes) override;
/// Compute the embedded mesh
void
buildResultFromQueryList(const std::list<K::Segment_3> & query_list) override;
void setPhysicalName(const std::string & other) {
current_physical_name = other;
}
protected:
/// Compute segments from intersection list
void computeSegments(const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query);
protected:
/// Result mesh
Mesh & result_mesh;
/// Physical name of the current batch of queries
std::string current_physical_name;
};
} // namespace akantu
#include "mesh_segment_intersector_tmpl.hh"
#endif // AKANTU_MESH_SEGMENT_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_segment_intersector_tmpl.hh b/src/geometry/mesh_segment_intersector_tmpl.hh
index 31e1de1b8..eb4eb7792 100644
--- a/src/geometry/mesh_segment_intersector_tmpl.hh
+++ b/src/geometry/mesh_segment_intersector_tmpl.hh
@@ -1,283 +1,285 @@
/**
* @file mesh_segment_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with segments
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
#define AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSegmentIntersector<dim, type>::MeshSegmentIntersector(Mesh & mesh,
Mesh & result_mesh)
: parent_type(mesh), result_mesh(result_mesh) {
this->intersection_points = new Array<Real>(0, dim);
this->constructData();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeIntersectionQuery(
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
result_mesh.addConnectivityType(_segment_2, _not_ghost);
result_mesh.addConnectivityType(_segment_2, _ghost);
std::list<result_type> result_list;
std::set<std::pair<K::Segment_3, UInt>, segmentPairsLess> segment_set;
this->factory.getTree().all_intersections(query,
std::back_inserter(result_list));
this->computeSegments(result_list, segment_set, query);
// Arrays for storing nodes and connectivity
Array<Real> & nodes = result_mesh.getNodes();
Array<UInt> & connectivity = result_mesh.getConnectivity(_segment_2);
// Arrays for storing associated element and physical name
bool valid_elemental_data = true;
Array<Element> * associated_element = nullptr;
Array<std::string> * associated_physical_name = nullptr;
try {
associated_element =
&result_mesh.getData<Element>("associated_element", _segment_2);
associated_physical_name =
&result_mesh.getData<std::string>("physical_names", _segment_2);
} catch (debug::Exception & e) {
valid_elemental_data = false;
}
auto it = segment_set.begin();
auto end = segment_set.end();
// Loop over the segment pairs
for (; it != end; ++it) {
if (!it->first.is_degenerate()) {
Vector<UInt> segment_connectivity(2);
segment_connectivity(0) = result_mesh.getNbNodes();
segment_connectivity(1) = result_mesh.getNbNodes() + 1;
connectivity.push_back(segment_connectivity);
// Copy nodes
Vector<Real> source(dim);
Vector<Real> target(dim);
for (UInt j = 0; j < dim; j++) {
source(j) = it->first.source()[j];
target(j) = it->first.target()[j];
}
nodes.push_back(source);
nodes.push_back(target);
// Copy associated element info
if (valid_elemental_data) {
associated_element->push_back(Element{type, it->second, _not_ghost});
associated_physical_name->push_back(current_physical_name);
}
}
}
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const K::Segment_3 & /*query*/, UInt /*nb_old_nodes*/) {
AKANTU_ERROR("The method: computeMeshQueryIntersectionPoint has not "
"been implemented in class MeshSegmentIntersector!");
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::buildResultFromQueryList(
const std::list<K::Segment_3> & query_list) {
AKANTU_DEBUG_IN();
this->computeIntersectionQueryList(query_list);
AKANTU_DEBUG_OUT();
}
template <UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeSegments(
const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
/*
* Number of intersections = 0 means
*
* - query is completely outside mesh
* - query is completely inside primitive
*
* We try to determine the case and still construct the segment list
*/
if (intersections.empty()) {
// We look at all the primitives intersected by two rays
// If there is one primitive in common, then query is inside
// that primitive
K::Ray_3 ray1(query.source(), query.target());
K::Ray_3 ray2(query.target(), query.source());
std::set<UInt> ray1_results;
std::set<UInt> ray2_results;
this->factory.getTree().all_intersected_primitives(
ray1, std::inserter(ray1_results, ray1_results.begin()));
this->factory.getTree().all_intersected_primitives(
ray2, std::inserter(ray2_results, ray2_results.begin()));
bool inside_primitive = false;
UInt primitive_id = 0;
auto ray2_it = ray2_results.begin();
auto ray2_end = ray2_results.end();
// Test if first list contains an element of second list
for (; ray2_it != ray2_end && !inside_primitive; ++ray2_it) {
if (ray1_results.find(*ray2_it) != ray1_results.end()) {
inside_primitive = true;
primitive_id = *ray2_it;
}
}
if (inside_primitive) {
segments.insert(std::make_pair(query, primitive_id));
}
}
else {
auto it = intersections.begin();
auto end = intersections.end();
for (; it != end; ++it) {
UInt el = (*it)->second;
// Result of intersection is a segment
if (const K::Segment_3 * segment =
boost::get<K::Segment_3>(&((*it)->first))) {
// Check if the segment was alread created
segments.insert(std::make_pair(*segment, el));
}
// Result of intersection is a point
else if (const K::Point_3 * point =
boost::get<K::Point_3>(&((*it)->first))) {
// We only want to treat points differently if we're in 3D with Tetra4
// elements This should be optimized by compilator
if (dim == 3 && type == _tetrahedron_4) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
TreeTypeHelper<Triangle<K>, K>::container_type facets;
const Array<Real> & nodes = this->mesh.getNodes();
Array<UInt>::const_vector_iterator connectivity_vec =
this->mesh.getConnectivity(type).begin(nb_nodes_per_element);
const Vector<UInt> & el_connectivity = connectivity_vec[el];
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
for (UInt i = 0; i < nb_nodes_per_element; i++) {
for (UInt j = 0; j < dim; j++) {
node_coordinates(j, i) = nodes(el_connectivity(i), j);
}
}
this->factory.addPrimitive(node_coordinates, el, facets);
// Local tree
auto * local_tree =
new TreeTypeHelper<Triangle<K>, K>::tree(facets.begin(),
facets.end());
// Compute local intersections (with current element)
std::list<result_type> local_intersections;
local_tree->all_intersections(
query, std::back_inserter(local_intersections));
bool out_point_found = false;
auto local_it = local_intersections.begin();
auto local_end = local_intersections.end();
for (; local_it != local_end; ++local_it) {
if (const auto * local_point =
boost::get<K::Point_3>(&((*local_it)->first))) {
if (!comparePoints(*point, *local_point)) {
K::Segment_3 seg(*point, *local_point);
segments.insert(std::make_pair(seg, el));
out_point_found = true;
}
}
}
if (!out_point_found) {
using Point = TreeTypeHelper<Triangle<K>, K>::point_type;
Point a(node_coordinates(0, 0), node_coordinates(1, 0),
node_coordinates(2, 0));
Point b(node_coordinates(0, 1), node_coordinates(1, 1),
node_coordinates(2, 1));
Point c(node_coordinates(0, 2), node_coordinates(1, 2),
node_coordinates(2, 2));
Point d(node_coordinates(0, 3), node_coordinates(1, 3),
node_coordinates(2, 3));
K::Tetrahedron_3 tetra(a, b, c, d);
const K::Point_3 * inside_point = nullptr;
if (tetra.has_on_bounded_side(query.source()) &&
!tetra.has_on_boundary(query.source())) {
inside_point = &query.source();
} else if (tetra.has_on_bounded_side(query.target()) &&
!tetra.has_on_boundary(query.target())) {
inside_point = &query.target();
}
if (inside_point != nullptr) {
K::Segment_3 seg(*inside_point, *point);
segments.insert(std::make_pair(seg, el));
}
}
delete local_tree;
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif // AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/mesh_sphere_intersector.hh b/src/geometry/mesh_sphere_intersector.hh
index dbd19cd46..4de042f1f 100644
--- a/src/geometry/mesh_sphere_intersector.hh
+++ b/src/geometry/mesh_sphere_intersector.hh
@@ -1,118 +1,120 @@
/**
* @file mesh_sphere_intersector.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
* @date last modification: Tue Feb 20 2018
*
* @brief Computation of mesh intersection with sphere(s)
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_SPHERE_INTERSECTOR_HH_
#define AKANTU_MESH_SPHERE_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt dim, ElementType type>
class MeshSphereIntersector
: public MeshGeomIntersector<dim, type, Line_arc<cgal::Spherical>,
cgal::Spherical::Sphere_3, cgal::Spherical> {
using SK = cgal::Spherical;
using K = cgal::Cartesian;
/// Parent class type
typedef MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>
parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type
result_type;
/// Pair of intersection points and element id
typedef std::pair<SK::Circular_arc_point_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSphereIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshSphereIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @brief Computes the intersection of the mesh with a sphere
*/
virtual void computeIntersectionQuery(const SK::Sphere_3 & /* query */) {
AKANTU_ERROR("This function is not implemented for spheres (It was "
"to generic and has been replaced by "
"computeMeshQueryIntersectionPoint");
}
/**
* Compute intersection points between the mesh primitives (segments) and a
* query (surface in 3D or a curve in 2D), double intersection points for the
* same primitives are not considered. A maximum is set to the number of
* intersection nodes per element: 2 in 2D and 4 in 3D
*/
virtual void computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query,
UInt nb_old_nodes);
/// Build the IGFEM mesh
virtual void
buildResultFromQueryList(const std::list<SK::Sphere_3> & /*query*/) {
AKANTU_ERROR("This function is no longer implemented to split "
"geometrical operations and dedicated result "
"construction");
}
/// Set the tolerance
void setToleranceIntersectionOnNode(UInt tol) {
this->tol_intersection_on_node = tol;
}
protected:
/// tolerance for which the intersection is considered on the mesh node
/// (relative to the segment lenght)
Real tol_intersection_on_node;
};
} // namespace akantu
#include "mesh_sphere_intersector_tmpl.hh"
#endif // AKANTU_MESH_SPHERE_INTERSECTOR_HH_
diff --git a/src/geometry/mesh_sphere_intersector_tmpl.hh b/src/geometry/mesh_sphere_intersector_tmpl.hh
index e11373440..f5460850d 100644
--- a/src/geometry/mesh_sphere_intersector_tmpl.hh
+++ b/src/geometry/mesh_sphere_intersector_tmpl.hh
@@ -1,214 +1,216 @@
/**
* @file mesh_sphere_intersector_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Dec 04 2018
*
* @brief Computation of mesh intersection with spheres
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
#define AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_sphere_intersector.hh"
#include "tree_type_helper.hh"
namespace akantu {
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::MeshSphereIntersector(Mesh & mesh)
: parent_type(mesh), tol_intersection_on_node(1e-10) {
#if defined(AKANTU_IGFEM)
if ((type == _triangle_3) || (type == _igfem_triangle_4) ||
(type == _igfem_triangle_5)) {
const_cast<UInt &>(this->nb_seg_by_el) = 3;
} else {
AKANTU_ERROR("Not ready for mesh type " << type);
}
#else
if ((type != _triangle_3))
AKANTU_ERROR("Not ready for mesh type " << type);
#endif
// initialize the intersection pointsss array with the spatial dimension
this->intersection_points = new Array<Real>(0, dim);
// A maximum is set to the number of intersection nodes per element to limit
// the size of new_node_per_elem: 2 in 2D and 4 in 3D
this->new_node_per_elem = new Array<UInt>(0, 1 + 4 * (dim - 1));
}
template <UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::~MeshSphereIntersector() {
delete this->new_node_per_elem;
delete this->intersection_points;
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::constructData(GhostType ghost_type) {
this->new_node_per_elem->resize(this->mesh.getNbElement(type, ghost_type));
this->new_node_per_elem->clear();
MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>::constructData(
ghost_type);
}
template <UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::computeMeshQueryIntersectionPoint(
const SK::Sphere_3 & query, UInt nb_old_nodes) {
/// function to replace computeIntersectionQuery in a more generic geometry
/// module version
// The newNodeEvent is not send from this method who only compute the
// intersection points
AKANTU_DEBUG_IN();
Array<Real> & nodes = this->mesh.getNodes();
UInt nb_node = nodes.size() + this->intersection_points->size();
// Tolerance for proximity checks should be defined by user
Real global_tolerance = Math::getTolerance();
Math::setTolerance(tol_intersection_on_node);
typedef boost::variant<pair_type> sk_inter_res;
TreeTypeHelper<Line_arc<cgal::Spherical>, cgal::Spherical>::const_iterator
it = this->factory.getPrimitiveList().begin(),
end = this->factory.getPrimitiveList().end();
for (; it != end; ++it) { // loop on the primitives (segments)
std::list<sk_inter_res> s_results;
CGAL::intersection(*it, query, std::back_inserter(s_results));
if (s_results.size() == 1) { // just one point
if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
if (pair->second == 1) { // not a point tangent to the sphere
// the intersection point written as a vector
Vector<Real> new_node(dim, 0.0);
cgal::Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
CGAL::to_double(pair->first.y()),
CGAL::to_double(pair->first.z()));
for (UInt i = 0; i < dim; i++) {
new_node(i) = point[i];
}
/// boolean to decide wheter intersection point is on a standard node
/// of the mesh or not
bool is_on_mesh = false;
/// boolean to decide if this intersection point has been already
/// computed for a neighbor element
bool is_new = true;
/// check if intersection point has already been computed
UInt n = nb_old_nodes;
// check if we already compute this intersection and add it as a node
// for a neighboor element of another type
auto existing_node = nodes.begin(dim);
for (; n < nodes.size(); ++n) { // loop on the nodes from nb_old_nodes
if (Math::are_vector_equal(dim, new_node.storage(),
existing_node[n].storage())) {
is_new = false;
break;
}
}
if (is_new) {
auto intersection_points_it = this->intersection_points->begin(dim);
auto intersection_points_end = this->intersection_points->end(dim);
for (; intersection_points_it != intersection_points_end;
++intersection_points_it, ++n) {
if (Math::are_vector_equal(dim, new_node.storage(),
intersection_points_it->storage())) {
is_new = false;
break;
}
}
}
// get the initial and final points of the primitive (segment) and
// write them as vectors
cgal::Cartesian::Point_3 source_cgal(
CGAL::to_double(it->source().x()),
CGAL::to_double(it->source().y()),
CGAL::to_double(it->source().z()));
cgal::Cartesian::Point_3 target_cgal(
CGAL::to_double(it->target().x()),
CGAL::to_double(it->target().y()),
CGAL::to_double(it->target().z()));
Vector<Real> source(dim), target(dim);
for (UInt i = 0; i < dim; i++) {
source(i) = source_cgal[i];
target(i) = target_cgal[i];
}
// Check if we are close from a node of the primitive (segment)
if (Math::are_vector_equal(dim, source.storage(),
new_node.storage()) ||
Math::are_vector_equal(dim, target.storage(),
new_node.storage())) {
is_on_mesh = true;
is_new = false;
}
if (is_new) { // if the intersection point is a new one add it to the
// list
this->intersection_points->push_back(new_node);
nb_node++;
}
// deduce the element id
UInt element_id = it->id();
// fill the new_node_per_elem array
if (!is_on_mesh) { // if the node is not on a mesh node
UInt & nb_new_nodes_per_el =
(*this->new_node_per_elem)(element_id, 0);
nb_new_nodes_per_el += 1;
AKANTU_DEBUG_ASSERT(
2 * nb_new_nodes_per_el <
this->new_node_per_elem->getNbComponent(),
"You might have to interface crossing the same material");
(*this->new_node_per_elem)(element_id,
(2 * nb_new_nodes_per_el) - 1) = n;
(*this->new_node_per_elem)(element_id, 2 * nb_new_nodes_per_el) =
it->segId();
}
}
}
}
}
Math::setTolerance(global_tolerance);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif // AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH_
diff --git a/src/geometry/tree_type_helper.hh b/src/geometry/tree_type_helper.hh
index c7d846983..9f4d0dd66 100644
--- a/src/geometry/tree_type_helper.hh
+++ b/src/geometry/tree_type_helper.hh
@@ -1,109 +1,111 @@
/**
* @file tree_type_helper.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Feb 01 2018
*
* @brief Converts element types of a mesh to CGAL primitive types
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TREE_TYPE_HELPER_HH_
#define AKANTU_TREE_TYPE_HELPER_HH_
#include "aka_common.hh"
#include "line_arc.hh"
#include "tetrahedron.hh"
#include "triangle.hh"
#include "aabb_primitive.hh"
#include "mesh_geom_common.hh"
#include <CGAL/AABB_traits.h>
#include <CGAL/AABB_tree.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Replacement class for algorithm that can't use the AABB tree types
template <typename iterator> struct VoidTree {
VoidTree(const iterator & /*begin*/, const iterator & /*end*/) {}
};
/// Helper class used to ease the use of CGAL AABB tree algorithm
template <class Primitive, class Kernel> struct TreeTypeHelper {
static const bool is_valid = false;
using primitive_type = Primitive;
using container_type = typename std::list<primitive_type>;
using iterator = typename container_type::iterator;
using const_iterator = typename container_type::const_iterator;
using point_type = typename CGAL::Point_3<Kernel>;
using tree = VoidTree<iterator>;
};
/// Helper class used to ease the use of intersections
template <class TTHelper, class Query> struct IntersectionTypeHelper;
/**
* Macro used to specialize TreeTypeHelper
* @param my_primitive associated primitive type
* @param my_query query_type
* @param my_kernel kernel type
*/
#define TREE_TYPE_HELPER_MACRO(my_primitive, my_query, my_kernel) \
template <> \
struct TreeTypeHelper<my_primitive<my_kernel> /*NOLINT*/, my_kernel> { \
static const bool is_valid = true; \
using primitive_type = my_primitive<my_kernel>; /*NOLINT*/ \
using aabb_primitive_type = my_primitive##_primitive; \
using point_type = CGAL::Point_3<my_kernel>; \
using container_type = std::list<primitive_type>; \
using iterator = container_type::iterator; \
using aabb_traits_type = \
CGAL::AABB_traits<my_kernel, aabb_primitive_type>; \
using tree = CGAL::AABB_tree<aabb_traits_type>; \
using id_type = tree::Primitive_id; \
}; \
\
template <> \
struct IntersectionTypeHelper< \
TreeTypeHelper<my_primitive<my_kernel>, /*NOLINT*/ my_kernel>, \
my_query> { \
typedef boost::optional<TreeTypeHelper< \
my_primitive<my_kernel>, /*NOLINT*/ \
my_kernel>::tree::Intersection_and_primitive_id<my_query>::Type> \
intersection_type; \
}
TREE_TYPE_HELPER_MACRO(Triangle, cgal::Cartesian::Segment_3, cgal::Cartesian);
// TREE_TYPE_HELPER_MACRO(Line_arc, cgal::Spherical::Sphere_3, cgal::Spherical);
#undef TREE_TYPE_HELPER_MACRO
} // namespace akantu
#endif // AKANTU_TREE_TYPE_HELPER_HH_
diff --git a/src/io/dumper/dumpable.cc b/src/io/dumper/dumpable.cc
index 0a3df6a52..8ae9559a8 100644
--- a/src/io/dumper/dumpable.cc
+++ b/src/io/dumper/dumpable.cc
@@ -1,277 +1,279 @@
/**
* @file dumpable.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Feb 28 2020
*
* @brief Implementation of the dumpable interface
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include <io_helper.hh>
#include <utility>
namespace akantu {
/* -------------------------------------------------------------------------- */
Dumpable::Dumpable() = default;
/* -------------------------------------------------------------------------- */
Dumpable::~Dumpable() = default;
/* -------------------------------------------------------------------------- */
void Dumpable::registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
const bool is_default) {
this->dumpers[dumper_name] = std::move(dumper);
if (is_default) {
this->default_dumper = dumper_name;
}
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMesh(const Mesh & mesh, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind) {
this->addDumpMeshToDumper(this->default_dumper, mesh, spatial_dimension,
ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh, UInt spatial_dimension,
GhostType ghost_type,
ElementKind element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerMesh(mesh, spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind) {
this->addDumpFilteredMeshToDumper(this->default_dumper, mesh, elements_filter,
nodes_filter, spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerFilteredMesh(mesh, elements_filter, nodes_filter,
spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id,
std::move(field));
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, std::move(field));
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpField(const std::string & field_id) {
this->removeDumpFieldFromDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.unRegisterField(field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVectorToDumper(const std::string & /*dumper_name*/,
const std::string & /*field_id*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectory(const std::string & directory) {
this->setDirectoryToDumper(this->default_dumper, directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseName(const std::string & basename) {
this->setBaseNameToDumper(this->default_dumper, basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(Real time_step) {
this->setTimeStepToDumper(this->default_dumper, time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(const std::string & dumper_name,
Real time_step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper() {
DumperIOHelper & dumper = this->getDumper(this->default_dumper);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump();
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump() { this->dump(this->default_dumper); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(UInt step) { this->dump(this->default_dumper, step); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, Real time, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(Real time, UInt step) {
this->dump(this->default_dumper, time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::internalAddDumpFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, std::move(field));
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper() {
return this->getDumper(this->default_dumper);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper(const std::string & dumper_name) {
auto it = this->dumpers.find(dumper_name);
auto end = this->dumpers.end();
if (it == end) {
AKANTU_EXCEPTION("Dumper " << dumper_name
<< "has not been registered, yet.");
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
std::string Dumpable::getDefaultDumperName() const {
return this->default_dumper;
}
} // namespace akantu
#endif
diff --git a/src/io/dumper/dumpable.hh b/src/io/dumper/dumpable.hh
index 913c184bf..a5f5840d2 100644
--- a/src/io/dumper/dumpable.hh
+++ b/src/io/dumper/dumpable.hh
@@ -1,46 +1,48 @@
/**
* @file dumpable.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Tue Oct 01 2019
*
* @brief Interface for object who wants to dump themselves
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPABLE_HH_
#define AKANTU_DUMPABLE_HH_
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_iohelper.hh"
#else
#include "dumpable_dummy.hh"
#endif // AKANTU_USE_IOHELPER
#endif /* AKANTU_DUMPABLE_HH_ */
diff --git a/src/io/dumper/dumpable_dummy.hh b/src/io/dumper/dumpable_dummy.hh
index 15e0f05a9..8faf9f80c 100644
--- a/src/io/dumper/dumpable_dummy.hh
+++ b/src/io/dumper/dumpable_dummy.hh
@@ -1,267 +1,270 @@
/**
* @file dumpable_dummy.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Interface for object who wants to dump themselves
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#if !defined(DOXYGEN)
#ifndef AKANTU_DUMPABLE_DUMMY_HH_
#define AKANTU_DUMPABLE_DUMMY_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused"
namespace dumpers {
class Field;
}
class DumperIOHelper;
class Mesh;
/* -------------------------------------------------------------------------- */
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable(){};
virtual ~Dumpable(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false) {}
void registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
const bool is_default = false) {}
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {}
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {
}
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {
}
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {}
virtual void addDumpField(const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_TO_IMPLEMENT();
}
virtual void addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
virtual void
addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <typename T>
void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpField(const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirecory(const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseName(const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name, Real current_time, UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
protected:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
DumperIOHelper & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
template <class T> T & getDumper(const std::string & dumper_name) {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
std::string getDefaultDumperName() {
AKANTU_ERROR("No dumper activated at compilation, turn on "
"AKANTU_USE_IOHELPER in cmake.");
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
#pragma GCC diagnostic pop
} // namespace akantu
#endif /* AKANTU_DUMPABLE_DUMMY_HH_ */
#endif // DOXYGEN
diff --git a/src/io/dumper/dumpable_inline_impl.hh b/src/io/dumper/dumpable_inline_impl.hh
index ddf4d2c8b..0fd69200c 100644
--- a/src/io/dumper/dumpable_inline_impl.hh
+++ b/src/io/dumper/dumpable_inline_impl.hh
@@ -1,135 +1,137 @@
/**
* @file dumpable_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the Dumpable class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPABLE_INLINE_IMPL_HH_
#define AKANTU_DUMPABLE_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
inline void Dumpable::registerDumper(const std::string & dumper_name,
const std::string & file_name,
const bool is_default) {
if (this->dumpers.find(dumper_name) != this->dumpers.end()) {
AKANTU_DEBUG_INFO("Dumper " + dumper_name + "is already registered.");
}
std::string name = file_name;
if (name.empty()) {
name = dumper_name;
}
this->dumpers[dumper_name] = std::make_shared<T>(name);
if (is_default) {
this->default_dumper = dumper_name;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
this->addDumpFieldExternalToDumper<T>(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void
Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
auto field_cont = std::make_shared<dumpers::NodalField<T>>(field);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension,
GhostType ghost_type,
ElementKind element_kind) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field,
spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field_cont;
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
field_cont = std::make_shared<dumpers::IGFEMElementalField<T>>(
field, spatial_dimension, ghost_type, element_kind);
} else
#endif
field_cont = std::make_shared<dumpers::ElementalField<T>>(
field, spatial_dimension, ghost_type, element_kind);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline T & Dumpable::getDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
try {
auto & templated_dumper = aka::as_type<T>(dumper);
return templated_dumper;
} catch (std::bad_cast &) {
AKANTU_EXCEPTION("Dumper " << dumper_name << " is not of type: "
<< debug::demangle(typeid(T).name()));
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif
#endif /* AKANTU_DUMPABLE_INLINE_IMPL_HH_ */
diff --git a/src/io/dumper/dumpable_iohelper.hh b/src/io/dumper/dumpable_iohelper.hh
index 02597fa7a..381044d06 100644
--- a/src/io/dumper/dumpable_iohelper.hh
+++ b/src/io/dumper/dumpable_iohelper.hh
@@ -1,192 +1,194 @@
/**
* @file dumpable_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 06 2015
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Feb 28 2020
*
* @brief Interface for object who wants to dump themselves
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPABLE_IOHELPER_HH_
#define AKANTU_DUMPABLE_IOHELPER_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable();
virtual ~Dumpable();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create a new dumper (of templated type T) and register it under
/// dumper_name. file_name is used for construction of T. is default states if
/// this dumper is the default dumper.
template <class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
bool is_default = false);
/// register an externally created dumper
void registerExternalDumper(std::shared_ptr<DumperIOHelper> dumper,
const std::string & dumper_name,
bool is_default = false);
/// register a mesh to the default dumper
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// register a mesh to the default identified by its name
void addDumpMeshToDumper(const std::string & dumper_name, const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// register a filtered mesh as the default dumper
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// register a filtered mesh and provides a name
void addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// to implement
virtual void addDumpField(const std::string & field_id);
/// to implement
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/// add a field
virtual void addDumpFieldExternal(const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
virtual void
addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
template <typename T>
inline void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field);
template <typename T>
inline void
addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
template <typename T>
inline void addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
void removeDumpField(const std::string & field_id);
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
void setBaseName(const std::string & basename);
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
void setTimeStepToDumper(Real time_step);
void setTimeStepToDumper(const std::string & dumper_name, Real time_step);
void setTextModeToDumper(const std::string & dumper_name);
void setTextModeToDumper();
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
public:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper();
DumperIOHelper & getDumper(const std::string & dumper_name);
template <class T> T & getDumper(const std::string & dumper_name);
std::string getDefaultDumperName() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DumperMap = std::map<std::string, std::shared_ptr<DumperIOHelper>>;
using DumperSet = std::set<std::string>;
DumperMap dumpers;
std::string default_dumper;
};
} // namespace akantu
#endif /* AKANTU_DUMPABLE_IOHELPER_HH_ */
diff --git a/src/io/dumper/dumper_compute.hh b/src/io/dumper/dumper_compute.hh
index b6c7bbeb8..a45832117 100644
--- a/src/io/dumper/dumper_compute.hh
+++ b/src/io/dumper/dumper_compute.hh
@@ -1,408 +1,411 @@
/**
* @file dumper_compute.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Field that map a function to another field
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_COMPUTE_HH_
#define AKANTU_DUMPER_COMPUTE_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_type_traits.hh"
/* -------------------------------------------------------------------------- */
#include <aka_iterators.hh>
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
class ComputeFunctorInterface {
public:
virtual ~ComputeFunctorInterface() = default;
virtual UInt getDim() = 0;
virtual UInt getNbComponent(UInt old_nb_comp) = 0;
};
/* ------------------------------------------------------------------------ */
template <typename return_type>
class ComputeFunctorOutput : public ComputeFunctorInterface {
public:
ComputeFunctorOutput() = default;
~ComputeFunctorOutput() override = default;
};
/* ------------------------------------------------------------------------ */
template <typename input_type, typename return_type>
class ComputeFunctor : public ComputeFunctorOutput<return_type> {
public:
ComputeFunctor() = default;
~ComputeFunctor() override = default;
virtual return_type func(const input_type & /*d*/,
Element /*global_index*/) {
AKANTU_TO_IMPLEMENT();
}
virtual return_type func(const input_type & /*d*/) {
AKANTU_TO_IMPLEMENT();
}
};
/* ------------------------------------------------------------------------ */
template <class EnumType>
class ComputeUIntFromEnum
: public ComputeFunctor<Vector<EnumType>, Vector<UInt>> {
public:
ComputeUIntFromEnum() = default;
inline Vector<UInt> func(const Vector<EnumType> & in) override {
Vector<UInt> out(in.size());
for (auto && data : zip(in, out)) {
std::get<1>(data) =
static_cast<std::underlying_type_t<EnumType>>(std::get<0>(data));
}
return out;
}
UInt getDim() override { return 1; };
UInt getNbComponent(UInt old_nb_comp) override { return old_nb_comp; };
};
/* ------------------------------------------------------------------------ */
template <typename SubFieldCompute, typename _return_type,
class support_type_ = typename SubFieldCompute::support_type>
class FieldCompute : public Field {
/* ---------------------------------------------------------------------- */
/* Typedefs */
/* ---------------------------------------------------------------------- */
public:
using return_type = _return_type;
using support_type = support_type_;
using sub_iterator = typename SubFieldCompute::iterator;
using sub_types = typename SubFieldCompute::types;
using sub_return_type = typename sub_types::return_type;
using data_type = typename return_type::value_type;
using functor_type = ComputeFunctor<sub_return_type, return_type>;
using types = TypeTraits<data_type, return_type, Array<data_type>>;
public:
class iterator {
public:
iterator(const sub_iterator & it, functor_type & func)
: it(it), func(func) {}
bool operator!=(const iterator & it) const { return it.it != this->it; }
iterator operator++() {
++this->it;
return *this;
}
return_type operator*() { return func.func(*it); }
/// Do to IOHelper the needs it...
UInt element_type() { return this->it.element_type(); }
protected:
sub_iterator it;
functor_type & func;
};
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
FieldCompute(SubFieldCompute & cont,
std::unique_ptr<ComputeFunctorInterface> func)
: sub_field(aka::as_type<SubFieldCompute>(cont.shared_from_this())),
func(aka::as_type<functor_type>(func.release())) {
this->checkHomogeneity();
};
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
public:
iterator begin() { return iterator(sub_field->begin(), *func); }
iterator end() { return iterator(sub_field->end(), *func); }
UInt getDim() { return func->getDim(); }
UInt size() {
throw;
// return Functor::size();
return 0;
}
void checkHomogeneity() override { this->homogeneous = true; };
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
/// for connection to a FieldCompute
inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override;
/// for connection to a FieldCompute
std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & proxy) override;
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
public:
std::shared_ptr<SubFieldCompute> sub_field;
std::unique_ptr<functor_type> func;
};
/* ------------------------------------------------------------------------ */
template <typename SubFieldCompute, typename _return_type>
class FieldCompute<SubFieldCompute, _return_type, Element> : public Field {
/* ---------------------------------------------------------------------- */
/* Typedefs */
/* ---------------------------------------------------------------------- */
public:
using return_type = _return_type;
using support_type = Element;
using sub_iterator = typename SubFieldCompute::iterator;
using sub_types = typename SubFieldCompute::types;
using sub_return_type = typename sub_types::return_type;
using data_type = typename sub_types::data_type;
using functor_type = ComputeFunctor<sub_return_type, return_type>;
using types =
TypeTraits<data_type, return_type, ElementTypeMapArray<data_type>>;
public:
class iterator {
public:
iterator(const sub_iterator & it, functor_type & func)
: it(it), func(func) {}
bool operator!=(const iterator & it) const { return it.it != this->it; }
iterator operator++() {
++this->it;
return *this;
}
UInt currentGlobalIndex() { return this->it.currentGlobalIndex(); }
return_type operator*() { return func.func(*it, it.getCurrentElement()); }
Element getCurrentElement() { return this->it.getCurrentElement(); }
UInt element_type() { return this->it.element_type(); }
protected:
sub_iterator it;
functor_type & func;
};
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
FieldCompute(SubFieldCompute & cont,
std::unique_ptr<ComputeFunctorInterface> func)
: sub_field(aka::as_type<SubFieldCompute>(cont.shared_from_this())),
func(aka::as_type<functor_type>(func.release())) {
this->checkHomogeneity();
};
~FieldCompute() override = default;
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
}
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
public:
iterator begin() { return iterator(sub_field->begin(), *func); }
iterator end() { return iterator(sub_field->end(), *func); }
UInt getDim() { return func->getDim(); }
UInt size() {
throw;
// return Functor::size();
return 0;
}
void checkHomogeneity() override { this->homogeneous = true; };
template <class T1 = data_type,
std::enable_if_t<std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<UInt>();
}
template <class T1 = data_type,
std::enable_if_t<not std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
/// get the number of components of the hosted field
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) override {
ElementTypeMap<UInt> nb_components;
const auto & old_nb_components =
this->sub_field->getNbComponents(dim, ghost_type, kind);
for (auto type : old_nb_components.elementTypes(dim, ghost_type, kind)) {
UInt nb_comp = old_nb_components(type, ghost_type);
nb_components(type, ghost_type) = func->getNbComponent(nb_comp);
}
return nb_components;
};
/// for connection to a FieldCompute
inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override;
/// for connection to a FieldCompute
std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & proxy) override;
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
public:
std::shared_ptr<SubFieldCompute> sub_field;
std::unique_ptr<functor_type> func;
};
/* ------------------------------------------------------------------------ */
class FieldComputeProxy {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
FieldComputeProxy(std::unique_ptr<ComputeFunctorInterface> func)
: func(std::move(func)){};
inline static std::shared_ptr<Field>
createFieldCompute(std::shared_ptr<Field> & field,
std::unique_ptr<ComputeFunctorInterface> func) {
FieldComputeProxy compute_proxy(std::move(func));
return field->connect(compute_proxy);
}
template <typename T> std::shared_ptr<Field> connectToField(T * ptr) {
if (aka::is_of_type<ComputeFunctorOutput<Vector<Real>>>(func)) {
return this->connectToFunctor<Vector<Real>>(ptr);
}
if (aka::is_of_type<ComputeFunctorOutput<Vector<UInt>>>(func)) {
return this->connectToFunctor<Vector<UInt>>(ptr);
}
if (aka::is_of_type<ComputeFunctorOutput<Matrix<UInt>>>(func)) {
return this->connectToFunctor<Matrix<UInt>>(ptr);
}
if (aka::is_of_type<ComputeFunctorOutput<Matrix<Real>>>(func)) {
return this->connectToFunctor<Matrix<Real>>(ptr);
}
throw;
}
template <typename output, typename T>
std::shared_ptr<Field> connectToFunctor(T * ptr) {
return std::make_shared<FieldCompute<T, output>>(*ptr, std::move(func));
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2>
std::shared_ptr<Field>
connectToFunctor(FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
return_type2> * /*ptr*/) {
throw; // return new FieldCompute<T,output>(*ptr,func);
return nullptr;
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2, typename return_type3,
typename return_type4>
std::shared_ptr<Field> connectToFunctor(
FieldCompute<FieldCompute<FieldCompute<FieldCompute<SubFieldCompute,
return_type1>,
return_type2>,
return_type3>,
return_type4> * /*ptr*/) {
throw; // return new FieldCompute<T,output>(*ptr,func);
return nullptr;
}
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
public:
std::unique_ptr<ComputeFunctorInterface> func;
};
/* ------------------------------------------------------------------------ */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type,
typename support_type_>
inline std::shared_ptr<Field>
FieldCompute<SubFieldCompute, return_type, support_type_>::connect(
FieldComputeProxy & proxy) {
return proxy.connectToField(this);
}
template <typename SubFieldCompute, typename return_type>
inline std::shared_ptr<Field>
FieldCompute<SubFieldCompute, return_type, Element>::connect(
FieldComputeProxy & proxy) {
return proxy.connectToField(this);
}
/* ------------------------------------------------------------------------ */
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_COMPUTE_HH_ */
diff --git a/src/io/dumper/dumper_element_iterator.hh b/src/io/dumper/dumper_element_iterator.hh
index 97db57d48..f2df0326f 100644
--- a/src/io/dumper/dumper_element_iterator.hh
+++ b/src/io/dumper/dumper_element_iterator.hh
@@ -1,178 +1,180 @@
/**
* @file dumper_element_iterator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Iterators for elemental fields
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_ELEMENT_ITERATOR_HH_
#define AKANTU_DUMPER_ELEMENT_ITERATOR_HH_
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class types, template <class> class final_iterator>
class element_iterator {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using iterator = final_iterator<types>;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
element_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: field(field), tit(t_it), tit_end(t_it_end), array_it(array_it),
array_it_end(array_it_end), ghost_type(ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
bool operator!=(const iterator & it) const {
return (ghost_type != it.ghost_type) ||
(tit != it.tit || (array_it != it.array_it));
}
iterator & operator++() {
++array_it;
while (array_it == array_it_end && tit != tit_end) {
++tit;
if (tit != tit_end) {
const array_type & vect = field(*tit, ghost_type);
UInt _nb_data_per_elem = getNbDataPerElem(*tit);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / _nb_data_per_elem;
array_it = vect.begin_reinterpret(_nb_data_per_elem, size);
array_it_end = vect.end_reinterpret(_nb_data_per_elem, size);
}
}
return *(static_cast<iterator *>(this));
};
ElementType getType() { return *tit; }
UInt element_type() { return getIOHelperType(*tit); }
Element getCurrentElement() {
return Element{*tit, array_it.getCurrentIndex(), _not_ghost};
}
UInt getNbDataPerElem(ElementType type) const {
if (!nb_data_per_elem.exists(type, ghost_type)) {
return field(type, ghost_type).getNbComponent();
}
return nb_data_per_elem(type, ghost_type);
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) {
this->nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the field to iterate on
const field_type & field;
/// field iterator
typename field_type::type_iterator tit;
/// field iterator end
typename field_type::type_iterator tit_end;
/// array iterator
array_iterator array_it;
/// internal iterator end
array_iterator array_it_end;
/// ghost type identification
const GhostType ghost_type;
/// number of data per element
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
template <typename types>
class elemental_field_iterator
: public element_iterator<types, elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
using parent =
element_iterator<types, ::akantu::dumpers::elemental_field_iterator>;
using it_type = typename types::it_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
elemental_field_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*() { return *this->array_it; }
private:
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_DUMPER_ELEMENT_ITERATOR_HH_ */
diff --git a/src/io/dumper/dumper_element_partition.hh b/src/io/dumper/dumper_element_partition.hh
index fb26796a6..1b3bf50b4 100644
--- a/src/io/dumper/dumper_element_partition.hh
+++ b/src/io/dumper/dumper_element_partition.hh
@@ -1,136 +1,138 @@
/**
* @file dumper_element_partition.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief ElementPartition field
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
#ifdef AKANTU_IGFEM
#include "dumper_igfem_element_partition.hh"
#endif
/* --------------------------------------------------------------------------
*/
template <class types>
class element_partition_field_iterator
: public element_iterator<types, element_partition_field_iterator> {
/* ------------------------------------------------------------------------
*/
/* Typedefs */
/* ------------------------------------------------------------------------
*/
public:
using parent =
element_iterator<types, dumpers::element_partition_field_iterator>;
using return_type =
typename SingleType<unsigned int, Vector, true>::return_type;
using array_iterator = typename types::array_iterator;
using field_type = typename types::field_type;
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
element_partition_field_iterator(
const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {
prank = Communicator::getStaticCommunicator().whoAmI();
}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
return_type operator*() { return return_type(1, prank); }
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
protected:
UInt prank;
};
/* --------------------------------------------------------------------------
*/
template <bool filtered = false>
class ElementPartitionField
: public GenericElementalField<SingleType<UInt, Vector, filtered>,
element_partition_field_iterator> {
public:
/* ------------------------------------------------------------------------
*/
/* Typedefs */
/* ------------------------------------------------------------------------
*/
using types = SingleType<UInt, Vector, filtered>;
using iterator = element_partition_field_iterator<types>;
using parent =
GenericElementalField<types, element_partition_field_iterator>;
using field_type = typename types::field_type;
public:
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
ElementPartitionField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind) {
this->homogeneous = true;
}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
UInt getDim() override { return 1; }
};
/* --------------------------------------------------------------------------
*/
} // namespace dumper
} // namespace akantu
diff --git a/src/io/dumper/dumper_elemental_field.hh b/src/io/dumper/dumper_elemental_field.hh
index 7a8e739c4..29c201308 100644
--- a/src/io/dumper/dumper_elemental_field.hh
+++ b/src/io/dumper/dumper_elemental_field.hh
@@ -1,75 +1,77 @@
/**
* @file dumper_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief description of elemental fields
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_ELEMENTAL_FIELD_HH_
#define AKANTU_DUMPER_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dumper_field.hh"
#include "dumper_generic_elemental_field.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class ret = Vector,
bool filtered = false>
class ElementalField
: public GenericElementalField<SingleType<T, ret, filtered>,
elemental_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, ret, filtered>;
using field_type = typename types::field_type;
using iterator = elemental_field_iterator<types>;
using support_type = Element;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: GenericElementalField<types, elemental_field_iterator>(
field, spatial_dimension, ghost_type, element_kind) {}
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_ELEMENTAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_field.hh b/src/io/dumper/dumper_field.hh
index 87106bc9b..8d935070d 100644
--- a/src/io/dumper/dumper_field.hh
+++ b/src/io/dumper/dumper_field.hh
@@ -1,136 +1,138 @@
/**
* @file dumper_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Common interface for fields
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_FIELD_HH_
#define AKANTU_DUMPER_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
class FieldComputeProxy;
class FieldComputeBaseInterface;
class ComputeFunctorInterface;
class HomogenizerProxy;
/* -------------------------------------------------------------------------- */
/// Field interface
class Field : public std::enable_shared_from_this<Field> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Field() = default;
virtual ~Field() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
#ifdef AKANTU_USE_IOHELPER
/// register this to the provided dumper
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
#endif
/// set the number of data per item (used for elements fields at the moment)
virtual void setNbData([[gnu::unused]] UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem([
[gnu::unused]] const ElementTypeMap<UInt> & nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem([[gnu::unused]] UInt nb_data) {
AKANTU_TO_IMPLEMENT();
};
/// get the number of components of the hosted field
virtual ElementTypeMap<UInt>
getNbComponents([[gnu::unused]] UInt dim = _all_dimensions,
[[gnu::unused]] GhostType ghost_type = _not_ghost,
[[gnu::unused]] ElementKind kind = _ek_not_defined) {
throw;
};
/// for connection to a FieldCompute
inline virtual std::shared_ptr<Field> connect([
[gnu::unused]] FieldComputeProxy & proxy) {
throw;
};
/// for connection to a FieldCompute
inline virtual std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & /*proxy*/) {
throw;
};
/// check if the same quantity of data for all element types
virtual void checkHomogeneity() = 0;
/// return the dumper name
std::string getGroupName() { return group_name; };
/// return the id of the field
std::string getID() { return field_id; };
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the flag to know if the field is homogeneous/contiguous
virtual bool isHomogeneous() { return homogeneous; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the flag to know if it is homogeneous
bool homogeneous{false};
/// the name of the group it was associated to
std::string group_name;
/// the name of the dumper it was associated to
std::string field_id;
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_filtered_connectivity.hh b/src/io/dumper/dumper_filtered_connectivity.hh
index ad5b1313d..3517122b6 100644
--- a/src/io/dumper/dumper_filtered_connectivity.hh
+++ b/src/io/dumper/dumper_filtered_connectivity.hh
@@ -1,172 +1,174 @@
/**
* @file dumper_filtered_connectivity.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief FilteredConnectivities field
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* --------------------------------------------------------------------------
*/
template <class types>
class filtered_connectivity_field_iterator
: public element_iterator<types, filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------
*/
/* Typedefs */
/* ------------------------------------------------------------------------
*/
public:
using parent =
element_iterator<types, dumpers::filtered_connectivity_field_iterator>;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
filtered_connectivity_field_iterator(
const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it, const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
return_type operator*() {
const Vector<UInt> & old_connect = *this->array_it;
Vector<UInt> new_connect(old_connect.size());
Array<UInt>::const_iterator<UInt> nodes_begin = nodal_filter->begin();
Array<UInt>::const_iterator<UInt> nodes_end = nodal_filter->end();
for (UInt i(0); i < old_connect.size(); ++i) {
Array<UInt>::const_iterator<UInt> new_id =
std::find(nodes_begin, nodes_end, old_connect(i));
if (new_id == nodes_end) {
AKANTU_EXCEPTION("Node not found in the filter!");
}
new_connect(i) = new_id - nodes_begin;
}
return new_connect;
}
void setNodalFilter(const Array<UInt> & new_nodal_filter) {
nodal_filter = &new_nodal_filter;
}
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
private:
const Array<UInt> * nodal_filter;
};
/* --------------------------------------------------------------------------
*/
class FilteredConnectivityField
: public GenericElementalField<SingleType<UInt, Vector, true>,
filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------
*/
/* Typedefs */
/* ------------------------------------------------------------------------
*/
public:
using types = SingleType<UInt, Vector, true>;
using iterator = filtered_connectivity_field_iterator<types>;
using field_type = types::field_type;
using parent =
GenericElementalField<types, filtered_connectivity_field_iterator>;
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
FilteredConnectivityField(const field_type & field,
const Array<UInt> & nodal_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind),
nodal_filter(nodal_filter) {}
~FilteredConnectivityField() override {
// since the field is created in registerFilteredMesh it is destroyed here
delete const_cast<field_type *>(&this->field);
}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
iterator begin() override {
iterator it = parent::begin();
it.setNodalFilter(nodal_filter);
return it;
}
iterator end() override {
iterator it = parent::end();
it.setNodalFilter(nodal_filter);
return it;
}
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
private:
const Array<UInt> & nodal_filter;
};
/* --------------------------------------------------------------------------
*/
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
diff --git a/src/io/dumper/dumper_generic_elemental_field.hh b/src/io/dumper/dumper_generic_elemental_field.hh
index 8a4a2f7ff..0b9c0dd89 100644
--- a/src/io/dumper/dumper_generic_elemental_field.hh
+++ b/src/io/dumper/dumper_generic_elemental_field.hh
@@ -1,229 +1,231 @@
/**
* @file dumper_generic_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Generic interface for elemental fields
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_
#define AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_element_iterator.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <class _types, template <class> class iterator_type>
class GenericElementalField : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
// check dumper_type_traits.hh for additional information over these types
using types = _types;
using data_type = typename types::data_type;
using it_type = typename types::it_type;
using field_type = typename types::field_type;
using array_type = typename types::array_type;
using array_iterator = typename types::array_iterator;
using field_type_iterator = typename field_type::type_iterator;
using iterator = iterator_type<types>;
using support_type = Element;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GenericElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: field(field), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {
this->checkHomogeneity();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the number of components of the hosted field
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) override {
return this->field.getNbComponents(dim, ghost_type, kind);
};
/// return the size of the contained data: i.e. the number of elements ?
virtual UInt size() {
checkHomogeneity();
return this->nb_total_element;
}
/// return the iohelper datatype to be dumped
template <class T1 = data_type,
std::enable_if_t<std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<UInt>();
}
template <class T1 = data_type,
std::enable_if_t<not std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
protected:
/// return the number of entries per element
UInt getNbDataPerElem(ElementType type,
GhostType ghost_type = _not_ghost) const {
if (!nb_data_per_elem.exists(type, ghost_type)) {
return field(type, ghost_type).getNbComponent();
}
return nb_data_per_elem(type, this->ghost_type);
}
/// check if the same quantity of data for all element types
void checkHomogeneity() override;
public:
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
}
/// for connection to a FieldCompute
inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
inline std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & proxy) override {
return proxy.connectToField(this);
}
virtual iterator begin() {
/// type iterators on the elemental field
auto types = this->field.elementTypes(this->spatial_dimension,
this->ghost_type, this->element_kind);
auto tit = types.begin();
auto end = types.end();
/// skip all types without data
for (; tit != end and this->field(*tit, this->ghost_type).empty();
++tit) {
}
auto type = *tit;
if (tit == end) {
return this->end();
}
/// getting information for the field of the given type
const auto & vect = this->field(type, this->ghost_type);
UInt nb_data_per_elem = this->getNbDataPerElem(type);
/// define element-wise iterator
auto view = make_view(vect, nb_data_per_elem);
auto it = view.begin();
auto it_end = view.end();
/// define data iterator
iterator rit =
iterator(this->field, tit, end, it, it_end, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual iterator end() {
auto types = this->field.elementTypes(this->spatial_dimension,
this->ghost_type, this->element_kind);
auto tit = types.begin();
auto end = types.end();
auto type = *tit;
for (; tit != end; ++tit) {
type = *tit;
}
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data = this->getNbDataPerElem(type);
auto it = make_view(vect, nb_data).end();
auto rit = iterator(this->field, end, end, it, it, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual UInt getDim() {
if (this->homogeneous) {
auto tit = this->field
.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind)
.begin();
return this->getNbDataPerElem(*tit);
}
throw;
return 0;
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) override {
nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ElementTypeMapArray embedded in the field
const field_type & field;
/// total number of elements
UInt nb_total_element;
/// the spatial dimension of the problem
UInt spatial_dimension;
/// whether this is a ghost field or not (for type selection)
GhostType ghost_type;
/// The element kind to operate on
ElementKind element_kind;
/// The number of data per element type
ElementTypeMap<UInt> nb_data_per_elem;
};
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
index 3ac648b7b..777f6e387 100644
--- a/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
+++ b/src/io/dumper/dumper_generic_elemental_field_tmpl.hh
@@ -1,73 +1,76 @@
/**
* @file dumper_generic_elemental_field_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of the template functions of the ElementalField
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
template <class types, template <class> class iterator>
void GenericElementalField<types, iterator>::checkHomogeneity() {
auto types =
field.elementTypes(spatial_dimension, ghost_type, element_kind);
auto tit = types.begin();
auto end = types.end();
this->nb_total_element = 0;
UInt nb_comp = 0;
bool homogen = true;
if (tit != end) {
nb_comp = this->field(*tit, ghost_type).getNbComponent();
for (; tit != end; ++tit) {
const auto & vect = this->field(*tit, ghost_type);
auto nb_element = vect.size();
auto nb_comp_cur = vect.getNbComponent();
if (homogen && nb_comp != nb_comp_cur) {
homogen = false;
}
this->nb_total_element += nb_element;
// this->nb_data_per_elem(*tit,this->ghost_type) = nb_comp_cur;
}
if (!homogen) {
nb_comp = 0;
}
}
this->homogeneous = homogen;
}
/* --------------------------------------------------------------------------
*/
} // namespace dumpers
} // namespace akantu
diff --git a/src/io/dumper/dumper_homogenizing_field.hh b/src/io/dumper/dumper_homogenizing_field.hh
index 8fc41cf8a..478f8ff70 100644
--- a/src/io/dumper/dumper_homogenizing_field.hh
+++ b/src/io/dumper/dumper_homogenizing_field.hh
@@ -1,199 +1,201 @@
/**
* @file dumper_homogenizing_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief description of field homogenizing field
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_
#define AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
template <typename type>
inline type
typeConverter(const type & input,
[[gnu::unused]] Vector<typename type::value_type> & res,
[[gnu::unused]] UInt nb_data) {
throw;
return input;
}
/* ------------------------------------------------------------------------ */
template <typename type>
inline Matrix<type> typeConverter(const Matrix<type> & input,
Vector<type> & res, UInt nb_data) {
Matrix<type> tmp(res.storage(), input.rows(), nb_data / input.rows());
Matrix<type> tmp2(tmp, true);
return tmp2;
}
/* ------------------------------------------------------------------------ */
template <typename type>
inline Vector<type> typeConverter(const Vector<type> & /*unused*/,
Vector<type> & res, UInt /*unused*/) {
return res;
}
/* ------------------------------------------------------------------------ */
template <typename type>
class AvgHomogenizingFunctor : public ComputeFunctor<type, type> {
/* ---------------------------------------------------------------------- */
/* Typedefs */
/* ---------------------------------------------------------------------- */
private:
using value_type = typename type::value_type;
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
AvgHomogenizingFunctor(ElementTypeMap<UInt> & nb_datas) {
auto types = nb_datas.elementTypes();
auto tit = types.begin();
auto end = types.end();
nb_data = nb_datas(*tit);
for (; tit != end; ++tit) {
if (nb_data != nb_datas(*tit)) {
throw;
}
}
}
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
public:
type func(const type & d, Element /*global_index*/) override {
Vector<value_type> res(this->nb_data);
if (d.size() % this->nb_data) {
throw;
}
UInt nb_to_average = d.size() / this->nb_data;
value_type * ptr = d.storage();
for (UInt i = 0; i < nb_to_average; ++i) {
Vector<value_type> tmp(ptr, this->nb_data);
res += tmp;
ptr += this->nb_data;
}
res /= nb_to_average;
return typeConverter(d, res, this->nb_data);
};
UInt getDim() override { return nb_data; };
UInt getNbComponent(UInt /*old_nb_comp*/) override { throw; };
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
/// The size of data: i.e. the size of the vector to be returned
UInt nb_data;
};
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
class HomogenizerProxy {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
HomogenizerProxy() = default;
public:
inline static std::unique_ptr<ComputeFunctorInterface>
createHomogenizer(Field & field);
template <typename T>
inline std::unique_ptr<ComputeFunctorInterface> connectToField(T * field) {
ElementTypeMap<UInt> nb_components = field->getNbComponents();
using ret_type = typename T::types::return_type;
return this->instantiateHomogenizer<ret_type>(nb_components);
}
template <typename ret_type>
inline std::unique_ptr<ComputeFunctorInterface>
instantiateHomogenizer(ElementTypeMap<UInt> & nb_components);
};
/* ------------------------------------------------------------------------ */
template <typename ret_type>
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::instantiateHomogenizer(
ElementTypeMap<UInt> & nb_components) {
using Homogenizer = dumpers::AvgHomogenizingFunctor<ret_type>;
return std::make_unique<Homogenizer>(nb_components);
}
template <>
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::instantiateHomogenizer<Vector<iohelper::ElemType>>(
[[gnu::unused]] ElementTypeMap<UInt> & nb_components) {
throw;
return nullptr;
}
/* ------------------------------------------------------------------------ */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type,
typename support_type_>
inline std::unique_ptr<ComputeFunctorInterface>
FieldCompute<SubFieldCompute, return_type, support_type_>::connect(
HomogenizerProxy & proxy) {
return proxy.connectToField(this);
}
template <typename SubFieldCompute, typename return_type>
inline std::unique_ptr<ComputeFunctorInterface>
FieldCompute<SubFieldCompute, return_type, Element>::connect(
HomogenizerProxy & proxy) {
return proxy.connectToField(this);
}
/* ------------------------------------------------------------------------ */
inline std::unique_ptr<ComputeFunctorInterface>
HomogenizerProxy::createHomogenizer(Field & field) {
HomogenizerProxy homogenizer_proxy;
return field.connect(homogenizer_proxy);
}
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_HOMOGENIZING_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_internal_material_field.hh b/src/io/dumper/dumper_internal_material_field.hh
index ba233717e..c94d68d78 100644
--- a/src/io/dumper/dumper_internal_material_field.hh
+++ b/src/io/dumper/dumper_internal_material_field.hh
@@ -1,72 +1,74 @@
/**
* @file dumper_internal_material_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Mar 04 2020
*
* @brief description of material internal field
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_
#define AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_quadrature_point_iterator.hh"
#ifdef AKANTU_IGFEM
#include "dumper_igfem_material_internal_field.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename T, bool filtered = false>
class InternalMaterialField
: public GenericElementalField<SingleType<T, Vector, filtered>,
quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using types = SingleType<T, Vector, filtered>;
using parent = GenericElementalField<types, quadrature_point_iterator>;
using field_type = typename types::field_type;
using support_type = Element;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
InternalMaterialField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: parent(field, spatial_dimension, ghost_type, element_kind) {}
};
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_iohelper.cc b/src/io/dumper/dumper_iohelper.cc
index 7aedfd549..3f6b33f52 100644
--- a/src/io/dumper/dumper_iohelper.cc
+++ b/src/io/dumper/dumper_iohelper.cc
@@ -1,320 +1,322 @@
/**
* @file dumper_iohelper.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of DumperIOHelper
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
#include "dumper_elemental_field.hh"
#include "dumper_filtered_connectivity.hh"
#include "dumper_iohelper.hh"
#include "dumper_nodal_field.hh"
#include "dumper_variable.hh"
#include "mesh.hh"
#if defined(AKANTU_IGFEM)
#include "dumper_igfem_connectivity.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperIOHelper::DumperIOHelper() = default;
/* -------------------------------------------------------------------------- */
DumperIOHelper::~DumperIOHelper() = default;
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setParallelContext(bool is_parallel) {
UInt whoami = Communicator::getStaticCommunicator().whoAmI();
UInt nb_proc = Communicator::getStaticCommunicator().getNbProc();
if (is_parallel) {
dumper->setParallelContext(whoami, nb_proc);
} else {
dumper->setParallelContext(0, 1);
}
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setDirectory(const std::string & directory) {
this->directory = directory;
dumper->setPrefix(directory);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setBaseName(const std::string & basename) {
filename = basename;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setTimeStep(Real time_step) {
if (!time_activated) {
this->dumper->activateTimeDescFiles(time_step);
} else {
this->dumper->setTimeStep(time_step);
}
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump() {
try {
dumper->dump(filename, count);
} catch (iohelper::IOHelperException & e) {
AKANTU_ERROR(
"I was not able to dump your data with a Dumper: " << e.what());
}
++count;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(UInt step) {
this->count = step;
this->dump();
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(Real current_time, UInt step) {
this->dumper->setCurrentTime(current_time);
this->dump(step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerMesh(const Mesh & mesh, UInt spatial_dimension,
GhostType ghost_type,
ElementKind element_kind) {
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
registerField("connectivities",
new dumpers::IGFEMConnectivityField(
mesh.getConnectivities(), spatial_dimension, ghost_type));
} else
#endif
registerField("connectivities",
std::make_shared<dumpers::ElementalField<UInt>>(
mesh.getConnectivities(), spatial_dimension, ghost_type,
element_kind));
registerField("positions",
std::make_shared<dumpers::NodalField<Real>>(mesh.getNodes()));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind) {
auto * f_connectivities = new ElementTypeMapArrayFilter<UInt>(
mesh.getConnectivities(), elements_filter);
this->registerField("connectivities",
std::make_shared<dumpers::FilteredConnectivityField>(
*f_connectivities, nodes_filter, spatial_dimension,
ghost_type, element_kind));
this->registerField("positions",
std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &nodes_filter));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerField(
const std::string & field_id,
std::shared_ptr<dumpers::Field>
field) // NOLINT(performance-unnecessary-value-param)
{
auto it = fields.find(field_id);
if (it != fields.end()) {
AKANTU_DEBUG_WARNING(
"The field "
<< field_id << " is already registered in this Dumper. Field ignored.");
return;
}
fields[field_id] = field;
field->registerToDumper(field_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterField(const std::string & field_id) {
auto it = fields.find(field_id);
if (it == fields.end()) {
AKANTU_DEBUG_WARNING(
"The field " << field_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
fields.erase(it);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerVariable(
const std::string & variable_id,
std::shared_ptr<dumpers::VariableBase>
variable) // NOLINT(performance-unnecessary-value-param)
{
auto it = variables.find(variable_id);
if (it != variables.end()) {
AKANTU_DEBUG_WARNING(
"The Variable "
<< variable_id
<< " is already registered in this Dumper. Variable ignored.");
return;
}
variables[variable_id] = variable;
variable->registerToDumper(variable_id, *dumper);
} // namespace akantu
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterVariable(const std::string & variable_id) {
auto it = variables.find(variable_id);
if (it == variables.end()) {
AKANTU_DEBUG_WARNING(
"The variable " << variable_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
variables.erase(it);
}
/* -------------------------------------------------------------------------- */
template <ElementType type> iohelper::ElemType getIOHelperType() {
AKANTU_TO_IMPLEMENT();
return iohelper::MAX_ELEM_TYPE;
}
template <> iohelper::ElemType getIOHelperType<_point_1>() {
return iohelper::POINT_SET;
}
template <> iohelper::ElemType getIOHelperType<_segment_2>() {
return iohelper::LINE1;
}
template <> iohelper::ElemType getIOHelperType<_segment_3>() {
return iohelper::LINE2;
}
template <> iohelper::ElemType getIOHelperType<_triangle_3>() {
return iohelper::TRIANGLE1;
}
template <> iohelper::ElemType getIOHelperType<_triangle_6>() {
return iohelper::TRIANGLE2;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_4>() {
return iohelper::QUAD1;
}
template <> iohelper::ElemType getIOHelperType<_quadrangle_8>() {
return iohelper::QUAD2;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_4>() {
return iohelper::TETRA1;
}
template <> iohelper::ElemType getIOHelperType<_tetrahedron_10>() {
return iohelper::TETRA2;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_8>() {
return iohelper::HEX1;
}
template <> iohelper::ElemType getIOHelperType<_hexahedron_20>() {
return iohelper::HEX2;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_6>() {
return iohelper::PRISM1;
}
template <> iohelper::ElemType getIOHelperType<_pentahedron_15>() {
return iohelper::PRISM2;
}
#if defined(AKANTU_COHESIVE_ELEMENT)
template <> iohelper::ElemType getIOHelperType<_cohesive_1d_2>() {
return iohelper::COH1D2;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_4>() {
return iohelper::COH2D4;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_2d_6>() {
return iohelper::COH2D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_6>() {
return iohelper::COH3D6;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_12>() {
return iohelper::COH3D12;
}
template <> iohelper::ElemType getIOHelperType<_cohesive_3d_8>() {
return iohelper::COH3D8;
}
// template <>
// iohelper::ElemType getIOHelperType<_cohesive_3d_16>() { return
// iohelper::COH3D16; }
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_2>() {
return iohelper::BEAM2;
}
template <> iohelper::ElemType getIOHelperType<_bernoulli_beam_3>() {
return iohelper::BEAM3;
}
#endif
/* -------------------------------------------------------------------------- */
UInt getIOHelperType(ElementType type) {
UInt ioh_type = iohelper::MAX_ELEM_TYPE;
#define GET_IOHELPER_TYPE(type) ioh_type = getIOHelperType<type>();
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_IOHELPER_TYPE);
#undef GET_IOHELPER_TYPE
return ioh_type;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
namespace iohelper {
template <> DataType getDataType<akantu::NodeFlag>() {
return getDataType<std::underlying_type_t<akantu::NodeFlag>>();
}
} // namespace iohelper
diff --git a/src/io/dumper/dumper_iohelper.hh b/src/io/dumper/dumper_iohelper.hh
index 8404ff193..038deacc5 100644
--- a/src/io/dumper/dumper_iohelper.hh
+++ b/src/io/dumper/dumper_iohelper.hh
@@ -1,160 +1,162 @@
/**
* @file dumper_iohelper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Define the akantu dumper interface for IOhelper dumpers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPER_IOHELPER_HH_
#define AKANTU_DUMPER_IOHELPER_HH_
/* -------------------------------------------------------------------------- */
namespace iohelper {
class Dumper;
}
namespace akantu {
UInt getIOHelperType(ElementType type);
namespace dumpers {
class Field;
class VariableBase;
} // namespace dumper
class Mesh;
class DumperIOHelper : public std::enable_shared_from_this<DumperIOHelper> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper();
virtual ~DumperIOHelper();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a given Mesh for the current dumper
virtual void registerMesh(const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// register a filtered Mesh (provided filter lists) for the current dumper
virtual void
registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
/// register a Field object identified by name and provided by pointer
void registerField(const std::string & field_id,
std::shared_ptr<dumpers::Field> field);
/// remove the Field identified by name from managed fields
void unRegisterField(const std::string & field_id);
/// register a VariableBase object identified by name and provided by pointer
void registerVariable(const std::string & variable_id,
std::shared_ptr<dumpers::VariableBase> variable);
/// remove a VariableBase identified by name from managed fields
void unRegisterVariable(const std::string & variable_id);
/// request dump: this calls IOHelper dump routine
virtual void dump();
/// request dump: this first set the current step and then calls IOHelper dump
/// routine
virtual void dump(UInt step);
/// request dump: this first set the current step and current time and then
/// calls IOHelper dump routine
virtual void dump(Real current_time, UInt step);
/// set the parallel context for IOHeper
virtual void setParallelContext(bool is_parallel);
/// set the directory where to generate the dumped files
virtual void setDirectory(const std::string & directory);
/// set the base name (needed by most IOHelper dumpers)
virtual void setBaseName(const std::string & basename);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// direct access to the iohelper::Dumper object
AKANTU_GET_MACRO(Dumper, *dumper, iohelper::Dumper &)
/// set the timestep of the iohelper::Dumper
void setTimeStep(Real time_step);
public:
/* ------------------------------------------------------------------------ */
/* Variable wrapper */
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// internal iohelper::Dumper
std::unique_ptr<iohelper::Dumper> dumper;
using Fields = std::map<std::string, std::shared_ptr<dumpers::Field>>;
using Variables =
std::map<std::string, std::shared_ptr<dumpers::VariableBase>>;
/// list of registered fields to dump
Fields fields;
Variables variables;
/// dump counter
UInt count{0};
/// directory name
std::string directory;
/// filename prefix
std::string filename;
/// is time tracking activated in the dumper
bool time_activated{false};
};
} // namespace akantu
#endif /* AKANTU_DUMPER_IOHELPER_HH_ */
diff --git a/src/io/dumper/dumper_iohelper_paraview.cc b/src/io/dumper/dumper_iohelper_paraview.cc
index 7cdcc76f0..c1ab9c0f3 100644
--- a/src/io/dumper/dumper_iohelper_paraview.cc
+++ b/src/io/dumper/dumper_iohelper_paraview.cc
@@ -1,64 +1,67 @@
/**
* @file dumper_iohelper_paraview.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Mon Jan 22 2018
*
* @brief implementations of DumperParaview
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
DumperParaview::DumperParaview(const std::string & filename,
const std::string & directory, bool parallel)
{
dumper = std::make_unique<iohelper::DumperParaview>();
setBaseName(filename);
this->setParallelContext(parallel);
dumper->setMode(iohelper::BASE64);
dumper->setPrefix(directory);
dumper->init();
}
/* -------------------------------------------------------------------------- */
DumperParaview::~DumperParaview() = default;
/* -------------------------------------------------------------------------- */
void DumperParaview::setBaseName(const std::string & basename) {
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperParaview *>(dumper.get())
->setVTUSubDirectory(filename + "-VTU");
}
} // namespace akantu
diff --git a/src/io/dumper/dumper_iohelper_paraview.hh b/src/io/dumper/dumper_iohelper_paraview.hh
index 67f9b9ee2..c9a96412d 100644
--- a/src/io/dumper/dumper_iohelper_paraview.hh
+++ b/src/io/dumper/dumper_iohelper_paraview.hh
@@ -1,70 +1,72 @@
/**
* @file dumper_iohelper_paraview.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jan 22 2018
*
* @brief Dumper Paraview using IOHelper
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPER_PARAVIEW_HH_
#define AKANTU_DUMPER_PARAVIEW_HH_
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperParaview : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & filename,
const std::string & directory = "./paraview",
bool parallel = true);
~DumperParaview() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// void dump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setBaseName(const std::string & basename) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#endif /* AKANTU_DUMPER_PARAVIEW_HH_ */
diff --git a/src/io/dumper/dumper_material_padders.hh b/src/io/dumper/dumper_material_padders.hh
index d3b02a5f0..20c1022d2 100644
--- a/src/io/dumper/dumper_material_padders.hh
+++ b/src/io/dumper/dumper_material_padders.hh
@@ -1,305 +1,307 @@
/**
* @file dumper_material_padders.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 29 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Material padders for plane stress/ plane strain
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_MATERIAL_PADDERS_HH_
#define AKANTU_DUMPER_MATERIAL_PADDERS_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_padding_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
class MaterialFunctor {
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
MaterialFunctor(const SolidMechanicsModel & model)
: model(model), material_index(model.getMaterialByElement()),
nb_data_per_element("nb_data_per_element", model.getID()),
spatial_dimension(model.getSpatialDimension()) {}
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
/// return the material from the global element index
const Material & getMaterialFromGlobalIndex(Element global_index) {
UInt index = global_index.element;
UInt material_id = material_index(global_index.type)(index);
const Material & material = model.getMaterial(material_id);
return material;
}
/// return the type of the element from global index
ElementType
getElementTypeFromGlobalIndex( // NOLINT(readability-convert-member-functions-to-static)
Element global_index) {
return global_index.type;
}
protected:
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
/// all material padders probably need access to solid mechanics model
const SolidMechanicsModel & model;
/// they also need an access to the map from global ids to material id and
/// local ids
const ElementTypeMapArray<UInt> & material_index;
/// the number of data per element
const ElementTypeMapArray<UInt> nb_data_per_element;
UInt spatial_dimension;
};
/* ------------------------------------------------------------------------ */
template <class T, class R>
class MaterialPadder : public MaterialFunctor,
public PadderGeneric<Vector<T>, R> {
public:
MaterialPadder(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
};
/* ------------------------------------------------------------------------ */
template <UInt spatial_dimension>
class StressPadder : public MaterialPadder<Real, Matrix<Real>> {
public:
StressPadder(const SolidMechanicsModel & model)
: MaterialPadder<Real, Matrix<Real>>(model) {
this->setPadding(3, 3);
}
inline Matrix<Real> func(const Vector<Real> & in,
Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> stress = this->pad(in, nrows, ncols, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_strain = true;
if (spatial_dimension == 2) {
plane_strain = !((bool)material.getParam("Plane_Stress"));
}
if (plane_strain) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
stress(2, 2 + 3 * d) =
nu * (stress(0, 0 + 3 * d) + stress(1, 1 + 3 * d));
}
}
return stress;
}
UInt getDim() override { return 9; };
UInt getNbComponent(UInt /*old_nb_comp*/) override {
return this->getDim();
};
};
/* ------------------------------------------------------------------------ */
template <UInt spatial_dimension>
class StrainPadder : public MaterialFunctor,
public PadderGeneric<Matrix<Real>, Matrix<Real>> {
public:
StrainPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {
this->setPadding(3, 3);
}
inline Matrix<Real> func(const Matrix<Real> & in,
Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> strain = this->pad(in, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_stress = material.getParam("Plane_Stress");
if (plane_stress) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
strain(2, 2 + 3 * d) =
nu / (nu - 1) * (strain(0, 0 + 3 * d) + strain(1, 1 + 3 * d));
}
}
return strain;
}
UInt getDim() override { return 9; };
UInt getNbComponent(UInt /*old_nb_comp*/) override {
return this->getDim();
};
};
/* ------------------------------------------------------------------------ */
template <bool green_strain>
class ComputeStrain : public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real>> {
public:
ComputeStrain(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
inline Matrix<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, ncols);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Tensor3<Real> all_strain(ret_all_strain.storage(), nrows, nrows, nb_data);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
Matrix<Real> strain = all_strain(d);
if (spatial_dimension == 2) {
if (green_strain) {
Material::gradUToE<2>(grad_u, strain);
} else {
Material::gradUToEpsilon<2>(grad_u, strain);
}
} else if (spatial_dimension == 3) {
if (green_strain) {
Material::gradUToE<3>(grad_u, strain);
} else {
Material::gradUToEpsilon<3>(grad_u, strain);
}
}
}
return ret_all_strain;
}
UInt getDim() override { return spatial_dimension * spatial_dimension; };
UInt getNbComponent(UInt /*old_nb_comp*/) override {
return this->getDim();
};
};
/* ------------------------------------------------------------------------ */
template <bool green_strain>
class ComputePrincipalStrain
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real>> {
public:
ComputePrincipalStrain(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Matrix<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, nb_data);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Matrix<Real> strain(nrows, nrows);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
if (spatial_dimension == 2) {
if (green_strain) {
Material::gradUToE<2>(grad_u, strain);
} else {
Material::gradUToEpsilon<2>(grad_u, strain);
}
} else if (spatial_dimension == 3) {
if (green_strain) {
Material::gradUToE<3>(grad_u, strain);
} else {
Material::gradUToEpsilon<3>(grad_u, strain);
}
}
Vector<Real> principal_strain(ret_all_strain(d));
strain.eig(principal_strain);
}
return ret_all_strain;
}
UInt getDim() override { return spatial_dimension; };
UInt getNbComponent(UInt /*old_nb_comp*/) override {
return this->getDim();
};
};
/* ------------------------------------------------------------------------ */
class ComputeVonMisesStress
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Vector<Real>> {
public:
ComputeVonMisesStress(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Vector<Real> func(const Vector<Real> & in,
Element /*global_element_id*/) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Vector<Real> von_mises_stress(nb_data);
Matrix<Real> deviatoric_stress(3, 3);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> cauchy_stress(in.storage() + d * nrows * nrows, nrows,
nrows);
von_mises_stress(d) = Material::stressToVonMises(cauchy_stress);
}
return von_mises_stress;
}
UInt getDim() override { return 1; };
UInt getNbComponent(UInt /*old_nb_comp*/) override {
return this->getDim();
};
};
/* ------------------------------------------------------------------------ */
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_MATERIAL_PADDERS_HH_ */
diff --git a/src/io/dumper/dumper_nodal_field.hh b/src/io/dumper/dumper_nodal_field.hh
index 377332706..7b87c585c 100644
--- a/src/io/dumper/dumper_nodal_field.hh
+++ b/src/io/dumper/dumper_nodal_field.hh
@@ -1,187 +1,189 @@
/**
* @file dumper_nodal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Description of nodal fields
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPER_NODAL_FIELD_HH_
#define AKANTU_DUMPER_NODAL_FIELD_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
#include "dumper_field.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
// This represents a iohelper compatible field
template <typename T, bool filtered = false, class Container = Array<T>,
class Filter = Array<UInt>>
class NodalField : public dumpers::Field {
/* ---------------------------------------------------------------------- */
/* Typedefs */
/* ---------------------------------------------------------------------- */
public:
using support_type = UInt;
using types = TypeTraits<T, Vector<T>, Container>;
class iterator : public iohelper::iterator<T, iterator, Vector<T>> {
public:
iterator(T * vect, UInt _offset, UInt _n, UInt _stride,
const UInt * filter)
: internal_it(vect), offset(_offset), n(_n), stride(_stride),
filter(filter) {}
bool operator!=(const iterator & it) const override {
if (filter != nullptr) {
return filter != it.filter;
}
return internal_it != it.internal_it;
}
iterator & operator++() override {
if (filter != nullptr) {
++filter;
} else {
internal_it += offset;
}
return *this;
}
Vector<T> operator*() override {
if (filter != nullptr) {
return Vector<T>(internal_it + *(filter)*offset + stride, n);
}
return Vector<T>(internal_it + stride, n);
}
private:
T * internal_it;
UInt offset, n, stride;
const UInt * filter{nullptr};
};
/* ---------------------------------------------------------------------- */
/* Constructors/Destructors */
/* ---------------------------------------------------------------------- */
public:
NodalField(const Container & _field, UInt _n = 0, UInt _stride = 0,
const Filter * filter = nullptr)
: field(_field), n(_n), stride(_stride), filter(filter), padding(0) {
AKANTU_DEBUG_ASSERT(((not filtered) and filter == nullptr) or filtered,
"Filter passed to unfiltered NodalField!");
AKANTU_DEBUG_ASSERT((filtered and this->filter != nullptr) or
(not filtered),
"No filter passed to filtered NodalField!");
AKANTU_DEBUG_ASSERT(
(filter != nullptr and this->filter->getNbComponent() == 1) or
(filter == nullptr),
"Multi-component filter given to NodalField ("
<< this->filter->getNbComponent()
<< " components detected, sould be 1");
if (n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ---------------------------------------------------------------------- */
/* Methods */
/* ---------------------------------------------------------------------- */
public:
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter == nullptr ? nullptr : filter->storage());
}
inline iterator end() {
return iterator(field.storage(), field.getNbComponent(), n, stride,
filter == nullptr ? nullptr
: filter->storage() + filter->size());
}
bool isHomogeneous() override { return true; }
void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
if (this->padding) {
return this->padding;
}
return n;
}
void setPadding(UInt padding) { this->padding = padding; }
UInt size() {
if (filter != nullptr) {
return filter->size();
}
return field.size();
}
inline std::shared_ptr<Field> connect(FieldComputeProxy & proxy) override {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
inline std::unique_ptr<ComputeFunctorInterface>
connect(HomogenizerProxy & /*proxy*/) override {
throw;
}
template <class T1 = T,
std::enable_if_t<std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<UInt>();
}
template <class T1 = T,
std::enable_if_t<not std::is_enum<T1>::value> * = nullptr>
iohelper::DataType getDataType() {
return iohelper::getDataType<T>();
}
/* ---------------------------------------------------------------------- */
/* Class Members */
/* ---------------------------------------------------------------------- */
private:
const Container & field;
UInt n, stride;
const Filter * filter{nullptr};
UInt padding;
};
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_DUMPER_NODAL_FIELD_HH_ */
diff --git a/src/io/dumper/dumper_padding_helper.hh b/src/io/dumper/dumper_padding_helper.hh
index 396e20d3e..cc621d931 100644
--- a/src/io/dumper/dumper_padding_helper.hh
+++ b/src/io/dumper/dumper_padding_helper.hh
@@ -1,150 +1,152 @@
/**
* @file dumper_padding_helper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Padding helper for field iterators
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_PADDING_HELPER_HH_
#define AKANTU_DUMPER_PADDING_HELPER_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* --------------------------------------------------------------------------
*/
class PadderInterface {
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
PadderInterface() {
padding_m = 0;
padding_n = 0;
}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
void setPadding(UInt m, UInt n = 0) {
padding_m = m;
padding_n = n;
}
virtual UInt getPaddedDim(UInt nb_data) { return nb_data; }
/* ------------------------------------------------------------------------
*/
/* Class Members */
/* ------------------------------------------------------------------------
*/
public:
/// padding informations
UInt padding_n, padding_m;
};
/* --------------------------------------------------------------------------
*/
template <class input_type, class output_type>
class PadderGeneric : public ComputeFunctor<input_type, output_type>,
public PadderInterface {
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
PadderGeneric() : PadderInterface() {}
/* ------------------------------------------------------------------------
*/
/* Methods */
/* ------------------------------------------------------------------------
*/
public:
inline output_type pad(const input_type & in,
__attribute__((unused)) UInt nb_data) {
return in; // trick due to the fact that IOHelper padds the vectors (avoid
// a copy of data)
}
};
/* --------------------------------------------------------------------------
*/
template <class T>
class PadderGeneric<Vector<T>, Matrix<T>>
: public ComputeFunctor<Vector<T>, Matrix<T>>, public PadderInterface {
/* ------------------------------------------------------------------------
*/
/* Constructors/Destructors */
/* ------------------------------------------------------------------------
*/
public:
inline Matrix<T> pad(const Vector<T> & _in, UInt nrows, UInt ncols,
UInt nb_data) {
Matrix<T> in(_in.storage(), nrows, ncols);
if (padding_m <= nrows && padding_n * nb_data <= ncols) {
return in;
}
Matrix<T> ret(padding_m, padding_n * nb_data);
UInt nb_cols_per_data = in.cols() / nb_data;
for (UInt d = 0; d < nb_data; ++d) {
for (UInt i = 0; i < in.rows(); ++i) {
for (UInt j = 0; j < nb_cols_per_data; ++j) {
ret(i, j + d * padding_n) = in(i, j + d * nb_cols_per_data);
}
}
}
return ret;
}
};
/* --------------------------------------------------------------------------
*/
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_PADDING_HELPER_HH_ */
diff --git a/src/io/dumper/dumper_quadrature_point_iterator.hh b/src/io/dumper/dumper_quadrature_point_iterator.hh
index 2356d5c2a..a81fd81f7 100644
--- a/src/io/dumper/dumper_quadrature_point_iterator.hh
+++ b/src/io/dumper/dumper_quadrature_point_iterator.hh
@@ -1,73 +1,75 @@
/**
* @file dumper_quadrature_point_iterator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Description of quadrature point iterator
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_
#define AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_
/* -------------------------------------------------------------------------- */
#include "dumper_elemental_field.hh"
namespace akantu {
namespace dumpers {
/* -------------------------------------------------------------------------- */
template <typename types>
class quadrature_point_iterator
: public element_iterator<types, quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using parent = element_iterator<types, dumpers::quadrature_point_iterator>;
using data_type = typename types::data_type;
using return_type = typename types::return_type;
using field_type = typename types::field_type;
using array_iterator = typename types::array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
quadrature_point_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost)
: parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {}
return_type operator*() { return *this->array_it; }
};
/* -------------------------------------------------------------------------- */
} // namespace dumpers
} // namespace akantu
#endif /* AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH_ */
diff --git a/src/io/dumper/dumper_text.cc b/src/io/dumper/dumper_text.cc
index 377d41179..83579d7be 100644
--- a/src/io/dumper/dumper_text.cc
+++ b/src/io/dumper/dumper_text.cc
@@ -1,103 +1,105 @@
/**
* @file dumper_text.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of text dumper
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_text.hh"
#include "communicator.hh"
#include "dumper_compute.hh"
#include "dumper_homogenizing_field.hh"
#include "dumper_nodal_field.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DumperText::DumperText(const std::string & basename,
iohelper::TextDumpMode mode, bool parallel) {
this->dumper = std::make_unique<iohelper::DumperText>(mode);
this->setBaseName(basename);
this->setParallelContext(parallel);
}
/* -------------------------------------------------------------------------- */
void DumperText::registerMesh(const Mesh & mesh, UInt /*spatial_dimension*/,
GhostType /*ghost_type*/,
ElementKind /*element_kind*/) {
registerField("position",
std::make_shared<dumpers::NodalField<Real>>(mesh.getNodes()));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
auto func = std::make_unique<dumpers::ComputeUIntFromEnum<ContactState>>();
std::shared_ptr<dumpers::Field> field =
std::make_shared<dumpers::NodalField<NodeFlag>>(mesh.getNodesFlags());
field =
dumpers::FieldComputeProxy::createFieldCompute(field, std::move(func));
registerField("nodes_type", field);
}
}
/* -------------------------------------------------------------------------- */
void DumperText::registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & /*elements_filter*/,
const Array<UInt> & nodes_filter, UInt /*spatial_dimension*/,
GhostType /*ghost_type*/, ElementKind /*element_kind*/) {
registerField("position", std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &nodes_filter));
// in parallel we need node type
UInt nb_proc = mesh.getCommunicator().getNbProc();
if (nb_proc > 1) {
auto func = std::make_unique<dumpers::ComputeUIntFromEnum<ContactState>>();
std::shared_ptr<dumpers::Field> field =
std::make_shared<dumpers::NodalField<NodeFlag, true>>(
mesh.getNodesFlags(), 0, 0, &nodes_filter);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, std::move(func));
registerField("nodes_type", field);
}
}
/* -------------------------------------------------------------------------- */
void DumperText::setBaseName(const std::string & basename) {
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperText *>(this->dumper.get())
->setDataSubDirectory(this->filename + "-DataFiles");
}
/* -------------------------------------------------------------------------- */
void DumperText::setPrecision(UInt prec) {
static_cast<iohelper::DumperText *>(this->dumper.get())->setPrecision(prec);
}
} // namespace akantu
diff --git a/src/io/dumper/dumper_text.hh b/src/io/dumper/dumper_text.hh
index 379ab374f..671ea2113 100644
--- a/src/io/dumper/dumper_text.hh
+++ b/src/io/dumper/dumper_text.hh
@@ -1,83 +1,85 @@
/**
* @file dumper_text.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief to dump into a text file
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPER_TEXT_HH_
#define AKANTU_DUMPER_TEXT_HH_
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperText : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperText(const std::string & basename = "dumper_text",
iohelper::TextDumpMode mode = iohelper::_tdm_space,
bool parallel = true);
~DumperText() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void
registerMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) override;
void registerFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) override;
void setBaseName(const std::string & basename) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setPrecision(UInt prec);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#endif /* AKANTU_DUMPER_TEXT_HH_ */
diff --git a/src/io/dumper/dumper_type_traits.hh b/src/io/dumper/dumper_type_traits.hh
index 46395d22c..dace0430a 100644
--- a/src/io/dumper/dumper_type_traits.hh
+++ b/src/io/dumper/dumper_type_traits.hh
@@ -1,88 +1,90 @@
/**
* @file dumper_type_traits.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Type traits for field properties
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_DUMPER_TYPE_TRAITS_HH_
#define AKANTU_DUMPER_TYPE_TRAITS_HH_
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* ------------------------------------------------------------------------ */
template <class data, class ret, class field> struct TypeTraits {
//! the stored data (real, int, uint, ...)
using data_type = data;
//! the type returned by the operator *
using return_type = ret;
//! the field type (ElementTypeMap or ElementTypeMapFilter)
using field_type = field;
//! the type over which we iterate
using it_type = typename field_type::value_type;
//! the type of array (Array<T> or ArrayFilter<T>)
using array_type = typename field_type::array_type;
//! the iterator over the array
using array_iterator = typename array_type::const_vector_iterator;
};
/* ------------------------------------------------------------------------ */
// specialization for the case in which input and output types are the same
template <class T, template <class> class ret, bool filtered>
struct SingleType : public TypeTraits<T, ret<T>, ElementTypeMapArray<T>> {};
/* ------------------------------------------------------------------------ */
// same as before but for filtered data
template <class T, template <class> class ret>
struct SingleType<T, ret, true>
: public TypeTraits<T, ret<T>, ElementTypeMapArrayFilter<T>> {};
/* ------------------------------------------------------------------------ */
// specialization for the case in which input and output types are different
template <class it_type, class data_type, template <class> class ret,
bool filtered>
struct DualType : public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArray<it_type>> {};
/* ------------------------------------------------------------------------ */
// same as before but for filtered data
template <class it_type, class data_type, template <class> class ret>
struct DualType<it_type, data_type, ret, true>
: public TypeTraits<data_type, ret<data_type>,
ElementTypeMapArrayFilter<it_type>> {};
/* ------------------------------------------------------------------------ */
} // namespace dumpers
} // namespace akantu
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_DUMPER_TYPE_TRAITS_HH_ */
diff --git a/src/io/dumper/dumper_variable.hh b/src/io/dumper/dumper_variable.hh
index 49d4524fa..d72be196c 100644
--- a/src/io/dumper/dumper_variable.hh
+++ b/src/io/dumper/dumper_variable.hh
@@ -1,119 +1,121 @@
/**
* @file dumper_variable.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Wed Nov 08 2017
*
* @brief template of variable
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_
#define AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace dumpers {
/* --------------------------------------------------------------------------
*/
/// Variable interface
class VariableBase {
public:
VariableBase() = default;
virtual ~VariableBase() = default;
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
};
/* --------------------------------------------------------------------------
*/
template <typename T, bool is_scal = std::is_arithmetic<T>::value>
class Variable : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<Vector<T>, false> : public VariableBase {
public:
Variable(const Vector<T> & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const { return vari[i]; }
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const Vector<T> & vari;
};
/* --------------------------------------------------------------------------
*/
template <typename T> class Variable<T, true> : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) override {
dumper.addVariable(id, *this);
}
const T & operator[](__attribute__((unused)) UInt i) const { return vari; }
UInt getDim() { return 1; }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
} // namespace dumper
} // namespace akantu
#endif /* AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH_ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index 001575922..f7dbd4bc3 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -1,139 +1,141 @@
/**
* @file mesh_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Fri Jun 07 2019
*
* @brief common part for all mesh io classes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "aka_common.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIO::MeshIO() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIO::~MeshIO() = default;
/* -------------------------------------------------------------------------- */
std::unique_ptr<MeshIO> MeshIO::getMeshIO(const std::string & filename,
const MeshIOType & type) {
MeshIOType t = type;
if (type == _miot_auto) {
std::string::size_type idx = filename.rfind('.');
std::string ext;
if (idx != std::string::npos) {
ext = filename.substr(idx + 1);
}
if (ext == "msh") {
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
} else {
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
<< "Please provide the MeshIOType to the read function");
}
}
switch (t) {
case _miot_gmsh:
return std::make_unique<MeshIOMSH>();
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _miot_gmsh_struct:
return std::make_unique<MeshIOMSHStruct>();
#endif
case _miot_diana:
return std::make_unique<MeshIODiana>();
default:
return nullptr;
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::read(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->read(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::write(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
std::unique_ptr<MeshIO> mesh_io = getMeshIO(filename, type);
mesh_io->write(filename, mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIO::constructPhysicalNames(const std::string & tag_name, Mesh & mesh) {
if (not physical_names.empty()) {
for (auto type : mesh.elementTypes()) {
auto & name_vec =
mesh.getDataPointer<std::string>("physical_names", type);
const auto & tags_vec = mesh.getData<UInt>(tag_name, type);
for (auto && pair : zip(tags_vec, name_vec)) {
auto tag = std::get<0>(pair);
auto & name = std::get<1>(pair);
auto map_it = physical_names.find(tag);
if (map_it == physical_names.end()) {
std::stringstream sstm;
sstm << tag;
name = sstm.str();
} else {
name = map_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
if (not physical_names.empty()) {
stream << space << "Physical map:" << std::endl;
for (const auto & pair : physical_names) {
stream << space << pair.first << ": " << pair.second << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index b0de9ca2d..12aa47618 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -1,113 +1,115 @@
/**
* @file mesh_io.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Aug 09 2017
+ * @date last modification: Fri Jun 07 2019
*
* @brief interface of a mesh io class, reader and writer
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_IO_HH_
#define AKANTU_MESH_IO_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIO();
virtual ~MeshIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
static void read(const std::string & filename, Mesh & mesh,
const MeshIOType & type);
static void write(const std::string & filename, Mesh & mesh,
const MeshIOType & type);
/// read a mesh from the file
virtual void read(const std::string & /*filename*/, Mesh & /*mesh*/) {}
/// write a mesh to a file
virtual void write(const std::string & /*filename*/, const Mesh & /*mesh*/) {}
/// function to request the manual construction of the physical names maps
virtual void constructPhysicalNames(const std::string & tag_name,
Mesh & mesh);
/// method to permit to be printed to a generic stream
virtual void printself(std::ostream & stream, int indent = 0) const;
/// static contruction of a meshio object
static std::unique_ptr<MeshIO> getMeshIO(const std::string & filename,
const MeshIOType & type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
auto & getPhysicalNames() { return this->physical_names; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
bool canReadSurface{false};
bool canReadExtendedData{false};
/// correspondance between a tag and physical names (if applicable)
std::map<int, std::string> physical_names;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "mesh_io_diana.hh"
#include "mesh_io_msh.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "mesh_io_msh_struct.hh"
#endif
#endif /* AKANTU_MESH_IO_HH_ */
diff --git a/src/io/mesh_io/mesh_io_diana.cc b/src/io/mesh_io/mesh_io_diana.cc
index d2acb15a0..7573a9c67 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,610 +1,612 @@
/**
* @file mesh_io_diana.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Sat Mar 26 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Feb 28 2020
*
* @brief handles diana meshes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io_diana.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIODiana::MeshIODiana() {
canReadSurface = true;
canReadExtendedData = true;
_diana_to_akantu_element_types["T9TM"] = _triangle_3;
_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
_diana_to_akantu_mat_prop["YOUNG"] = "E";
_diana_to_akantu_mat_prop["DENSIT"] = "rho";
_diana_to_akantu_mat_prop["POISON"] = "nu";
std::map<std::string, ElementType>::iterator it;
for (it = _diana_to_akantu_element_types.begin();
it != _diana_to_akantu_element_types.end(); ++it) {
UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);
auto * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->second) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 8;
tmp[2] = 0;
tmp[3] = 6;
tmp[4] = 1;
tmp[5] = 7;
tmp[6] = 11;
tmp[7] = 9;
tmp[8] = 10;
tmp[9] = 5;
tmp[10] = 14;
tmp[11] = 3;
tmp[12] = 12;
tmp[13] = 4;
tmp[14] = 13;
break;
case _hexahedron_20:
tmp[0] = 5;
tmp[1] = 16;
tmp[2] = 4;
tmp[3] = 19;
tmp[4] = 7;
tmp[5] = 18;
tmp[6] = 6;
tmp[7] = 17;
tmp[8] = 13;
tmp[9] = 12;
tmp[10] = 15;
tmp[11] = 14;
tmp[12] = 1;
tmp[13] = 8;
tmp[14] = 0;
tmp[15] = 11;
tmp[16] = 3;
tmp[17] = 10;
tmp[18] = 2;
tmp[19] = 9;
break;
default:
// nothing to change
break;
}
_read_order[it->second] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIODiana::~MeshIODiana() = default;
/* -------------------------------------------------------------------------- */
inline void my_getline(std::ifstream & infile, std::string & line) {
std::getline(infile, line); // read the line
size_t pos = line.find('\r'); /// remove the extra \\r if needed
line = line.substr(0, pos);
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::read(const std::string & filename, Mesh & mesh) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max();
diana_element_number_to_elements.clear();
if (!infile.good()) {
AKANTU_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
/// read all nodes
if (line == "'COORDINATES'") {
line = readCoordinates(infile, mesh, first_node_number);
}
/// read all elements
if (line == "'ELEMENTS'") {
line = readElements(infile, mesh, first_node_number);
}
/// read the material properties and write a .dat file
if (line == "'MATERIALS'") {
line = readMaterial(infile, filename);
}
/// read the material properties and write a .dat file
if (line == "'GROUPS'") {
line = readGroups(infile, mesh, first_node_number);
}
}
infile.close();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
MeshUtils::fillElementToSubElementsData(mesh);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::
readCoordinates( // NOLINT(readability-convert-member-functions-to-static)
std::ifstream & infile, Mesh & mesh, UInt & first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
std::string line;
UInt index;
Vector<Real> coord(3);
do {
my_getline(infile, line);
if ("'ELEMENTS'" == line) {
break;
}
std::stringstream sstr_node(line);
sstr_node >> index >> coord(0) >> coord(1) >> coord(2);
first_node_number = first_node_number < index ? first_node_number : index;
nodes.push_back(coord);
} while (true);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
UInt MeshIODiana::
readInterval( // NOLINT(readability-convert-member-functions-to-static)
std::stringstream & line, std::set<UInt> & interval) {
UInt first;
line >> first;
if (line.fail()) {
return 0;
}
interval.insert(first);
UInt second;
int dash;
dash = line.get();
if (dash == '-') {
line >> second;
interval.insert(second);
return 2;
}
if (line.fail()) {
line.clear(std::ios::eofbit); // in case of get at end of the line
} else {
line.unget();
}
return 1;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
bool reading_nodes_group = false;
while (line != "'SUPPORTS'") {
if (line == "NODES") {
reading_nodes_group = true;
my_getline(infile, line);
}
if (line == "ELEMEN") {
reading_nodes_group = false;
my_getline(infile, line);
}
auto * str = new std::stringstream(line);
UInt id;
std::string name;
char c;
*str >> id >> name >> c;
auto * list_ids = new Array<UInt>(0, 1, name);
UInt s = 1;
bool end = false;
while (!end) {
while (!str->eof() && s != 0) {
std::set<UInt> interval;
s = readInterval(*str, interval);
auto it = interval.begin();
if (s == 1) {
list_ids->push_back(*it);
}
if (s == 2) {
UInt first = *it;
++it;
UInt second = *it;
for (UInt i = first; i <= second; ++i) {
list_ids->push_back(i);
}
}
}
if (str->fail()) {
end = true;
} else {
my_getline(infile, line);
delete str;
str = new std::stringstream(line);
}
}
delete str;
if (reading_nodes_group) {
NodeGroup & ng = mesh.createNodeGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
UInt node = (*list_ids)(i)-first_node_number;
ng.add(node, false);
}
delete list_ids;
} else {
ElementGroup & eg = mesh.createElementGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
if (elem.type != _not_defined) {
eg.add(elem, false, false);
}
}
eg.optimize();
delete list_ids;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
if ("CONNECTIVITY" == line) {
line = readConnectivity(infile, mesh, first_node_number);
}
/// read the line corresponding to the materials
if ("MATERIALS" == line) {
line = readMaterialElement(infile, mesh);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Int index;
std::string lline;
std::string diana_type;
ElementType akantu_type;
ElementType akantu_type_old = _not_defined;
Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
Element elem;
UInt * read_order = nullptr;
while (true) {
my_getline(infile, lline);
// std::cerr << lline << std::endl;
std::stringstream sstr_elem(lline);
if (lline == "MATERIALS") {
break;
}
/// traiter les coordonnees
sstr_elem >> index;
sstr_elem >> diana_type;
akantu_type = _diana_to_akantu_element_types[diana_type];
if (akantu_type == _not_defined) {
continue;
}
if (akantu_type != akantu_type_old) {
connectivity = &(mesh_accessor.getConnectivity(akantu_type));
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = _read_order[akantu_type];
}
Vector<UInt> local_connect(node_per_element);
// used if element is written on two lines
UInt j_last = 0;
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
// check s'il y a pas plus rien après un certain point
if (sstr_elem.fail()) {
sstr_elem.clear();
sstr_elem.ignore();
break;
}
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
j_last = j;
}
// check if element is written in two lines
if (j_last != (node_per_element - 1)) {
// if this is the case, read on more line
my_getline(infile, lline);
std::stringstream sstr_elem(lline);
for (UInt j = (j_last + 1); j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
}
connectivity->push_back(local_connect);
elem.type = akantu_type;
elem.element = connectivity->size() - 1;
diana_element_number_to_elements[index] = elem;
akantu_number_to_diana_number[elem] = index;
}
AKANTU_DEBUG_OUT();
return lline;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
Mesh & mesh) {
AKANTU_DEBUG_IN();
std::string line;
for (auto type : mesh.elementTypes()) {
UInt nb_element = mesh.getNbElement(type);
mesh.getDataPointer<UInt>("material", type, _not_ghost, 1)
.resize(nb_element);
}
my_getline(infile, line);
while (line != "'MATERIALS'") {
line =
line.substr(line.find('/') + 1,
std::string::npos); // erase the first slash / of the line
char tutu[250] = {'\0'};
strncpy(tutu, line.c_str(), 249);
AKANTU_DEBUG_WARNING("reading line " << line);
Array<UInt> temp_id(0, 2);
UInt mat;
while (true) {
std::stringstream sstr_intervals_elements(line);
Vector<UInt> id(2);
char temp;
while (sstr_intervals_elements.good()) {
sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
if (!sstr_intervals_elements.fail()) {
temp_id.push_back(id);
}
}
if (sstr_intervals_elements.fail()) {
sstr_intervals_elements.clear();
sstr_intervals_elements.ignore();
sstr_intervals_elements >> mat;
break;
}
my_getline(infile, line);
}
// loop over elements
// UInt * temp_id_val = temp_id.storage();
for (UInt i = 0; i < temp_id.size(); ++i) {
for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
Element & element = diana_element_number_to_elements[j];
if (element.type == _not_defined) {
continue;
}
UInt elem = element.element;
ElementType type = element.type;
Array<UInt> & data =
mesh.getDataPointer<UInt>("material", type, _not_ghost);
data(elem) = mat;
}
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterial(std::ifstream & infile,
const std::string & filename) {
AKANTU_DEBUG_IN();
std::stringstream mat_file_name;
mat_file_name << "material_" << filename;
std::ofstream material_file;
material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());
UInt mat_index;
std::string line;
bool first_mat = true;
bool end = false;
UInt mat_id = 0;
using MatProp = std::map<std::string, Real>;
MatProp mat_prop;
do {
my_getline(infile, line);
std::stringstream sstr_material(line);
if (("'GROUPS'" == line) || ("'END'" == line)) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it) {
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
}
material_file << "]" << std::endl;
mat_prop.clear();
}
end = true;
} else {
/// traiter les caractéristiques des matériaux
sstr_material >> mat_index;
if (!sstr_material.fail()) {
if (!first_mat) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (auto it = mat_prop.begin(); it != mat_prop.end(); ++it) {
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
}
material_file << "]" << std::endl;
mat_prop.clear();
}
}
first_mat = false;
} else {
sstr_material.clear();
}
std::string prop_name;
sstr_material >> prop_name;
std::map<std::string, std::string>::iterator it;
it = _diana_to_akantu_mat_prop.find(prop_name);
if (it != _diana_to_akantu_mat_prop.end()) {
Real value;
sstr_material >> value;
mat_prop[it->second] = value;
} else {
AKANTU_DEBUG_INFO("In material reader, property " << prop_name
<< "not recognized");
}
}
} while (!end);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_diana.hh b/src/io/mesh_io/mesh_io_diana.hh
index c145a1024..8051e5104 100644
--- a/src/io/mesh_io/mesh_io_diana.hh
+++ b/src/io/mesh_io/mesh_io_diana.hh
@@ -1,107 +1,109 @@
/**
* @file mesh_io_diana.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief diana mesh reader description
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_IO_DIANA_HH_
#define AKANTU_MESH_IO_DIANA_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIODiana : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIODiana();
~MeshIODiana() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
private:
std::string readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number);
std::string readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readMaterialElement(std::ifstream & infile, Mesh & mesh);
std::string readMaterial(std::ifstream & infile,
const std::string & filename);
UInt readInterval(std::stringstream & line, std::set<UInt> & interval);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::map<std::string, ElementType> _diana_to_akantu_element_types;
std::map<std::string, std::string> _diana_to_akantu_mat_prop;
/// order in witch element as to be read, akantu_node_order =
/// _read_order[diana_node_order]
std::map<ElementType, UInt *> _read_order;
std::map<UInt, Element> diana_element_number_to_elements;
std::map<Element, UInt> akantu_number_to_diana_number;
};
} // namespace akantu
#endif /* AKANTU_MESH_IO_DIANA_HH_ */
diff --git a/src/io/mesh_io/mesh_io_msh.cc b/src/io/mesh_io/mesh_io_msh.cc
index c6c76f2d3..d6a160a8e 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,1123 +1,1125 @@
/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Oct 29 2020
*
* @brief Read/Write for MSH files generated by gmsh
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() = default;
/* -------------------------------------------------------------------------- */
namespace {
struct File {
std::string filename;
std::ifstream infile;
std::string line;
size_t current_line{0};
size_t first_node_number{std::numeric_limits<UInt>::max()},
last_node_number{0};
bool has_physical_names{false};
std::unordered_map<size_t, size_t> node_tags;
std::unordered_map<size_t, Element> element_tags;
double version{0};
int size_of_size_t{0};
Mesh & mesh;
MeshAccessor mesh_accessor;
std::multimap<std::pair<int, int>, int> entity_tag_to_physical_tags;
File(const std::string & filename, Mesh & mesh)
: filename(filename), mesh(mesh), mesh_accessor(mesh) {
infile.open(filename.c_str());
if (not infile.good()) {
AKANTU_EXCEPTION("Cannot open file " << filename);
}
}
~File() { infile.close(); }
auto good() { return infile.good(); }
std::stringstream get_line() {
std::string tmp_str;
if (infile.eof()) {
AKANTU_EXCEPTION("Reached the end of the file " << filename);
}
std::getline(infile, tmp_str);
line = trim(tmp_str);
++current_line;
return std::stringstream(line);
}
template <typename... Ts> void read_line(Ts &&... ts) {
auto && sstr = get_line();
(void)std::initializer_list<int>{
(sstr >> std::forward<decltype(ts)>(ts), 0)...};
}
};
} // namespace
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders2(File & file, Readers & readers) {
readers["$NOD"] = readers["$Nodes"] = [&](const std::string & /*unused*/) {
UInt nb_nodes;
file.read_line(nb_nodes);
Array<Real> & nodes = file.mesh_accessor.getNodes();
nodes.resize(nb_nodes);
file.mesh_accessor.setNbGlobalNodes(nb_nodes);
size_t index;
Vector<double> coord(3);
/// for each node, read the coordinates
for (auto && data : enumerate(make_view(nodes, nodes.getNbComponent()))) {
file.read_line(index, coord(0), coord(1), coord(2));
if (index > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
file.first_node_number = std::min(file.first_node_number, index);
file.last_node_number = std::max(file.last_node_number, index);
for (auto && coord_data : zip(std::get<1>(data), coord)) {
std::get<0>(coord_data) = std::get<1>(coord_data);
}
file.node_tags[index] = std::get<0>(data);
}
};
readers["$ELM"] = readers["$Elements"] = [&](const std::string & /*unused*/) {
UInt nb_elements;
file.read_line(nb_elements);
Int index;
UInt msh_type;
ElementType akantu_type;
for (UInt i = 0; i < nb_elements; ++i) {
auto && sstr_elem = file.get_line();
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type =
this->_msh_to_akantu_element_types[MSHElementType(msh_type)];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
auto node_per_element = connectivity.getNbComponent();
auto & read_order = this->_read_order[akantu_type];
/// read tags informations
if (file.version < 2) {
Int tag0;
Int tag1;
Int nb_nodes; // reg-phys, reg-elem, number-of-nodes
sstr_elem >> tag0 >> tag1 >> nb_nodes;
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.push_back(tag0);
auto & data1 =
file.mesh_accessor.template getData<UInt>("tag_1", akantu_type);
data1.push_back(tag1);
} else if (file.version < 4) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
auto & data = file.mesh_accessor.template getData<UInt>(
"tag_" + std::to_string(j), akantu_type);
data.push_back(tag);
}
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
local_connect(read_order[j]) = file.node_tags[node_index];
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[index] = elem;
}
};
readers["$Periodic"] = [&](const std::string & /*unused*/) {
UInt nb_periodic_entities;
file.read_line(nb_periodic_entities);
file.mesh_accessor.getNodesFlags().resize(file.mesh.getNbNodes(),
NodeFlag::_normal);
for (UInt p = 0; p < nb_periodic_entities; ++p) {
// dimension slave-tag master-tag
UInt dimension;
file.read_line(dimension);
// transformation
file.get_line();
// nb nodes
UInt nb_nodes;
file.read_line(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
// slave master
auto && sstr = file.get_line();
// The info in the mesh seem inconsistent so they are ignored for now.
continue;
if (dimension == file.mesh.getSpatialDimension() - 1) {
UInt slave;
UInt master;
sstr >> slave;
sstr >> master;
file.mesh_accessor.addPeriodicSlave(file.node_tags[slave],
file.node_tags[master]);
}
}
}
// mesh_accessor.markMeshPeriodic();
};
}
/* -------------------------------------------------------------------------- */
template <typename File, typename Readers>
void MeshIOMSH::populateReaders4(File & file, Readers & readers) {
static std::map<int, std::string> entity_type{
{0, "points"},
{1, "curve"},
{2, "surface"},
{3, "volume"},
};
readers["$Entities"] = [&](const std::string & /*unused*/) {
size_t num_entity[4];
file.read_line(num_entity[0], num_entity[1], num_entity[2], num_entity[3]);
for (auto entity_dim : arange(4)) {
for (auto _ [[gnu::unused]] : arange(num_entity[entity_dim])) {
auto && sstr = file.get_line();
int tag;
double min_x;
double min_y;
double min_z;
double max_x;
double max_y;
double max_z;
size_t num_physical_tags;
sstr >> tag >> min_x >> min_y >> min_z;
if (entity_dim > 0 or file.version < 4.1) {
sstr >> max_x >> max_y >> max_z;
}
sstr >> num_physical_tags;
for (auto _ [[gnu::unused]] : arange(num_physical_tags)) {
int phys_tag;
sstr >> phys_tag;
std::string physical_name;
if (this->physical_names.find(phys_tag) ==
this->physical_names.end()) {
physical_name = "msh_block_" + std::to_string(phys_tag);
} else {
physical_name = this->physical_names[phys_tag];
}
if (not file.mesh.elementGroupExists(physical_name)) {
file.mesh.createElementGroup(physical_name, entity_dim);
} else {
file.mesh.getElementGroup(physical_name).addDimension(entity_dim);
}
file.entity_tag_to_physical_tags.insert(
std::make_pair(std::make_pair(tag, entity_dim), phys_tag));
}
}
}
};
readers["$Nodes"] = [&](const std::string & /*unused*/) {
size_t num_blocks;
size_t num_nodes;
if (file.version >= 4.1) {
file.read_line(num_blocks, num_nodes, file.first_node_number,
file.last_node_number);
} else {
file.read_line(num_blocks, num_nodes);
}
auto & nodes = file.mesh_accessor.getNodes();
nodes.reserve(num_nodes);
file.mesh_accessor.setNbGlobalNodes(num_nodes);
if (num_nodes > std::numeric_limits<UInt>::max()) {
AKANTU_EXCEPTION(
"There are more nodes in this files than the index type of akantu "
"can handle, consider recompiling with a bigger index type");
}
size_t node_id{0};
for (auto block [[gnu::unused]] : arange(num_blocks)) {
int entity_dim;
int entity_tag;
int parametric;
size_t num_nodes_in_block;
Vector<double> pos(3);
Vector<double> real_pos(nodes.getNbComponent());
if (file.version >= 4.1) {
file.read_line(entity_dim, entity_tag, parametric, num_nodes_in_block);
if (parametric) {
AKANTU_EXCEPTION(
"Akantu does not support parametric nodes in msh files");
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag);
file.node_tags[tag] = node_id;
++node_id;
}
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
file.read_line(pos(_x), pos(_y), pos(_z));
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
}
} else {
file.read_line(entity_tag, entity_dim, parametric, num_nodes_in_block);
for (auto _ [[gnu::unused]] : arange(num_nodes_in_block)) {
size_t tag;
file.read_line(tag, pos(_x), pos(_y), pos(_z));
if (file.version < 4.1) {
file.first_node_number = std::min(file.first_node_number, tag);
file.last_node_number = std::max(file.last_node_number, tag);
}
for (auto && data : zip(real_pos, pos)) {
std::get<0>(data) = std::get<1>(data);
}
nodes.push_back(real_pos);
file.node_tags[tag] = node_id;
++node_id;
}
}
}
};
readers["$Elements"] = [&](const std::string & /*unused*/) {
size_t num_blocks;
size_t num_elements;
file.read_line(num_blocks, num_elements);
for (auto block [[gnu::unused]] : arange(num_blocks)) {
int entity_dim;
int entity_tag;
int element_type;
size_t num_elements_in_block;
if (file.version >= 4.1) {
file.read_line(entity_dim, entity_tag, element_type,
num_elements_in_block);
} else {
file.read_line(entity_tag, entity_dim, element_type,
num_elements_in_block);
}
/// get the connectivity vector depending on the element type
auto && akantu_type =
this->_msh_to_akantu_element_types[(MSHElementType)element_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind " << element_type
<< " at line "
<< file.current_line);
continue;
}
Element elem{akantu_type, 0, _not_ghost};
auto & connectivity = file.mesh_accessor.getConnectivity(akantu_type);
Vector<UInt> local_connect(connectivity.getNbComponent());
auto && read_order = this->_read_order[akantu_type];
auto & data0 =
file.mesh_accessor.template getData<UInt>("tag_0", akantu_type);
data0.resize(data0.size() + num_elements_in_block, 0);
auto & physical_data = file.mesh_accessor.template getData<std::string>(
"physical_names", akantu_type);
physical_data.resize(physical_data.size() + num_elements_in_block, "");
for (auto _ [[gnu::unused]] : arange(num_elements_in_block)) {
auto && sstr_elem = file.get_line();
size_t elem_tag;
sstr_elem >> elem_tag;
for (auto && c : arange(connectivity.getNbComponent())) {
size_t node_tag;
sstr_elem >> node_tag;
AKANTU_DEBUG_ASSERT(node_tag <= file.last_node_number,
"Node number not in range : line "
<< file.current_line);
node_tag = file.node_tags[node_tag];
local_connect(read_order[c]) = node_tag;
}
connectivity.push_back(local_connect);
elem.element = connectivity.size() - 1;
file.element_tags[elem_tag] = elem;
auto range = file.entity_tag_to_physical_tags.equal_range(
std::make_pair(entity_tag, entity_dim));
bool first = true;
for (auto it = range.first; it != range.second; ++it) {
auto phys_it = this->physical_names.find(it->second);
if (first) {
data0(elem.element) =
it->second; // for compatibility with version 2
if (phys_it != this->physical_names.end()) {
physical_data(elem.element) = phys_it->second;
}
first = false;
}
if (phys_it != this->physical_names.end()) {
file.mesh.getElementGroup(phys_it->second).add(elem, true, false);
}
}
}
}
for (auto && element_group : file.mesh.iterateElementGroups()) {
element_group.getNodeGroup().optimize();
}
};
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
File file(filename, mesh);
std::map<std::string, std::function<void(const std::string &)>> readers;
readers["$MeshFormat"] = [&](const std::string & /*unused*/) {
auto && sstr = file.get_line();
int format;
sstr >> file.version >> format;
if (format != 0) {
AKANTU_ERROR("This reader can only read ASCII files.");
}
if (file.version > 2) {
sstr >> file.size_of_size_t;
if (file.size_of_size_t > int(sizeof(UInt))) {
AKANTU_DEBUG_INFO("The size of the indexes in akantu might be to small "
"to read this file (akantu "
<< sizeof(UInt) << " vs. msh file "
<< file.size_of_size_t << ")");
}
}
if (file.version < 4) {
this->populateReaders2(file, readers);
} else {
this->populateReaders4(file, readers);
}
};
auto && read_data = [&](auto && entity_tags, auto && get_data,
auto && read_data) {
auto read_data_tags = [&](auto x) {
UInt number_of_tags{0};
file.read_line(number_of_tags);
std::vector<decltype(x)> tags(number_of_tags);
for (auto && tag : tags) {
file.read_line(tag);
}
return tags;
};
auto && string_tags = read_data_tags(std::string{});
auto && real_tags [[gnu::unused]] = read_data_tags(double{});
auto && int_tags = read_data_tags(int{});
for (auto & s : string_tags) {
s = trim(s, '"');
}
auto id = string_tags[0];
auto size = int_tags[2];
auto nb_component = int_tags[1];
auto & data = get_data(id, size, nb_component);
for (auto n [[gnu::unused]] : arange(size)) {
auto && sstr = file.get_line();
size_t tag;
sstr >> tag;
const auto & entity = entity_tags[tag];
read_data(entity, sstr, data, nb_component);
}
};
readers["$NodeData"] = [&](const std::string & /*unused*/) {
/* $NodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
nodeTag(size_t) value(double) ...
...
$EndNodeData */
read_data(
file.node_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component [[gnu::unused]]) -> Array<double> & {
auto & data =
file.mesh.template getNodalData<double>(id, nb_component);
data.resize(size);
return data;
},
[&](auto && node, auto && sstr, auto && data,
auto && nb_component [[gnu::unused]]) {
for (auto c : arange(nb_component)) {
sstr >> data(node, c);
}
});
};
readers["$ElementData"] = [&](const std::string & /*unused*/) {
/* $ElementData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
return file.mesh.template getElementalData<double>(id);
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type), nb_component,
element.type, element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
readers["$ElementNodeData"] = [&](const std::string & /*unused*/) {
/* $ElementNodeData
numStringTags(ASCII int)
stringTag(string) ...
numRealTags(ASCII int)
realTag(ASCII double) ...
numIntegerTags(ASCII int)
integerTag(ASCII int) ...
elementTag(size_t) value(double) ...
...
$EndElementNodeData
*/
read_data(
file.element_tags,
[&](auto && id, auto && size [[gnu::unused]],
auto && nb_component
[[gnu::unused]]) -> ElementTypeMapArray<double> & {
file.mesh.template getElementalData<double>(id);
auto & data = file.mesh.template getElementalData<double>(id);
data.isNodal(true);
return data;
},
[&](auto && element, auto && sstr, auto && data, auto && nb_component) {
int nb_nodes_per_element;
sstr >> nb_nodes_per_element;
if (not data.exists(element.type)) {
data.alloc(mesh.getNbElement(element.type),
nb_component * nb_nodes_per_element, element.type,
element.ghost_type);
}
auto & data_array = data(element.type);
for (auto c : arange(nb_component)) {
sstr >> data_array(element.element, c);
}
});
};
readers["$PhysicalNames"] = [&](const std::string & /*unused*/) {
file.has_physical_names = true;
int num_of_phys_names;
file.read_line(num_of_phys_names); /// the format line
for (auto k [[gnu::unused]] : arange(num_of_phys_names)) {
int phys_name_id;
int phys_dim;
std::string phys_name;
file.read_line(phys_dim, phys_name_id, std::quoted(phys_name));
this->physical_names[phys_name_id] = phys_name;
}
};
readers["Unsupported"] = [&](const std::string & _block) {
std::string block = _block.substr(1);
AKANTU_DEBUG_WARNING("Unsupported block_kind " << block << " at line "
<< file.current_line);
auto && end_block = "$End" + block;
while (file.line != end_block) {
file.get_line();
}
};
while (file.good()) {
std::string block;
file.read_line(block);
auto && it = readers.find(block);
if (it != readers.end()) {
it->second(block);
std::string end_block;
file.read_line(end_block);
block = block.substr(1);
if (end_block != "$End" + block) {
AKANTU_EXCEPTION("The reader failed to properly read the block "
<< block << ". Expected a $End" << block << " at line "
<< file.current_line);
}
} else if (not block.empty()) {
readers["Unsupported"](block);
}
}
// mesh.updateTypesOffsets(_not_ghost);
if (file.version < 4) {
this->constructPhysicalNames("tag_0", mesh);
if (file.has_physical_names) {
mesh.createGroupsFromMeshData<std::string>("physical_names");
}
}
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat"
<< "\n";
outfile << "2.2 0 8"
<< "\n";
outfile << "$EndMeshFormat"
<< "\n";
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes"
<< "\n";
outfile << nodes.size() << "\n";
outfile << std::uppercase;
for (UInt i = 0; i < nodes.size(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
for (UInt p = nodes.getNbComponent(); p < 3; ++p) {
outfile << " " << 0.;
}
outfile << "\n";
;
}
outfile << std::nouppercase;
outfile << "$EndNodes"
<< "\n";
outfile << "$Elements"
<< "\n";
Int nb_elements = 0;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
nb_elements += connectivity.size();
}
outfile << nb_elements << "\n";
std::map<Element, size_t> element_to_msh_element;
UInt element_idx = 1;
auto element = ElementNull;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
element.type = type;
UInt * tag[2] = {nullptr, nullptr};
if (mesh.hasData<UInt>("tag_0", type, _not_ghost)) {
const auto & data_tag_0 = mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
}
if (mesh.hasData<UInt>("tag_1", type, _not_ghost)) {
const auto & data_tag_1 = mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
}
for (auto && data :
enumerate(make_view(connectivity, connectivity.getNbComponent()))) {
element.element = std::get<0>(data);
const auto & conn = std::get<1>(data);
element_to_msh_element.insert(std::make_pair(element, element_idx));
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
for (UInt t = 0; t < 2; ++t) {
if (tag[t] != nullptr) {
outfile << " " << tag[t][element.element];
} else {
outfile << " 0";
}
}
for (auto && c : conn) {
outfile << " " << c + 1;
}
outfile << "\n";
element_idx++;
}
}
outfile << "$EndElements"
<< "\n";
if (mesh.hasData(MeshDataType::_nodal)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto type = mesh.getTypeCode(tag, MeshDataType::_nodal);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
auto && data = mesh.getNodalData<double>(tag);
outfile << "$NodeData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << data.getNbComponent() << "\n";
outfile << data.size() << "\n";
for (auto && d : enumerate(make_view(data, data.getNbComponent()))) {
outfile << std::get<0>(d) + 1;
for (auto && v : std::get<1>(d)) {
outfile << " " << v;
}
outfile << "\n";
}
outfile << "$EndNodeData"
<< "\n";
}
}
if (mesh.hasData(MeshDataType::_elemental)) {
auto && tags = mesh.getTagNames();
for (auto && tag : tags) {
auto && data = mesh.getElementalData<double>(tag);
auto type = mesh.getTypeCode(tag, MeshDataType::_elemental);
if (type != MeshDataTypeCode::_real) {
AKANTU_DEBUG_WARNING(
"The field "
<< tag << " is ignored by the MSH writer, msh files do not support "
<< type << " data");
continue;
}
if (data.isNodal()) {
continue;
}
auto size = data.size();
if (size == 0) {
continue;
}
auto && nb_components = data.getNbComponents();
auto nb_component = nb_components(*(data.elementTypes().begin()));
outfile << "$ElementData"
<< "\n";
outfile << "1"
<< "\n";
outfile << "\"" << tag << "\"\n";
outfile << "1\n0.0"
<< "\n";
outfile << "3\n0"
<< "\n";
outfile << nb_component << "\n";
outfile << size << "\n";
Element element;
for (auto type : data.elementTypes()) {
element.type = type;
for (auto && _ :
enumerate(make_view(data(type), nb_components(type)))) {
element.element = std::get<0>(_);
outfile << element_to_msh_element[element];
for (auto && v : std::get<1>(_)) {
outfile << " " << v;
}
outfile << "\n";
}
}
outfile << "$EndElementData"
<< "\n";
}
}
outfile.close();
}
/* --------------------------------------------------------------------------
*/
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh.hh b/src/io/mesh_io/mesh_io_msh.hh
index 56f2927a4..e8a0fe0ca 100644
--- a/src/io/mesh_io/mesh_io_msh.hh
+++ b/src/io/mesh_io/mesh_io_msh.hh
@@ -1,115 +1,117 @@
/**
* @file mesh_io_msh.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue May 21 2019
*
* @brief Read/Write for MSH files
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_IO_MSH_HH_
#define AKANTU_MESH_IO_MSH_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSH : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
~MeshIOMSH() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
void write(const std::string & filename, const Mesh & mesh) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// MSH element types
enum MSHElementType {
_msh_not_defined = 0,
_msh_segment_2 = 1, // 2-node line.
_msh_triangle_3 = 2, // 3-node triangle.
_msh_quadrangle_4 = 3, // 4-node quadrangle.
_msh_tetrahedron_4 = 4, // 4-node tetrahedron.
_msh_hexahedron_8 = 5, // 8-node hexahedron.
_msh_prism_1 = 6, // 6-node prism.
_msh_pyramid_1 = 7, // 5-node pyramid.
_msh_segment_3 = 8, // 3-node second order line
_msh_triangle_6 = 9, // 6-node second order triangle
_msh_quadrangle_9 = 10, // 9-node second order quadrangle
_msh_tetrahedron_10 = 11, // 10-node second order tetrahedron
_msh_hexahedron_27 = 12, // 27-node second order hexahedron
_msh_prism_18 = 13, // 18-node second order prism
_msh_pyramid_14 = 14, // 14-node second order pyramid
_msh_point = 15, // 1-node point.
_msh_quadrangle_8 = 16, // 8-node second order quadrangle
_msh_hexahedron_20 = 17, // 20-node second order hexahedron
_msh_prism_15 = 18 // 15-node second order prism
};
#define MAX_NUMBER_OF_NODE_PER_ELEMENT 10 // tetrahedron of second order
/// order in witch element as to be read
std::map<ElementType, std::vector<UInt>> _read_order;
/// number of nodes per msh element
std::map<MSHElementType, UInt> _msh_nodes_per_elem;
/// correspondence between msh element types and akantu element types
std::map<MSHElementType, ElementType> _msh_to_akantu_element_types;
/// correspondence between akantu element types and msh element types
std::map<ElementType, MSHElementType> _akantu_to_msh_element_types;
protected:
template <typename File, typename Readers>
void populateReaders2(File & file, Readers & readers);
template <typename File, typename Readers>
void populateReaders4(File & file, Readers & readers);
};
} // namespace akantu
#endif /* AKANTU_MESH_IO_MSH_HH_ */
diff --git a/src/io/mesh_io/mesh_io_msh_struct.cc b/src/io/mesh_io/mesh_io_msh_struct.cc
index 789f9b80a..b966639b5 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.cc
+++ b/src/io/mesh_io/mesh_io_msh_struct.cc
@@ -1,79 +1,81 @@
/**
* @file mesh_io_msh_struct.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files generated by gmsh
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh_struct.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOMSHStruct::MeshIOMSHStruct() {
canReadSurface = true;
canReadExtendedData = true;
_msh_to_akantu_element_types.clear();
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
_msh_to_akantu_element_types[_msh_triangle_3] =
_discrete_kirchhoff_triangle_18;
_akantu_to_msh_element_types.clear();
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_discrete_kirchhoff_triangle_18] =
_msh_triangle_3;
for (auto & kv_pair : _akantu_to_msh_element_types) {
UInt nb_nodes = _msh_nodes_per_elem[kv_pair.second];
std::vector<UInt> tmp(nb_nodes);
std::iota(tmp.begin(), tmp.end(), 0);
_read_order[kv_pair.first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
void MeshIOMSHStruct::read(const std::string & filename, Mesh & mesh) {
if (mesh.getSpatialDimension() == 2) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_2;
} else if (mesh.getSpatialDimension() == 3) {
_msh_to_akantu_element_types[_msh_segment_2] = _bernoulli_beam_3;
AKANTU_DEBUG_WARNING("The MeshIOMSHStruct is reading bernoulli beam 3D be "
"sure to provide the missing normals with the element "
"data \"extra_normal\"");
}
MeshIOMSH::read(filename, mesh);
}
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh_struct.hh b/src/io/mesh_io/mesh_io_msh_struct.hh
index 7c3f64aa8..e528f7978 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.hh
+++ b/src/io/mesh_io/mesh_io_msh_struct.hh
@@ -1,53 +1,55 @@
/**
* @file mesh_io_msh_struct.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 26 2018
*
* @brief Read/Write for MSH files
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_IO_MSH_STRUCT_HH_
#define AKANTU_MESH_IO_MSH_STRUCT_HH_
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSHStruct : public MeshIOMSH {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSHStruct();
/// read a mesh from the file
void read(const std::string & filename, Mesh & mesh) override;
};
} // namespace akantu
#endif /* AKANTU_MESH_IO_MSH_STRUCT_HH_ */
diff --git a/src/io/parser/algebraic_parser.hh b/src/io/parser/algebraic_parser.hh
index 870c3d963..0ef86d064 100644
--- a/src/io/parser/algebraic_parser.hh
+++ b/src/io/parser/algebraic_parser.hh
@@ -1,515 +1,517 @@
/**
* @file algebraic_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Mar 03 2020
*
* @brief algebraic_parser definition of the grammar
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
// Boost
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/spirit/include/qi.hpp>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ALGEBRAIC_PARSER_HH_
#define AKANTU_ALGEBRAIC_PARSER_HH_
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct algebraic_error_handler_ {
template <typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos,
Iterator last) const {
AKANTU_EXCEPTION(
"Error! Expecting "
<< what // what failed?
<< " here: \""
<< std::string(err_pos, last) // iterators to error-pos, end
<< "\"");
}
};
static Real my_min(Real a, Real b) { return std::min(a, b); }
static Real my_max(Real a, Real b) { return std::max(a, b); }
static Real my_pow(Real a, Real b) { return std::pow(a, b); }
static Real eval_param(const ID & a, const ParserSection & section) {
return section.getParameter(a, _ppsc_current_and_parent_scope);
}
static Real unary_func(Real (*func)(Real), Real a) { return func(a); }
static Real binary_func(Real (*func)(Real, Real), Real a, Real b) {
return func(a, b);
}
template <class Iterator, typename Skipper = spirit::unused_type>
struct AlgebraicGrammar : qi::grammar<Iterator, Real(), Skipper> {
AlgebraicGrammar(const ParserSection & section)
: AlgebraicGrammar::base_type(start, "algebraic_grammar"),
section(section) {
// phx::function<lazy_pow_> lazy_pow;
// phx::function<lazy_unary_func_> lazy_unary_func;
// phx::function<lazy_binary_func_> lazy_binary_func;
// phx::function<lazy_eval_param_> lazy_eval_param;
/* clang-format off */
start
= expr.alias()
;
expr
= term [ lbs::_val = lbs::_1 ]
>> *( ('+' > term [ lbs::_val += lbs::_1 ])
| ('-' > term [ lbs::_val -= lbs::_1 ])
)
;
term
= factor [ lbs::_val = lbs::_1 ]
>> *( ('*' > factor [ lbs::_val *= lbs::_1 ])
| ('/' > factor [ lbs::_val /= lbs::_1 ])
)
;
factor
= number [ lbs::_val = lbs::_1 ]
>> *("**" > number [ lbs::_val = phx::bind(&my_pow, lbs::_val, lbs::_1) ])
;
number
= real [ lbs::_val = lbs::_1 ]
| ('-' > number [ lbs::_val = -lbs::_1 ])
| ('+' > number [ lbs::_val = lbs::_1 ])
| constant [ lbs::_val = lbs::_1 ]
| function [ lbs::_val = lbs::_1 ]
| ('(' > expr > ')') [ lbs::_val = lbs::_1 ]
| variable [ lbs::_val = lbs::_1 ]
;
function
= (qi::no_case[unary_function]
> '('
> expr
> ')') [ lbs::_val = phx::bind(&unary_func, lbs::_1, lbs::_2) ]
| (qi::no_case[binary_function]
> '(' >> expr
> ',' >> expr
> ')') [ lbs::_val = phx::bind(&binary_func ,lbs::_1, lbs::_2, lbs::_3) ]
;
variable
= key [ lbs::_val = phx::bind(&eval_param, lbs::_1, section) ]
;
key
= qi::no_skip[qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")] // coming from the InputFileGrammar
;
#ifndef M_PI
# define M_PI 3.14159265358979323846
#endif
#ifndef M_E
# define M_E 2.7182818284590452354
#endif
constant.add
("pi", M_PI)
("e", M_E);
unary_function.add
("abs" , &std::abs )
("acos" , &std::acos )
("asin" , &std::asin )
("atan" , &std::atan )
("ceil" , &std::ceil )
("cos" , &std::cos )
("cosh" , &std::cosh )
("exp" , &std::exp )
("floor" , &std::floor )
("log10" , &std::log10 )
("log" , &std::log )
("sin" , &std::sin )
("sinh" , &std::sinh )
("sqrt" , &std::sqrt )
("tan" , &std::tan )
("tanh" , &std::tanh )
("acosh" , &std::acosh )
("asinh" , &std::asinh )
("atanh" , &std::atanh )
("exp2" , &std::exp2 )
("expm1" , &std::expm1 )
("log1p" , &std::log1p )
("log2" , &std::log2 )
("erf" , &std::erf )
("erfc" , &std::erfc )
("lgamma", &std::lgamma)
("tgamma", &std::tgamma)
("trunc" , &std::trunc )
("round" , &std::round )
// ("crbt" , &std::crbt )
;
binary_function.add
("pow" , &std::pow )
("min" , &parser::my_min)
("max" , &parser::my_max)
("atan2", &std::atan2 )
("fmod" , &std::fmod )
("hypot", &std::hypot )
;
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler = algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
expr .name("expression");
term .name("term");
factor .name("factor");
number .name("numerical-value");
variable.name("variable");
function.name("function");
constant.name("constants-list");
unary_function.name("unary-functions-list");
binary_function.name("binary-functions-list");
#if !defined AKANTU_NDEBUG
if(AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(expr);
qi::debug(term);
qi::debug(factor);
qi::debug(number);
qi::debug(variable);
qi::debug(function);
}
#endif
}
/* clang-format on */
private:
qi::rule<Iterator, Real(), Skipper> start;
qi::rule<Iterator, Real(), Skipper> expr;
qi::rule<Iterator, Real(), Skipper> term;
qi::rule<Iterator, Real(), Skipper> factor;
qi::rule<Iterator, Real(), Skipper> number;
qi::rule<Iterator, Real(), Skipper> variable;
qi::rule<Iterator, Real(), Skipper> function;
qi::rule<Iterator, std::string(), Skipper> key;
qi::real_parser<Real, qi::real_policies<Real>> real;
qi::symbols<char, Real> constant;
qi::symbols<char, Real (*)(Real)> unary_function;
qi::symbols<char, Real (*)(Real, Real)> binary_function;
const ParserSection & section;
};
/* ---------------------------------------------------------------------- */
/* Vector Parser */
/* ---------------------------------------------------------------------- */
struct parsable_vector {
operator Vector<Real>() {
Vector<Real> tmp(_cells.size());
auto it = _cells.begin();
for (UInt i = 0; it != _cells.end(); ++it, ++i) {
tmp(i) = *it;
}
return tmp;
}
std::vector<Real> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_vector & pv) {
stream << "pv[";
auto it = pv._cells.begin();
if (it != pv._cells.end()) {
stream << *it;
for (++it; it != pv._cells.end(); ++it) {
stream << ", " << *it;
}
}
stream << "]";
return stream;
}
struct parsable_matrix {
operator Matrix<Real>() {
size_t cols = 0;
auto it_rows = _cells.begin();
for (; it_rows != _cells.end(); ++it_rows) {
cols = std::max(cols, it_rows->_cells.size());
}
Matrix<Real> tmp(_cells.size(), _cells[0]._cells.size(), 0.);
it_rows = _cells.begin();
for (UInt i = 0; it_rows != _cells.end(); ++it_rows, ++i) {
auto it_cols = it_rows->_cells.begin();
for (UInt j = 0; it_cols != it_rows->_cells.end(); ++it_cols, ++j) {
tmp(i, j) = *it_cols;
}
}
return tmp;
}
std::vector<parsable_vector> _cells;
};
inline std::ostream & operator<<(std::ostream & stream,
const parsable_matrix & pm) {
stream << "pm[";
auto it = pm._cells.begin();
if (it != pm._cells.end()) {
stream << *it;
for (++it; it != pm._cells.end(); ++it) {
stream << ", " << *it;
}
}
stream << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <typename T1, typename T2>
static void cont_add(T1 & cont, T2 & value) {
cont._cells.push_back(value);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct VectorGrammar : qi::grammar<Iterator, parsable_vector(), Skipper> {
VectorGrammar(const ParserSection & section)
: VectorGrammar::base_type(start, "vector_algebraic_grammar"),
number(section) {
start = '[' > vector > ']';
vector =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' >> number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("start");
vector.name("vector");
number.name("value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(vector);
}
#endif
}
private:
qi::rule<Iterator, parsable_vector(), Skipper> start;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
vector;
qi::rule<Iterator, Real(), Skipper> value;
AlgebraicGrammar<Iterator, Skipper> number;
};
/* ---------------------------------------------------------------------- */
static inline bool vector_eval(const ID & a, const ParserSection & section,
parsable_vector & result) {
std::string value = section.getParameter(a, _ppsc_current_and_parent_scope);
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
parser::VectorGrammar<std::string::const_iterator, qi::space_type> grammar(
section);
return qi::phrase_parse(b, e, grammar, qi::space, result);
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct MatrixGrammar : qi::grammar<Iterator, parsable_matrix(), Skipper> {
MatrixGrammar(const ParserSection & section)
: MatrixGrammar::base_type(start, "matrix_algebraic_grammar"),
vector(section) {
start = '[' >> matrix >> ']';
matrix =
(rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>, lbs::_a,
lbs::_1)] >>
*(',' >> rows[phx::bind(&cont_add<parsable_matrix, parsable_vector>,
lbs::_a, lbs::_1)]))[lbs::_val = lbs::_a];
rows = eval_vector | vector;
eval_vector = (key[lbs::_pass = phx::bind(&vector_eval, lbs::_1, section,
lbs::_a)])[lbs::_val = lbs::_a];
key = qi::char_("a-zA-Z_") >>
*qi::char_("a-zA-Z_0-9") // coming from the InputFileGrammar
;
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("matrix");
matrix.name("all_rows");
rows.name("rows");
vector.name("vector");
eval_vector.name("eval_vector");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(start);
qi::debug(matrix);
qi::debug(rows);
qi::debug(eval_vector);
qi::debug(key);
}
#endif
}
private:
qi::rule<Iterator, parsable_matrix(), Skipper> start;
qi::rule<Iterator, parsable_matrix(), qi::locals<parsable_matrix>, Skipper>
matrix;
qi::rule<Iterator, parsable_vector(), Skipper> rows;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
eval_vector;
qi::rule<Iterator, std::string(), Skipper> key;
VectorGrammar<Iterator, Skipper> vector;
};
/* ---------------------------------------------------------------------- */
/* Randon Generator */
/* ---------------------------------------------------------------------- */
struct ParsableRandomGenerator {
ParsableRandomGenerator(
Real base = Real(),
const RandomDistributionType & type = _rdt_not_defined,
const parsable_vector & parameters = parsable_vector())
: base(base), type(type), parameters(parameters) {}
Real base;
RandomDistributionType type;
parsable_vector parameters;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParsableRandomGenerator & prg) {
stream << "prg[" << prg.base << " " << UInt(prg.type) << " "
<< prg.parameters << "]";
return stream;
}
/* ---------------------------------------------------------------------- */
template <class Iterator, typename Skipper = spirit::unused_type>
struct RandomGeneratorGrammar
: qi::grammar<Iterator, ParsableRandomGenerator(), Skipper> {
RandomGeneratorGrammar(const ParserSection & section)
: RandomGeneratorGrammar::base_type(start, "random_generator_grammar"),
number(section) {
start = generator.alias();
generator =
qi::hold[distribution[lbs::_val = lbs::_1]] |
number[lbs::_val = phx::construct<ParsableRandomGenerator>(lbs::_1)];
distribution = (number >> generator_type >> '[' >> generator_params >>
']')[lbs::_val = phx::construct<ParsableRandomGenerator>(
lbs::_1, lbs::_2, lbs::_3)];
generator_params =
(number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)] >>
*(',' > number[phx::bind(&cont_add<parsable_vector, Real>, lbs::_a,
lbs::_1)]))[lbs::_val = lbs::_a];
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)), \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem)))
generator_type.add BOOST_PP_SEQ_FOR_EACH(
AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES);
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG)
phx::function<algebraic_error_handler_> const error_handler =
algebraic_error_handler_();
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start.name("random-generator");
generator.name("random-generator");
distribution.name("random-distribution");
generator_type.name("generator-type");
generator_params.name("generator-parameters");
number.name("number");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
qi::debug(generator);
qi::debug(distribution);
qi::debug(generator_params);
}
#endif
}
private:
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> start;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> generator;
qi::rule<Iterator, ParsableRandomGenerator(), Skipper> distribution;
qi::rule<Iterator, parsable_vector(), qi::locals<parsable_vector>, Skipper>
generator_params;
AlgebraicGrammar<Iterator, Skipper> number;
qi::symbols<char, RandomDistributionType> generator_type;
};
} // namespace parser
} // namespace akantu
#endif /* AKANTU_ALGEBRAIC_PARSER_HH_ */
diff --git a/src/io/parser/cppargparse/cppargparse.cc b/src/io/parser/cppargparse/cppargparse.cc
index 95fadd974..b85927c1b 100644
--- a/src/io/parser/cppargparse/cppargparse.cc
+++ b/src/io/parser/cppargparse/cppargparse.cc
@@ -1,536 +1,538 @@
/**
* @file cppargparse.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Jun 12 2019
*
* @brief implementation of the ArgumentParser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cppargparse.hh"
#include <cstdlib>
#include <cstring>
#include <libgen.h>
#include <algorithm>
#include <iomanip>
#include <iostream>
#include <queue>
#include <sstream>
#include <string>
#include <exception>
#include <stdexcept>
#include <string.h>
namespace cppargparse {
/* -------------------------------------------------------------------------- */
static inline std::string to_upper(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(),
(int (*)(int))std::toupper);
return lstr;
}
/* -------------------------------------------------------------------------- */
/* ArgumentParser */
/* -------------------------------------------------------------------------- */
ArgumentParser::ArgumentParser() {
this->addArgument("-h;--help", "show this help message and exit", 0, _boolean,
false, true);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::~ArgumentParser() {
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::setParallelContext(int prank, int psize) {
this->prank = prank;
this->psize = psize;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::_exit(const std::string & msg, int status) {
if (prank == 0) {
if (not msg.empty()) {
std::cerr << msg << std::endl;
std::cerr << std::endl;
}
this->print_help(std::cerr);
}
if (external_exit != nullptr) {
(*external_exit)(status);
} else {
exit(status);
}
}
/* -------------------------------------------------------------------------- */
const ArgumentParser::Argument &
ArgumentParser::operator[](const std::string & name) const {
auto it = success_parsed.find(name);
if (it != success_parsed.end()) {
return *(it->second);
}
throw std::range_error("No argument named \'" + name +
"\' was found in the parsed argument," +
" make sur to specify it \'required\'" +
" or to give it a default value");
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::has(const std::string & name) const {
return (success_parsed.find(name) != success_parsed.end());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type) {
_addArgument(name_or_flag, help, nargs, type);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::Argument_ &
ArgumentParser::_addArgument(const std::string & name, const std::string & help,
int nargs, ArgumentType type) {
Argument_ * arg = nullptr;
switch (type) {
case _string: {
arg = new ArgumentStorage<std::string>();
break;
}
case _float: {
arg = new ArgumentStorage<double>();
break;
}
case _integer: {
arg = new ArgumentStorage<long int>();
break;
}
case _boolean: {
arg = new ArgumentStorage<bool>();
break;
}
}
arg->help = help;
arg->nargs = nargs;
arg->type = type;
std::stringstream sstr(name);
std::string item;
std::vector<std::string> tmp_keys;
while (std::getline(sstr, item, ';')) {
tmp_keys.push_back(item);
}
int long_key = -1;
int short_key = -1;
bool problem = (tmp_keys.size() > 2) || name.empty();
for (auto it = tmp_keys.begin(); it != tmp_keys.end(); ++it) {
if (it->find("--") == 0) {
problem |= (long_key != -1);
long_key = it - tmp_keys.begin();
} else if (it->find("-") == 0) {
problem |= (long_key != -1);
short_key = it - tmp_keys.begin();
}
}
problem |= ((tmp_keys.size() == 2) && (long_key == -1 || short_key == -1));
if (problem) {
delete arg;
throw std::invalid_argument("Synthax of name or flags is not correct. "
"Possible synthax are \'-f\', \'-f;--foo\', "
"\'--foo\', \'bar\'");
}
if (long_key != -1) {
arg->name = tmp_keys[long_key];
arg->name.erase(0, 2);
} else if (short_key != -1) {
arg->name = tmp_keys[short_key];
arg->name.erase(0, 1);
} else {
arg->name = tmp_keys[0];
pos_args.push_back(arg);
arg->required = (nargs != _one_if_possible);
arg->is_positional = true;
}
arguments[arg->name] = arg;
if (!arg->is_positional) {
if (short_key != -1) {
std::string key = tmp_keys[short_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
if (long_key != -1) {
std::string key = tmp_keys[long_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
}
return *arg;
}
#if not HAVE_STRDUP
static char * strdup(const char * str) {
size_t len = strlen(str);
auto * x = (char *)malloc(len + 1); /* 1 for the null terminator */
if (x == nullptr) {
return nullptr; /* malloc could not allocate memory */
}
memcpy(x, str, len + 1); /* copy the string into the new buffer */
return x;
}
#endif
/* -------------------------------------------------------------------------- */
void ArgumentParser::parse(int & argc, char **& argv, int flags,
bool parse_help) {
bool stop_in_not_parsed = (flags & _stop_on_not_parsed) != 0;
bool remove_parsed = (flags & _remove_parsed) != 0;
std::vector<std::string> argvs;
argvs.reserve(argc);
for (int i = 0; i < argc; ++i) {
argvs.emplace_back(argv[i]);
}
unsigned int current_position = 0;
if (this->program_name.empty() and argc > 0) {
std::string prog = argvs[current_position];
const char * c_prog = prog.c_str();
char * c_prog_tmp = strdup(c_prog);
std::string base_prog(basename(c_prog_tmp));
this->program_name = base_prog;
std::free(c_prog_tmp);
}
std::queue<Argument_ *> positional_queue;
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
positional_queue.push(*it);
}
std::vector<int> argvs_to_remove;
++current_position; // consume argv[0]
while (current_position < argvs.size()) {
std::string arg = argvs[current_position];
++current_position;
auto key_it = key_args.find(arg);
bool is_positional = false;
Argument_ * argument_ptr = nullptr;
if (key_it == key_args.end()) {
if (positional_queue.empty()) {
if (stop_in_not_parsed) {
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
}
continue;
}
argument_ptr = positional_queue.front();
is_positional = true;
--current_position;
} else {
argument_ptr = key_it->second;
}
if (remove_parsed && !is_positional && argument_ptr->name != "help") {
argvs_to_remove.push_back(current_position - 1);
}
Argument_ & argument = *argument_ptr;
unsigned int min_nb_val{};
unsigned int max_nb_val{};
switch (argument.nargs) {
case _one_if_possible:
max_nb_val = 1;
break; // "?"
case _at_least_one:
min_nb_val = 1; // "+"
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it*/
case _any:
max_nb_val = argc - current_position;
break; // "*"
default:
min_nb_val = max_nb_val = argument.nargs; // "N"
}
std::vector<std::string> values;
unsigned int arg_consumed = 0;
if (max_nb_val <= (argc - current_position)) {
for (; arg_consumed < max_nb_val; ++arg_consumed) {
std::string v = argvs[current_position];
++current_position;
bool is_key = key_args.find(v) != key_args.end();
bool is_good_type = checkType(argument.type, v);
if (!is_key && is_good_type) {
values.push_back(v);
if (remove_parsed) {
argvs_to_remove.push_back(current_position - 1);
}
} else {
// unconsume not parsed argument for optional
if (!is_positional || is_key) {
--current_position;
}
break;
}
}
}
if (arg_consumed < min_nb_val) {
if (!is_positional) {
this->_exit("Not enought values for the argument " + argument.name +
" where provided",
EXIT_FAILURE);
} else {
if (stop_in_not_parsed) {
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
}
}
} else {
if (is_positional) {
positional_queue.pop();
}
if (!argument.parsed) {
success_parsed[argument.name] = &argument;
argument.parsed = true;
if ((argument.nargs == _one_if_possible || argument.nargs == 0) &&
arg_consumed == 0) {
if (argument.has_const) {
argument.setToConst();
} else if (argument.has_default) {
argument.setToDefault();
}
} else {
argument.setValues(values);
}
} else {
this->_exit("Argument " + argument.name +
" already present in the list of argument",
EXIT_FAILURE);
}
}
}
for (auto ait = arguments.begin(); ait != arguments.end(); ++ait) {
Argument_ & argument = *(ait->second);
if (!argument.parsed) {
if (argument.has_default) {
argument.setToDefault();
success_parsed[argument.name] = &argument;
}
if (argument.required) {
this->_exit("Argument " + argument.name + " required but not given!",
EXIT_FAILURE);
}
}
}
// removing the parsed argument if remove_parsed is true
if (not argvs_to_remove.empty()) {
std::vector<int>::const_iterator next_to_remove = argvs_to_remove.begin();
for (int i = 0, c = 0; i < argc; ++i) {
if (next_to_remove == argvs_to_remove.end() || i != *next_to_remove) {
argv[c] = argv[i];
++c;
} else {
if (next_to_remove != argvs_to_remove.end()) {
++next_to_remove;
}
}
}
argc -= argvs_to_remove.size();
}
this->argc = &argc;
this->argv = &argv;
if (this->arguments["help"]->parsed && parse_help) {
this->_exit();
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::checkType(ArgumentType type, const std::string & value) {
std::stringstream sstr(value);
switch (type) {
case _string: {
std::string s;
sstr >> s;
break;
}
case _float: {
double d;
sstr >> d;
break;
}
case _integer: {
long int i;
sstr >> i;
break;
}
case _boolean: {
bool b;
sstr >> b;
break;
}
}
return (not sstr.fail());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::printself(std::ostream & stream) const {
for (auto it = success_parsed.begin(); it != success_parsed.end(); ++it) {
const Argument & argument = *(it->second);
argument.printself(stream);
stream << std::endl;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage(std::ostream & stream) const {
stream << "Usage: " << this->program_name;
// print shorten usage
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
const Argument_ & argument = *(it->second);
if (!argument.is_positional) {
if (!argument.required) {
stream << " [";
}
stream << argument.keys[0];
ArgumentParser::print_usage_nargs(stream, argument);
if (!argument.required) {
stream << "]";
}
}
}
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
const Argument_ & argument = **it;
ArgumentParser::print_usage_nargs(stream, argument);
}
stream << std::endl;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage_nargs(std::ostream & stream,
const Argument_ & argument) {
std::string u_name = to_upper(argument.name);
switch (argument.nargs) {
case _one_if_possible:
stream << " [" << u_name << "]";
break;
case _at_least_one:
stream << " " << u_name;
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _any:
stream << " [" << u_name << " ...]";
break;
default:
for (int i = 0; i < argument.nargs; ++i) {
stream << " " << u_name;
}
}
}
void ArgumentParser::print_help(std::ostream & stream) const {
this->print_usage(stream);
if (!pos_args.empty()) {
stream << std::endl;
stream << "positional arguments:" << std::endl;
for (auto it = pos_args.begin(); it != pos_args.end(); ++it) {
const Argument_ & argument = **it;
this->print_help_argument(stream, argument);
}
}
if (!key_args.empty()) {
stream << std::endl;
stream << "optional arguments:" << std::endl;
for (auto it = arguments.begin(); it != arguments.end(); ++it) {
const Argument_ & argument = *(it->second);
if (!argument.is_positional) {
this->print_help_argument(stream, argument);
}
}
}
}
void ArgumentParser::print_help_argument(std::ostream & stream,
const Argument_ & argument) const {
std::string key;
if (argument.is_positional) {
key = argument.name;
} else {
std::stringstream sstr;
for (unsigned int i = 0; i < argument.keys.size(); ++i) {
if (i != 0) {
sstr << ", ";
}
sstr << argument.keys[i];
this->print_usage_nargs(sstr, argument);
}
key = sstr.str();
}
stream << " " << std::left << std::setw(15) << key << " " << argument.help;
argument.printDefault(stream);
stream << std::endl;
}
} // namespace cppargparse
diff --git a/src/io/parser/cppargparse/cppargparse.hh b/src/io/parser/cppargparse/cppargparse.hh
index b6fe478c3..abfdc09b1 100644
--- a/src/io/parser/cppargparse/cppargparse.hh
+++ b/src/io/parser/cppargparse/cppargparse.hh
@@ -1,200 +1,202 @@
/**
* @file cppargparse.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Wed Jun 12 2019
*
* @brief Get the commandline options and store them as short, long and others
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <map>
#include <string>
#include <vector>
#ifndef CPPARGPARSE_HH_
#define CPPARGPARSE_HH_
/* -------------------------------------------------------------------------- */
namespace cppargparse {
/// define the types of the arguments
enum ArgumentType { _string, _integer, _float, _boolean };
/// Defines how many arguments to expect
enum ArgumentNargs { _one_if_possible = -1, _at_least_one = -2, _any = -3 };
/// Flags for the parse function of ArgumentParser
enum ParseFlags {
_no_flags = 0x0, ///< Default behavior
_stop_on_not_parsed = 0x1, ///< Stop on unknown arguments
_remove_parsed = 0x2 ///< Remove parsed arguments from argc argv
};
/// Helps to combine parse flags
inline ParseFlags operator|(const ParseFlags & a, const ParseFlags & b) {
auto tmp = ParseFlags(int(a) | int(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
/**
* ArgumentParser is a class that mimics the Python argparse module
*/
class ArgumentParser {
public:
/// public definition of an argument
class Argument {
public:
Argument() : name(std::string()) {}
virtual ~Argument() = default;
virtual void printself(std::ostream & stream) const = 0;
template <class T> operator T() const;
std::string name;
};
/// constructor
ArgumentParser();
/// destroy everything
~ArgumentParser();
/// add an argument with a description
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs = 1, ArgumentType type = _string);
/// add an argument with an help and a default value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def);
/// add an argument with an help and a default + const value
template <class T>
void addArgument(const std::string & name_or_flag, const std::string & help,
int nargs, ArgumentType type, T def, T cons);
/// parse argc, argv
void parse(int & argc, char **& argv, int flags = _stop_on_not_parsed,
bool parse_help = true);
/// get the last argc parsed
int & getArgC() { return *(this->argc); }
/// get the last argv parsed
char **& getArgV() { return *(this->argv); }
/// print the content in the stream
void printself(std::ostream & stream) const;
/// print the help text
void print_help(std::ostream & stream = std::cout) const;
/// print the usage text
void print_usage(std::ostream & stream = std::cout) const;
/// set an external function to replace the exit function from the stdlib
void setExternalExitFunction(void (*external_exit)(int)) {
this->external_exit = external_exit;
}
/// accessor for a registered argument that was parsed, throw an exception if
/// the argument does not exist or was not set (parsed or default value)
const Argument & operator[](const std::string & name) const;
/// is the argument present
bool has(const std::string & /*name*/) const;
/// set the parallel context to avoid multiple help messages in
/// multiproc/thread cases
void setParallelContext(int prank, int psize);
public:
/// Internal class describing the arguments
struct Argument_;
/// Stores that value of an argument
template <class T> class ArgumentStorage;
private:
/// Internal function to be used by the public addArgument
Argument_ & _addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type);
void _exit(const std::string & msg = "", int status = 0);
static bool checkType(ArgumentType type, const std::string & value);
/// function to help to print help
static void print_usage_nargs(std::ostream & stream,
const Argument_ & argument);
/// function to help to print help
void print_help_argument(std::ostream & stream,
const Argument_ & argument) const;
private:
/// public arguments storage
using Arguments = std::map<std::string, Argument *>;
/// internal arguments storage
using Arguments_ = std::map<std::string, Argument_ *>;
/// association key argument
using ArgumentKeyMap = std::map<std::string, Argument_ *>;
/// position arguments
using PositionalArgument = std::vector<Argument_ *>;
/// internal storage of arguments declared by the user
Arguments_ arguments;
/// list of arguments successfully parsed
Arguments success_parsed;
/// keys associated to arguments
ArgumentKeyMap key_args;
/// positional arguments
PositionalArgument pos_args;
/// program name
std::string program_name;
/// exit function to use
void (*external_exit)(int){nullptr};
/// Parallel context, rank and size of communicator
int prank{0}, psize{1};
/// The last argc parsed (those are the modified version after parse)
int * argc;
/// The last argv parsed (those are the modified version after parse)
char *** argv;
};
inline std::ostream & operator<<(std::ostream & stream,
const ArgumentParser & argparse) {
argparse.printself(stream);
return stream;
}
} // namespace cppargparse
#endif /* CPPARGPARSE_HH_ */
#include "cppargparse_tmpl.hh"
diff --git a/src/io/parser/cppargparse/cppargparse_tmpl.hh b/src/io/parser/cppargparse/cppargparse_tmpl.hh
index 7e138944e..64edce693 100644
--- a/src/io/parser/cppargparse/cppargparse_tmpl.hh
+++ b/src/io/parser/cppargparse/cppargparse_tmpl.hh
@@ -1,241 +1,243 @@
/**
* @file cppargparse_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Wed Nov 08 2017
*
* @brief Implementation of the templated part of the commandline argument
* parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <sstream>
#include <stdexcept>
#ifndef CPPARGPARSE_TMPL_HH_
#define CPPARGPARSE_TMPL_HH_
namespace cppargparse {
/* -------------------------------------------------------------------------- */
/* Argument */
/* -------------------------------------------------------------------------- */
/// internal description of arguments
struct ArgumentParser::Argument_ : public Argument {
Argument_() = default;
~Argument_() override = default;
void setValues(std::vector<std::string> & values) {
for (auto it = values.begin(); it != values.end(); ++it) {
this->addValue(*it);
}
}
virtual void addValue(std::string & value) = 0;
virtual void setToDefault() = 0;
virtual void setToConst() = 0;
std::ostream & printDefault(std::ostream & stream) const {
stream << std::boolalpha;
if (has_default) {
stream << " (default: ";
this->_printDefault(stream);
stream << ")";
}
if (has_const) {
stream << " (const: ";
this->_printConst(stream);
stream << ")";
}
return stream;
}
virtual std::ostream & _printDefault(std::ostream & stream) const = 0;
virtual std::ostream & _printConst(std::ostream & stream) const = 0;
std::string help;
int nargs{1};
ArgumentType type{_string};
bool required{false};
bool parsed{false};
bool has_default{false};
bool has_const{false};
std::vector<std::string> keys;
bool is_positional{false};
};
/* -------------------------------------------------------------------------- */
/// typed storage of the arguments
template <class T>
class ArgumentParser::ArgumentStorage : public ArgumentParser::Argument_ {
public:
ArgumentStorage() : _default(T()), _const(T()), values(std::vector<T>()) {}
void addValue(std::string & value) override {
std::stringstream sstr(value);
T t;
sstr >> t;
values.push_back(t);
}
void setToDefault() override {
values.clear();
values.push_back(_default);
}
void setToConst() override {
values.clear();
values.push_back(_const);
}
void printself(std::ostream & stream) const override {
stream << this->name << " =";
stream << std::boolalpha; // for boolean
for (auto vit = this->values.begin(); vit != this->values.end(); ++vit) {
stream << " " << *vit;
}
}
std::ostream & _printDefault(std::ostream & stream) const override {
stream << _default;
return stream;
}
std::ostream & _printConst(std::ostream & stream) const override {
stream << _const;
return stream;
}
T _default;
T _const;
std::vector<T> values;
};
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::ArgumentStorage<std::string>::addValue(std::string & value) {
values.push_back(value);
}
template <class T> struct is_vector {
enum { value = false };
};
template <class T> struct is_vector<std::vector<T>> {
enum { value = true };
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_vector = cppargparse::is_vector<T>::value>
struct cast_helper {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
if (_arg.values.size() == 1) {
return _arg.values[0];
}
throw std::length_error("Not enougth or too many argument where passed "
"for the command line argument: " +
arg.name);
}
};
template <class T> struct cast_helper<T, true> {
static T cast(const ArgumentParser::Argument & arg) {
const auto & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
return _arg.values;
}
};
/* -------------------------------------------------------------------------- */
template <class T> ArgumentParser::Argument::operator T() const {
return cast_helper<T>::cast(*this);
}
#if !defined(DOXYGEN)
template <>
inline ArgumentParser::Argument::operator std::string() const {
return cast_helper<std::string>::cast(*this);
}
template <> inline ArgumentParser::Argument::operator unsigned int() const {
return cast_helper<int>::cast(*this);
}
#endif
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def) {
Argument_ & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
}
template <class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, T def, T cons) {
Argument_ & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
dynamic_cast<ArgumentStorage<T> &>(arg)._const = cons;
arg.has_const = true;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::addArgument<const char *>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, const char * def) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def);
}
template <>
inline void
ArgumentParser::addArgument<unsigned int>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, unsigned int def) {
this->addArgument<int>(name_or_flag, help, nargs, type, def);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ArgumentParser::addArgument<const char *>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, const char * def, const char * cons) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def, cons);
}
template <>
inline void ArgumentParser::addArgument<unsigned int>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, unsigned int def, unsigned int cons) {
this->addArgument<int>(name_or_flag, help, nargs, type, def, cons);
}
} // namespace cppargparse
#endif /* AKANTU_CPPARGPARSE_TMPL_HH_ */
diff --git a/src/io/parser/input_file_parser.hh b/src/io/parser/input_file_parser.hh
index 72f3b21a4..b610ca943 100644
--- a/src/io/parser/input_file_parser.hh
+++ b/src/io/parser/input_file_parser.hh
@@ -1,269 +1,271 @@
/**
* @file input_file_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Wed Sep 04 2019
*
* @brief Grammar definition for the input files
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// Boost
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/spirit/include/phoenix_core.hpp>
#include <boost/spirit/include/phoenix_fusion.hpp>
#include <boost/spirit/include/phoenix_operator.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/variant/recursive_variant.hpp>
#ifndef AKANTU_INPUT_FILE_PARSER_HH_
#define AKANTU_INPUT_FILE_PARSER_HH_
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
namespace akantu {
namespace parser {
struct error_handler_ {
template <typename, typename, typename, typename> struct result {
using type = void;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos, Iterator /*first*/,
Iterator /*last*/) const {
spirit::classic::file_position pos = err_pos.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< "Expecting " << what << " instead of \"" << *err_pos
<< "\" ]"
<< " in file " << pos.file << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << err_pos.get_currentline() << "'" << std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
private:
};
static ParserSection & create_subsection(
const ParserType & type, const boost::optional<std::string> & opt_name,
const boost::optional<std::string> & opt_option, ParserSection & sect) {
std::string option;
if (opt_option) {
option = *opt_option;
}
static size_t id = 12;
std::string name = "anonymous_" + std::to_string(id++);
if (opt_name) {
name = *opt_name;
}
ParserSection sect_tmp(name, type, option, sect);
return sect.addSubSection(sect_tmp);
}
template <typename Iter>
static bool create_parameter(boost::iterator_range<Iter> & rng,
std::string & value, ParserSection & sect) {
try {
std::string name(rng.begin(), rng.end());
name = trim(name);
spirit::classic::file_position pos = rng.begin().get_position();
ParserParameter param_tmp(name, value, sect);
param_tmp.setDebugInfo(pos.file, pos.line, pos.column);
sect.addParameter(param_tmp);
} catch (debug::Exception & e) {
return false;
}
return true;
}
static std::string concatenate(const std::string & t1,
const std::string & t2) {
return (t1 + t2);
}
/* ---------------------------------------------------------------------- */
/* Grammars definitions */
/* ---------------------------------------------------------------------- */
template <class Iterator>
struct InputFileGrammar
: qi::grammar<Iterator, void(), typename Skipper<Iterator>::type> {
InputFileGrammar(ParserSection * sect)
: InputFileGrammar::base_type(start, "input_file_grammar"),
parent_section(sect) {
/* clang-format off */
start
= mini_section(parent_section)
;
mini_section
= *(
entry (lbs::_r1)
| section(lbs::_r1)
)
;
entry
= (
qi::raw[key]
>> '='
> value
) [ lbs::_pass = phx::bind(&create_parameter<Iterator>,
lbs::_1,
lbs::_2,
*lbs::_r1) ]
;
section
= (
qi::no_case[section_type]
> qi::lexeme
[
-section_name
> -section_option
]
) [ lbs::_a = &phx::bind(&create_subsection,
lbs::_1,
phx::at_c<0>(lbs::_2),
phx::at_c<1>(lbs::_2),
*lbs::_r1) ]
> '['
> mini_section(lbs::_a)
> ']'
;
section_name
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
section_option
= (+ascii::space >> section_name) [ lbs::_val = lbs::_2 ]
;
key
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
value
= (
mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
> *(
'\\' > mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
)
) [ lbs::_val = lbs::_a ]
;
mono_line_value
= qi::lexeme
[
+(qi::char_ - (qi::char_('=') | spirit::eol | '#' | ';' | '\\'))
]
;
skipper
= ascii::space
| "#" >> *(qi::char_ - spirit::eol)
;
/* clang-format on */
#define AKANTU_SECTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(elem), BOOST_PP_CAT(ParserType::_, elem))
section_type.add BOOST_PP_SEQ_FOR_EACH(AKANTU_SECTION_TYPE_ADD, _,
AKANTU_SECTION_TYPES);
#undef AKANTU_SECTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG)
phx::function<error_handler_> const error_handler = error_handler_();
qi::on_error<qi::fail>(start,
error_handler(lbs::_4, lbs::_3, lbs::_1, lbs::_2));
#endif
section.name("section");
section_name.name("section-name");
section_option.name("section-option");
mini_section.name("section-content");
entry.name("parameter");
key.name("parameter-name");
value.name("parameter-value");
section_type.name("section-types-list");
mono_line_value.name("mono-line-value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
// qi::debug(section);
qi::debug(section_name);
qi::debug(section_option);
// qi::debug(mini_section);
// qi::debug(entry);
qi::debug(key);
qi::debug(value);
qi::debug(mono_line_value);
}
#endif
}
const std::string & getErrorMessage() const { return error_message; };
using skipper_type = typename Skipper<Iterator>::type;
skipper_type skipper;
private:
std::string error_message;
qi::rule<Iterator, void(ParserSection *), skipper_type> mini_section;
qi::rule<Iterator, void(ParserSection *), qi::locals<ParserSection *>,
skipper_type>
section;
qi::rule<Iterator, void(), skipper_type> start;
qi::rule<Iterator, std::string()> section_name;
qi::rule<Iterator, std::string()> section_option;
qi::rule<Iterator, void(ParserSection *), skipper_type> entry;
qi::rule<Iterator, std::string(), skipper_type> key;
qi::rule<Iterator, std::string(), qi::locals<std::string>, skipper_type>
value;
qi::rule<Iterator, std::string(), skipper_type> mono_line_value;
qi::symbols<char, ParserType> section_type;
ParserSection * parent_section;
};
} // namespace parser
} // namespace akantu
#endif /* AKANTU_INPUT_FILE_PARSER_HH_ */
diff --git a/src/io/parser/parameter_registry.cc b/src/io/parser/parameter_registry.cc
index 008c7613d..39b695a58 100644
--- a/src/io/parser/parameter_registry.cc
+++ b/src/io/parser/parameter_registry.cc
@@ -1,154 +1,156 @@
/**
* @file parameter_registry.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 04 2016
* @date last modification: Thu Feb 01 2018
*
* @brief Parameter Registry and derived classes implementation
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "parameter_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
Parameter::Parameter() = default;
/* -------------------------------------------------------------------------- */
Parameter::Parameter(std::string name, std::string description,
ParameterAccessType param_type)
: name(std::move(name)), description(std::move(description)),
param_type(param_type) {}
/* -------------------------------------------------------------------------- */
bool Parameter::isWritable() const { return (param_type & _pat_writable) != 0; }
/* -------------------------------------------------------------------------- */
bool Parameter::isReadable() const { return (param_type & _pat_readable) != 0; }
/* -------------------------------------------------------------------------- */
bool Parameter::isInternal() const { return (param_type & _pat_internal) != 0; }
/* -------------------------------------------------------------------------- */
bool Parameter::isParsable() const { return (param_type & _pat_parsable) != 0; }
/* -------------------------------------------------------------------------- */
void Parameter::setAccessType(ParameterAccessType ptype) {
this->param_type = ptype;
}
/* -------------------------------------------------------------------------- */
void Parameter::printself(std::ostream & stream) const {
stream << " ";
if (isInternal()) {
stream << "iii";
} else {
if (isReadable()) {
stream << "r";
} else {
stream << "-";
}
if (isWritable()) {
stream << "w";
} else {
stream << "-";
}
if (isParsable()) {
stream << "p";
} else {
stream << "-";
}
}
stream << " ";
std::stringstream sstr;
sstr << name;
UInt width = std::max(int(10 - sstr.str().length()), 0);
sstr.width(width);
if (not description.empty()) {
sstr << " [" << description << "]";
}
stream << sstr.str();
width = std::max(int(50 - sstr.str().length()), 0);
stream.width(width);
stream << " : ";
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
ParameterRegistry::ParameterRegistry() = default;
/* -------------------------------------------------------------------------- */
ParameterRegistry::~ParameterRegistry() {
for (auto && data : params) {
delete data.second;
data.second = NULL;
}
this->params.clear();
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
Parameters::const_iterator it;
for (it = params.begin(); it != params.end(); ++it) {
stream << space;
it->second->printself(stream);
}
SubRegisteries::const_iterator sub_it;
for (sub_it = sub_registries.begin(); sub_it != sub_registries.end();
++sub_it) {
stream << space << "Registry [" << std::endl;
sub_it->second->printself(stream, indent + 1);
stream << space << "]";
}
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::registerSubRegistry(const ID & id,
ParameterRegistry & registry) {
sub_registries[id] = &registry;
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::setParameterAccessType(const std::string & name,
ParameterAccessType ptype) {
auto it = params.find(name);
if (it == params.end()) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
param.setAccessType(ptype);
}
} // namespace akantu
diff --git a/src/io/parser/parameter_registry.hh b/src/io/parser/parameter_registry.hh
index 5dbd40df1..29e582909 100644
--- a/src/io/parser/parameter_registry.hh
+++ b/src/io/parser/parameter_registry.hh
@@ -1,225 +1,227 @@
/**
* @file parameter_registry.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
- * @date last modification: Tue Jan 30 2018
+ * @date last modification: Wed Oct 17 2018
*
* @brief Interface of the parameter registry
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARAMETER_REGISTRY_HH_
#define AKANTU_PARAMETER_REGISTRY_HH_
namespace akantu {
class ParserParameter;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Defines the access modes of parsable parameters
enum ParameterAccessType {
_pat_internal = 0x0001,
_pat_writable = 0x0010,
_pat_readable = 0x0100,
_pat_modifiable = 0x0110, //<_pat_readable | _pat_writable,
_pat_parsable = 0x1000,
_pat_parsmod = 0x1110 //< _pat_parsable | _pat_modifiable
};
/// Bit-wise operator between access modes
inline ParameterAccessType operator|(const ParameterAccessType & a,
const ParameterAccessType & b) {
auto tmp = ParameterAccessType(UInt(a) | UInt(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped;
/**
* Interface for the Parameter
*/
class Parameter {
public:
Parameter();
Parameter(std::string name, std::string description,
ParameterAccessType param_type);
virtual ~Parameter() = default;
/* ------------------------------------------------------------------------ */
bool isInternal() const;
bool isWritable() const;
bool isReadable() const;
bool isParsable() const;
void setAccessType(ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void set(const V & value);
virtual void setAuto(const ParserParameter & param);
template <typename T> T & get();
template <typename T> const T & get() const;
virtual inline operator Real() const { throw std::bad_cast(); };
template <typename T> inline operator T() const;
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream) const;
virtual const std::type_info & type() const = 0;
protected:
/// Returns const instance of templated sub-class ParameterTyped
template <typename T> const ParameterTyped<T> & getParameterTyped() const;
/// Returns instance of templated sub-class ParameterTyped
template <typename T> ParameterTyped<T> & getParameterTyped();
protected:
/// Name of parameter
std::string name;
private:
/// Description of parameter
std::string description;
/// Type of access
ParameterAccessType param_type{_pat_internal};
};
/* -------------------------------------------------------------------------- */
/* Typed Parameter */
/* -------------------------------------------------------------------------- */
/**
* Type parameter transfering a ParserParameter (string: string) to a typed
* parameter in the memory of the p
*/
template <typename T> class ParameterTyped : public Parameter {
public:
ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, T & param);
/* ------------------------------------------------------------------------ */
template <typename V> void setTyped(const V & value);
void setAuto(const ParserParameter & value) override;
T & getTyped();
const T & getTyped() const;
void printself(std::ostream & stream) const override;
inline operator Real() const override;
inline const std::type_info & type() const override { return typeid(T); }
private:
/// Value of parameter
T & param;
};
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class ParameterRegistry {
public:
ParameterRegistry();
virtual ~ParameterRegistry();
/* ------------------------------------------------------------------------ */
/// Add parameter to the params map
template <typename T>
void registerParam(const std::string & name, T & variable, ParameterAccessType type,
const std::string & description = "");
/// Add parameter to the params map (with default value)
template <typename T>
void registerParam(const std::string &name, T & variable, const T & default_value,
ParameterAccessType type,
const std::string & description = "");
/*------------------------------------------------------------------------- */
protected:
void registerSubRegistry(const ID & id, ParameterRegistry & registry);
/* ------------------------------------------------------------------------ */
public:
/// Set value to a parameter (with possible different type)
template <typename T, typename V>
void setMixed(const std::string & name, const V & value);
/// Set value to a parameter
template <typename T> void set(const std::string & name, const T & value);
/// Get value of a parameter
inline const Parameter & get(const std::string & name) const;
/// Get value of a parameter
inline Parameter & get(const std::string & name);
std::vector<ID> listParameters() const {
std::vector<ID> params;
for (const auto & pair : this->params) {
params.push_back(pair.first);
}
return params;
}
std::vector<ID> listSubRegisteries() const {
std::vector<ID> subs;
for (const auto & pair : this->sub_registries) {
subs.push_back(pair.first);
}
return subs;
}
protected:
template <typename T> T & get_(const std::string & name);
protected:
void setParameterAccessType(const std::string & name,
ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream, int indent) const;
protected:
/// Parameters map
using Parameters = std::map<std::string, Parameter *>;
Parameters params;
/// list of sub-registries
using SubRegisteries = std::map<std::string, ParameterRegistry *>;
SubRegisteries sub_registries;
/// should accessor check in sub registries
bool consisder_sub{true};
};
} // namespace akantu
#include "parameter_registry_tmpl.hh"
#endif /* AKANTU_PARAMETER_REGISTRY_HH_ */
diff --git a/src/io/parser/parameter_registry_tmpl.hh b/src/io/parser/parameter_registry_tmpl.hh
index ad6cc226f..ee0815b64 100644
--- a/src/io/parser/parameter_registry_tmpl.hh
+++ b/src/io/parser/parameter_registry_tmpl.hh
@@ -1,457 +1,459 @@
/**
* @file parameter_registry_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed May 04 2016
- * @date last modification: Tue Jan 30 2018
+ * @date last modification: Thu Mar 19 2020
*
* @brief implementation of the templated part of ParameterRegistry class and
* the derivated ones
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_error.hh"
#include "aka_iterators.hh"
//#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <set>
#include <string>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARAMETER_REGISTRY_TMPL_HH_
#define AKANTU_PARAMETER_REGISTRY_TMPL_HH_
namespace akantu {
namespace debug {
class ParameterException : public Exception {
public:
ParameterException(const std::string & name, const std::string & message)
: Exception(message), name(name) {}
const std::string & name;
};
class ParameterUnexistingException : public ParameterException {
public:
ParameterUnexistingException(const std::string & name,
const ParameterRegistry & registery)
: ParameterException(name, "Parameter " + name +
" does not exists in this scope") {
auto && params = registery.listParameters();
this->_info =
std::accumulate(params.begin(), params.end(),
this->_info + "\n Possible parameters are: ",
[](auto && str, auto && param) {
static auto first = true;
auto ret = str + (first ? " " : ", ") + param;
first = false;
return ret;
});
}
};
class ParameterAccessRightException : public ParameterException {
public:
ParameterAccessRightException(const std::string & name,
const std::string & perm)
: ParameterException(name, "Parameter " + name + " is not " + perm) {}
};
class ParameterWrongTypeException : public ParameterException {
public:
ParameterWrongTypeException(const std::string & name,
const std::type_info & wrong_type,
const std::type_info & type)
: ParameterException(name, "Parameter " + name +
" type error, cannot convert " +
debug::demangle(type.name()) + " to " +
debug::demangle(wrong_type.name())) {}
};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <typename T>
const ParameterTyped<T> & Parameter::getParameterTyped() const {
try {
const auto & tmp = aka::as_type<ParameterTyped<T>>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* -------------------------------------------------------------------------- */
template <typename T> ParameterTyped<T> & Parameter::getParameterTyped() {
try {
auto & tmp = aka::as_type<ParameterTyped<T>>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterWrongTypeException(name, typeid(T), this->type()));
}
}
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void Parameter::set(const V & value) {
if (not isWritable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "writable"));
}
ParameterTyped<T> & typed_param = getParameterTyped<T>();
typed_param.setTyped(value);
}
/* ------------------------------------------------------------------------ */
inline void Parameter::setAuto(const ParserParameter & /*value*/) {
if (not isParsable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "parsable"));
}
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & Parameter::get() const {
if (not isReadable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "readable"));
}
const ParameterTyped<T> & typed_param = getParameterTyped<T>();
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> T & Parameter::get() {
ParameterTyped<T> & typed_param = getParameterTyped<T>();
if (not isReadable() or not this->isWritable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
}
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> inline Parameter::operator T() const {
return this->get<T>();
}
/* -------------------------------------------------------------------------- */
template <typename T>
ParameterTyped<T>::ParameterTyped(const std::string & name,
const std::string & description,
ParameterAccessType param_type, T & param)
: Parameter(name, description, param_type), param(param) {}
/* -------------------------------------------------------------------------- */
template <typename T>
template <typename V>
void ParameterTyped<T>::setTyped(const V & value) {
param = value;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = static_cast<T>(value);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<std::string>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = value.getValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Vector<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Vector<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.size(); ++i) {
param(i) = tmp(i);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Matrix<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Matrix<Real> tmp = in_param;
if (param.size() == 0) {
param = tmp;
} else {
for (UInt i = 0; i < param.rows(); ++i) {
for (UInt j = 0; j < param.cols(); ++j) {
param(i, j) = tmp(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & ParameterTyped<T>::getTyped() const {
return param;
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterTyped<T>::getTyped() { return param; }
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped<std::vector<T>> : public Parameter {
public:
ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, std::vector<T> & param)
: Parameter(name, description, param_type), param(param) {}
/* ------------------------------------------------------------------------
*/
template <typename V> void setTyped(const V & value) { param = value; }
void setAuto(const ParserParameter & value) override {
Parameter::setAuto(value);
param.zero();
const std::vector<T> & tmp = value;
for (auto && z : tmp) {
param.emplace_back(z);
}
}
std::vector<T> & getTyped() { return param; }
const std::vector<T> & getTyped() const { return param; }
void printself(std::ostream & stream) const override {
Parameter::printself(stream);
stream << "[ ";
for (auto && v : param) {
stream << v << " ";
}
stream << "]\n";
}
inline const std::type_info & type() const override {
return typeid(std::vector<T>);
}
private:
/// Value of parameter
std::vector<T> & param;
};
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped<std::set<T>> : public Parameter {
public:
ParameterTyped(const std::string & name, const std::string & description,
ParameterAccessType param_type, std::set<T> & param)
: Parameter(name, description, param_type), param(param) {}
/* ------------------------------------------------------------------------
*/
template <typename V> void setTyped(const V & value) { param = value; }
void setAuto(const ParserParameter & value) override {
Parameter::setAuto(value);
param.clear();
const std::set<T> & tmp = value;
for (auto && z : tmp) {
param.emplace(z);
}
}
std::set<T> & getTyped() { return param; }
const std::set<T> & getTyped() const { return param; }
void printself(std::ostream & stream) const override {
Parameter::printself(stream);
stream << "[ ";
for (auto && v : param) {
stream << v << " ";
}
stream << "]\n";
}
inline const std::type_info & type() const override {
return typeid(std::set<T>);
}
private:
/// Value of parameter
std::set<T> & param;
};
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<bool>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << std::boolalpha << param << "\n";
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(const std::string & name, T & variable,
ParameterAccessType type,
const std::string & description) {
auto it = params.find(name);
if (it != params.end()) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterException(
name, "Parameter named " + name + " already registered."));
}
auto * param = new ParameterTyped<T>(name, description, type, variable);
params[name] = param;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(const std::string & name, T & variable,
const T & default_value,
ParameterAccessType type,
const std::string & description) {
variable = default_value;
registerParam(name, variable, type, description);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename V>
void ParameterRegistry::setMixed(const std::string & name, const V & value) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
it->second->setMixed<T>(name, value);
}
} else {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
} else {
Parameter & param = *(it->second);
param.set<T>(value);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::set(const std::string & name, const T & value) {
this->template setMixed<T>(name, value);
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterRegistry::get_(const std::string & name) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get_<T>(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param.get<T>();
}
/* -------------------------------------------------------------------------- */
const Parameter & ParameterRegistry::get(const std::string & name) const {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param;
}
/* -------------------------------------------------------------------------- */
Parameter & ParameterRegistry::get(const std::string & name) {
auto it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (auto it = sub_registries.begin(); it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name, *this));
}
Parameter & param = *(it->second);
return param;
}
/* -------------------------------------------------------------------------- */
namespace {
namespace details {
template <class T, class R, class Enable = void> struct CastHelper {
static R convert(const T & /*unused*/) { throw std::bad_cast(); }
};
template <class T, class R>
struct CastHelper<T, R,
std::enable_if_t<std::is_convertible<T, R>::value>> {
static R convert(const T & val) { return val; }
};
} // namespace details
} // namespace
template <typename T> inline ParameterTyped<T>::operator Real() const {
if (not isReadable()) {
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
}
return details::CastHelper<T, Real>::convert(param);
}
} // namespace akantu
#endif /* AKANTU_PARAMETER_REGISTRY_TMPL_HH_ */
diff --git a/src/io/parser/parsable.cc b/src/io/parser/parsable.cc
index 9e6dfff6d..99d9d43a1 100644
--- a/src/io/parser/parsable.cc
+++ b/src/io/parser/parsable.cc
@@ -1,110 +1,112 @@
/**
* @file parsable.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Feb 08 2018
*
* @brief Parsable implementation
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "parsable.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Parsable::Parsable(const ParserType & section_type, const ID & id)
: section_type(section_type), pid(id) {
this->consisder_sub = false;
}
/* -------------------------------------------------------------------------- */
Parsable::~Parsable() = default;
/* -------------------------------------------------------------------------- */
void Parsable::registerSubSection(const ParserType & type,
const std::string & name,
Parsable & sub_section) {
SubSectionKey key(type, name);
sub_sections[key] = &sub_section;
this->registerSubRegistry(name, sub_section);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseParam(const ParserParameter & in_param) {
auto it = params.find(in_param.getName());
if (it == params.end()) {
if (Parser::isPermissive()) {
AKANTU_DEBUG_WARNING("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
return;
}
AKANTU_EXCEPTION("No parameter named " << in_param.getName()
<< " registered in " << pid << ".");
}
Parameter & param = *(it->second);
param.setAuto(in_param);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSection(const ParserSection & section) {
if (section_type != section.getType()) {
AKANTU_EXCEPTION("The object "
<< pid << " is meant to parse section of type "
<< section_type << ", so it cannot parse section of type "
<< section.getType());
}
auto params = section.getParameters();
auto it = params.first;
for (; it != params.second; ++it) {
parseParam(*it);
}
auto sit = section.getSubSections().first;
for (; sit != section.getSubSections().second; ++sit) {
parseSubSection(*sit);
}
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSubSection(const ParserSection & section) {
SubSectionKey key(section.getType(), section.getName());
auto it = sub_sections.find(key);
if (it != sub_sections.end()) {
it->second->parseSection(section);
} else if (!Parser::isPermissive()) {
AKANTU_EXCEPTION("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
} else {
AKANTU_DEBUG_WARNING("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
}
}
} // namespace akantu
diff --git a/src/io/parser/parsable.hh b/src/io/parser/parsable.hh
index d01694238..5aa957288 100644
--- a/src/io/parser/parsable.hh
+++ b/src/io/parser/parsable.hh
@@ -1,72 +1,74 @@
/**
* @file parsable.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Fri Dec 08 2017
*
* @brief Interface of the parameter registry
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parameter_registry.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARSABLE_HH_
#define AKANTU_PARSABLE_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class Parsable : public ParameterRegistry {
public:
Parsable(const ParserType & section_type, const ID & id = std::string());
~Parsable() override;
/// Add subsection to the sub_sections map
void registerSubSection(const ParserType & type, const std::string & name,
Parsable & sub_section);
/* ------------------------------------------------------------------------ */
public:
virtual void parseSection(const ParserSection & section);
virtual void parseSubSection(const ParserSection & section);
virtual void parseParam(const ParserParameter & in_param);
private:
ParserType section_type;
/// ID of parsable object
ID pid;
using SubSectionKey = std::pair<ParserType, std::string>;
using SubSections = std::map<SubSectionKey, Parsable *>;
/// Subsections map
SubSections sub_sections;
};
} // namespace akantu
#endif /* AKANTU_PARSABLE_HH_ */
diff --git a/src/io/parser/parser.cc b/src/io/parser/parser.cc
index bc4252069..968b2ae9c 100644
--- a/src/io/parser/parser.cc
+++ b/src/io/parser/parser.cc
@@ -1,98 +1,100 @@
/**
* @file parser.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Feb 01 2018
*
* @brief implementation of the parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// STL
#include <fstream>
#include <iomanip>
#include <map>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ParserSection::~ParserSection() { this->clean(); }
/* -------------------------------------------------------------------------- */
ParserParameter & ParserSection::addParameter(const ParserParameter & param) {
if (parameters.find(param.getName()) != parameters.end()) {
AKANTU_EXCEPTION("The parameter \"" + param.getName() +
"\" is already defined in this section");
}
return (parameters
.insert(std::pair<std::string, ParserParameter>(param.getName(),
param))
.first->second);
}
/* -------------------------------------------------------------------------- */
ParserSection & ParserSection::addSubSection(const ParserSection & section) {
return ((sub_sections_by_type.insert(std::pair<ParserType, ParserSection>(
section.getType(), section)))
->second);
}
/* -------------------------------------------------------------------------- */
std::string Parser::getLastParsedFile() const { return last_parsed_file; }
/* -------------------------------------------------------------------------- */
void ParserSection::printself(std::ostream & stream,
unsigned int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Section(" << this->type << ") " << this->name
<< ((not option.empty()) ? (" " + option) : "") << " [" << std::endl;
if (!this->parameters.empty()) {
stream << space << " Parameters [" << std::endl;
auto pit = this->parameters.begin();
for (; pit != this->parameters.end(); ++pit) {
stream << space << " + ";
pit->second.printself(stream, indent);
stream << "\n";
}
stream << space << " ]" << std::endl;
}
if (!this->sub_sections_by_type.empty()) {
stream << space << " Subsections [" << std::endl;
auto sit = this->sub_sections_by_type.begin();
for (; sit != this->sub_sections_by_type.end(); ++sit) {
sit->second.printself(stream, indent + 2);
}
stream << std::endl;
stream << space << " ]" << std::endl;
}
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/io/parser/parser.hh b/src/io/parser/parser.hh
index c39b2a9db..1666886b6 100644
--- a/src/io/parser/parser.hh
+++ b/src/io/parser/parser.hh
@@ -1,541 +1,543 @@
/**
* @file parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Fri Apr 02 2021
*
* @brief File parser interface
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARSER_HH_
#define AKANTU_PARSER_HH_
namespace akantu {
#if !defined(DOXYGEN)
// clang-format off
#define AKANTU_SECTION_TYPES \
(cohesive_inserter) \
(contact) \
(embedded_interface) \
(friction) \
(global) \
(heat) \
(integration_scheme) \
(material) \
(phasefield) \
(mesh) \
(model) \
(model_solver) \
(neighborhood) \
(neighborhoods) \
(non_linear_solver) \
(non_local) \
(rules) \
(solver) \
(time_step_solver) \
(user) \
(weight_function) \
(contact_detector) \
(contact_resolution) \
(not_defined)
// clang-format on
/// Defines the possible section types
AKANTU_CLASS_ENUM_DECLARE(ParserType, AKANTU_SECTION_TYPES)
AKANTU_CLASS_ENUM_OUTPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
AKANTU_CLASS_ENUM_INPUT_STREAM(ParserType, AKANTU_SECTION_TYPES)
#else
enum class ParserType {
cohesive_inserter,
contact,
embedded_interface,
friction,
global,
heat,
integration_scheme,
material,
phasefield,
mesh,
model,
model_solver,
neighborhood,
neighborhoods,
non_linear_solver,
non_local,
rules,
solver,
time_step_solver,
user,
weight_function,
not_defined
};
#endif
/// Defines the possible search contexts/scopes (for parameter search)
enum ParserParameterSearchCxt {
_ppsc_current_scope = 0x1,
_ppsc_parent_scope = 0x2,
_ppsc_current_and_parent_scope = 0x3
};
/* ------------------------------------------------------------------------ */
/* Parameters Class */
/* ------------------------------------------------------------------------ */
class ParserSection;
/// @brief The ParserParameter objects represent the end of tree branches as
/// they
/// are the different informations contained in the input file.
class ParserParameter {
public:
ParserParameter()
: name(std::string()), value(std::string()), dbg_filename(std::string()) {
}
ParserParameter(const std::string & name, const std::string & value,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), value(value),
dbg_filename(std::string()) {}
ParserParameter(const ParserParameter & param) = default;
virtual ~ParserParameter() = default;
/// Get parameter name
const std::string & getName() const { return name; }
/// Get parameter value
const std::string & getValue() const { return value; }
/// Set info for debug output
void setDebugInfo(const std::string & filename, UInt line, UInt column) {
dbg_filename = filename;
dbg_line = line;
dbg_column = column;
}
template <typename T> inline operator T() const;
// template <typename T> inline operator Vector<T>() const;
// template <typename T> inline operator Matrix<T>() const;
/// Print parameter info in stream
void printself(std::ostream & stream,
__attribute__((unused)) unsigned int indent = 0) const {
stream << name << ": " << value << " (" << dbg_filename << ":" << dbg_line
<< ":" << dbg_column << ")";
}
private:
void setParent(const ParserSection & sect) { parent_section = &sect; }
friend class ParserSection;
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of the parameter
std::string name;
/// Value of the parameter
std::string value;
/// File for debug output
std::string dbg_filename;
/// Position of parameter in parsed file
UInt dbg_line, dbg_column;
};
/* ------------------------------------------------------------------------ */
/* Sections Class */
/* ------------------------------------------------------------------------ */
/// ParserSection represents a branch of the parsing tree.
class ParserSection {
public:
using SubSections = std::multimap<ParserType, ParserSection>;
using Parameters = std::map<std::string, ParserParameter>;
private:
using const_section_iterator_ = SubSections::const_iterator;
public:
/* ------------------------------------------------------------------------ */
/* SubSection iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on sections
class const_section_iterator {
public:
using iterator_category = std::forward_iterator_tag;
using value_type = ParserSection;
using pointer = ParserSection *;
using reference = ParserSection &;
const_section_iterator() = default;
const_section_iterator(const const_section_iterator_ & it) : it(it) {}
const_section_iterator(const const_section_iterator & other) = default;
const_section_iterator &
operator=(const const_section_iterator & other) = default;
const ParserSection & operator*() const { return it->second; }
const ParserSection * operator->() const { return &(it->second); }
bool operator==(const const_section_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_section_iterator & other) const {
return it != other.it;
}
const_section_iterator & operator++() {
++it;
return *this;
}
const_section_iterator operator++(int) {
const_section_iterator tmp = *this;
operator++();
return tmp;
}
private:
const_section_iterator_ it;
};
/* ------------------------------------------------------------------------ */
/* Parameters iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on parameters
class const_parameter_iterator {
public:
const_parameter_iterator(const const_parameter_iterator & other) = default;
const_parameter_iterator(const Parameters::const_iterator & it) : it(it) {}
const_parameter_iterator &
operator=(const const_parameter_iterator & other) {
if (this != &other) {
it = other.it;
}
return *this;
}
const ParserParameter & operator*() const { return it->second; }
const ParserParameter * operator->() { return &(it->second); };
bool operator==(const const_parameter_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_parameter_iterator & other) const {
return it != other.it;
}
const_parameter_iterator & operator++() {
++it;
return *this;
}
const_parameter_iterator operator++(int) {
const_parameter_iterator tmp = *this;
operator++();
return tmp;
}
private:
Parameters::const_iterator it;
};
/* ---------------------------------------------------------------------- */
ParserSection() : name(std::string()) {}
ParserSection(const std::string & name, ParserType type)
: name(name), type(type) {}
ParserSection(const std::string & name, ParserType type,
const std::string & option,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), type(type),
option(option) {}
ParserSection(const ParserSection & section)
: parent_section(section.parent_section), name(section.name),
type(section.type), option(section.option),
parameters(section.parameters),
sub_sections_by_type(section.sub_sections_by_type) {
setChldrenPointers();
}
ParserSection & operator=(const ParserSection & other) {
if (&other != this) {
parent_section = other.parent_section;
name = other.name;
type = other.type;
option = other.option;
parameters = other.parameters;
sub_sections_by_type = other.sub_sections_by_type;
setChldrenPointers();
}
return *this;
}
virtual ~ParserSection();
virtual void printself(std::ostream & stream, unsigned int indent = 0) const;
/* ---------------------------------------------------------------------- */
/* Creation functions */
/* ---------------------------------------------------------------------- */
public:
ParserParameter & addParameter(const ParserParameter & param);
ParserSection & addSubSection(const ParserSection & section);
protected:
/// Clean ParserSection content
void clean() {
parameters.clear();
sub_sections_by_type.clear();
}
private:
void setChldrenPointers() {
for (auto && param_pair : this->parameters) {
param_pair.second.setParent(*this);
}
for (auto && sub_sect_pair : this->sub_sections_by_type) {
sub_sect_pair.second.setParent(*this);
}
}
/* ---------------------------------------------------------------------- */
/* Accessors */
/* ---------------------------------------------------------------------- */
public:
class SubSectionsRange
: public std::pair<const_section_iterator, const_section_iterator> {
public:
SubSectionsRange(const const_section_iterator & first,
const const_section_iterator & second)
: std::pair<const_section_iterator, const_section_iterator>(first,
second) {}
auto begin() { return this->first; }
auto end() { return this->second; }
};
/// Get begin and end iterators on subsections of certain type
auto getSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
auto range = sub_sections_by_type.equal_range(type);
return SubSectionsRange(range.first, range.second);
}
return SubSectionsRange(sub_sections_by_type.begin(),
sub_sections_by_type.end());
}
/// Get number of subsections of certain type
UInt getNbSubSections(ParserType type = ParserType::_not_defined) const {
if (type != ParserType::_not_defined) {
return this->sub_sections_by_type.count(type);
}
return this->sub_sections_by_type.size();
}
/// Get begin and end iterators on parameters
auto getParameters() const {
return std::pair<const_parameter_iterator, const_parameter_iterator>(
parameters.begin(), parameters.end());
}
/* ---------------------------------------------------------------------- */
/// Get parameter within specified context
const ParserParameter & getParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if ((search_ctx & _ppsc_current_scope) != 0) {
it = parameters.find(name);
}
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) != 0 and
parent_section != nullptr) {
return parent_section->getParameter(name, search_ctx);
}
AKANTU_SILENT_EXCEPTION(
"The parameter " << name
<< " has not been found in the specified context");
}
return it->second;
}
/* ------------------------------------------------------------------------ */
/// Get parameter within specified context, with a default value in case the
/// parameter does not exists
template <class T>
T getParameter(
const std::string & name, const T & default_value,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
try {
T tmp = this->getParameter(name, search_ctx);
return tmp;
} catch (debug::Exception &) {
return default_value;
}
}
/* ------------------------------------------------------------------------ */
/// Check if parameter exists within specified context
bool hasParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if ((search_ctx & _ppsc_current_scope) != 0) {
it = parameters.find(name);
}
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) != 0 and
parent_section != nullptr) {
return parent_section->hasParameter(name, search_ctx);
}
return false;
}
return true;
}
/* --------------------------------------------------------------------------
*/
/// Get value of given parameter in context
template <class T>
T getParameterValue(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
const ParserParameter & tmp_param = getParameter(name, search_ctx);
T t = tmp_param;
return t;
}
/* --------------------------------------------------------------------------
*/
/// Get section name
std::string getName() const { return name; }
/// Get section type
ParserType getType() const { return type; }
/// Get section option
std::string getOption(const std::string & def = "") const {
return (not option.empty()) ? option : def;
}
protected:
void setParent(const ParserSection & sect) { parent_section = &sect; }
/* ---------------------------------------------------------------------- */
/* Members */
/* ---------------------------------------------------------------------- */
private:
/// Pointer to the parent section
const ParserSection * parent_section{nullptr};
/// Name of section
std::string name;
/// Type of section, see AKANTU_SECTION_TYPES
ParserType type{ParserType::_not_defined};
/// Section option
std::string option;
/// Map of parameters in section
Parameters parameters;
/// Multi-map of subsections
SubSections sub_sections_by_type;
};
/* ------------------------------------------------------------------------ */
/* Parser Class */
/* ------------------------------------------------------------------------ */
/// Root of parsing tree, represents the global ParserSection
class Parser : public ParserSection {
public:
Parser() : ParserSection("global", ParserType::_global) {}
void parse(const std::string & filename);
std::string getLastParsedFile() const;
static bool isPermissive() { return permissive_parser; }
public:
/// Parse real scalar
static Real parseReal(const std::string & value,
const ParserSection & section);
/// Parse real vector
static Vector<Real> parseVector(const std::string & value,
const ParserSection & section);
/// Parse real matrix
static Matrix<Real> parseMatrix(const std::string & value,
const ParserSection & section);
/// Parse real random parameter
static RandomParameter<Real>
parseRandomParameter(const std::string & value,
const ParserSection & section);
protected:
/// General parse function
template <class T, class Grammar>
static T parseType(const std::string & value, Grammar & grammar);
protected:
// friend class Parsable;
static bool permissive_parser;
std::string last_parsed_file;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParserParameter & _this) {
_this.printself(stream);
return stream;
}
inline std::ostream & operator<<(std::ostream & stream,
const ParserSection & section) {
section.printself(stream);
return stream;
}
} // namespace akantu
namespace std {
template <> struct iterator_traits<::akantu::Parser::const_section_iterator> {
using iterator_category = input_iterator_tag;
using value_type = ::akantu::ParserParameter;
using difference_type = ptrdiff_t;
using pointer = const ::akantu::ParserParameter *;
using reference = const ::akantu::ParserParameter &;
};
} // namespace std
#include "parser_tmpl.hh"
#endif /* AKANTU_PARSER_HH_ */
diff --git a/src/io/parser/parser_grammar_tmpl.hh b/src/io/parser/parser_grammar_tmpl.hh
index a31b09119..32649ed05 100644
--- a/src/io/parser/parser_grammar_tmpl.hh
+++ b/src/io/parser/parser_grammar_tmpl.hh
@@ -1,81 +1,83 @@
/**
* @file parser_grammar_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
* @date last modification: Sun Dec 03 2017
*
* @brief implementation of the templated part of ParsableParam Parsable and
* ParsableParamTyped
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
//#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/classic_position_iterator.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/support_multi_pass.hpp>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARSER_GRAMMAR_TMPL_HH
#define AKANTU_PARSER_GRAMMAR_TMPL_HH
namespace akantu {
namespace qi = boost::spirit::qi;
/* -------------------------------------------------------------------------- */
template <class T, class Grammar>
T Parser::parseType(const std::string & value, Grammar & grammar) {
using boost::spirit::ascii::space;
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
T resultat = T();
bool res = false;
try {
res = qi::phrase_parse(b, e, grammar, space, resultat);
} catch (debug::Exception & ex) {
AKANTU_EXCEPTION("Could not parse '"
<< value << "' as a " << debug::demangle(typeid(T).name())
<< ", an unknown error append '" << ex.what());
}
if (!res || (b != e)) {
AKANTU_EXCEPTION("Could not parse '"
<< value << "' as a " << debug::demangle(typeid(T).name())
<< ", an unknown error append '"
<< std::string(value.begin(), b) << "<HERE>"
<< std::string(b, e) << "'");
}
return resultat;
}
namespace parser {
template <class Iterator> struct Skipper {
using type = qi::rule<Iterator, void()>;
};
} // namespace parser
} // namespace akantu
#endif // AKANTU_PARSER_GRAMMAR_TMPL_HH
diff --git a/src/io/parser/parser_input_files.cc b/src/io/parser/parser_input_files.cc
index cfd0d9fd8..adbf8d16a 100644
--- a/src/io/parser/parser_input_files.cc
+++ b/src/io/parser/parser_input_files.cc
@@ -1,118 +1,120 @@
/**
* @file parser_input_files.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
* @date last modification: Wed Nov 08 2017
*
* @brief implementation of the parser
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "input_file_parser.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Parser::parse(const std::string & filename) {
this->clean();
std::ifstream input(filename.c_str());
if (!input.good()) {
AKANTU_EXCEPTION("Could not open file " << filename << "!");
}
input.unsetf(std::ios::skipws);
// wrap istream into iterator
spirit::istream_iterator fwd_begin(input);
spirit::istream_iterator fwd_end;
// wrap forward iterator with position iterator, to record the position
using pos_iterator_type =
spirit::classic::position_iterator2<spirit::istream_iterator>;
pos_iterator_type position_begin(fwd_begin, fwd_end, filename);
pos_iterator_type position_end;
// parse
parser::InputFileGrammar<pos_iterator_type> ag(this);
bool result = qi::phrase_parse(position_begin, position_end, ag, ag.skipper);
if (!result || position_begin != position_end) {
spirit::classic::file_position pos = position_begin.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< ag.getErrorMessage() << " ]"
<< " in file " << filename << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << position_begin.get_currentline() << "'"
<< std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
try {
bool permissive = getParameter("permissive_parser", _ppsc_current_scope);
permissive_parser = permissive;
AKANTU_DEBUG_INFO("Parser switched permissive mode to "
<< std::boolalpha << permissive_parser);
} catch (debug::Exception & e) {
}
last_parsed_file = filename;
input.close();
}
} // namespace akantu
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif defined(__GNUG__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic pop
#else
#pragma GCC diagnostic warning "-Wunused-local-typedefs"
#endif
#endif
diff --git a/src/io/parser/parser_random.cc b/src/io/parser/parser_random.cc
index 6def53c0c..33f651d5e 100644
--- a/src/io/parser/parser_random.cc
+++ b/src/io/parser/parser_random.cc
@@ -1,113 +1,116 @@
/**
* @file parser_random.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Jul 09 2017
*
* @brief implementation of the parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#if !defined(DOXYGEN)
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
RandomParameter<Real>
Parser::parseRandomParameter(const std::string & value,
const ParserSection & section) {
#if !defined(DOXYGEN)
using boost::spirit::ascii::space_type;
parser::RandomGeneratorGrammar<std::string::const_iterator, space_type>
grammar(section);
grammar.name("random_grammar");
parser::ParsableRandomGenerator rg =
Parser::parseType<parser::ParsableRandomGenerator>(value, grammar);
Vector<Real> params = rg.parameters;
switch (rg.type) {
case _rdt_not_defined:
return RandomParameter<Real>(rg.base,
std::uniform_real_distribution<Real>(0, 0));
case _rdt_uniform:
return RandomParameter<Real>(
rg.base, std::uniform_real_distribution<Real>(params(0), params(1)));
case _rdt_exponential:
return RandomParameter<Real>(
rg.base, std::exponential_distribution<Real>(params(0)));
case _rdt_gamma:
return RandomParameter<Real>(
rg.base, std::gamma_distribution<Real>(params(0), params(1)));
case _rdt_weibull:
return RandomParameter<Real>(
rg.base, std::weibull_distribution<Real>(params(1), params(0)));
case _rdt_extreme_value:
return RandomParameter<Real>(
rg.base, std::extreme_value_distribution<Real>(params(0), params(1)));
case _rdt_normal:
return RandomParameter<Real>(
rg.base, std::normal_distribution<Real>(params(0), params(1)));
case _rdt_lognormal:
return RandomParameter<Real>(
rg.base, std::lognormal_distribution<Real>(params(0), params(1)));
case _rdt_chi_squared:
return RandomParameter<Real>(
rg.base, std::chi_squared_distribution<Real>(params(0)));
case _rdt_cauchy:
return RandomParameter<Real>(
rg.base, std::cauchy_distribution<Real>(params(0), params(1)));
case _rdt_fisher_f:
return RandomParameter<Real>(
rg.base, std::fisher_f_distribution<Real>(params(0), params(1)));
case _rdt_student_t:
return RandomParameter<Real>(rg.base,
std::student_t_distribution<Real>(params(0)));
default:
AKANTU_EXCEPTION("This is an unknown random distribution in the parser");
}
#endif
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/parser/parser_real.cc b/src/io/parser/parser_real.cc
index 235608558..19558a8b0 100644
--- a/src/io/parser/parser_real.cc
+++ b/src/io/parser/parser_real.cc
@@ -1,62 +1,65 @@
/**
* @file parser_real.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Wed Apr 20 2016
*
* @brief implementation of the parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Real Parser::parseReal(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::AlgebraicGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("algebraic_grammar");
return Parser::parseType<Real>(value, grammar);
}
} // namespace akantu
diff --git a/src/io/parser/parser_tmpl.hh b/src/io/parser/parser_tmpl.hh
index 0e531778d..19bb0c6c5 100644
--- a/src/io/parser/parser_tmpl.hh
+++ b/src/io/parser/parser_tmpl.hh
@@ -1,123 +1,125 @@
/**
* @file parser_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Thu Mar 19 2020
*
* @brief Implementation of the parser templated methods
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <regex>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> inline ParserParameter::operator T() const {
T t;
std::stringstream sstr(value);
sstr >> t;
if (sstr.bad()) {
AKANTU_EXCEPTION("No known conversion of a ParserParameter \""
<< name << "\" to the type " << typeid(T).name());
}
return t;
}
#if !defined(DOXYGEN)
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator const char *() const {
return value.c_str();
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator Real() const {
return Parser::parseReal(value, *parent_section);
}
/* --------------------------------------------------------- -----------------
*/
template <> inline ParserParameter::operator bool() const {
bool b;
std::stringstream sstr(value);
sstr >> std::boolalpha >> b;
if (sstr.fail()) {
sstr.clear();
sstr >> std::noboolalpha >> b;
}
return b;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator std::vector<std::string>() const {
std::vector<std::string> tmp;
auto string =
std::regex_replace(value, std::regex("[[:space:]]|\\[|\\]"), "");
std::smatch sm;
while (std::regex_search(string, sm, std::regex("[^,]+"))) {
tmp.push_back(sm.str());
string = sm.suffix();
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator std::set<std::string>() const {
std::set<std::string> tmp;
auto string =
std::regex_replace(value, std::regex("[[:space:]]|\\[|\\]"), "");
std::smatch sm;
while (std::regex_search(string, sm, std::regex("[^,]+"))) {
tmp.emplace(sm.str());
string = sm.suffix();
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator Vector<Real>() const {
return Parser::parseVector(value, *parent_section);
}
/* --------------------------------------------------------- ---------------- */
template <> inline ParserParameter::operator Vector<UInt>() const {
Vector<Real> tmp = Parser::parseVector(value, *parent_section);
Vector<UInt> tmp_uint(tmp.size());
for (UInt i = 0; i < tmp.size(); ++i) {
tmp_uint(i) = UInt(tmp(i));
}
return tmp_uint;
}
/* --------------------------------------------------------- ---------------- */
template <> inline ParserParameter::operator Matrix<Real>() const {
return Parser::parseMatrix(value, *parent_section);
}
/* -------------------------------------------------------------------------- */
template <> inline ParserParameter::operator RandomParameter<Real>() const {
return Parser::parseRandomParameter(value, *parent_section);
}
#endif
} // namespace akantu
diff --git a/src/io/parser/parser_types.cc b/src/io/parser/parser_types.cc
index 8c292d0ce..4c1c4c0cf 100644
--- a/src/io/parser/parser_types.cc
+++ b/src/io/parser/parser_types.cc
@@ -1,74 +1,77 @@
/**
* @file parser_types.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Wed Apr 20 2016
*
* @brief implementation of the parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Vector<Real> Parser::parseVector(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::VectorGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("vector_grammar");
return Parser::parseType<parser::parsable_vector>(value, grammar);
}
/* -------------------------------------------------------------------------- */
Matrix<Real> Parser::parseMatrix(const std::string & value,
const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::MatrixGrammar<std::string::const_iterator, space_type> grammar(
section);
grammar.name("matrix_grammar");
return Parser::parseType<parser::parsable_matrix>(value, grammar);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh/element_group.cc b/src/mesh/element_group.cc
index 4de478fbb..7e6d20a6b 100644
--- a/src/mesh/element_group.cc
+++ b/src/mesh/element_group.cc
@@ -1,213 +1,215 @@
/**
* @file element_group.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Jan 22 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "group_manager.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include <algorithm>
#include <iterator>
#include <sstream>
#include "element_group.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const std::string & group_name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension,
const std::string & id)
: mesh(mesh), name(group_name),
elements("elements", id), node_group(node_group),
dimension(dimension) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + group_name, group_name,
true);
this->addDumpFilteredMesh(mesh, elements, node_group.getNodes(),
_all_dimensions);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const ElementGroup & /*other*/) = default;
/* -------------------------------------------------------------------------- */
void ElementGroup::clear() {
elements.free();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::clear(ElementType type, GhostType ghost_type) {
if (elements.exists(type, ghost_type)) {
elements(type, ghost_type).clear();
}
}
/* -------------------------------------------------------------------------- */
bool ElementGroup::empty() const { return elements.empty(); }
/* -------------------------------------------------------------------------- */
void ElementGroup::append(const ElementGroup & other_group) {
AKANTU_DEBUG_IN();
node_group.append(other_group.node_group);
/// loop on all element types in all dimensions
for (auto ghost_type : ghost_types) {
for (auto type : other_group.elementTypes(_ghost_type = ghost_type,
_element_kind = _ek_not_defined)) {
const Array<UInt> & other_elem_list =
other_group.elements(type, ghost_type);
UInt nb_other_elem = other_elem_list.size();
Array<UInt> * elem_list;
UInt nb_elem = 0;
/// create current type if doesn't exists, otherwise get information
if (elements.exists(type, ghost_type)) {
elem_list = &elements(type, ghost_type);
nb_elem = elem_list->size();
} else {
elem_list = &(elements.alloc(0, 1, type, ghost_type));
}
/// append new elements to current list
elem_list->resize(nb_elem + nb_other_elem);
std::copy(other_elem_list.begin(), other_elem_list.end(),
elem_list->begin() + nb_elem);
/// remove duplicates
std::sort(elem_list->begin(), elem_list->end());
Array<UInt>::iterator<> end =
std::unique(elem_list->begin(), elem_list->end());
elem_list->resize(end - elem_list->begin());
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << space << "ElementGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
stream << space << " + dimension: " << dimension << std::endl;
elements.printself(stream, indent + 1);
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ElementGroup::optimize() {
// increasing the locality of data when iterating on the element of a group
for (auto ghost_type : ghost_types) {
for (auto type : elements.elementTypes(_ghost_type = ghost_type)) {
Array<UInt> & els = elements(type, ghost_type);
std::sort(els.begin(), els.end());
Array<UInt>::iterator<> end = std::unique(els.begin(), els.end());
els.resize(end - els.begin());
}
}
node_group.optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::fillFromNodeGroup() {
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(this->mesh, node_to_elem, this->dimension);
std::set<Element> seen;
Array<UInt>::const_iterator<> itn = this->node_group.begin();
Array<UInt>::const_iterator<> endn = this->node_group.end();
for (; itn != endn; ++itn) {
CSR<Element>::iterator ite = node_to_elem.begin(*itn);
CSR<Element>::iterator ende = node_to_elem.end(*itn);
for (; ite != ende; ++ite) {
const Element & elem = *ite;
if (this->dimension != _all_dimensions &&
this->dimension != Mesh::getSpatialDimension(elem.type)) {
continue;
}
if (seen.find(elem) != seen.end()) {
continue;
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(elem.type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
this->mesh.getConnectivity(elem.type, elem.ghost_type)
.begin(nb_nodes_per_element);
const Vector<UInt> & conn = conn_it[elem.element];
UInt count = 0;
for (UInt n = 0; n < conn.size(); ++n) {
count +=
(this->node_group.getNodes().find(conn(n)) != UInt(-1) ? 1 : 0);
}
if (count == nb_nodes_per_element) {
this->add(elem);
}
seen.insert(elem);
}
}
this->optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::addDimension(UInt dimension) {
this->dimension = std::max(dimension, this->dimension);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh/element_group.hh b/src/mesh/element_group.hh
index b8dab597a..6bf7c208d 100644
--- a/src/mesh/element_group.hh
+++ b/src/mesh/element_group.hh
@@ -1,203 +1,205 @@
/**
* @file element_group.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Mon Mar 08 2021
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumpable.hh"
#include "element_type_map.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_GROUP_HH_
#define AKANTU_ELEMENT_GROUP_HH_
namespace akantu {
class Mesh;
class Element;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class ElementGroup : public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementGroup(const std::string & name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension = _all_dimensions,
const std::string & id = "element_group");
ElementGroup(const ElementGroup & /*unused*/);
/* ------------------------------------------------------------------------ */
/* Type definitions */
/* ------------------------------------------------------------------------ */
public:
using ElementList = ElementTypeMapArray<UInt>;
using NodeList = Array<UInt>;
/* ------------------------------------------------------------------------ */
/* Element iterator */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementList::type_iterator;
[[deprecated("Use elementTypes instead")]] inline type_iterator
firstType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
[[deprecated("Use elementTypes instead")]] inline type_iterator
lastType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
template <typename... pack>
inline decltype(auto) elementTypes(pack &&... _pack) const {
return elements.elementTypes(_pack...);
}
using const_element_iterator = Array<UInt>::const_iterator<UInt>;
inline const_element_iterator begin(ElementType type,
GhostType ghost_type = _not_ghost) const;
inline const_element_iterator end(ElementType type,
GhostType ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty the element group
void clear();
void clear(ElementType type, GhostType ghost_type = _not_ghost);
bool empty() const __attribute__((warn_unused_result));
/// append another group to this group
/// BE CAREFUL: it doesn't conserve the element order
void append(const ElementGroup & other_group);
/// add an element to the group. By default the it does not add the nodes to
/// the group
inline void add(const Element & el, bool add_nodes = false,
bool check_for_duplicate = true);
/// \todo fix the default for add_nodes : make it coherent with the other
/// method
inline void add(ElementType type, UInt element,
GhostType ghost_type = _not_ghost, bool add_nodes = true,
bool check_for_duplicate = true);
inline void addNode(UInt node_id, bool check_for_duplicate = true);
inline void removeNode(UInt node_id);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// fill the elements based on the underlying node group.
virtual void fillFromNodeGroup();
// sort and remove duplicated values
void optimize();
/// change the dimension if needed
void addDimension(UInt dimension);
private:
inline void addElement(ElementType elem_type, UInt elem_id,
GhostType ghost_type);
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
const Array<UInt> & getElements(ElementType type,
GhostType ghost_type = _not_ghost) const;
AKANTU_GET_MACRO(Elements, elements, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_NOT_CONST(Elements, elements, ElementTypeMapArray<UInt> &);
template <class... Args> auto size(Args &&... pack) const {
return elements.size(std::forward<Args>(pack)...);
}
decltype(auto) getElementsIterable(ElementType type,
GhostType ghost_type = _not_ghost) const;
// AKANTU_GET_MACRO(Nodes, node_group.getNodes(), const Array<UInt> &);
AKANTU_GET_MACRO(NodeGroup, node_group, const NodeGroup &);
AKANTU_GET_MACRO_NOT_CONST(NodeGroup, node_group, NodeGroup &);
AKANTU_GET_MACRO(Dimension, dimension, UInt);
AKANTU_GET_MACRO(Name, name, std::string);
inline UInt getNbNodes() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Mesh to which this group belongs
const Mesh & mesh;
/// name of the group
std::string name;
/// list of elements composing the group
ElementList elements;
/// sub list of nodes which are composing the elements
NodeGroup & node_group;
/// group dimension
UInt dimension{_all_dimensions};
/// empty arry for the iterator to work when an element type not present
Array<UInt> empty_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ElementGroup & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "element.hh"
#include "element_group_inline_impl.hh"
#endif /* AKANTU_ELEMENT_GROUP_HH_ */
diff --git a/src/mesh/element_group_inline_impl.hh b/src/mesh/element_group_inline_impl.hh
index 9ade23bc3..d2e447805 100644
--- a/src/mesh/element_group_inline_impl.hh
+++ b/src/mesh/element_group_inline_impl.hh
@@ -1,146 +1,148 @@
/**
* @file element_group_inline_impl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Tue Mar 09 2021
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_
#define AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const Element & el, bool add_nodes,
bool check_for_duplicate) {
this->add(el.type, el.element, el.ghost_type, add_nodes, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(ElementType type, UInt element,
GhostType ghost_type, bool add_nodes,
bool check_for_duplicate) {
addElement(type, element, ghost_type);
if (add_nodes) {
Array<UInt>::const_vector_iterator it =
mesh.getConnectivity(type, ghost_type)
.begin(mesh.getNbNodesPerElement(type)) +
element;
const Vector<UInt> & conn = *it;
for (UInt i = 0; i < conn.size(); ++i) {
addNode(conn[i], check_for_duplicate);
}
}
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addNode(UInt node_id, bool check_for_duplicate) {
node_group.add(node_id, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::removeNode(UInt node_id) {
node_group.remove(node_id);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addElement(ElementType elem_type, UInt elem_id,
GhostType ghost_type) {
if (!(elements.exists(elem_type, ghost_type))) {
elements.alloc(0, 1, elem_type, ghost_type);
}
elements(elem_type, ghost_type).push_back(elem_id);
this->dimension = UInt(
std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
}
/* -------------------------------------------------------------------------- */
inline UInt ElementGroup::getNbNodes() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
ElementGroup::firstType(UInt dim, GhostType ghost_type,
ElementKind kind) const {
return elements.elementTypes(dim, ghost_type, kind).begin();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator
ElementGroup::lastType(UInt dim, GhostType ghost_type, ElementKind kind) const {
return elements.elementTypes(dim, ghost_type, kind).end();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
ElementGroup::begin(ElementType type, GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).begin();
}
return empty_elements.begin();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator
ElementGroup::end(ElementType type, GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type).end();
}
return empty_elements.end();
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
ElementGroup::getElements(ElementType type, GhostType ghost_type) const {
if (elements.exists(type, ghost_type)) {
return elements(type, ghost_type);
}
return empty_elements;
}
/* -------------------------------------------------------------------------- */
inline decltype(auto)
ElementGroup::getElementsIterable(ElementType type,
GhostType ghost_type) const {
return make_transform_adaptor(this->elements(type, ghost_type),
[type, ghost_type](auto && el) {
return Element{type, el, ghost_type};
});
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_GROUP_INLINE_IMPL_HH_ */
diff --git a/src/mesh/element_type_map.cc b/src/mesh/element_type_map.cc
index 1e8a45c53..62ed6ee7e 100644
--- a/src/mesh/element_type_map.cc
+++ b/src/mesh/element_type_map.cc
@@ -1,73 +1,75 @@
/**
* @file element_type_map.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Mar 04 2020
*
- * @brief A Documented file.
+ * @brief storage class by element type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component, UInt spatial_dimension,
GhostType ghost_type, ElementKind element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
FEEngineElementTypeMapArrayInitializer::FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
UInt spatial_dimension, GhostType ghost_type,
ElementKind element_kind)
: MeshElementTypeMapArrayInitializer(
fe_engine.getMesh(), nb_component,
spatial_dimension == UInt(-2)
? fe_engine.getMesh().getSpatialDimension()
: spatial_dimension,
ghost_type, element_kind, true, false),
fe_engine(fe_engine) {}
UInt FEEngineElementTypeMapArrayInitializer::size(
ElementType type) const {
return MeshElementTypeMapArrayInitializer::size(type) *
fe_engine.getNbIntegrationPoints(type, this->ghost_type);
}
FEEngineElementTypeMapArrayInitializer::ElementTypesIteratorHelper
FEEngineElementTypeMapArrayInitializer::elementTypes() const {
return this->fe_engine.elementTypes(spatial_dimension, ghost_type,
element_kind);
}
} // namespace akantu
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index 171fb7559..8df2e43bb 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,490 +1,492 @@
/**
* @file element_type_map.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Mar 11 2021
*
* @brief storage class by element type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_named_argument.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_TYPE_MAP_HH_
#define AKANTU_ELEMENT_TYPE_MAP_HH_
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(all_ghost_types);
DECLARE_NAMED_ARGUMENT(default_value);
DECLARE_NAMED_ARGUMENT(element_kind);
DECLARE_NAMED_ARGUMENT(ghost_type);
DECLARE_NAMED_ARGUMENT(nb_component);
DECLARE_NAMED_ARGUMENT(nb_component_functor);
DECLARE_NAMED_ARGUMENT(with_nb_element);
DECLARE_NAMED_ARGUMENT(with_nb_nodes_per_element);
DECLARE_NAMED_ARGUMENT(spatial_dimension);
DECLARE_NAMED_ARGUMENT(do_not_default);
DECLARE_NAMED_ARGUMENT(element_filter);
} // namespace
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase() = default;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
~ElementTypeMap() override;
inline static std::string printType(const SupportType & type,
GhostType ghost_type);
/*! Tests whether a type is present in the object
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return true if the type is present. */
inline bool exists(const SupportType & type,
GhostType ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline const Stored & operator()(const SupportType & type,
GhostType ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const SupportType & type,
GhostType ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map. THIS METHOD IS
* NOT ARRAY SAFE, when using ElementTypeMapArray, use setArray instead
* @param data to insert
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
template <typename U>
inline Stored & operator()(U && insertee, const SupportType & type,
GhostType ghost_type = _not_ghost);
public:
/// print helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
/*! iterator allows to iterate over type-data pairs of the map. The interface
* expects the SupportType to be ElementType. */
using DataMap = std::map<SupportType, Stored>;
/// helper class to use in range for constructions
class type_iterator
: private std::iterator<std::forward_iterator_tag, const SupportType> {
public:
using value_type = const SupportType;
using pointer = const SupportType *;
using reference = const SupportType &;
protected:
using DataMapIterator =
typename ElementTypeMap<Stored>::DataMap::const_iterator;
public:
type_iterator(DataMapIterator & list_begin, DataMapIterator & list_end,
UInt dim, ElementKind ek);
type_iterator(const type_iterator & it);
type_iterator() = default;
inline reference operator*();
inline reference operator*() const;
inline type_iterator & operator++();
type_iterator operator++(int);
inline bool operator==(const type_iterator & other) const;
inline bool operator!=(const type_iterator & other) const;
type_iterator & operator=(const type_iterator & it);
private:
DataMapIterator list_begin;
DataMapIterator list_end;
UInt dim;
ElementKind kind;
};
/// helper class to use in range for constructions
class ElementTypesIteratorHelper {
public:
using Container = ElementTypeMap<Stored, SupportType>;
using iterator = typename Container::type_iterator;
ElementTypesIteratorHelper(const Container & container, UInt dim,
GhostType ghost_type, ElementKind kind)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type),
kind(kind) {}
template <typename... pack>
ElementTypesIteratorHelper(const Container & container,
use_named_args_t /*unused*/, pack &&... _pack)
: ElementTypesIteratorHelper(
container, OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
OPTIONAL_NAMED_ARG(ghost_type, _not_ghost),
OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined)) {}
ElementTypesIteratorHelper(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(ElementTypesIteratorHelper &&) noexcept = default;
iterator begin();
iterator end();
private:
std::reference_wrapper<const Container> container;
UInt dim;
GhostType ghost_type;
ElementKind kind;
};
private:
ElementTypesIteratorHelper
elementTypesImpl(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
template <typename... pack>
ElementTypesIteratorHelper
elementTypesImpl(const use_named_args_t & /*unused*/, pack &&... _pack) const;
public:
/*!
* \param _pack
* \parblock
* represent optional parameters:
* \li \c _spatial_dimension filter for elements of given spatial
* dimension
* \li \c _ghost_type filter for a certain ghost_type
* \li \c _element_kind filter for elements of given kind
* \endparblock
*/
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(use_named_args,
std::forward<decltype(_pack)>(_pack)...);
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value,
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(std::forward<decltype(_pack)>(_pack)...);
}
/*! Get an iterator to the beginning of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the first stored data matching the filters
* or an iterator to the end of the map if none match*/
[[deprecated("Use elementTypes instead")]] inline type_iterator
firstType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Get an iterator to the end of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the last stored data matching the filters
* or an iterator to the end of the map if none match */
[[deprecated("Use elementTypes instead")]] inline type_iterator
lastType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline DataMap & getData(GhostType ghost_type);
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline const DataMap & getData(GhostType ghost_type) const;
/* ------------------------------------------------------------------------ */
protected:
DataMap data;
DataMap ghost_data;
};
/* -------------------------------------------------------------------------- */
/* Some typedefs */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
class ElementTypeMapArray
: public ElementTypeMap<std::unique_ptr<Array<T>>, SupportType> {
public:
using value_type = T;
using array_type = Array<T>;
protected:
using parent = ElementTypeMap<std::unique_ptr<Array<T>>, SupportType>;
using DataMap = typename parent::DataMap;
public:
using type_iterator = typename parent::type_iterator;
/// standard assigment (copy) operator
void operator=(const ElementTypeMapArray &) = delete;
ElementTypeMapArray(const ElementTypeMapArray & /*other*/);
/// explicit copy
void copy(const ElementTypeMapArray & other);
/*! Constructor
* @param id optional: identifier (string)
* @param parent_id optional: parent identifier. for organizational purposes
* only
*/
ElementTypeMapArray(const ID & id = "by_element_type_array",
const ID & parent_id = "no_parent")
: parent(), id(parent_id + ":" + id), name(id){};
/*! allocate memory for a new array
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param ghost_type whether to add the field to the data map or the
* ghost_data map
* @param default_value the default value to use to fill the array
* @return a reference to the allocated array */
inline Array<T> & alloc(UInt size, UInt nb_component,
const SupportType & type, GhostType ghost_type,
const T & default_value = T());
/*! allocate memory for a new array in both the data and the ghost_data map
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param default_value the default value to use to fill the array
*/
inline void alloc(UInt size, UInt nb_component, const SupportType & type,
const T & default_value = T());
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a reference to the array */
inline const Array<T> & operator()(const SupportType & type,
GhostType ghost_type = _not_ghost) const;
/// access the data of an element, this combine the map and array accessor
inline const T & operator()(const Element & element,
UInt component = 0) const;
/// access the data of an element, this combine the map and array accessor
inline T & operator()(const Element & element, UInt component = 0);
/// access the data of an element, this combine the map and array accessor
inline decltype(auto) get(const Element & element);
inline decltype(auto) get(const Element & element) const;
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a const reference to the array */
inline Array<T> & operator()(const SupportType & type,
GhostType ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map.
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @param vect the vector to include into the map
* @return stored data corresponding to type. */
inline void setArray(const SupportType & type, GhostType ghost_type,
const Array<T> & vect);
/*! frees all memory related to the data*/
inline void free();
inline void clear();
inline bool empty() const __attribute__((warn_unused_result));
/*! set all values in the ElementTypeMap to zero*/
inline void zero() { this->set(T()); }
/*! set all values in the ElementTypeMap to value */
template <typename ST> inline void set(const ST & value);
/*! deletes and reorders entries in the stored arrays
* @param new_numbering a ElementTypeMapArray of new indices. UInt(-1)
* indicates
* deleted entries. */
inline void
onElementsRemoved(const ElementTypeMapArray<UInt> & new_numbering);
/// text output helper
void printself(std::ostream & stream, int indent = 0) const override;
/*! set the id
* @param id the new name
*/
inline void setID(const ID & id) { this->id = id; }
/// return the id
inline auto getID() const -> ID { return this->id; }
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions,
GhostType requested_ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
ElementTypeMap<UInt> nb_components;
bool all_ghost_types = requested_ghost_type == _casper;
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
}
for (auto & type : this->elementTypes(dim, ghost_type, kind)) {
UInt nb_comp = (*this)(type, ghost_type).getNbComponent();
nb_components(type, ghost_type) = nb_comp;
}
}
return nb_components;
}
/* ------------------------------------------------------------------------ */
/* more evolved allocators */
/* ------------------------------------------------------------------------ */
public:
/// initialize the arrays in accordance to a functor
template <class Func>
void initialize(const Func & f, const T & default_value, bool do_not_default);
/// initialize with sizes and number of components in accordance of a mesh
/// content
template <typename... pack>
void initialize(const Mesh & mesh, pack &&... _pack);
/// initialize with sizes and number of components in accordance of a fe
/// engine content (aka integration points)
template <typename... pack>
void initialize(const FEEngine & fe_engine, pack &&... _pack);
/* ------------------------------------------------------------------------ */
/* Accesssors */
/* ------------------------------------------------------------------------ */
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
/**
* get the size of the ElementTypeMapArray<T>
* @param[in] _pack
* \parblock
* optional arguments can be any of:
* \li \c _spatial_dimension the dimension to consider (default:
* _all_dimensions)
* \li \c _ghost_type (default: _not_ghost)
* \li \c _element_kind (default: _ek_not_defined)
* \li \c _all_ghost_types (default: false)
* \endparblock
**/
template <typename... pack> UInt size(pack &&... _pack) const;
bool isNodal() const { return is_nodal; }
void isNodal(bool is_nodal) { this->is_nodal = is_nodal; }
private:
UInt sizeImpl(UInt spatial_dimension, GhostType ghost_type,
ElementKind kind) const;
private:
ID id;
protected:
/// name of the element type map: e.g. connectivity, grad_u
ID name;
/// Is the data stored by node of the element
bool is_nodal{false};
};
/// to store data Array<Real> by element type
using ElementTypeMapReal = ElementTypeMapArray<Real>;
/// to store data Array<Int> by element type
using ElementTypeMapInt = ElementTypeMapArray<Int>;
/// to store data Array<UInt> by element type
using ElementTypeMapUInt = ElementTypeMapArray<UInt, ElementType>;
} // namespace akantu
#endif /* AKANTU_ELEMENT_TYPE_MAP_HH_ */
diff --git a/src/mesh/element_type_map_filter.hh b/src/mesh/element_type_map_filter.hh
index c3d52ec00..8713d0300 100644
--- a/src/mesh/element_type_map_filter.hh
+++ b/src/mesh/element_type_map_filter.hh
@@ -1,128 +1,130 @@
/**
* @file element_type_map_filter.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Filtered version based on a an akantu::ElementGroup of a
* akantu::ElementTypeMap
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array_filter.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BY_ELEMENT_TYPE_FILTER_HH_
#define AKANTU_BY_ELEMENT_TYPE_FILTER_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ElementTypeMapFilter */
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType = ElementType>
class ElementTypeMapArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
using array_type = ArrayFilter<T>;
using value_type = typename array_type::value_type;
using type_iterator =
typename ElementTypeMapArray<UInt, SupportType>::type_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter,
const ElementTypeMap<UInt, SupportType> & nb_data_per_elem)
: array(array), filter(filter), nb_data_per_elem(nb_data_per_elem) {}
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter)
: array(array), filter(filter) {}
~ElementTypeMapArrayFilter() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline ArrayFilter<T> operator()(const SupportType & type,
GhostType ghost_type = _not_ghost) const {
if (filter.exists(type, ghost_type)) {
if (nb_data_per_elem.exists(type, ghost_type)) {
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
nb_data_per_elem(type, ghost_type) /
array(type, ghost_type).getNbComponent());
}
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
1);
}
return ArrayFilter<T>(empty_array, empty_filter, 1);
};
template <typename... Args>
decltype(auto) elementTypes(Args &&... args) const {
return filter.elementTypes(std::forward<decltype(args)>(args)...);
}
decltype(auto) getNbComponents(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return this->array.getNbComponents(dim, ghost_type, kind);
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
std::string getID() {
return std::string("filtered:" + this->array().getID());
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const ElementTypeMapArray<T, SupportType> & array;
const ElementTypeMapArray<UInt, SupportType> & filter;
ElementTypeMap<UInt> nb_data_per_elem;
/// Empty array to be able to return consistent filtered arrays
Array<T> empty_array;
Array<UInt> empty_filter;
};
} // namespace akantu
#endif /* AKANTU_BY_ELEMENT_TYPE_FILTER_HH_ */
diff --git a/src/mesh/element_type_map_tmpl.hh b/src/mesh/element_type_map_tmpl.hh
index 2ed347b00..ca6ee7313 100644
--- a/src/mesh/element_type_map_tmpl.hh
+++ b/src/mesh/element_type_map_tmpl.hh
@@ -1,849 +1,852 @@
/**
* @file element_type_map_tmpl.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Mar 11 2021
*
* @brief implementation of template functions of the ElementTypeMap and
* ElementTypeMapArray classes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_static_if.hh"
#include "element_type_map.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include "element_type_conversion.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_
#define AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline std::string
ElementTypeMap<Stored, SupportType>::printType(const SupportType & type,
GhostType ghost_type) {
std::stringstream sstr;
sstr << "(" << ghost_type << ":" << type << ")";
return sstr.str();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool
ElementTypeMap<Stored, SupportType>::exists(const SupportType & type,
GhostType ghost_type) const {
return this->getData(ghost_type).find(type) !=
this->getData(ghost_type).end();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const Stored &
ElementTypeMap<Stored, SupportType>::operator()(const SupportType & type,
GhostType ghost_type) const {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline Stored &
ElementTypeMap<Stored, SupportType>::operator()(const SupportType & type,
GhostType ghost_type) {
return this->getData(ghost_type)[type];
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename U>
inline Stored & ElementTypeMap<Stored, SupportType>::operator()(
U && insertee, const SupportType & type, GhostType ghost_type) {
auto it = this->getData(ghost_type).find(type);
if (it != this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("Element of type "
<< ElementTypeMap::printType(type, ghost_type)
<< " already in this ElementTypeMap<"
<< debug::demangle(typeid(Stored).name())
<< "> class");
} else {
auto & data = this->getData(ghost_type);
const auto & res =
data.insert(std::make_pair(type, std::forward<U>(insertee)));
it = res.first;
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) {
if (ghost_type == _not_ghost) {
return data;
}
return ghost_data;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline const typename ElementTypeMap<Stored, SupportType>::DataMap &
ElementTypeMap<Stored, SupportType>::getData(GhostType ghost_type) const {
if (ghost_type == _not_ghost) {
return data;
}
return ghost_data;
}
/* -------------------------------------------------------------------------- */
/// Works only if stored is a pointer to a class with a printself method
template <class Stored, typename SupportType>
void ElementTypeMap<Stored, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "ElementTypeMap<" << debug::demangle(typeid(Stored).name())
<< "> [" << std::endl;
for (auto && gt : ghost_types) {
const DataMap & data = getData(gt);
for (auto & pair : data) {
stream << space << space << ElementTypeMap::printType(pair.first, gt)
<< std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::~ElementTypeMap() = default;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapArray */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::copy(
const ElementTypeMapArray & other) {
for (auto ghost_type : ghost_types) {
for (auto type :
this->elementTypes(_all_dimensions, ghost_type, _ek_not_defined)) {
const auto & array_to_copy = other(type, ghost_type);
auto & array =
this->alloc(0, array_to_copy.getNbComponent(), type, ghost_type);
array.copy(array_to_copy);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
ElementTypeMapArray<T, SupportType>::ElementTypeMapArray(
const ElementTypeMapArray & other)
: parent(), id(other.id + "_copy"), name(other.name + "_copy") {
this->copy(other);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> & ElementTypeMapArray<T, SupportType>::alloc(
UInt size, UInt nb_component, const SupportType & type,
GhostType ghost_type, const T & default_value) {
std::string ghost_id;
if (ghost_type == _ghost) {
ghost_id = ":ghost";
}
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
auto id = this->id + ":" + std::to_string(type) + ghost_id;
this->getData(ghost_type)[type] =
std::make_unique<Array<T>>(size, nb_component, default_value, id);
return *(this->getData(ghost_type)[type]);
}
AKANTU_DEBUG_INFO("The vector "
<< this->id << this->printType(type, ghost_type)
<< " already exists, it is resized instead of allocated.");
auto && array = *(it->second);
array.resize(size);
return array;
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void
ElementTypeMapArray<T, SupportType>::alloc(UInt size, UInt nb_component,
const SupportType & type,
const T & default_value) {
this->alloc(size, nb_component, type, _not_ghost, default_value);
this->alloc(size, nb_component, type, _ghost, default_value);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::free() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
data.clear();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::clear() {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->clear();
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline bool ElementTypeMapArray<T, SupportType>::empty() const {
bool is_empty = true;
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
is_empty &= vect.second->empty();
if (not is_empty) {
return false;
}
}
}
return is_empty;
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <typename ST>
inline void ElementTypeMapArray<T, SupportType>::set(const ST & value) {
for (auto gt : ghost_types) {
auto & data = this->getData(gt);
for (auto & vect : data) {
vect.second->set(value);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline const Array<T> &
ElementTypeMapArray<T, SupportType>::operator()(const SupportType & type,
GhostType ghost_type) const {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this const ElementTypeMapArray<"
<< debug::demangle(typeid(T).name()) << "> class(\""
<< this->id << "\")");
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline Array<T> &
ElementTypeMapArray<T, SupportType>::operator()(const SupportType & type,
GhostType ghost_type) {
auto it = this->getData(ghost_type).find(type);
if (it == this->getData(ghost_type).end()) {
AKANTU_SILENT_EXCEPTION("No element of type "
<< ElementTypeMapArray::printType(type, ghost_type)
<< " in this ElementTypeMapArray<"
<< debug::demangle(typeid(T).name())
<< "> class (\"" << this->id << "\")");
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::setArray(
const SupportType & type, GhostType ghost_type, const Array<T> & vect) {
auto it = this->getData(ghost_type).find(type);
if (AKANTU_DEBUG_TEST(dblWarning) && it != this->getData(ghost_type).end() &&
it->second != &vect) {
AKANTU_DEBUG_WARNING(
"The Array "
<< this->printType(type, ghost_type)
<< " is already registred, this call can lead to a memory leak.");
}
this->getData(ghost_type)[type] = &(const_cast<Array<T> &>(vect));
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
inline void ElementTypeMapArray<T, SupportType>::onElementsRemoved(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto gt : ghost_types) {
for (auto && type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
auto support_type = convertType<ElementType, SupportType>(type);
if (this->exists(support_type, gt)) {
const auto & renumbering = new_numbering(type, gt);
if (renumbering.empty()) {
continue;
}
auto & vect = this->operator()(support_type, gt);
auto nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size(), nb_component);
UInt new_size = 0;
for (UInt i = 0; i < vect.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
std::copy_n(vect.storage() + i * nb_component, nb_component,
tmp.storage() + new_i * nb_component);
++new_size;
}
}
tmp.resize(new_size);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
void ElementTypeMapArray<T, SupportType>::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "ElementTypeMapArray<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
for (UInt g = _not_ghost; g <= _ghost; ++g) {
auto gt = (GhostType)g;
const DataMap & data = this->getData(gt);
typename DataMap::const_iterator it;
for (it = data.begin(); it != data.end(); ++it) {
stream << space << space << ElementTypeMapArray::printType(it->first, gt)
<< " [" << std::endl;
it->second->printself(stream, indent + 3);
stream << space << space << " ]" << std::endl;
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* SupportType Iterator */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
DataMapIterator & list_begin, DataMapIterator & list_end, UInt dim,
ElementKind ek)
: list_begin(list_begin), list_end(list_end), dim(dim), kind(ek) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
ElementTypeMap<Stored, SupportType>::type_iterator::type_iterator(
const type_iterator & it)
: list_begin(it.list_begin), list_end(it.list_end), dim(it.dim),
kind(it.kind) {}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::operator=(
const type_iterator & it) {
if (this != &it) {
list_begin = it.list_begin;
list_end = it.list_end;
dim = it.dim;
kind = it.kind;
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator::reference
ElementTypeMap<Stored, SupportType>::type_iterator::operator*() const {
return list_begin->first;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline typename ElementTypeMap<Stored, SupportType>::type_iterator &
ElementTypeMap<Stored, SupportType>::type_iterator::operator++() {
++list_begin;
while ((list_begin != list_end) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(list_begin->first))) ||
((kind != _ek_not_defined) &&
(kind != Mesh::getKind(list_begin->first))))) {
++list_begin;
}
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
typename ElementTypeMap<Stored, SupportType>::type_iterator
ElementTypeMap<Stored, SupportType>::type_iterator::operator++(int) {
type_iterator tmp(*this);
operator++();
return tmp;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::operator==(
const type_iterator & other) const {
return this->list_begin == other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline bool ElementTypeMap<Stored, SupportType>::type_iterator::operator!=(
const type_iterator & other) const {
return this->list_begin != other.list_begin;
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper::begin()
-> iterator {
auto b = container.get().getData(ghost_type).begin();
auto e = container.get().getData(ghost_type).end();
// loop until the first valid type
while ((b != e) &&
(((dim != _all_dimensions) &&
(dim != Mesh::getSpatialDimension(b->first))) ||
((kind != _ek_not_defined) && (kind != Mesh::getKind(b->first))))) {
++b;
}
return iterator(b, e, dim, kind);
}
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::ElementTypesIteratorHelper::end()
-> iterator {
auto e = container.get().getData(ghost_type).end();
return iterator(e, e, dim, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
auto ElementTypeMap<Stored, SupportType>::elementTypesImpl(
UInt dim, GhostType ghost_type, ElementKind kind) const
-> ElementTypesIteratorHelper {
return ElementTypesIteratorHelper(*this, dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
template <typename... pack>
auto ElementTypeMap<Stored, SupportType>::elementTypesImpl(
const use_named_args_t & unused, pack &&... _pack) const
-> ElementTypesIteratorHelper {
return ElementTypesIteratorHelper(*this, unused, _pack...);
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline auto ElementTypeMap<Stored, SupportType>::firstType(
UInt dim, GhostType ghost_type, ElementKind kind) const -> type_iterator {
return elementTypes(dim, ghost_type, kind).begin();
}
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
inline auto ElementTypeMap<Stored, SupportType>::lastType(
UInt dim, GhostType ghost_type, ElementKind kind) const -> type_iterator {
typename DataMap::const_iterator e;
e = getData(ghost_type).end();
return typename ElementTypeMap<Stored, SupportType>::type_iterator(e, e, dim,
kind);
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator
template <class Stored, typename SupportType>
inline std::ostream &
operator<<(std::ostream & stream,
const ElementTypeMap<Stored, SupportType> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
class ElementTypeMapArrayInitializer {
protected:
using CompFunc = std::function<UInt(ElementType, GhostType)>;
public:
ElementTypeMapArrayInitializer(const CompFunc & comp_func,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: comp_func(comp_func), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {}
GhostType ghostType() const { return ghost_type; }
virtual UInt nbComponent(ElementType type) const {
return comp_func(type, ghostType());
}
virtual bool isNodal() const { return false; }
protected:
CompFunc comp_func;
UInt spatial_dimension;
GhostType ghost_type;
ElementKind element_kind;
};
/* -------------------------------------------------------------------------- */
class MeshElementTypeMapArrayInitializer
: public ElementTypeMapArrayInitializer {
using CompFunc = ElementTypeMapArrayInitializer::CompFunc;
public:
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined, bool with_nb_element = false,
bool with_nb_nodes_per_element = false,
const ElementTypeMapArray<UInt> * filter = nullptr)
: MeshElementTypeMapArrayInitializer(
mesh,
[nb_component](ElementType /*unused*/, GhostType /*unused*/)
-> UInt { return nb_component; },
spatial_dimension, ghost_type, element_kind, with_nb_element,
with_nb_nodes_per_element, filter) {}
MeshElementTypeMapArrayInitializer(
const Mesh & mesh, const CompFunc & comp_func,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined, bool with_nb_element = false,
bool with_nb_nodes_per_element = false,
const ElementTypeMapArray<UInt> * filter = nullptr)
: ElementTypeMapArrayInitializer(comp_func, spatial_dimension, ghost_type,
element_kind),
mesh(mesh), with_nb_element(with_nb_element),
with_nb_nodes_per_element(with_nb_nodes_per_element), filter(filter) {}
decltype(auto) elementTypes() const {
if (filter) {
return filter->elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind);
}
return mesh.elementTypes(this->spatial_dimension, this->ghost_type,
this->element_kind);
}
virtual UInt size(ElementType type) const {
if (with_nb_element) {
if (filter) {
return (*filter)(type, this->ghost_type).size();
}
return mesh.getNbElement(type, this->ghost_type);
}
return 0;
}
UInt nbComponent(ElementType type) const override {
UInt res = ElementTypeMapArrayInitializer::nbComponent(type);
if (with_nb_nodes_per_element) {
return (res * Mesh::getNbNodesPerElement(type));
}
return res;
}
bool isNodal() const override { return with_nb_nodes_per_element; }
protected:
const Mesh & mesh;
bool with_nb_element{false};
bool with_nb_nodes_per_element{false};
const ElementTypeMapArray<UInt> * filter{nullptr};
};
/* -------------------------------------------------------------------------- */
class FEEngineElementTypeMapArrayInitializer
: public MeshElementTypeMapArrayInitializer {
public:
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine, UInt nb_component = 1,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
FEEngineElementTypeMapArrayInitializer(
const FEEngine & fe_engine,
const ElementTypeMapArrayInitializer::CompFunc & nb_component,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined);
UInt size(ElementType type) const override;
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes() const;
protected:
const FEEngine & fe_engine;
};
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
template <class Func>
void ElementTypeMapArray<T, SupportType>::initialize(const Func & f,
const T & default_value,
bool do_not_default) {
this->is_nodal = f.isNodal();
auto ghost_type = f.ghostType();
for (auto & type : f.elementTypes()) {
if (not this->exists(type, ghost_type)) {
if (do_not_default) {
auto & array = this->alloc(0, f.nbComponent(type), type, ghost_type);
array.resize(f.size(type));
} else {
this->alloc(f.size(type), f.nbComponent(type), type, ghost_type,
default_value);
}
} else {
auto & array = this->operator()(type, ghost_type);
if (not do_not_default) {
array.resize(f.size(type), default_value);
} else {
array.resize(f.size(type));
}
}
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _with_nb_element allocate the arrays with the number of elements for
* each
* type in the mesh
* \param _with_nb_nodes_per_element multiply the number of components by the
* number of nodes per element
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a type of ghost
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const Mesh & mesh,
pack &&... _pack) {
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types =
OPTIONAL_NAMED_ARG(all_ghost_types, requested_ghost_type == _casper);
for (GhostType ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
}
auto functor = MeshElementTypeMapArrayInitializer(
mesh, OPTIONAL_NAMED_ARG(nb_component, 1),
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension()),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined),
OPTIONAL_NAMED_ARG(with_nb_element, false),
OPTIONAL_NAMED_ARG(with_nb_nodes_per_element, false),
OPTIONAL_NAMED_ARG(element_filter, nullptr));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
/**
* All parameters are named optionals
* \param _nb_component a functor giving the number of components per
* (ElementType, GhostType) pair or a scalar giving a unique number of
* components
* regardless of type
* \param _spatial_dimension a filter for the elements of a specific dimension
* \param _element_kind filter with element kind (_ek_regular, _ek_structural,
* ...)
* \param _default_value default inital value
* \param _do_not_default do not initialize the allocated arrays
* \param _ghost_type filter a specific ghost type
* \param _all_ghost_types get all ghost types
*/
template <typename T, typename SupportType>
template <typename... pack>
void ElementTypeMapArray<T, SupportType>::initialize(const FEEngine & fe_engine,
pack &&... _pack) {
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types =
OPTIONAL_NAMED_ARG(all_ghost_types, requested_ghost_type == _casper);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
}
auto functor = FEEngineElementTypeMapArrayInitializer(
fe_engine, OPTIONAL_NAMED_ARG(nb_component, 1),
OPTIONAL_NAMED_ARG(spatial_dimension, UInt(-2)), ghost_type,
OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined));
this->initialize(functor, OPTIONAL_NAMED_ARG(default_value, T()),
OPTIONAL_NAMED_ARG(do_not_default, false));
}
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline T &
ElementTypeMapArray<T, SupportType>::operator()(const Element & element,
UInt component) {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline const T &
ElementTypeMapArray<T, SupportType>::operator()(const Element & element,
UInt component) const {
return this->operator()(element.type, element.ghost_type)(element.element,
component);
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline decltype(auto)
ElementTypeMapArray<T, SupportType>::get(const Element & element) {
auto & array = operator()(element.type, element.ghost_type);
auto it = array.begin(array.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
inline decltype(auto)
ElementTypeMapArray<T, SupportType>::get(const Element & element) const {
auto & array = operator()(element.type, element.ghost_type);
auto it = array.begin(array.getNbComponent());
return it[element.element];
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
UInt ElementTypeMapArray<T, SupportType>::sizeImpl(UInt spatial_dimension,
GhostType ghost_type,
ElementKind kind) const {
UInt size = 0;
for (auto && type : this->elementTypes(spatial_dimension, ghost_type, kind)) {
size += this->operator()(type, ghost_type).size();
}
return size;
}
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType>
template <typename... pack>
UInt ElementTypeMapArray<T, SupportType>::size(pack &&... _pack) const {
UInt size = 0;
GhostType requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
bool all_ghost_types =
OPTIONAL_NAMED_ARG(all_ghost_types, requested_ghost_type == _casper);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
}
size +=
sizeImpl(OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
ghost_type, OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined));
}
return size;
}
} // namespace akantu
#endif /* AKANTU_ELEMENT_TYPE_MAP_TMPL_HH_ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index c10def800..d2d9984be 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1033 +1,1035 @@
/**
* @file group_manager.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Nov 12 2020
*
* @brief Stores information about ElementGroup and NodeGroup
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
#include "aka_csr.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
#include <utility>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GroupManager::GroupManager(Mesh & mesh, const ID & id)
: id(id), mesh(mesh) {
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
GroupManager::~GroupManager() = default;
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = node_groups.find(group_name);
if (it != node_groups.end()) {
if (replace_group) {
it->second.reset();
} else {
AKANTU_EXCEPTION(
"Trying to create a node group that already exists:" << group_name);
}
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_node_group";
auto && ptr =
std::make_unique<NodeGroup>(group_name, mesh, sstr.str());
auto & node_group = *ptr;
// \todo insert_or_assign in c++17
if (it != node_groups.end()) {
it->second = std::move(ptr);
} else {
node_groups[group_name] = std::move(ptr);
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
NodeGroup &
GroupManager::createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & source_node_group,
T & filter) {
AKANTU_DEBUG_IN();
NodeGroup & node_group = this->createNodeGroup(group_name);
node_group.append(source_node_group);
if (T::type == FilterFunctor::_node_filter_functor) {
node_group.applyNodeFilter(filter);
} else {
AKANTU_ERROR("ElementFilter cannot be applied to NodeGroup yet."
<< " Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = element_groups.find(group_name);
if (it != element_groups.end()) {
if (replace_group) {
it->second.reset();
} else {
AKANTU_EXCEPTION("Trying to create a element group that already exists:"
<< group_name);
}
}
NodeGroup & new_node_group =
createNodeGroup(group_name + "_nodes", replace_group);
auto && ptr = std::make_unique<ElementGroup>(
group_name, mesh, new_node_group, dimension,
this->id + ":" + group_name + "_element_group");
auto & element_group = *ptr;
if (it != element_groups.end()) {
it->second = std::move(ptr);
} else {
element_groups[group_name] = std::move(ptr);
}
AKANTU_DEBUG_OUT();
return element_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyElementGroup(const std::string & group_name,
bool destroy_node_group) {
AKANTU_DEBUG_IN();
auto eit = element_groups.find(group_name);
if (eit != element_groups.end()) {
if (destroy_node_group) {
destroyNodeGroup(eit->second->getNodeGroup().getName());
}
element_groups.erase(eit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyNodeGroup(const std::string & group_name) {
AKANTU_DEBUG_IN();
auto nit = node_groups.find(group_name);
if (nit != node_groups.end()) {
node_groups.erase(nit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
NodeGroup & node_group) {
AKANTU_DEBUG_IN();
if (element_groups.find(group_name) != element_groups.end()) {
AKANTU_EXCEPTION(
"Trying to create a element group that already exists:" << group_name);
}
auto && ptr = std::make_unique<ElementGroup>(
group_name, mesh, node_group, dimension,
id + ":" + group_name + "_element_group");
auto & element_group = *ptr;
element_groups[group_name] = std::move(ptr);
AKANTU_DEBUG_OUT();
return element_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementGroup & GroupManager::createFilteredElementGroup(
const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter) {
AKANTU_DEBUG_IN();
if (T::type == FilterFunctor::_node_filter_functor) {
auto & filtered_node_group = this->createFilteredNodeGroup(
group_name + "_nodes", node_group, filter);
AKANTU_DEBUG_OUT();
return this->createElementGroup(group_name, dimension, filtered_node_group);
}
if (T::type == FilterFunctor::_element_filter_functor) {
AKANTU_ERROR(
"Cannot handle an ElementFilter yet. Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class ClusterSynchronizer : public DataAccessor<Element> {
using DistantIDs = std::set<std::pair<UInt, UInt>>;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
const ElementSynchronizer & element_synchronizer,
UInt nb_cluster)
: group_manager(group_manager), element_dimension(element_dimension),
cluster_name_prefix(std::move(cluster_name_prefix)),
element_to_fragment(element_to_fragment),
element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}
UInt synchronize() {
Communicator & comm = Communicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
UInt nb_proc = comm.getNbProc();
/// find starting index to renumber local clusters
Array<UInt> nb_cluster_per_proc(nb_proc);
nb_cluster_per_proc(rank) = nb_cluster;
comm.allGather(nb_cluster_per_proc);
starting_index = std::accumulate(nb_cluster_per_proc.begin(),
nb_cluster_per_proc.begin() + rank, 0U);
UInt global_nb_fragment =
std::accumulate(nb_cluster_per_proc.begin() + rank,
nb_cluster_per_proc.end(), starting_index);
/// create the local to distant cluster pairs with neighbors
element_synchronizer.synchronizeOnce(*this,
SynchronizationTag::_gm_clusters);
/// count total number of pairs
Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
// 2**31 pairs, but due to a all gatherv after
// it must be int to match MPI interfaces
nb_pairs(rank) = distant_ids.size();
comm.allGather(nb_pairs);
UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);
/// generate pairs global array
UInt local_pair_index =
std::accumulate(nb_pairs.storage(), nb_pairs.storage() + rank, 0);
Array<UInt> total_pairs(total_nb_pairs, 2);
for (const auto & ids : distant_ids) {
total_pairs(local_pair_index, 0) = ids.first;
total_pairs(local_pair_index, 1) = ids.second;
++local_pair_index;
}
/// communicate pairs to all processors
nb_pairs *= 2;
comm.allGatherV(total_pairs, nb_pairs);
/// renumber clusters
/// generate fragment list
std::vector<std::set<UInt>> global_clusters;
UInt total_nb_cluster = 0;
Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
std::queue<UInt> fragment_check_list;
while (not total_pairs.empty()) {
/// create a new cluster
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];
UInt first_fragment = total_pairs(0, 0);
UInt second_fragment = total_pairs(0, 1);
total_pairs.erase(0);
fragment_check_list.push(first_fragment);
fragment_check_list.push(second_fragment);
while (!fragment_check_list.empty()) {
UInt current_fragment = fragment_check_list.front();
UInt * total_pairs_end = total_pairs.storage() + total_pairs.size() * 2;
UInt * fragment_found =
std::find(total_pairs.storage(), total_pairs_end, current_fragment);
if (fragment_found != total_pairs_end) {
UInt position = fragment_found - total_pairs.storage();
UInt pair = position / 2;
UInt other_index = (position + 1) % 2;
fragment_check_list.push(total_pairs(pair, other_index));
total_pairs.erase(pair);
} else {
fragment_check_list.pop();
current_cluster.insert(current_fragment);
is_fragment_in_cluster(current_fragment) = true;
}
}
}
/// add to FragmentToCluster all local fragments
for (UInt c = 0; c < global_nb_fragment; ++c) {
if (!is_fragment_in_cluster(c)) {
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster =
global_clusters[total_nb_cluster - 1];
current_cluster.insert(c);
}
}
/// reorganize element groups to match global clusters
for (UInt c = 0; c < global_clusters.size(); ++c) {
/// create new element group corresponding to current cluster
std::stringstream sstr;
sstr << cluster_name_prefix << "_" << c;
ElementGroup & cluster =
group_manager.createElementGroup(sstr.str(), element_dimension, true);
auto it = global_clusters[c].begin();
auto end = global_clusters[c].end();
/// append to current element group all fragments that belong to
/// the same cluster if they exist
for (; it != end; ++it) {
Int local_index = *it - starting_index;
if (local_index < 0 || local_index >= Int(nb_cluster)) {
continue;
}
std::stringstream tmp_sstr;
tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
AKANTU_DEBUG_ASSERT(group_manager.elementGroupExists(tmp_sstr.str()),
"Temporary fragment \"" << tmp_sstr.str()
<< "\" not found");
cluster.append(group_manager.getElementGroup(tmp_sstr.str()));
group_manager.destroyElementGroup(tmp_sstr.str(), true);
}
}
return total_nb_cluster;
}
private:
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_gm_clusters) {
return elements.size() * sizeof(UInt);
}
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag != SynchronizationTag::_gm_clusters) {
return;
}
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
/// for each element pack its global cluster index
buffer << element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
}
}
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag != SynchronizationTag::_gm_clusters) {
return;
}
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
UInt distant_cluster;
buffer >> distant_cluster;
const Element & el = *el_it;
UInt local_cluster =
element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
}
}
private:
GroupManager & group_manager;
UInt element_dimension;
std::string cluster_name_prefix;
ElementTypeMapArray<UInt> & element_to_fragment;
const ElementSynchronizer & element_synchronizer;
UInt nb_cluster;
DistantIDs distant_ids;
UInt starting_index;
};
/* -------------------------------------------------------------------------- */
/// \todo this function doesn't work in 1D
UInt GroupManager::createBoundaryGroupFromGeometry() {
UInt spatial_dimension = mesh.getSpatialDimension();
return createClusters(spatial_dimension - 1, "boundary");
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, Mesh & mesh_facets,
const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
return createClusters(element_dimension, cluster_name_prefix, filter,
mesh_facets);
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
MeshAccessor mesh_accessor(mesh);
auto mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
mesh_accessor.getNodesSharedPtr(),
"mesh_facets_for_clusters");
mesh_facets->defineMeshParent(mesh);
MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
element_dimension - 1);
return createClusters(element_dimension, cluster_name_prefix, filter,
*mesh_facets);
}
/* -------------------------------------------------------------------------- */
//// \todo if needed element list construction can be optimized by
//// templating the filter class
UInt GroupManager::createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const GroupManager::ClusteringFilter & filter,
Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = mesh.getCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = nullptr;
if (nb_proc > 1 && mesh.isDistributed()) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id);
element_to_fragment->initialize(
mesh, _nb_component = 1, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined, _with_nb_element = true);
// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
// false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
ElementTypeMapArray<bool> seen_elements("seen_elements", id);
seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true);
// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
// _ek_not_defined, true);
for (auto ghost_type : ghost_types) {
Element el;
el.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(_spatial_dimension = element_dimension,
_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
el.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<bool> & seen_elements_array = seen_elements(type, ghost_type);
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
if (!filter(el)) {
seen_elements_array(e) = true;
}
}
}
}
Array<bool> checked_node(mesh.getNbNodes(), 1, false);
UInt nb_cluster = 0;
for (auto ghost_type : ghost_types) {
Element uns_el;
uns_el.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(_spatial_dimension = element_dimension,
_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
uns_el.type = type;
Array<bool> & seen_elements_vec =
seen_elements(uns_el.type, uns_el.ghost_type);
for (UInt e = 0; e < seen_elements_vec.size(); ++e) {
// skip elements that have been already seen
if (seen_elements_vec(e)) {
continue;
}
// set current element
uns_el.element = e;
seen_elements_vec(e) = true;
/// create a new cluster
std::stringstream sstr;
sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
ElementGroup & cluster =
createElementGroup(sstr.str(), element_dimension, true);
++nb_cluster;
// point element are cluster by themself
if (element_dimension == 0) {
cluster.add(uns_el);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
Vector<UInt> connect =
mesh.getConnectivity(uns_el.type, uns_el.ghost_type)
.begin(nb_nodes_per_element)[uns_el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node);
checked_node(node) = true;
}
}
continue;
}
std::queue<Element> element_to_add;
element_to_add.push(uns_el);
/// keep looping until current cluster is complete (no more
/// connected elements)
while (!element_to_add.empty()) {
/// take first element and erase it in the queue
Element el = element_to_add.front();
element_to_add.pop();
/// if parallel, store cluster index per element
if (nb_proc > 1 && mesh.isDistributed()) {
(*element_to_fragment)(el.type, el.ghost_type)(el.element) =
nb_cluster - 1;
}
/// add current element to the cluster
cluster.add(el);
const Array<Element> & element_to_facet =
mesh_facets.getSubelementToElement(el.type, el.ghost_type);
UInt nb_facet_per_element = element_to_facet.getNbComponent();
for (UInt f = 0; f < nb_facet_per_element; ++f) {
const Element & facet = element_to_facet(el.element, f);
if (facet == ElementNull) {
continue;
}
const std::vector<Element> & connected_elements =
mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
const Element & check_el = connected_elements[elem];
// check if this element has to be skipped
if (check_el == ElementNull || check_el == el) {
continue;
}
Array<bool> & seen_elements_vec_current =
seen_elements(check_el.type, check_el.ghost_type);
if (not seen_elements_vec_current(check_el.element)) {
seen_elements_vec_current(check_el.element) = true;
element_to_add.push(check_el);
}
}
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Vector<UInt> connect = mesh.getConnectivity(el.type, el.ghost_type)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node, false);
checked_node(node) = true;
}
}
}
}
}
}
if (nb_proc > 1 && mesh.isDistributed()) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
this->mesh.getElementSynchronizer(), nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
if (mesh.isDistributed()) {
this->synchronizeGroupNames();
}
AKANTU_DEBUG_OUT();
return nb_cluster;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
std::set<std::string> group_names;
const auto & datas = mesh.getData<T>(dataset_name);
std::map<std::string, UInt> group_dim;
for (auto ghost_type : ghost_types) {
for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
const Array<T> & dataset = datas(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements ("
<< type << ":" << ghost_type
<< ") in the map from MeshData ("
<< dataset.size() << ") " << dataset_name
<< " and in the mesh (" << nb_element << ")!");
for (UInt e(0); e < nb_element; ++e) {
std::stringstream sstr;
sstr << dataset(e);
std::string gname = sstr.str();
group_names.insert(gname);
auto it = group_dim.find(gname);
if (it == group_dim.end()) {
group_dim[gname] = mesh.getSpatialDimension(type);
} else {
it->second = std::max(it->second, mesh.getSpatialDimension(type));
}
}
}
}
for (auto && name : group_names) {
createElementGroup(name, group_dim[name]);
}
if (mesh.isDistributed()) {
this->synchronizeGroupNames();
}
Element el;
for (auto ghost_type : ghost_types) {
el.ghost_type = ghost_type;
for (auto type : datas.elementTypes(_ghost_type = ghost_type)) {
el.type = type;
const Array<T> & dataset = datas(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements in the map from "
"MeshData and in the mesh!");
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);
Array<UInt>::const_iterator<Vector<UInt>> cit =
mesh.getConnectivity(type, ghost_type).begin(nb_nodes_per_element);
for (UInt e(0); e < nb_element; ++e, ++cit) {
el.element = e;
std::stringstream sstr;
sstr << dataset(e);
ElementGroup & group = getElementGroup(sstr.str());
group.add(el, false, false);
const Vector<UInt> & connect = *cit;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
group.addNode(node, false);
}
}
}
}
for (auto && name : group_names) {
getElementGroup(name).optimize();
}
}
template void GroupManager::createGroupsFromMeshData<std::string>(
const std::string & dataset_name);
template void
GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);
/* -------------------------------------------------------------------------- */
void GroupManager::createElementGroupFromNodeGroup(
const std::string & name, const std::string & node_group_name,
UInt dimension) {
NodeGroup & node_group = getNodeGroup(node_group_name);
ElementGroup & group = createElementGroup(name, dimension, node_group);
group.fillFromNodeGroup();
}
/* -------------------------------------------------------------------------- */
void GroupManager::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "GroupManager [" << std::endl;
std::set<std::string> node_group_seen;
for (auto & group : iterateElementGroups()) {
group.printself(stream, indent + 1);
node_group_seen.insert(group.getNodeGroup().getName());
}
for (auto & group : iterateNodeGroups()) {
if (node_group_seen.find(group.getName()) == node_group_seen.end()) {
group.printself(stream, indent + 1);
}
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::getNbElementGroups(UInt dimension) const {
if (dimension == _all_dimensions) {
return element_groups.size();
}
return std::count_if(
element_groups.begin(), element_groups.end(),
[dimension](auto && eg) { return eg.second->getDimension() == dimension; });
}
/* -------------------------------------------------------------------------- */
void GroupManager::checkAndAddGroups(DynamicCommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
UInt nb_node_group;
buffer >> nb_node_group;
AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");
for (UInt ng = 0; ng < nb_node_group; ++ng) {
std::string node_group_name;
buffer >> node_group_name;
if (node_groups.find(node_group_name) == node_groups.end()) {
this->createNodeGroup(node_group_name);
}
AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
}
UInt nb_element_group;
buffer >> nb_element_group;
AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
for (UInt eg = 0; eg < nb_element_group; ++eg) {
std::string element_group_name;
buffer >> element_group_name;
std::string node_group_name;
buffer >> node_group_name;
UInt dim;
buffer >> dim;
AKANTU_DEBUG_INFO("Received element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with node group "
<< node_group_name);
NodeGroup & node_group = *node_groups[node_group_name];
if (element_groups.find(element_group_name) == element_groups.end()) {
this->createElementGroup(element_group_name, dim, node_group);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::fillBufferWithGroupNames(
DynamicCommunicationBuffer & comm_buffer) const {
AKANTU_DEBUG_IN();
// packing node group names;
UInt nb_groups = this->node_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");
auto nnames_it = node_groups.begin();
auto nnames_end = node_groups.end();
for (; nnames_it != nnames_end; ++nnames_it) {
std::string node_group_name = nnames_it->first;
comm_buffer << node_group_name;
AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
}
// packing element group names with there associated node group name
nb_groups = this->element_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
auto gnames_it = this->element_groups.begin();
auto gnames_end = this->element_groups.end();
for (; gnames_it != gnames_end; ++gnames_it) {
ElementGroup & element_group = *(gnames_it->second);
std::string element_group_name = gnames_it->first;
std::string node_group_name = element_group.getNodeGroup().getName();
UInt dim = element_group.getDimension();
comm_buffer << element_group_name;
comm_buffer << node_group_name;
comm_buffer << dim;
AKANTU_DEBUG_INFO("Sending element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with the node group "
<< node_group_name);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::synchronizeGroupNames() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
Int my_rank = comm.whoAmI();
if (nb_proc == 1) {
return;
}
if (my_rank == 0) {
for (Int p = 1; p < nb_proc; ++p) {
DynamicCommunicationBuffer recv_buffer;
auto tag = Tag::genTag(p, 0, Tag::_element_group);
comm.receive(recv_buffer, p, tag);
AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(recv_buffer.size())
<< " from proc " << p << " " << tag);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
comm.broadcast(comm_buffer);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
auto tag = Tag::genTag(my_rank, 0, Tag::_element_group);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
<< " to proc " << 0 << " " << tag);
comm.send(comm_buffer, 0, tag);
DynamicCommunicationBuffer recv_buffer;
comm.broadcast(recv_buffer);
AKANTU_DEBUG_INFO("Receiving broadcast with "
<< printMemorySize<char>(recv_buffer.size()));
this->checkAndAddGroups(recv_buffer);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const ElementGroup &
GroupManager::getElementGroup(const std::string & name) const {
auto it = element_groups.find(name);
if (it == element_groups.end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::getElementGroup(const std::string & name) {
auto it = element_groups.find(name);
if (it == element_groups.end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
auto it = node_groups.find(name);
if (it == node_groups.end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
auto it = node_groups.find(name);
if (it == node_groups.end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
template <typename GroupsType>
void GroupManager::renameGroup(GroupsType & groups, const std::string & name,
const std::string & new_name) {
auto it = groups.find(name);
if (it == groups.end()) {
AKANTU_EXCEPTION("There are no group named "
<< name << " associated to the group manager: " << id);
}
auto && group_ptr = std::move(it->second);
group_ptr->name = new_name;
groups.erase(it);
groups[new_name] = std::move(group_ptr);
}
/* -------------------------------------------------------------------------- */
void GroupManager::renameElementGroup(const std::string & name,
const std::string & new_name) {
renameGroup(element_groups, name, new_name);
}
/* -------------------------------------------------------------------------- */
void GroupManager::renameNodeGroup(const std::string & name,
const std::string & new_name) {
renameGroup(node_groups, name, new_name);
}
/* -------------------------------------------------------------------------- */
void GroupManager::copyElementGroup(const std::string & name,
const std::string & new_name) {
const auto & grp = getElementGroup(name);
auto & new_grp = createElementGroup(new_name, grp.getDimension());
new_grp.getElements().copy(grp.getElements());
}
/* -------------------------------------------------------------------------- */
void GroupManager::copyNodeGroup(const std::string & name,
const std::string & new_name) {
const auto & grp = getNodeGroup(name);
auto & new_grp = createNodeGroup(new_name);
new_grp.getNodes().copy(grp.getNodes());
}
} // namespace akantu
diff --git a/src/mesh/group_manager.hh b/src/mesh/group_manager.hh
index 43da4e554..4cd70f563 100644
--- a/src/mesh/group_manager.hh
+++ b/src/mesh/group_manager.hh
@@ -1,348 +1,350 @@
/**
* @file group_manager.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Feb 07 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Stores information relevent to the notion of element and nodes
* groups.
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GROUP_MANAGER_HH_
#define AKANTU_GROUP_MANAGER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_iterators.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementGroup;
class NodeGroup;
class Mesh;
class Element;
class ElementSynchronizer;
template <bool> class CommunicationBufferTemplated;
namespace dumpers {
class Field;
}
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
class GroupManager {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using ElementGroups = std::map<std::string, std::unique_ptr<ElementGroup>>;
using NodeGroups = std::map<std::string, std::unique_ptr<NodeGroup>>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GroupManager(Mesh & mesh, const ID & id = "group_manager");
virtual ~GroupManager();
/* ------------------------------------------------------------------------ */
/* Groups iterators */
/* ------------------------------------------------------------------------ */
public:
using node_group_iterator = NodeGroups::iterator;
using element_group_iterator = ElementGroups::iterator;
using const_node_group_iterator = NodeGroups::const_iterator;
using const_element_group_iterator = ElementGroups::const_iterator;
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(group_type, function, \
param_in, param_out) \
[[deprecated( \
"use iterate(Element|Node)Groups or " \
"(element|node)GroupExists")]] inline BOOST_PP_CAT(BOOST_PP_CAT(const_, \
group_type), \
_iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) const { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}; \
\
[[deprecated("use iterate(Element|Node)Groups or " \
"(element|node)GroupExists")]] inline BOOST_PP_CAT(group_type, \
_iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(group_type, function) \
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION( \
group_type, function, BOOST_PP_EMPTY(), BOOST_PP_EMPTY())
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(element_group, find,
const std::string & name, name);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(node_group, find,
const std::string & name, name);
public:
decltype(auto) iterateNodeGroups() {
return make_dereference_adaptor(make_values_adaptor(node_groups));
}
decltype(auto) iterateNodeGroups() const {
return make_dereference_adaptor(make_values_adaptor(node_groups));
}
decltype(auto) iterateElementGroups() {
return make_dereference_adaptor(make_values_adaptor(element_groups));
}
decltype(auto) iterateElementGroups() const {
return make_dereference_adaptor(make_values_adaptor(element_groups));
}
/* ------------------------------------------------------------------------ */
/* Clustering filter */
/* ------------------------------------------------------------------------ */
public:
class ClusteringFilter {
public:
virtual bool operator()(const Element & /*unused*/) const { return true; }
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create an empty node group
NodeGroup & createNodeGroup(const std::string & group_name,
bool replace_group = false);
/// create an element group and the associated node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension = _all_dimensions,
bool replace_group = false);
/* ------------------------------------------------------------------------ */
/// renames an element group
void renameElementGroup(const std::string & name,
const std::string & new_name);
/// renames a node group
void renameNodeGroup(const std::string & name, const std::string & new_name);
/// copy an existing element group
void copyElementGroup(const std::string & name, const std::string & new_name);
/// copy an existing node group
void copyNodeGroup(const std::string & name, const std::string & new_name);
/* ------------------------------------------------------------------------ */
/// create a node group from another node group but filtered
template <typename T>
NodeGroup & createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & node_group, T & filter);
/// create an element group from another element group but filtered
template <typename T>
ElementGroup &
createFilteredElementGroup(const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter);
/// destroy a node group
void destroyNodeGroup(const std::string & group_name);
/// destroy an element group and the associated node group
void destroyElementGroup(const std::string & group_name,
bool destroy_node_group = false);
// /// destroy all element groups and the associated node groups
// void destroyAllElementGroups(bool destroy_node_groups = false);
/// create a element group using an existing node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension, NodeGroup & node_group);
/// create groups based on values stored in a given mesh data
template <typename T>
void createGroupsFromMeshData(const std::string & dataset_name);
/// create boundaries group by a clustering algorithm \todo extend to parallel
UInt createBoundaryGroupFromGeometry();
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension, Mesh & mesh_facets,
const std::string & cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
const std::string & cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter());
private:
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
const std::string & cluster_name_prefix,
const ClusteringFilter & filter, Mesh & mesh_facets);
public:
/// Create an ElementGroup based on a NodeGroup
void createElementGroupFromNodeGroup(const std::string & name,
const std::string & node_group,
UInt dimension = _all_dimensions);
virtual void printself(std::ostream & stream, int indent = 0) const;
/// this function insure that the group names are present on all processors
/// /!\ it is a SMP call
void synchronizeGroupNames();
/// register an elemental field to the given group name (overloading for
/// ElementalPartionField)
template <typename T, template <bool> class dump_type>
std::shared_ptr<dumpers::Field> createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// ElementalField)
template <typename T, template <class> class ret_type,
template <class, template <class> class, bool> class dump_type>
std::shared_ptr<dumpers::Field> createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// MaterialInternalField)
template <typename T,
/// type of InternalMaterialField
template <typename, bool filtered> class dump_type>
std::shared_ptr<dumpers::Field>
createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name, UInt spatial_dimension,
ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem);
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
createNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt padding_size = 0);
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size);
protected:
/// fill a buffer with all the group names
void fillBufferWithGroupNames(
CommunicationBufferTemplated<false> & comm_buffer) const;
/// take a buffer and create the missing groups localy
void checkAndAddGroups(CommunicationBufferTemplated<false> & buffer);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline std::shared_ptr<dumpers::Field>
createElementalField(const field_type & field, const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
const ElementTypeMap<UInt> & nb_data_per_elem);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline std::shared_ptr<dumpers::Field>
createElementalFilteredField(const field_type & field,
const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
// AKANTU_GET_MACRO(ElementGroups, element_groups, const ElementGroups &);
const ElementGroup & getElementGroup(const std::string & name) const;
const NodeGroup & getNodeGroup(const std::string & name) const;
ElementGroup & getElementGroup(const std::string & name);
NodeGroup & getNodeGroup(const std::string & name);
UInt getNbElementGroups(UInt dimension = _all_dimensions) const;
UInt getNbNodeGroups() { return node_groups.size(); };
bool elementGroupExists(const std::string & name) {
return element_groups.find(name) != element_groups.end();
}
bool nodeGroupExists(const std::string & name) {
return node_groups.find(name) != node_groups.end();
}
private:
template <typename GroupsType>
void renameGroup(GroupsType & groups, const std::string & name,
const std::string & new_name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id to create element and node groups
ID id;
/// list of the node groups managed
NodeGroups node_groups;
/// list of the element groups managed
ElementGroups element_groups;
/// Mesh to which the element belongs
Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const GroupManager & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_GROUP_MANAGER_HH_ */
diff --git a/src/mesh/group_manager_inline_impl.hh b/src/mesh/group_manager_inline_impl.hh
index 98f6af47a..32942bc13 100644
--- a/src/mesh/group_manager_inline_impl.hh
+++ b/src/mesh/group_manager_inline_impl.hh
@@ -1,196 +1,198 @@
/**
* @file group_manager_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Tue Mar 03 2020
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "element_group.hh"
#include "element_type_map_filter.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <bool> class dump_type>
std::shared_ptr<dumpers::Field>
GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr) {
return nullptr;
}
if (group_name == "all") {
return this->createElementalField<dump_type<false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
return this->createElementalFilteredField<dump_type<true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class T2,
template <class, template <class> class, bool> class dump_type>
std::shared_ptr<dumpers::Field>
GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr) {
return nullptr;
}
if (group_name == "all") {
return this->createElementalField<dump_type<T, T2, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
return this->createElementalFilteredField<dump_type<T, T2, true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename T2, bool filtered>
class dump_type> ///< type of InternalMaterialField
std::shared_ptr<dumpers::Field>
GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
if (field_ptr == nullptr) {
return nullptr;
}
if (group_name == "all") {
return this->createElementalField<dump_type<T, false>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
return this->createElementalFilteredField<dump_type<T, true>>(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
std::shared_ptr<dumpers::Field> GroupManager::createElementalField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
const ElementTypeMap<UInt> & nb_data_per_elem) {
const field_type * field_ptr = &field;
if (field_ptr == nullptr) {
return nullptr;
}
if (group_name != "all") {
throw;
}
auto dumper =
std::make_shared<dump_type>(field, spatial_dimension, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
std::shared_ptr<dumpers::Field> GroupManager::createElementalFilteredField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, ElementKind kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const field_type * field_ptr = &field;
if (field_ptr == nullptr) {
return nullptr;
}
if (group_name == "all") {
throw;
}
using T = typename field_type::value_type;
ElementGroup & group = this->getElementGroup(group_name);
UInt dim = group.getDimension();
if (dim != spatial_dimension) {
throw;
}
const ElementTypeMapArray<UInt> & elemental_filter = group.getElements();
auto * filtered = new ElementTypeMapArrayFilter<T>(field, elemental_filter,
nb_data_per_elem);
auto dumper = std::make_shared<dump_type>(*filtered, dim, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
GroupManager::createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size) {
return createStridedNodalField(field, group_name, 0, 0, padding_size);
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
std::shared_ptr<dumpers::Field>
GroupManager::createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size) {
if (not field) {
return nullptr;
}
if (group_name == "all") {
using DumpType = typename dumpers::NodalField<type, false>;
auto dumper = std::make_shared<DumpType>(*field, size, stride);
dumper->setPadding(padding_size);
return dumper;
}
ElementGroup & group = this->getElementGroup(group_name);
const Array<UInt> * nodal_filter = &(group.getNodeGroup().getNodes());
using DumpType = typename dumpers::NodalField<type, true>;
auto dumper = std::make_shared<DumpType>(*field, size, stride, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif
diff --git a/src/mesh/mesh.cc b/src/mesh/mesh.cc
index bb2c6741f..c450603d1 100644
--- a/src/mesh/mesh.cc
+++ b/src/mesh/mesh.cc
@@ -1,658 +1,661 @@
/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 09 2021
*
* @brief class handling meshes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.hh"
#include "mesh.hh"
#include "mesh_global_data_updater.hh"
#include "mesh_io.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, Communicator & communicator)
: GroupManager(*this, id + ":group_manager"), MeshData("mesh_data", id),
id(id), connectivities("connectivities", id),
ghosts_counters("ghosts_counters", id), normals("normals", id),
spatial_dimension(spatial_dimension), size(spatial_dimension, 0.),
bbox(spatial_dimension), bbox_local(spatial_dimension),
communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Communicator & communicator, const ID & id)
: Mesh(spatial_dimension, id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
this->nodes_flags = std::make_shared<Array<NodeFlag>>(0, 1, NodeFlag::_normal,
id + ":nodes_flags");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id)
: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id)
: Mesh(spatial_dimension, id, Communicator::getStaticCommunicator()) {
this->nodes = nodes;
this->nb_global_nodes = this->nodes->size();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getBarycenters(Array<Real> & barycenter, ElementType type,
GhostType ghost_type) const {
barycenter.resize(getNbElement(type, ghost_type));
for (auto && data : enumerate(make_view(barycenter, spatial_dimension))) {
getBarycenter(Element{type, UInt(std::get<0>(data)), ghost_type},
std::get<1>(data));
}
}
class FacetGlobalConnectivityAccessor : public DataAccessor<Element> {
public:
FacetGlobalConnectivityAccessor(Mesh & mesh)
: global_connectivity("global_connectivity",
"facet_connectivity_synchronizer") {
global_connectivity.initialize(
mesh, _spatial_dimension = _all_dimensions, _with_nb_element = true,
_with_nb_nodes_per_element = true, _element_kind = _ek_regular);
mesh.getGlobalConnectivity(global_connectivity);
}
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
UInt size = 0;
if (tag == SynchronizationTag::_smmc_facets_conn) {
UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
size += nb_nodes * sizeof(UInt);
}
return size;
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
const auto & conns =
global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer << conns(element.element, n);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_smmc_facets_conn) {
for (const auto & element : elements) {
auto & conns = global_connectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer >> conns(element.element, n);
}
}
}
}
AKANTU_GET_MACRO(GlobalConnectivity, (global_connectivity), decltype(auto));
protected:
ElementTypeMapArray<UInt> global_connectivity;
};
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (mesh_facets) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
getID() + ":" + id);
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
mesh_facets->nodes_flags = this->nodes_flags;
mesh_facets->nodes_global_ids = this->nodes_global_ids;
MeshUtils::buildAllFacets(*this, *mesh_facets, 0);
if (mesh.isDistributed()) {
mesh_facets->is_distributed = true;
mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
*mesh_facets, mesh.getElementSynchronizer());
FacetGlobalConnectivityAccessor data_accessor(*mesh_facets);
/// communicate
mesh_facets->element_synchronizer->synchronizeOnce(
data_accessor, SynchronizationTag::_smmc_facets_conn);
/// flip facets
MeshUtils::flipFacets(*mesh_facets, data_accessor.getGlobalConnectivity(),
_ghost);
}
/// transfers the the mesh physical names to the mesh facets
if (not this->hasData("physical_names")) {
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
auto & mesh_phys_data = this->getData<std::string>("physical_names");
auto & phys_data = mesh_facets->getData<std::string>("physical_names");
phys_data.initialize(*mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
ElementTypeMapArray<Real> barycenters(getID(), "temporary_barycenters");
barycenters.initialize(*mesh_facets, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
for (auto && ghost_type : ghost_types) {
for (auto && type :
barycenters.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh_facets->getBarycenters(barycenters(type, ghost_type), type,
ghost_type);
}
}
for_each_element(
mesh,
[&](auto && element) {
Vector<Real> barycenter(spatial_dimension);
mesh.getBarycenter(element, barycenter);
auto norm_barycenter = barycenter.norm();
auto tolerance = Math::getTolerance();
if (norm_barycenter > tolerance) {
tolerance *= norm_barycenter;
}
Vector<Real> barycenter_facet(spatial_dimension);
auto range = enumerate(make_view(
barycenters(element.type, element.ghost_type), spatial_dimension));
#ifndef AKANTU_NDEBUG
auto min_dist = std::numeric_limits<Real>::max();
#endif
// this is a spacial search coded the most inefficient way.
auto facet =
std::find_if(range.begin(), range.end(), [&](auto && data) {
auto norm_distance = barycenter.distance(std::get<1>(data));
#ifndef AKANTU_NDEBUG
min_dist = std::min(min_dist, norm_distance);
#endif
return (norm_distance < tolerance);
});
if (facet == range.end()) {
AKANTU_DEBUG_INFO("The element "
<< element
<< " did not find its associated facet in the "
"mesh_facets! Try to decrease math tolerance. "
"The closest element was at a distance of "
<< min_dist);
return;
}
// set physical name
auto && facet_element = Element{element.type, UInt(std::get<0>(*facet)),
element.ghost_type};
phys_data(facet_element) = mesh_phys_data(element);
},
_spatial_dimension = spatial_dimension - 1);
mesh_facets->createGroupsFromMeshData<std::string>("physical_names");
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
AKANTU_DEBUG_ASSERT(not is_distributed,
"You cannot read a mesh that is already distributed");
MeshIO::read(filename, *this, mesh_io_type);
auto types =
this->elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
auto it = types.begin();
auto last = types.end();
if (it == last) {
AKANTU_DEBUG_WARNING(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " were read.");
}
this->makeReady();
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO::write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::makeReady() {
this->nb_global_nodes = this->nodes->size();
this->computeBoundingBox();
this->nodes_flags->resize(nodes->size(), NodeFlag::_normal);
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
bbox_local.reset();
for (auto & pos : make_view(*nodes, spatial_dimension)) {
// if(!isPureGhostNode(i))
bbox_local += pos;
}
if (this->is_distributed) {
bbox = bbox_local.allSum(*communicator);
} else {
bbox = bbox_local;
}
size = bbox.size();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity) {
AKANTU_DEBUG_IN();
for (auto && ghost_type : ghost_types) {
for (auto type :
global_connectivity.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = ghost_type)) {
if (not connectivities.exists(type, ghost_type)) {
continue;
}
auto & local_conn = connectivities(type, ghost_type);
auto & g_connectivity = global_connectivity(type, ghost_type);
UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();
std::transform(local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[&](UInt l) -> UInt { return this->getNodeGlobalId(l); });
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
if (group_name == "all") {
return this->getDumper(dumper_name);
}
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays) {
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : arrays.elementTypes(_element_kind = _ek_not_defined)) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.size();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template <typename T>
std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem = this->getNbDataPerElem(*internal);
field = this->createElementalField<T, dumpers::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
template std::shared_ptr<dumpers::Field>
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distributeImpl(
Communicator & communicator,
const std::function<Int(const Element &, const Element &)> &
edge_weight_function [[gnu::unused]],
const std::function<Int(const Element &)> & vertex_weight_function
[[gnu::unused]]) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer = std::make_unique<ElementSynchronizer>(
*this, this->getID() + ":element_synchronizer", true);
this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", true);
Int psize = this->communicator->getNbProc();
if (psize > 1) {
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize, edge_weight_function,
vertex_weight_function);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (psize > 1) {
AKANTU_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
}
// if (psize > 1)
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) const {
for (const auto & node : node_list) {
for (const auto & element : *nodes_to_elements[node]) {
elements.push_back(element);
}
}
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const UInt & node,
Array<Element> & elements) const {
for (const auto & element : *nodes_to_elements[node]) {
elements.push_back(element);
}
}
/* -------------------------------------------------------------------------- */
void Mesh::fillNodesToElements(UInt dimension) {
Element e;
UInt nb_nodes = nodes->size();
this->nodes_to_elements.resize(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->nodes_to_elements[n]) {
this->nodes_to_elements[n]->clear();
} else {
this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
}
}
for (auto ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (const auto & type :
elementTypes(dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = this->getNbElement(type, ghost_type);
auto connectivity = connectivities(type, ghost_type);
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
const Vector<UInt> & conn = *conn_it;
for (auto node : conn) {
nodes_to_elements[node]->insert(e);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt>
Mesh::updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) {
if (global_data_updater) {
return this->global_data_updater->updateData(nodes_event, elements_event);
}
return std::make_tuple(nodes_event.getList().size(),
elements_event.getList().size());
}
/* -------------------------------------------------------------------------- */
void Mesh::registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
this->global_data_updater = std::move(global_data_updater);
}
/* -------------------------------------------------------------------------- */
void Mesh::eraseElements(const Array<Element> & elements) {
ElementTypeMap<UInt> last_element;
RemovedElementsEvent event(*this, "new_numbering", AKANTU_CURRENT_FUNCTION);
auto & remove_list = event.getList();
auto & new_numbering = event.getNewNumbering();
for (auto && el : elements) {
if (el.ghost_type != _not_ghost) {
auto & count = ghosts_counters(el);
--count;
if (count > 0) {
continue;
}
}
remove_list.push_back(el);
if (not new_numbering.exists(el.type, el.ghost_type)) {
auto nb_element = mesh.getNbElement(el.type, el.ghost_type);
auto & numbering =
new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
for (auto && pair : enumerate(numbering)) {
std::get<1>(pair) = std::get<0>(pair);
}
}
new_numbering(el) = UInt(-1);
}
auto find_last_not_deleted = [](auto && array, Int start) -> Int {
do {
--start;
} while (start >= 0 and array[start] == UInt(-1));
return start;
};
auto find_first_deleted = [](auto && array, Int start) -> Int {
auto begin = array.begin();
auto it = std::find_if(begin + start, array.end(),
[](auto & el) { return el == UInt(-1); });
return Int(it - begin);
};
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_ghost_type = ghost_type)) {
auto & numbering = new_numbering(type, ghost_type);
auto last_not_delete = find_last_not_deleted(numbering, numbering.size());
if (last_not_delete < 0) {
continue;
}
auto pos = find_first_deleted(numbering, 0);
while (pos < last_not_delete) {
std::swap(numbering[pos], numbering[last_not_delete]);
last_not_delete = find_last_not_deleted(numbering, last_not_delete);
pos = find_first_deleted(numbering, pos + 1);
}
}
}
this->sendEvent(event);
}
} // namespace akantu
diff --git a/src/mesh/mesh.hh b/src/mesh/mesh.hh
index 89e618daa..e2a5827de 100644
--- a/src/mesh/mesh.hh
+++ b/src/mesh/mesh.hh
@@ -1,699 +1,701 @@
/**
* @file mesh.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Thu Nov 12 2020
*
* @brief the class representing the meshes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_HH_
#define AKANTU_MESH_HH_
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_bbox.hh"
#include "aka_event_handler_manager.hh"
#include "communicator.hh"
#include "dumpable.hh"
#include "element.hh"
#include "element_class.hh"
#include "element_type_map.hh"
#include "group_manager.hh"
#include "mesh_data.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <set>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
class NodeSynchronizer;
class PeriodicNodeSynchronizer;
class MeshGlobalDataUpdater;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(communicator);
DECLARE_NAMED_ARGUMENT(edge_weight_function);
DECLARE_NAMED_ARGUMENT(vertex_weight_function);
} // namespace
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh mesh.hh
*
* This class contaisn the coordinates of the nodes in the Mesh.nodes
* akant::Array, and the connectivity. The connectivity are stored in by element
* types.
*
* In order to loop on all element you have to loop on all types like this :
* @code{.cpp}
for(auto & type : mesh.elementTypes()) {
UInt nb_element = mesh.getNbElement(type);
const Array<UInt> & conn = mesh.getConnectivity(type);
for(UInt e = 0; e < nb_element; ++e) {
...
}
}
or
for_each_element(mesh, [](Element & element) {
std::cout << element << std::endl
});
@endcode
*/
class Mesh : public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public MeshData,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(UInt spatial_dimension, const ID & id,
Communicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(UInt spatial_dimension, const ID & id = "mesh");
/// mesh not distributed and not using the default communicator
Mesh(UInt spatial_dimension, Communicator & communicator,
const ID & id = "mesh");
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
Mesh(UInt spatial_dimension, const std::shared_ptr<Array<Real>> & nodes,
const ID & id = "mesh");
~Mesh() override;
/// read the mesh from a file
void read(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
/// write the mesh to a file
void write(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
protected:
void makeReady();
private:
/// initialize the connectivity to NULL and other stuff
void init();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* Distributed memory methods and accessors */
/* ------------------------------------------------------------------------ */
public:
protected:
/// patitionate the mesh among the processors involved in their computation
virtual void distributeImpl(
Communicator & communicator,
const std::function<Int(const Element &, const Element &)> &
edge_weight_function,
const std::function<Int(const Element &)> & vertex_weight_function);
public:
/// with the arguments to pass to the partitionner
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
distribute(pack &&... _pack) {
distributeImpl(
OPTIONAL_NAMED_ARG(communicator, Communicator::getStaticCommunicator()),
OPTIONAL_NAMED_ARG(edge_weight_function,
[](auto &&, auto &&) { return 1; }),
OPTIONAL_NAMED_ARG(vertex_weight_function, [](auto &&) { return 1; }));
}
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
/* ------------------------------------------------------------------------ */
/* Periodicity methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the periodicity in a given direction
void makePeriodic(const SpatialDirection & direction);
void makePeriodic(const SpatialDirection & direction, const ID & list_1,
const ID & list_2);
protected:
void makePeriodic(const SpatialDirection & direction,
const Array<UInt> & list_left,
const Array<UInt> & list_right);
/// Removes the face that the mesh is periodic
void wipePeriodicInfo();
inline void addPeriodicSlave(UInt slave, UInt master);
template <typename T>
void synchronizePeriodicSlaveDataWithMaster(Array<T> & data);
// update the periodic synchronizer (creates it if it does not exists)
void updatePeriodicSynchronizer();
public:
/// defines if the mesh is periodic or not
inline bool isPeriodic() const { return this->is_periodic; }
inline bool isPeriodic(const SpatialDirection & /*direction*/) const {
return this->is_periodic;
}
class PeriodicSlaves;
/// get the master node for a given slave nodes, except if node not a slave
inline UInt getPeriodicMaster(UInt slave) const;
/// get an iterable list of slaves for a given master node
inline decltype(auto) getPeriodicSlaves(UInt master) const;
/* ------------------------------------------------------------------------ */
/* General Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// extract coordinates of nodes from an element
template <typename T>
inline void
extractNodalValuesFromElement(const Array<T> & nodal_values, T * local_coord,
const UInt * connectivity, UInt n_nodes,
UInt nb_degree_of_freedom) const;
// /// extract coordinates of nodes from a reversed element
// inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
// UInt * connectivity,
// UInt n_nodes);
/// add a Array of connectivity for the given ElementType and GhostType .
inline void addConnectivityType(ElementType type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().size() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/// prepare the event to remove the elements listed
void eraseElements(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering);
/// initialize normals
void initNormals();
/// init facets' mesh
Mesh & initMeshFacets(const ID & id = "mesh_facets");
/// define parent mesh
void defineMeshParent(const Mesh & mesh);
/// get global connectivity array
void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity);
public:
void getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) const;
void getAssociatedElements(const UInt & node,
Array<Element> & elements) const;
public:
/// fills the nodes_to_elements for given dimension elements
void fillNodesToElements(UInt dimension = _all_dimensions);
private:
/// update the global ids, nodes type, ...
std::tuple<UInt, UInt> updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event);
void registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
AKANTU_GET_MACRO(ID, id, const ID &);
/// get the spatial dimension of the mesh = number of component of the
/// coordinates
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the nodes Array aka coordinates
AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);
/// get the normals for the elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);
/// get the number of nodes
AKANTU_GET_MACRO(NbNodes, nodes->size(), UInt);
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Array<UInt> &);
// AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt>
// &);
/// get the global id of a node
inline UInt getNodeGlobalId(UInt local_id) const;
/// get the global id of a node
inline UInt getNodeLocalId(UInt global_id) const;
/// get the global number of nodes
inline UInt getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesFlags, *nodes_flags, const Array<NodeFlag> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesFlags, *nodes_flags, Array<NodeFlag> &);
public:
inline NodeFlag getNodeFlag(UInt local_id) const;
inline Int getNodePrank(UInt local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(UInt n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(UInt n) const;
inline bool isLocalNode(UInt n) const;
inline bool isMasterNode(UInt n) const;
inline bool isSlaveNode(UInt n) const;
inline bool isPeriodicSlave(UInt n) const;
inline bool isPeriodicMaster(UInt n) const;
const Vector<Real> & getLowerBounds() const { return bbox.getLowerBounds(); }
const Vector<Real> & getUpperBounds() const { return bbox.getUpperBounds(); }
AKANTU_GET_MACRO(BBox, bbox, const BBox &);
const Vector<Real> & getLocalLowerBounds() const {
return bbox_local.getLowerBounds();
}
const Vector<Real> & getLocalUpperBounds() const {
return bbox_local.getUpperBounds();
}
AKANTU_GET_MACRO(LocalBBox, bbox_local, const BBox &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<UInt> &);
/// get the number of element of a type in the mesh
inline UInt getNbElement(ElementType type,
GhostType ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
inline UInt getNbElement(UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/// compute the barycenter of a given element
inline void getBarycenter(const Element & element,
Vector<Real> & barycenter) const;
void getBarycenters(Array<Real> & barycenter, ElementType type,
GhostType ghost_type) const;
/// get the element connected to a subelement (element of lower dimension)
const auto & getElementToSubelement() const;
/// get the element connected to a subelement
const auto & getElementToSubelement(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get the elements connected to a subelement
const auto & getElementToSubelement(const Element & element) const;
/// get the subelement (element of lower dimension) connected to a element
const auto & getSubelementToElement() const;
/// get the subelement connected to an element
const auto &
getSubelementToElement(ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get the subelement (element of lower dimension) connected to a element
VectorProxy<Element> getSubelementToElement(const Element & element) const;
/// get connectivity of a given element
inline VectorProxy<UInt> getConnectivity(const Element & element) const;
inline Vector<UInt>
getConnectivityWithPeriodicity(const Element & element) const;
protected:
/// get the element connected to a subelement (element of lower dimension)
auto & getElementToSubelementNC();
auto & getSubelementToElementNC();
inline auto & getElementToSubelementNC(const Element & element);
inline VectorProxy<Element> getSubelementToElementNC(const Element & element);
/// get the element connected to a subelement
auto & getElementToSubelementNC(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// get the subelement connected to an element
auto & getSubelementToElementNC(ElementType el_type,
GhostType ghost_type = _not_ghost);
inline VectorProxy<UInt> getConnectivityNC(const Element & element);
public:
/// get a name field associated to the mesh
template <typename T>
inline const Array<T> & getData(const ID & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline Array<T> & getData(const ID & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost);
/// get a name field associated to the mesh
template <typename T>
inline const ElementTypeMapArray<T> & getData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline ElementTypeMapArray<T> & getData(const ID & data_name);
template <typename T>
ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array);
template <typename T>
std::shared_ptr<dumpers::Field>
createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
ElementKind element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
inline Array<T> &
getDataPointer(const std::string & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost, UInt nb_component = 1,
bool size_to_nb_element = true,
bool resize_with_parent = false);
template <typename T>
inline Array<T> & getDataPointer(const ID & data_name, ElementType el_type,
GhostType ghost_type, UInt nb_component,
bool size_to_nb_element,
bool resize_with_parent, const T & defaul_);
/// Facets mesh accessor
inline const Mesh & getMeshFacets() const;
inline Mesh & getMeshFacets();
inline auto hasMeshFacets() const { return mesh_facets != nullptr; }
/// Parent mesh accessor
inline const Mesh & getMeshParent() const;
inline bool isMeshFacets() const { return this->is_mesh_facets; }
/// return the dumper from a group and and a dumper name
DumperIOHelper & getGroupDumper(const std::string & dumper_name,
const std::string & group_name);
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
static inline UInt getNbNodesPerElement(ElementType type);
/// get the number of nodes per element for a given element type considered as
/// a first order element
static inline ElementType getP1ElementType(ElementType type);
/// get the kind of the element type
static inline ElementKind getKind(ElementType type);
/// get spatial dimension of a type of element
static inline UInt getSpatialDimension(ElementType type);
/// get the natural space dimension of a type of element
static inline UInt getNaturalSpaceDimension(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(ElementType type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(ElementType type, UInt t);
/// get local connectivity of a facet for a given facet type
static inline auto getFacetLocalConnectivity(ElementType type, UInt t = 0);
/// get connectivity of facets for a given element
inline auto getFacetConnectivity(const Element & element, UInt t = 0) const;
/// get the number of type of the surface element associated to a given
/// element type
static inline UInt getNbFacetTypes(ElementType type, UInt t = 0);
/// get the type of the surface element associated to a given element
static inline constexpr auto getFacetType(ElementType type, UInt t = 0);
/// get all the type of the surface element associated to a given element
static inline constexpr auto getAllFacetTypes(ElementType type);
/// get the number of nodes in the given element list
static inline UInt getNbNodesPerElementList(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
- using type_iterator [[deprecated]] =
+ using type_iterator =
ElementTypeMapArray<UInt, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
template <typename... pack>
ElementTypesIteratorHelper elementTypes(pack &&... _pack) const;
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
firstType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).begin();
}
[[deprecated("Use elementTypes instead")]] inline decltype(auto)
lastType(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.elementTypes(dim, ghost_type, kind).end();
}
AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
const ElementSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
NodeSynchronizer &);
AKANTU_GET_MACRO(PeriodicNodeSynchronizer, *periodic_node_synchronizer,
const PeriodicNodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(PeriodicNodeSynchronizer,
*periodic_node_synchronizer,
PeriodicNodeSynchronizer &);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
AKANTU_GET_MACRO(Communicator, *communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, auto &);
AKANTU_GET_MACRO(PeriodicMasterSlaves, periodic_master_slave, const auto &);
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
friend class MeshUtils;
AKANTU_GET_MACRO(NodesPointer, *nodes, Array<Real> &);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIdsPointer();
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeFlag> & getNodesFlagsPointer();
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
getConnectivityPointer(ElementType type, GhostType ghost_type = _not_ghost);
/// get the ghost element counter
inline Array<UInt> & getGhostsCounters(ElementType type,
GhostType ghost_type = _ghost) {
AKANTU_DEBUG_ASSERT(ghost_type != _not_ghost,
"No ghost counter for _not_ghost elements");
return ghosts_counters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline Array<std::vector<Element>> &
getElementToSubelementPointer(ElementType type,
GhostType ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
getSubelementToElementPointer(ElementType type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ID id;
/// array of the nodes coordinates
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::shared_ptr<Array<UInt>> nodes_global_ids;
/// node flags (shared/periodic/...)
std::shared_ptr<Array<NodeFlag>> nodes_flags;
/// processor handling the node when not local or master
std::unordered_map<UInt, Int> nodes_prank;
/// global number of nodes;
UInt nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<UInt> connectivities;
/// count the references on ghost elements
ElementTypeMapArray<UInt> ghosts_counters;
/// map to normals for all class of elements present in this mesh
ElementTypeMapArray<Real> normals;
/// the spatial dimension of this mesh
UInt spatial_dimension{0};
/// size covered by the mesh on each direction
Vector<Real> size;
/// global bounding box
BBox bbox;
/// local bounding box
BBox bbox_local;
/// Extra data loaded from the mesh file
// MeshData mesh_data;
/// facets' mesh
std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
bool is_distributed{false};
/// defines if the mesh is periodic
bool is_periodic{false};
/// Communicator on which mesh is distributed
Communicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
/// Node synchronizer for periodic nodes
std::unique_ptr<PeriodicNodeSynchronizer> periodic_node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// class to update global data using external knowledge
std::unique_ptr<MeshGlobalDataUpdater> global_data_updater;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
/// periodicity local info
std::unordered_map<UInt, UInt> periodic_slave_master;
std::unordered_multimap<UInt, UInt> periodic_master_slave;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.hh"
#endif /* AKANTU_MESH_HH_ */
diff --git a/src/mesh/mesh_accessor.hh b/src/mesh/mesh_accessor.hh
index 524c77fb9..0eff39457 100644
--- a/src/mesh/mesh_accessor.hh
+++ b/src/mesh/mesh_accessor.hh
@@ -1,219 +1,221 @@
/**
* @file mesh_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jun 30 2015
- * @date last modification: Tue Sep 19 2017
+ * @date last modification: Tue Feb 09 2021
*
* @brief this class allow to access some private member of mesh it is used for
* IO for examples
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_ACCESSOR_HH_
#define AKANTU_MESH_ACCESSOR_HH_
namespace akantu {
class NodeSynchronizer;
class ElementSynchronizer;
class MeshGlobalDataUpdater;
} // namespace akantu
namespace akantu {
class MeshAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MeshAccessor(Mesh & mesh) : _mesh(mesh) {}
virtual ~MeshAccessor() = default;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the global number of nodes
inline UInt getNbGlobalNodes() const { return this->_mesh.nb_global_nodes; }
/// set the global number of nodes
inline void setNbGlobalNodes(UInt nb_global_nodes) {
this->_mesh.nb_global_nodes = nb_global_nodes;
}
/// set the mesh as being distributed
inline void setDistributed() { this->_mesh.is_distributed = true; }
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline auto & getNodesGlobalIds() {
return this->_mesh.getNodesGlobalIdsPointer();
}
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline auto & getNodesFlags() { return this->_mesh.getNodesFlags(); }
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline void setNodePrank(UInt node, Int prank) {
this->_mesh.nodes_prank[node] = prank;
}
/// get a pointer to the coordinates Array
inline auto & getNodes() { return this->_mesh.getNodesPointer(); }
/// get a pointer to the coordinates Array
inline auto getNodesSharedPtr() { return this->_mesh.nodes; }
/// get the connectivities
inline auto & getConnectivities() { return this->_mesh.connectivities; }
/// get the connectivity Array for the given type and create it
/// if necessary
inline auto & getConnectivity(ElementType type,
GhostType ghost_type = _not_ghost) {
return this->_mesh.getConnectivityPointer(type, ghost_type);
}
/// resize the connectivity (use carefully)
inline void resizeConnectivity(UInt new_size, ElementType type,
GhostType ghost_type = _not_ghost) {
this->getConnectivity(type, ghost_type).resize(new_size, UInt(-1));
}
/// resize the nodes (use carefully)
inline void resizeNodes(UInt new_size) {
this->getNodes().resize(new_size, UInt(-1));
}
/// get the connectivity for the given element
inline decltype(auto) getConnectivity(const Element & element) {
return this->_mesh.getConnectivityNC(element);
}
/// get the ghost element counter
inline auto & getGhostsCounters(ElementType type,
GhostType ghost_type = _ghost) {
return this->_mesh.getGhostsCounters(type, ghost_type);
}
/// get the element_to_subelement Array for the given type and
/// create it if necessary
inline auto & getElementToSubelement(ElementType type,
GhostType ghost_type = _not_ghost) {
return this->_mesh.getElementToSubelementPointer(type, ghost_type);
}
inline decltype(auto)
getElementToSubelementNC(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return this->_mesh.getElementToSubelementNC(type, ghost_type);
}
/// get the subelement_to_element Array for the given type and
/// create it if necessary
inline auto & getSubelementToElement(ElementType type,
GhostType ghost_type = _not_ghost) {
return this->_mesh.getSubelementToElementPointer(type, ghost_type);
}
inline decltype(auto)
getSubelementToElementNC(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return this->_mesh.getSubelementToElementNC(type, ghost_type);
}
/// get the element_to_subelement, creates it if necessary
inline decltype(auto) getElementToSubelement() {
return this->_mesh.getElementToSubelementNC();
}
/// get subelement_to_element, creates it if necessary
inline decltype(auto) getSubelementToElement() {
return this->_mesh.getSubelementToElementNC();
}
/// get a pointer to the element_to_subelement Array for element and
/// create it if necessary
inline decltype(auto) getElementToSubelement(const Element & element) {
return this->_mesh.getElementToSubelementNC(element);
}
/// get a pointer to the subelement_to_element Array for the given element and
/// create it if necessary
inline decltype(auto) getSubelementToElement(const Element & element) {
return this->_mesh.getSubelementToElementNC(element);
}
template <typename T>
inline auto & getData(const std::string & data_name, ElementType el_type,
GhostType ghost_type = _not_ghost,
UInt nb_component = 1, bool size_to_nb_element = true,
bool resize_with_parent = false) {
return this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
nb_component, size_to_nb_element,
resize_with_parent);
}
/// get the node synchonizer
auto & getNodeSynchronizer() { return *this->_mesh.node_synchronizer; }
/// get the element synchonizer
auto & getElementSynchronizer() { return *this->_mesh.element_synchronizer; }
decltype(auto) updateGlobalData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) {
return this->_mesh.updateGlobalData(nodes_event, elements_event);
}
void registerGlobalDataUpdater(
std::unique_ptr<MeshGlobalDataUpdater> && global_data_updater) {
this->_mesh.registerGlobalDataUpdater(
std::forward<std::unique_ptr<MeshGlobalDataUpdater>>(
global_data_updater));
}
/* ------------------------------------------------------------------------ */
void makeReady() { this->_mesh.makeReady(); }
/* ------------------------------------------------------------------------ */
void addPeriodicSlave(UInt slave, UInt master) {
this->_mesh.addPeriodicSlave(slave, master);
}
void markMeshPeriodic() {
for (UInt s : arange(this->_mesh.spatial_dimension)) {
this->_mesh.is_periodic |= 1 << s;
}
}
void wipePeriodicInfo() { this->_mesh.wipePeriodicInfo(); }
private:
Mesh & _mesh;
};
} // namespace akantu
#endif /* AKANTU_MESH_ACCESSOR_HH_ */
diff --git a/src/mesh/mesh_data.cc b/src/mesh/mesh_data.cc
index ff1b628cc..1d4c1f322 100644
--- a/src/mesh/mesh_data.cc
+++ b/src/mesh/mesh_data.cc
@@ -1,38 +1,41 @@
/**
* @file mesh_data.cc
*
* @author Dana Christen <dana.christen@gmail.com>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Wed Sep 12 2018
*
* @brief Stores generic data loaded from the mesh file
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "mesh_data.hh"
#include "mesh.hh"
namespace akantu {
MeshData::MeshData(const ID & _id, const ID & parent_id)
: _id(parent_id + ":" + _id) {}
} // namespace akantu
diff --git a/src/mesh/mesh_data.hh b/src/mesh/mesh_data.hh
index ddab17361..e9c85f2e1 100644
--- a/src/mesh/mesh_data.hh
+++ b/src/mesh/mesh_data.hh
@@ -1,188 +1,190 @@
/**
* @file mesh_data.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Fri Dec 28 2018
*
* @brief Stores generic data loaded from the mesh file
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_DATA_HH_
#define AKANTU_MESH_DATA_HH_
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include <map>
#include <string>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_MESH_DATA_TYPES \
((_int, Int))((_uint, UInt))((_real, Real))((_bool, bool))( \
(_element, Element))((_std_string, std::string))( \
(_std_vector_element, std::vector<Element>))
#define AKANTU_MESH_DATA_TUPLE_FIRST_ELEM(s, data, elem) \
BOOST_PP_TUPLE_ELEM(2, 0, elem)
enum class MeshDataTypeCode : int {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_MESH_DATA_TUPLE_FIRST_ELEM, ,
AKANTU_MESH_DATA_TYPES)),
_unknown
};
enum class MeshDataType {
_nodal,
_elemental,
};
class MeshData {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
using TypeCode = MeshDataTypeCode;
using ElementalDataMap =
std::map<std::string, std::unique_ptr<ElementTypeMapBase>>;
using NodalDataMap = std::map<std::string, std::unique_ptr<ArrayBase>>;
using TypeCodeMap = std::map<std::string, TypeCode>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshData(const ID & id = "mesh_data", const ID & parent_id = "");
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// tells if the given array exists
template <typename T>
bool hasData(const ID & data_name, ElementType elem_type,
GhostType ghost_type = _not_ghost) const;
/// tells if the given data exists
bool hasData(const ID & data_name,
MeshDataType type = MeshDataType::_elemental) const;
bool hasData(MeshDataType type = MeshDataType::_elemental) const;
/// get the names of the data stored in elemental_data
inline auto getTagNames(ElementType type,
GhostType ghost_type = _not_ghost) const;
/// get the names of the data stored in elemental_data
inline auto getTagNames() const;
/// get the type of the data stored in elemental_data
template <typename T> TypeCode getTypeCode() const;
inline TypeCode
getTypeCode(const ID & name,
MeshDataType type = MeshDataType::_elemental) const;
/// Get an existing elemental data array
template <typename T>
const Array<T> &
getElementalDataArray(const ID & data_name, ElementType elem_type,
GhostType ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getElementalDataArray(const ID & data_name,
ElementType elem_type,
GhostType ghost_type = _not_ghost);
/// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> & getElementalDataArrayAlloc(
const ID & data_name, ElementType elem_type,
GhostType ghost_type = _not_ghost, UInt nb_component = 1);
template <typename T>
inline UInt getNbComponentTemplated(const ID & name,
ElementType el_type,
GhostType ghost_type) const;
inline UInt getNbComponent(const ID & name, ElementType el_type,
GhostType ghost_type = _not_ghost) const;
inline UInt getNbComponent(const ID & name) const;
/// Get an existing elemental data
template <typename T>
const ElementTypeMapArray<T> & getElementalData(const ID & name) const;
template <typename T>
ElementTypeMapArray<T> & getElementalData(const ID & name);
template <typename T>
Array<T> & getNodalData(const ID & name, UInt nb_components = 1);
template <typename T> const Array<T> & getNodalData(const ID & name) const;
private:
/// Register new elemental data (and alloc data) with check if the name is
/// new
template <typename T>
ElementTypeMapArray<T> & registerElementalData(const ID & name);
inline void registerElementalData(const ID & name, TypeCode type);
/// Register new nodal data (and alloc data) with check if the name is
/// new
template <typename T>
Array<T> & registerNodalData(const ID & name, UInt nb_components = 1);
inline void registerNodalData(const ID & name, UInt nb_components,
TypeCode type);
/// Register new elemental data (add alloc data)
template <typename T>
ElementTypeMapArray<T> & allocElementalData(const ID & name);
/// Register new nodal data (add alloc data)
template <typename T>
Array<T> & allocNodalData(const ID & name, UInt nb_components);
friend class SlaveNodeInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ID _id;
/// Map when elemental data is stored as ElementTypeMap
ElementalDataMap elemental_data;
/// Map when elemental data is stored as ElementTypeMap
NodalDataMap nodal_data;
/// Map when elementalType of the data stored in elemental_data
std::map<MeshDataType, TypeCodeMap> typecode_map{
{MeshDataType::_elemental, {}}, {MeshDataType::_nodal, {}}};
};
} // namespace akantu
#include "mesh_data_tmpl.hh"
#undef AKANTU_MESH_DATA_TUPLE_FIRST_ELEM
#endif /* AKANTU_MESH_DATA_HH_ */
diff --git a/src/mesh/mesh_data_tmpl.hh b/src/mesh/mesh_data_tmpl.hh
index 0d7294441..bdfccfb0e 100644
--- a/src/mesh/mesh_data_tmpl.hh
+++ b/src/mesh/mesh_data_tmpl.hh
@@ -1,412 +1,414 @@
/**
* @file mesh_data_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Dec 28 2018
*
* @brief Stores generic data loaded from the mesh file
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_data.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_DATA_TMPL_HH_
#define AKANTU_MESH_DATA_TMPL_HH_
namespace akantu {
#define AKANTU_MESH_DATA_OSTREAM(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, elem)); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
const MeshDataTypeCode & type_code) {
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_OSTREAM, name,
AKANTU_MESH_DATA_TYPES)
default:
stream << "(unknown type)";
}
return stream;
}
#undef AKANTU_MESH_DATA_OSTREAM
#define MESH_DATA_GET_TYPE(r, data, type) \
template <> \
inline MeshDataTypeCode \
MeshData::getTypeCode<BOOST_PP_TUPLE_ELEM(2, 1, type)>() const { \
return MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, type); \
}
/* -------------------------------------------------------------------------- */
// get the type of the data stored in elemental_data
template <typename T> inline MeshDataTypeCode MeshData::getTypeCode() const {
AKANTU_ERROR("Type " << debug::demangle(typeid(T).name())
<< " not implemented by MeshData.");
}
/* -------------------------------------------------------------------------- */
BOOST_PP_SEQ_FOR_EACH(MESH_DATA_GET_TYPE, void, AKANTU_MESH_DATA_TYPES)
#undef MESH_DATA_GET_TYPE
inline MeshDataTypeCode MeshData::getTypeCode(const ID & name,
MeshDataType type) const {
auto it = typecode_map.at(type).find(name);
if (it == typecode_map.at(type).end()) {
AKANTU_EXCEPTION("No dataset named " << name << " found.");
}
return it->second;
}
/* -------------------------------------------------------------------------- */
// Register new elemental data templated (and alloc data) with check if the
// name is new
template <typename T>
ElementTypeMapArray<T> & MeshData::registerElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
return allocElementalData<T>(name);
}
AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
return getElementalData<T>(name);
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the
// name is new
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
registerElementalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name); \
break; \
}
inline void MeshData::registerElementalData(const ID & name,
MeshDataTypeCode type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template <typename T>
ElementTypeMapArray<T> & MeshData::allocElementalData(const ID & name) {
auto dataset =
std::make_unique<ElementTypeMapArray<T>>(name, _id);
auto * dataset_typed = dataset.get();
elemental_data[name] = std::move(dataset);
typecode_map[MeshDataType::_elemental][name] = getTypeCode<T>();
return *dataset_typed;
}
/* -------------------------------------------------------------------------- */
// Register new nodal data templated (and alloc data) with check if the
// name is new
template <typename T>
Array<T> & MeshData::registerNodalData(const ID & name, UInt nb_components) {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
return allocNodalData<T>(name, nb_components);
}
AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
return getNodalData<T>(name);
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the
// name is new
#define AKANTU_MESH_NODAL_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
registerNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name, nb_components); \
break; \
}
inline void MeshData::registerNodalData(const ID & name, UInt nb_components,
MeshDataTypeCode type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_NODAL_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_NODAL_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template <typename T>
Array<T> & MeshData::allocNodalData(const ID & name, UInt nb_components) {
auto dataset =
std::make_unique<Array<T>>(0, nb_components, T(), _id + ":" + name);
auto * dataset_typed = dataset.get();
nodal_data[name] = std::move(dataset);
typecode_map[MeshDataType::_nodal][name] = getTypeCode<T>();
return *dataset_typed;
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> & MeshData::getNodalData(const ID & name) const {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
AKANTU_EXCEPTION("No nodal dataset named " << name << " found.");
}
return aka::as_type<Array<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template <typename T>
Array<T> & MeshData::getNodalData(const ID & name, UInt nb_components) {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
return allocNodalData<T>(name, nb_components);
}
return aka::as_type<Array<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
const ElementTypeMapArray<T> &
MeshData::getElementalData(const ID & name) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("No dataset named " << name << " found.");
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template <typename T>
ElementTypeMapArray<T> & MeshData::getElementalData(const ID & name) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
return allocElementalData<T>(name);
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool MeshData::hasData(const ID & name, ElementType elem_type,
GhostType ghost_type) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
return false;
}
auto & elem_map = aka::as_type<ElementTypeMapArray<T>>(*(it->second));
return elem_map.exists(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool MeshData::hasData(const ID & name, MeshDataType type) const {
if (type == MeshDataType::_elemental) {
auto it = elemental_data.find(name);
return (it != elemental_data.end());
}
if (type == MeshDataType::_nodal) {
auto it = nodal_data.find(name);
return (it != nodal_data.end());
}
return false;
}
/* -------------------------------------------------------------------------- */
inline bool MeshData::hasData(MeshDataType type) const {
switch (type) {
case MeshDataType::_elemental:
return (not elemental_data.empty());
case MeshDataType::_nodal:
return (not nodal_data.empty());
}
return false;
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> &
MeshData::getElementalDataArray(const ID & name, ElementType elem_type,
GhostType ghost_type) const {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second))(elem_type,
ghost_type);
}
template <typename T>
Array<T> & MeshData::getElementalDataArray(const ID & name,
ElementType elem_type,
GhostType ghost_type) {
auto it = elemental_data.find(name);
if (it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name
<< " not registered for type: " << elem_type
<< " - ghost_type:" << ghost_type << "!");
}
return aka::as_type<ElementTypeMapArray<T>>(*(it->second.get()))(elem_type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> & MeshData::getElementalDataArrayAlloc(const ID & name,
ElementType elem_type,
GhostType ghost_type,
UInt nb_component) {
auto it = elemental_data.find(name);
ElementTypeMapArray<T> * dataset;
if (it == elemental_data.end()) {
dataset = &allocElementalData<T>(name);
} else {
dataset = dynamic_cast<ElementTypeMapArray<T> *>(it->second.get());
}
AKANTU_DEBUG_ASSERT(
getTypeCode<T>() ==
typecode_map.at(MeshDataType::_elemental).find(name)->second,
"Function getElementalDataArrayAlloc called with the wrong type!");
if (!(dataset->exists(elem_type, ghost_type))) {
dataset->alloc(0, nb_component, elem_type, ghost_type);
}
return (*dataset)(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
nb_comp = getNbComponentTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>( \
name, el_type, ghost_type); \
break; \
}
inline UInt MeshData::getNbComponent(const ID & name,
ElementType el_type,
GhostType ghost_type) const {
auto it = typecode_map.at(MeshDataType::_elemental).find(name);
UInt nb_comp(0);
if (it == typecode_map.at(MeshDataType::_elemental).end()) {
AKANTU_EXCEPTION("Could not determine the type held in dataset "
<< name << " for type: " << el_type
<< " - ghost_type:" << ghost_type << ".");
}
MeshDataTypeCode type = it->second;
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR(
"Could not call the correct instance of getNbComponentTemplated.");
break;
}
return nb_comp;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
template <typename T>
inline UInt
MeshData::getNbComponentTemplated(const ID & name, ElementType el_type,
GhostType ghost_type) const {
return getElementalDataArray<T>(name, el_type, ghost_type).getNbComponent();
}
/* -------------------------------------------------------------------------- */
inline UInt MeshData::getNbComponent(const ID & name) const {
auto it = nodal_data.find(name);
if (it == nodal_data.end()) {
AKANTU_EXCEPTION("No nodal dataset registered with the name" << name
<< ".");
}
return it->second->getNbComponent();
}
/* -------------------------------------------------------------------------- */
// get the names of the data stored in elemental_data
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> * dataset; \
dataset = \
dynamic_cast<ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> *>( \
it->second.get()); \
exists = dataset->exists(el_type, ghost_type); \
break; \
}
inline auto MeshData::getTagNames(ElementType el_type,
GhostType ghost_type) const {
std::vector<std::string> tags;
bool exists(false);
auto it = elemental_data.begin();
auto it_end = elemental_data.end();
for (; it != it_end; ++it) {
MeshDataTypeCode type = getTypeCode(it->first);
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the proper type to (dynamic-)cast.");
break;
}
if (exists) {
tags.push_back(it->first);
}
}
return tags;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
inline auto MeshData::getTagNames() const {
std::vector<std::string> tags;
for (auto && data : nodal_data) {
tags.push_back(std::get<0>(data));
}
return tags;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_MESH_DATA_TMPL_HH_ */
diff --git a/src/mesh/mesh_events.hh b/src/mesh/mesh_events.hh
index 97fbbe209..eced63fb7 100644
--- a/src/mesh/mesh_events.hh
+++ b/src/mesh/mesh_events.hh
@@ -1,202 +1,204 @@
/**
* @file mesh_events.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 20 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Classes corresponding to mesh events type
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_array.hh"
#include "element.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_EVENTS_HH_
#define AKANTU_MESH_EVENTS_HH_
namespace akantu {
/// akantu::MeshEvent is the base event for meshes
template <class Entity> class MeshEvent {
public:
MeshEvent(const std::string & origin = "") : origin_(origin) {}
virtual ~MeshEvent() = default;
/// Get the list of entity modified by the event nodes or elements
const Array<Entity> & getList() const { return list; }
/// Get the list of entity modified by the event nodes or elements
Array<Entity> & getList() { return list; }
std::string origin() const { return origin_; }
protected:
Array<Entity> list;
private:
std::string origin_;
};
class Mesh;
/// akantu::MeshEvent related to new nodes in the mesh
class NewNodesEvent : public MeshEvent<UInt> {
public:
NewNodesEvent(const std::string & origin = "") : MeshEvent(origin) {}
~NewNodesEvent() override = default;
};
/// akantu::MeshEvent related to nodes removed from the mesh
class RemovedNodesEvent : public MeshEvent<UInt> {
public:
inline RemovedNodesEvent(const Mesh & mesh, const std::string & origin = "");
~RemovedNodesEvent() override = default;
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, Array<UInt> &);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering, const Array<UInt> &);
private:
Array<UInt> new_numbering;
};
/// akantu::MeshEvent related to new elements in the mesh
class NewElementsEvent : public MeshEvent<Element> {
public:
NewElementsEvent(const std::string & origin = "") : MeshEvent<Element>(origin) {}
~NewElementsEvent() override = default;
};
/// akantu::MeshEvent related to elements removed from the mesh
class RemovedElementsEvent : public MeshEvent<Element> {
public:
inline RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id = "new_numbering",
const std::string & origin = "");
~RemovedElementsEvent() override = default;
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering,
const ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering,
ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(NewNumbering, new_numbering, UInt);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NewNumbering, new_numbering, UInt);
protected:
ElementTypeMapArray<UInt> new_numbering;
};
/// akantu::MeshEvent for element that changed in some sort, can be seen as a
/// combination of removed and added elements
class ChangedElementsEvent : public RemovedElementsEvent {
public:
inline ChangedElementsEvent(
const Mesh & mesh, const ID & new_numbering_id = "changed_event:new_numbering",
const std::string & origin = "")
: RemovedElementsEvent(mesh, new_numbering_id, origin) {}
~ChangedElementsEvent() override = default;
AKANTU_GET_MACRO(ListOld, list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListOld, list, Array<Element> &);
AKANTU_GET_MACRO(ListNew, new_list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListNew, new_list, Array<Element> &);
protected:
Array<Element> new_list;
};
/* -------------------------------------------------------------------------- */
class MeshEventHandler {
public:
virtual ~MeshEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Internal code */
/* ------------------------------------------------------------------------ */
private:
/// send a akantu::NewNodesEvent
inline void sendEvent(const NewNodesEvent & event) {
onNodesAdded(event.getList(), event);
}
/// send a akantu::RemovedNodesEvent
inline void sendEvent(const RemovedNodesEvent & event) {
onNodesRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::NewElementsEvent
inline void sendEvent(const NewElementsEvent & event) {
onElementsAdded(event.getList(), event);
}
/// send a akantu::RemovedElementsEvent
inline void sendEvent(const RemovedElementsEvent & event) {
onElementsRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::ChangedElementsEvent
inline void sendEvent(const ChangedElementsEvent & event) {
onElementsChanged(event.getListOld(), event.getListNew(),
event.getNewNumbering(), event);
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::NewNodesEvent
virtual void onNodesAdded(const Array<UInt> & /*nodes_list*/,
const NewNodesEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedNodesEvent
virtual void onNodesRemoved(const Array<UInt> & /*nodes_list*/,
const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) {}
/// function to implement to react on akantu::NewElementsEvent
virtual void onElementsAdded(const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) {}
/// function to implement to react on akantu::RemovedElementsEvent
virtual void
onElementsRemoved(const Array<Element> & /*elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const RemovedElementsEvent & /*event*/) {}
/// function to implement to react on akantu::ChangedElementsEvent
virtual void
onElementsChanged(const Array<Element> & /*old_elements_list*/,
const Array<Element> & /*new_elements_list*/,
const ElementTypeMapArray<UInt> & /*new_numbering*/,
const ChangedElementsEvent & /*event*/) {}
};
} // namespace akantu
#endif /* AKANTU_MESH_EVENTS_HH_ */
diff --git a/src/mesh/mesh_filter.hh b/src/mesh/mesh_filter.hh
index 387bfb57a..4e227ec39 100644
--- a/src/mesh/mesh_filter.hh
+++ b/src/mesh/mesh_filter.hh
@@ -1,71 +1,73 @@
/**
* @file mesh_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Feb 20 2018
*
* @brief the class representing the meshes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_FILTER_HH_
#define AKANTU_MESH_FILTER_HH_
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Filter Functors */
/* -------------------------------------------------------------------------- */
/// struct for the possible filter functors
struct FilterFunctor {
enum Type { _node_filter_functor, _element_filter_functor };
};
/// class (functor) for the node filter
class NodeFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) UInt node) { AKANTU_TO_IMPLEMENT(); }
public:
static const Type type = _node_filter_functor;
};
/// class (functor) for the element filter
class ElementFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) const Element & element) {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _element_filter_functor;
};
} // namespace akantu
#endif /* AKANTU_MESH_FILTER_HH_ */
diff --git a/src/mesh/mesh_global_data_updater.hh b/src/mesh/mesh_global_data_updater.hh
index b4a01f896..b1bc7b5e9 100644
--- a/src/mesh/mesh_global_data_updater.hh
+++ b/src/mesh/mesh_global_data_updater.hh
@@ -1,50 +1,54 @@
/**
* @file mesh_global_data_updater.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Sat Mar 03 2018
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Oct 11 2017
*
- * @brief interface for the global data updater
+ * @brief interface for the global data updater
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_
#define AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_
namespace akantu {
class NewNodesEvent;
class NewElementsEvent;
class MeshGlobalDataUpdater {
public:
virtual ~MeshGlobalDataUpdater() = default;
virtual std::tuple<UInt, UInt>
updateData(NewNodesEvent & /*nodes_event*/,
NewElementsEvent & /*elements_event*/) {
return std::make_tuple(0, 0);
}
};
} // namespace akantu
#endif /* AKANTU_MESH_GLOBAL_DATA_UPDATER_HH_ */
diff --git a/src/mesh/mesh_inline_impl.hh b/src/mesh/mesh_inline_impl.hh
index 076cca8d0..e222a051e 100644
--- a/src/mesh/mesh_inline_impl.hh
+++ b/src/mesh/mesh_inline_impl.hh
@@ -1,761 +1,764 @@
/**
* @file mesh_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Fri Dec 11 2020
*
* @brief Implementation of the inline functions of the mesh class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "element_class.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_INLINE_IMPL_HH_
#define AKANTU_MESH_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline ElementKind Element::kind() const { return Mesh::getKind(type); }
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename... pack>
Mesh::ElementTypesIteratorHelper Mesh::elementTypes(pack &&... _pack) const {
return connectivities.elementTypes(_pack...);
}
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh,
const std::string & origin)
: MeshEvent<UInt>(origin),
new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
const ID & new_numbering_id,
const std::string & origin)
: MeshEvent<Element>(origin),
new_numbering(new_numbering_id, mesh.getID()) {}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
this->fillNodesToElements();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
this->computeBoundingBox();
this->nodes_flags->resize(this->nodes->size(), NodeFlag::_normal);
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
this->fillNodesToElements();
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
const auto & new_numbering = event.getNewNumbering();
this->removeNodesFromArray(*nodes, new_numbering);
if (nodes_global_ids and not is_mesh_facets) {
this->removeNodesFromArray(*nodes_global_ids, new_numbering);
}
if (not is_mesh_facets) {
this->removeNodesFromArray(*nodes_flags, new_numbering);
}
if (not nodes_to_elements.empty()) {
std::vector<std::unique_ptr<std::set<Element>>> tmp(
nodes_to_elements.size());
auto it = nodes_to_elements.begin();
UInt new_nb_nodes = 0;
for (auto new_i : new_numbering) {
if (new_i != UInt(-1)) {
tmp[new_i] = std::move(*it);
++new_nb_nodes;
}
++it;
}
tmp.resize(new_nb_nodes);
std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
}
computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.size(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.size(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (not nodes_global_ids) {
nodes_global_ids = std::make_shared<Array<UInt>>(
nodes->size(), 1, getID() + ":nodes_global_ids");
for (auto && global_ids : enumerate(*nodes_global_ids)) {
std::get<1>(global_ids) = std::get<0>(global_ids);
}
}
AKANTU_DEBUG_OUT();
return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getConnectivityPointer(ElementType type,
GhostType ghost_type) {
if (connectivities.exists(type, ghost_type)) {
return connectivities(type, ghost_type);
}
if (ghost_type != _not_ghost) {
ghosts_counters.alloc(0, 1, type, ghost_type, 1);
}
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
return connectivities.alloc(0, nb_nodes_per_element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelementPointer(ElementType type, GhostType ghost_type) {
return getDataPointer<std::vector<Element>>("element_to_subelement", type,
ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElementPointer(ElementType type, GhostType ghost_type) {
auto & array = getDataPointer<Element>(
"subelement_to_element", type, ghost_type, getNbFacetsPerElement(type),
false, is_mesh_facets, ElementNull);
return array;
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getElementToSubelement() const {
return getData<std::vector<Element>>("element_to_subelement");
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getElementToSubelementNC() {
return getData<std::vector<Element>>("element_to_subelement");
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getElementToSubelement(ElementType type,
GhostType ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getElementToSubelementNC(ElementType type,
GhostType ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const auto &
Mesh::getElementToSubelement(const Element & element) const {
return getData<std::vector<Element>>("element_to_subelement")(element, 0);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getElementToSubelementNC(const Element & element) {
return getData<std::vector<Element>>("element_to_subelement")(element, 0);
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getSubelementToElement() const {
return getData<Element>("subelement_to_element");
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getSubelementToElementNC() {
return getData<Element>("subelement_to_element");
}
/* -------------------------------------------------------------------------- */
inline const auto & Mesh::getSubelementToElement(ElementType type,
GhostType ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline auto & Mesh::getSubelementToElementNC(ElementType type,
GhostType ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<Element>
Mesh::getSubelementToElement(const Element & element) const {
return this->getSubelementToElement().get(element);
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<Element>
Mesh::getSubelementToElementNC(const Element & element) {
return this->getSubelementToElement().get(element);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
Mesh::getDataPointer(const ID & data_name, ElementType el_type,
GhostType ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = this->getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent) {
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
} else {
tmp.resize(this->getNbElement(el_type, ghost_type));
}
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
Mesh::getDataPointer(const ID & data_name, ElementType el_type,
GhostType ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent,
const T & defaul_) {
Array<T> & tmp = this->getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent) {
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type), defaul_);
} else {
tmp.resize(this->getNbElement(el_type, ghost_type), defaul_);
}
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const ID & data_name, ElementType el_type,
GhostType ghost_type) const {
return this->getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const ID & data_name, ElementType el_type,
GhostType ghost_type) {
return this->getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const ID & data_name) const {
return this->getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const ID & data_name) {
return this->getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(ElementType type, GhostType ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
GhostType ghost_type, ElementKind kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind)) {
nb_element += getNbElement(type, ghost_type);
}
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
Vector<UInt> conn = getConnectivity(element);
Matrix<Real> local_coord(spatial_dimension, conn.size());
auto node_begin = make_view(*nodes, spatial_dimension).begin();
for (auto && node : enumerate(conn)) {
local_coord(std::get<0>(node)) =
Vector<Real>(node_begin[std::get<1>(node)]);
}
Math::barycenter(local_coord.storage(), conn.size(), spatial_dimension,
barycenter.storage());
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElement(ElementType type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getP1ElementType(ElementType type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
inline ElementKind Mesh::getKind(ElementType type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getSpatialDimension(ElementType type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNaturalSpaceDimension(const ElementType & type) {
UInt natural_dimension = 0;
#define GET_NATURAL_DIMENSION(type) \
natural_dimension = ElementClass<type>::getNaturalSpaceDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NATURAL_DIMENSION);
#undef GET_NATURAL_DIMENSION
return natural_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetTypes(ElementType type, UInt /*t*/) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
inline constexpr auto Mesh::getFacetType(ElementType type, UInt t) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetType(t);
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return _not_defined;
}
/* -------------------------------------------------------------------------- */
inline constexpr auto Mesh::getAllFacetTypes(ElementType type) {
#define GET_FACET_TYPE(type) return ElementClass<type>::getFacetTypes();
AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return ElementClass<_not_defined>::getFacetTypes();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(ElementType type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(ElementType type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getFacetLocalConnectivity(ElementType type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return ElementClass<_not_defined>::getFacetLocalConnectivityPerElement(0);
// This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline auto Mesh::getFacetConnectivity(const Element & element, UInt t) const {
AKANTU_DEBUG_IN();
Matrix<const UInt> local_facets(getFacetLocalConnectivity(element.type, t));
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<UInt> Mesh::getConnectivity(const Element & element) const {
return connectivities.get(element);
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<UInt> Mesh::getConnectivityNC(const Element & element) {
return connectivities.get(element);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
const Array<T> & nodal_values, T * local_coord, const UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
inline void Mesh::addConnectivityType(ElementType type, GhostType ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_pure_ghost;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_local_master_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_master;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_shared_mask) == NodeFlag::_slave;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPeriodicSlave(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_slave;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPeriodicMaster(UInt n) const {
return ((*nodes_flags)(n)&NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_master;
}
/* -------------------------------------------------------------------------- */
inline NodeFlag Mesh::getNodeFlag(UInt local_id) const {
return (*nodes_flags)(local_id);
}
/* -------------------------------------------------------------------------- */
inline Int Mesh::getNodePrank(UInt local_id) const {
auto it = nodes_prank.find(local_id);
return it == nodes_prank.end() ? -1 : it->second;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
if (nodes_global_ids == nullptr) {
return global_id;
}
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->size();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
for (const auto & el : elements) {
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
if (this->mesh_facets == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
}
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
if (this->mesh_facets == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
}
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
if (this->mesh_parent == nullptr) {
AKANTU_SILENT_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
}
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
void Mesh::addPeriodicSlave(UInt slave, UInt master) {
if (master == slave) {
return;
}
// if pair already registered
auto master_slaves = periodic_master_slave.equal_range(master);
auto slave_it =
std::find_if(master_slaves.first, master_slaves.second,
[&](auto & pair) { return pair.second == slave; });
if (slave_it == master_slaves.second) {
// no duplicates
periodic_master_slave.insert(std::make_pair(master, slave));
AKANTU_DEBUG_INFO("adding periodic slave, slave gid:"
<< getNodeGlobalId(slave) << " [lid: " << slave << "]"
<< ", master gid:" << getNodeGlobalId(master)
<< " [lid: " << master << "]");
// std::cout << "adding periodic slave, slave gid:" <<
// getNodeGlobalId(slave)
// << " [lid: " << slave << "]"
// << ", master gid:" << getNodeGlobalId(master)
// << " [lid: " << master << "]" << std::endl;
}
periodic_slave_master[slave] = master;
auto set_flag = [&](auto node, auto flag) {
(*nodes_flags)[node] &= ~NodeFlag::_periodic_mask; // clean periodic flags
(*nodes_flags)[node] |= flag;
};
set_flag(slave, NodeFlag::_periodic_slave);
set_flag(master, NodeFlag::_periodic_master);
}
/* -------------------------------------------------------------------------- */
UInt Mesh::getPeriodicMaster(UInt slave) const {
return periodic_slave_master.at(slave);
}
/* -------------------------------------------------------------------------- */
class Mesh::PeriodicSlaves {
using internal_iterator = std::unordered_multimap<UInt, UInt>::const_iterator;
std::pair<internal_iterator, internal_iterator> pair;
public:
PeriodicSlaves(const Mesh & mesh, UInt master)
: pair(mesh.getPeriodicMasterSlaves().equal_range(master)) {}
PeriodicSlaves(const PeriodicSlaves & other) = default;
PeriodicSlaves(PeriodicSlaves && other) = default;
PeriodicSlaves & operator=(const PeriodicSlaves & other) = default;
class const_iterator {
internal_iterator it;
public:
const_iterator(internal_iterator it) : it(it) {}
const_iterator operator++() {
++it;
return *this;
}
bool operator!=(const const_iterator & other) { return other.it != it; }
auto operator*() { return it->second; }
};
auto begin() const { return const_iterator(pair.first); }
auto end() const { return const_iterator(pair.second); }
};
/* -------------------------------------------------------------------------- */
inline decltype(auto) Mesh::getPeriodicSlaves(UInt master) const {
return PeriodicSlaves(*this, master);
}
/* -------------------------------------------------------------------------- */
inline Vector<UInt>
Mesh::getConnectivityWithPeriodicity(const Element & element) const {
Vector<UInt> conn = getConnectivity(element);
if (not isPeriodic()) {
return conn;
}
for (auto && node : conn) {
if (isPeriodicSlave(node)) {
node = getPeriodicMaster(node);
}
}
return conn;
}
} // namespace akantu
#endif /* AKANTU_MESH_INLINE_IMPL_HH_ */
diff --git a/src/mesh/mesh_iterators.hh b/src/mesh/mesh_iterators.hh
index 4d14f8f69..cf3ff81ae 100644
--- a/src/mesh/mesh_iterators.hh
+++ b/src/mesh/mesh_iterators.hh
@@ -1,224 +1,226 @@
/**
* @file mesh_iterators.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 16 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Thu Mar 11 2021
*
* @brief Set of helper classes to have fun with range based for
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "aka_static_if.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_ITERATORS_HH_
#define AKANTU_MESH_ITERATORS_HH_
namespace akantu {
class MeshElementsByTypes {
using elements_iterator = Array<Element>::scalar_iterator;
public:
explicit MeshElementsByTypes(const Array<Element> & elements) {
this->elements.copy(elements);
std::sort(this->elements.begin(), this->elements.end());
}
/* ------------------------------------------------------------------------ */
class MeshElementsRange {
public:
MeshElementsRange() = default;
MeshElementsRange(const elements_iterator & begin,
const elements_iterator & end)
: type((*begin).type), ghost_type((*begin).ghost_type), begin(begin),
end(end) {}
AKANTU_GET_MACRO(Type, type, ElementType);
AKANTU_GET_MACRO(GhostType, ghost_type, GhostType);
const Array<UInt> & getElements() {
elements.resize(end - begin);
auto el_it = elements.begin();
for (auto it = begin; it != end; ++it, ++el_it) {
*el_it = it->element;
}
return elements;
}
private:
ElementType type{_not_defined};
GhostType ghost_type{_casper};
elements_iterator begin;
elements_iterator end;
Array<UInt> elements;
};
/* ------------------------------------------------------------------------ */
class iterator {
struct element_comparator {
bool operator()(const Element & lhs, const Element & rhs) const {
return ((rhs == ElementNull) || std::tie(lhs.ghost_type, lhs.type) <
std::tie(rhs.ghost_type, rhs.type));
}
};
public:
iterator(const iterator &) = default;
iterator(const elements_iterator & first, const elements_iterator & last)
: range(std::equal_range(first, last, *first, element_comparator())),
first(first), last(last) {}
decltype(auto) operator*() const {
return MeshElementsRange(range.first, range.second);
}
iterator operator++() {
first = range.second;
range = std::equal_range(first, last, *first, element_comparator());
return *this;
}
bool operator==(const iterator & other) const {
return (first == other.first and last == other.last);
}
bool operator!=(const iterator & other) const {
return (not operator==(other));
}
private:
std::pair<elements_iterator, elements_iterator> range;
elements_iterator first;
elements_iterator last;
};
iterator begin() { return iterator(elements.begin(), elements.end()); }
iterator end() { return iterator(elements.end(), elements.end()); }
private:
Array<Element> elements;
};
/* -------------------------------------------------------------------------- */
namespace mesh_iterators {
namespace details {
template <class internal_iterator> class delegated_iterator {
public:
using value_type = std::remove_pointer_t<
typename internal_iterator::value_type::second_type>;
using difference_type = std::ptrdiff_t;
using pointer = value_type *;
using reference = value_type &;
using iterator_category = std::input_iterator_tag;
explicit delegated_iterator(internal_iterator it) : it(std::move(it)) {}
decltype(auto) operator*() {
return std::forward<decltype(*(it->second))>(*(it->second));
}
delegated_iterator operator++() {
++it;
return *this;
}
bool operator==(const delegated_iterator & other) const {
return other.it == it;
}
bool operator!=(const delegated_iterator & other) const {
return other.it != it;
}
private:
internal_iterator it;
};
} // namespace details
} // namespace mesh_iterators
/* -------------------------------------------------------------------------- */
template <class Func>
void for_each_element(UInt nb_elements, const Array<UInt> & filter_elements,
Func && function) {
if (filter_elements != empty_filter) {
std::for_each(filter_elements.begin(), filter_elements.end(),
std::forward<Func>(function));
} else {
auto && range = arange(nb_elements);
std::for_each(range.begin(), range.end(), std::forward<Func>(function));
}
}
/* -------------------------------------------------------------------------- */
template <class Func, typename... pack>
void for_each_element(const Mesh & mesh, Func && function, pack &&... _pack) {
auto requested_ghost_type = OPTIONAL_NAMED_ARG(ghost_type, _casper);
const ElementTypeMapArray<UInt> * filter =
OPTIONAL_NAMED_ARG(element_filter, nullptr);
bool all_ghost_types = requested_ghost_type == _casper;
auto spatial_dimension =
OPTIONAL_NAMED_ARG(spatial_dimension, mesh.getSpatialDimension());
auto element_kind = OPTIONAL_NAMED_ARG(element_kind, _ek_not_defined);
for (auto ghost_type : ghost_types) {
if ((not(ghost_type == requested_ghost_type)) and (not all_ghost_types)) {
continue;
}
auto element_types =
mesh.elementTypes(spatial_dimension, ghost_type, element_kind);
if (filter) {
element_types =
filter->elementTypes(spatial_dimension, ghost_type, element_kind);
}
for (auto type : element_types) {
const Array<UInt> * filter_array;
if (filter) {
filter_array = &((*filter)(type, ghost_type));
} else {
filter_array = &empty_filter;
}
auto nb_elements = mesh.getNbElement(type, ghost_type);
for_each_element(nb_elements, *filter_array, [&](auto && el) {
auto element = Element{type, el, ghost_type};
std::forward<Func>(function)(element);
});
}
}
}
} // namespace akantu
#endif /* AKANTU_MESH_ITERATORS_HH_ */
diff --git a/src/mesh/mesh_periodic.cc b/src/mesh/mesh_periodic.cc
index e374b4033..55c2e67d5 100644
--- a/src/mesh/mesh_periodic.cc
+++ b/src/mesh/mesh_periodic.cc
@@ -1,462 +1,466 @@
/**
* @file mesh_periodic.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Sat Feb 10 2018
+ * @date creation: Mon Feb 12 2018
+ * @date last modification: Sun Mar 15 2020
*
- * @brief Implementation of the perdiodicity capabilities in the mesh
+ * @brief Implementation of the perdiodicity capabilities in the mesh
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "communication_tag.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction) {
Array<UInt> list_1;
Array<UInt> list_2;
Real tolerance = 1e-10;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
const auto & positions = *nodes;
for (auto && data : enumerate(make_view(positions, spatial_dimension))) {
UInt node = std::get<0>(data);
const auto & pos = std::get<1>(data);
if (std::abs((pos(direction) - lower_bound(direction)) / length) <
tolerance) {
list_1.push_back(node);
}
if (std::abs((pos(direction) - upper_bound(direction)) / length) <
tolerance) {
list_2.push_back(node);
}
}
this->makePeriodic(direction, list_1, list_2);
}
/* -------------------------------------------------------------------------- */
void Mesh::makePeriodic(const SpatialDirection & direction, const ID & list_1,
const ID & list_2) {
const auto & list_nodes_1 =
mesh.getElementGroup(list_1).getNodeGroup().getNodes();
const auto & list_nodes_2 =
mesh.getElementGroup(list_2).getNodeGroup().getNodes();
this->makePeriodic(direction, list_nodes_1, list_nodes_2);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace {
struct NodeInfo {
NodeInfo() = default;
NodeInfo(UInt spatial_dimension) : position(spatial_dimension) {}
NodeInfo(UInt node, const Vector<Real> & position,
const SpatialDirection & direction)
: node(node), position(position) {
this->direction_position = position(direction);
this->position(direction) = 0.;
}
NodeInfo(const NodeInfo & other) = default;
NodeInfo(NodeInfo && other) noexcept = default;
NodeInfo & operator=(const NodeInfo & other) = default;
NodeInfo & operator=(NodeInfo && other) = default;
UInt node{0};
Vector<Real> position;
Real direction_position{0.};
};
} // namespace
/* -------------------------------------------------------------------------- */
// left is for lower values on direction and right for highest values
void Mesh::makePeriodic(const SpatialDirection & direction,
const Array<UInt> & list_left,
const Array<UInt> & list_right) {
Real tolerance = 1e-10;
const auto & positions = *nodes;
auto lower_bound = this->getLowerBounds();
auto upper_bound = this->getUpperBounds();
auto length = upper_bound(direction) - lower_bound(direction);
lower_bound(direction) = 0;
upper_bound(direction) = 0;
auto prank = communicator->whoAmI();
std::vector<NodeInfo> nodes_left(list_left.size());
std::vector<NodeInfo> nodes_right(list_right.size());
BBox bbox(spatial_dimension);
auto to_position = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = positions(node, s);
}
auto && info = NodeInfo(node, pos, direction);
bbox += info.position;
return std::move(info);
};
std::transform(list_left.begin(), list_left.end(), nodes_left.begin(),
to_position);
BBox bbox_left = bbox;
bbox.reset();
std::transform(list_right.begin(), list_right.end(), nodes_right.begin(),
to_position);
BBox bbox_right = bbox;
std::vector<UInt> new_nodes;
if (is_distributed) {
NewNodesEvent event(AKANTU_CURRENT_FUNCTION);
/* ---------------------------------------------------------------------- */
// function to send nodes in bboxes intersections
auto extract_and_send_nodes = [&](const auto & bbox, const auto & node_list,
auto & buffers, auto proc, auto cnt) {
// buffers.resize(buffers.size() + 1);
buffers.push_back(std::make_unique<DynamicCommunicationBuffer>());
auto & buffer = *buffers.back();
// std::cout << "Sending to " << proc << std::endl;
for (auto & info : node_list) {
if (bbox.contains(info.position) and isLocalOrMasterNode(info.node)) {
Vector<Real> pos = info.position;
pos(direction) = info.direction_position;
NodeFlag flag = (*nodes_flags)(info.node) & NodeFlag::_periodic_mask;
UInt gnode = getNodeGlobalId(info.node);
buffer << gnode;
buffer << pos;
buffer << flag;
// std::cout << " - node " << getNodeGlobalId(info.node);
// if is slave sends master info
if (flag == NodeFlag::_periodic_slave) {
UInt master = getNodeGlobalId(periodic_slave_master[info.node]);
// std::cout << " slave of " << master << std::endl;
buffer << master;
}
// if is master sends list of slaves
if (flag == NodeFlag::_periodic_master) {
UInt nb_slaves = periodic_master_slave.count(info.node);
buffer << nb_slaves;
// std::cout << " master of " << nb_slaves << " nodes : [";
auto slaves = periodic_master_slave.equal_range(info.node);
for (auto it = slaves.first; it != slaves.second; ++it) {
UInt gslave = getNodeGlobalId(it->second);
// std::cout << (it == slaves.first ? "" : ", ") << gslave;
buffer << gslave;
}
// std::cout << "]";
}
// std::cout << std::endl;
}
}
auto tag = Tag::genTag(prank, 10 * direction + cnt, Tag::_periodic_nodes);
// std::cout << "SBuffer size " << buffer.size() << " " << tag <<
// std::endl;
return communicator->asyncSend(buffer, proc, tag);
};
/* ---------------------------------------------------------------------- */
// function to receive nodes in bboxes intersections
auto recv_and_extract_nodes = [&](auto & node_list, const auto proc,
auto cnt) {
DynamicCommunicationBuffer buffer;
auto tag = Tag::genTag(proc, 10 * direction + cnt, Tag::_periodic_nodes);
communicator->receive(buffer, proc, tag);
// std::cout << "RBuffer size " << buffer.size() << " " << tag <<
// std::endl; std::cout << "Receiving from " << proc << std::endl;
while (not buffer.empty()) {
Vector<Real> pos(spatial_dimension);
UInt global_node;
NodeFlag flag;
buffer >> global_node;
buffer >> pos;
buffer >> flag;
// std::cout << " - node " << global_node;
auto local_node = getNodeLocalId(global_node);
// get the master info of is slave
if (flag == NodeFlag::_periodic_slave) {
UInt master_node;
buffer >> master_node;
// std::cout << " slave of " << master_node << std::endl;
// auto local_master_node = getNodeLocalId(master_node);
// AKANTU_DEBUG_ASSERT(local_master_node != UInt(-1),
//"Should I know the master node " << master_node);
}
// get the list of slaves if is master
if ((flag & NodeFlag::_periodic_mask) == NodeFlag::_periodic_master) {
UInt nb_slaves;
buffer >> nb_slaves;
// std::cout << " master of " << nb_slaves << " nodes : [";
for (auto ns [[gnu::unused]] : arange(nb_slaves)) {
UInt gslave_node;
buffer >> gslave_node;
// std::cout << (ns == 0 ? "" : ", ") << gslave_node;
// auto lslave_node = getNodeLocalId(gslave_node);
// AKANTU_DEBUG_ASSERT(lslave_node != UInt(-1),
// "Should I know the slave node " <<
// gslave_node);
}
// std::cout << "]";
}
// std::cout << std::endl;
if (local_node != UInt(-1)) {
continue;
}
local_node = nodes->size();
NodeInfo info(local_node, pos, direction);
nodes->push_back(pos);
nodes_global_ids->push_back(global_node);
nodes_flags->push_back(flag | NodeFlag::_pure_ghost);
new_nodes.push_back(info.node);
node_list.push_back(info);
nodes_prank[info.node] = proc;
event.getList().push_back(local_node);
}
};
/* ---------------------------------------------------------------------- */
auto && intersections_with_right =
bbox_left.intersection(bbox_right, *communicator);
auto && intersections_with_left =
bbox_right.intersection(bbox_left, *communicator);
std::vector<CommunicationRequest> send_requests;
std::vector<std::unique_ptr<DynamicCommunicationBuffer>> send_buffers;
// sending nodes in the common zones
auto send_intersections = [&](auto & intersections, auto send_count) {
for (auto && data : intersections) {
auto proc = std::get<0>(data);
// Send local nodes if intersects with remote
const auto & intersection_with_proc = std::get<1>(data);
if (intersection_with_proc) {
send_requests.push_back(
extract_and_send_nodes(intersection_with_proc, nodes_right,
send_buffers, proc, send_count));
}
send_count += 2;
}
};
auto recv_intersections = [&](auto & intersections, auto recv_count) {
for (auto && data : intersections) {
auto proc = std::get<0>(data);
// receive remote nodes if intersects with local
const auto & intersection_with_proc = std::get<1>(data);
if (intersection_with_proc) {
recv_and_extract_nodes(nodes_right, proc, recv_count);
}
recv_count += 2;
}
};
send_intersections(intersections_with_left, 0);
send_intersections(intersections_with_right, 1);
recv_intersections(intersections_with_right, 0);
recv_intersections(intersections_with_right, 1);
Communicator::waitAll(send_requests);
Communicator::freeCommunicationRequest(send_requests);
this->sendEvent(event);
} // end distributed work
auto to_sort = [&](auto && info1, auto && info2) -> bool {
return info1.position < info2.position;
};
// sort nodes based on their distance to lower corner
std::sort(nodes_left.begin(), nodes_left.end(), to_sort);
std::sort(nodes_right.begin(), nodes_right.end(), to_sort);
// function to change the master of nodes
auto updating_master = [&](auto & old_master, auto & new_master) {
if (old_master == new_master) {
return;
}
auto slaves = periodic_master_slave.equal_range(old_master);
AKANTU_DEBUG_ASSERT(
isPeriodicMaster(
old_master), // slaves.first != periodic_master_slave.end(),
"Cannot update master " << old_master << ", its not a master node!");
decltype(periodic_master_slave) tmp_master_slave;
for (auto it = slaves.first; it != slaves.second; ++it) {
auto slave = it->second;
tmp_master_slave.insert(std::make_pair(new_master, slave));
periodic_slave_master[slave] = new_master;
}
periodic_master_slave.erase(old_master);
(*nodes_flags)[old_master] &= ~NodeFlag::_periodic_master;
addPeriodicSlave(old_master, new_master);
for (auto && data : tmp_master_slave) {
addPeriodicSlave(data.second, data.first);
}
};
// handling 2 nodes that are periodic
auto match_found = [&](auto & info1, auto & info2) {
const auto & node1 = info1.node;
const auto & node2 = info2.node;
auto master = node1;
bool node1_side_master = false;
if (isPeriodicMaster(node1)) {
node1_side_master = true;
} else if (isPeriodicSlave(node1)) {
node1_side_master = true;
master = periodic_slave_master[node1];
}
auto node2_master = node2;
if (isPeriodicSlave(node2)) {
node2_master = periodic_slave_master[node2];
}
if (node1_side_master) {
if (isPeriodicSlave(node2)) {
updating_master(node2_master, master);
return;
}
if (isPeriodicMaster(node2)) {
updating_master(node2, master);
return;
}
addPeriodicSlave(node2, master);
} else {
if (isPeriodicSlave(node2)) {
addPeriodicSlave(node1, node2_master);
return;
}
if (isPeriodicMaster(node2)) {
addPeriodicSlave(node1, node2);
return;
}
addPeriodicSlave(node2, node1);
}
};
// matching the nodes from 2 lists
auto match_pairs = [&](auto & nodes_1, auto & nodes_2) {
// Guillaume to Nico: It seems that the list of nodes is not sorted
// as it was: therefore the loop cannot be truncated anymore.
// Otherwise many pairs are missing.
// I replaced (temporarily?) for the N^2 loop so as not to miss
// any pbc pair.
//
// auto it = nodes_2.begin();
// for every nodes in 1st list
for (auto && info1 : nodes_1) {
auto & pos1 = info1.position;
// auto it_cur = it;
// try to find a match in 2nd list
for (auto && info2 : nodes_2) {
// auto & info2 = *it_cur;
auto & pos2 = info2.position;
auto dist = pos1.distance(pos2) / length;
if (dist < tolerance) {
// handles the found matches
match_found(info1, info2);
// it = it_cur;
break;
}
}
}
};
match_pairs(nodes_left, nodes_right);
// match_pairs(nodes_right, nodes_left);
this->updatePeriodicSynchronizer();
this->is_periodic = true;
}
/* -------------------------------------------------------------------------- */
void Mesh::wipePeriodicInfo() {
this->is_periodic = false;
this->periodic_slave_master.clear();
this->periodic_master_slave.clear();
for (auto && flags : *nodes_flags) {
flags &= ~NodeFlag::_periodic_mask;
}
}
/* -------------------------------------------------------------------------- */
void Mesh::updatePeriodicSynchronizer() {
if (not this->periodic_node_synchronizer) {
this->periodic_node_synchronizer =
std::make_unique<PeriodicNodeSynchronizer>(
*this, this->getID() + ":periodic_synchronizer", false);
}
this->periodic_node_synchronizer->update();
}
} // namespace akantu
diff --git a/src/mesh/node_group.cc b/src/mesh/node_group.cc
index cb788d6bb..e4983d36b 100644
--- a/src/mesh/node_group.cc
+++ b/src/mesh/node_group.cc
@@ -1,96 +1,99 @@
/**
* @file node_group.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Wed Mar 04 2020
*
* @brief Implementation of the node group
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_group.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "mesh.hh"
#if defined(AKANTU_USE_IOHELPER)
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeGroup::NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id)
: name(name),
node_group(0, 1, std::string(id + ":nodes")) {
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + name, name, true);
auto field = std::make_shared<dumpers::NodalField<Real, true>>(
mesh.getNodes(), 0, 0, &this->getNodes());
this->getDumper().registerField("positions", field);
#endif
}
/* -------------------------------------------------------------------------- */
NodeGroup::~NodeGroup() = default;
/* -------------------------------------------------------------------------- */
void NodeGroup::clear() { node_group.resize(0); }
/* -------------------------------------------------------------------------- */
// bool NodeGroup::empty() { return node_group.empty(); }
/* -------------------------------------------------------------------------- */
void NodeGroup::optimize() {
std::sort(node_group.begin(), node_group.end());
Array<UInt>::iterator<> end =
std::unique(node_group.begin(), node_group.end());
node_group.resize(end - node_group.begin());
}
/* -------------------------------------------------------------------------- */
void NodeGroup::append(const NodeGroup & other_group) {
AKANTU_DEBUG_IN();
UInt nb_nodes = node_group.size();
/// append new nodes to current list
node_group.resize(nb_nodes + other_group.node_group.size());
std::copy(other_group.node_group.begin(), other_group.node_group.end(),
node_group.begin() + nb_nodes);
optimize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeGroup::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "NodeGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index 804310797..c1f479d23 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,132 +1,134 @@
/**
* @file node_group.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Node group definition
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "dumpable.hh"
#include "mesh_filter.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NODE_GROUP_HH_
#define AKANTU_NODE_GROUP_HH_
namespace akantu {
class NodeGroup : public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NodeGroup(const std::string & name, const Mesh & mesh,
const std::string & id = "node_group");
~NodeGroup() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
using const_node_iterator = Array<UInt>::const_iterator<UInt>;
/// empty the node group
void clear();
/// returns treu if the group is empty \warning this changed beahavior if you
/// want to empty the group use clear
bool empty() const __attribute__((warn_unused_result));
/// iterator to the beginning of the node group
inline const_node_iterator begin() const;
/// iterator to the end of the node group
inline const_node_iterator end() const;
/// add a node and give the local position through an iterator
inline const_node_iterator add(UInt node, bool check_for_duplicate = true);
/// remove a node
inline void remove(UInt node);
inline decltype(auto) find(UInt node) const { return node_group.find(node); }
/// remove duplicated nodes
void optimize();
/// append a group to current one
void append(const NodeGroup & other_group);
/// apply a filter on current node group
template <typename T> void applyNodeFilter(T & filter);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(Nodes, node_group, Array<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group, const Array<UInt> &);
AKANTU_GET_MACRO(Name, name, const std::string &);
/// give the number of nodes in the current group
inline UInt size() const;
// UInt * storage() { return node_group.storage(); };
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// name of the group
std::string name;
/// list of nodes in the group
Array<UInt> node_group;
/// reference to the mesh in question
// const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const NodeGroup & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.hh"
#endif /* AKANTU_NODE_GROUP_HH_ */
diff --git a/src/mesh/node_group_inline_impl.hh b/src/mesh/node_group_inline_impl.hh
index f7ff2a079..1fdac9958 100644
--- a/src/mesh/node_group_inline_impl.hh
+++ b/src/mesh/node_group_inline_impl.hh
@@ -1,100 +1,102 @@
/**
* @file node_group_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Node group inline function definitions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::begin() const {
return node_group.begin();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::end() const {
return node_group.end();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::add(UInt node,
bool check_for_duplicate) {
if (check_for_duplicate) {
const_node_iterator it = std::find(begin(), end(), node);
if (it == node_group.end()) {
node_group.push_back(node);
return (node_group.end() - 1);
}
return it;
}
node_group.push_back(node);
return (node_group.end() - 1);
}
/* -------------------------------------------------------------------------- */
inline void NodeGroup::remove(UInt node) {
Array<UInt>::iterator<> it = this->node_group.begin();
Array<UInt>::iterator<> end = this->node_group.end();
AKANTU_DEBUG_ASSERT(it != end, "The node group is empty!!");
for (; it != node_group.end(); ++it) {
if (*it == node) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_ASSERT(it != end, "The node was not found!");
}
/* -------------------------------------------------------------------------- */
inline bool NodeGroup::empty() const { return node_group.empty(); }
/* -------------------------------------------------------------------------- */
inline UInt NodeGroup::size() const { return node_group.size(); }
/* -------------------------------------------------------------------------- */
struct FilterFunctor;
template <typename T> void NodeGroup::applyNodeFilter(T & filter) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(T::type == FilterFunctor::_node_filter_functor,
"NodeFilter can only apply node filter functor");
Array<UInt>::iterator<> it = this->node_group.begin();
for (; it != node_group.end(); ++it) {
/// filter == true -> keep node
if (!filter(*it)) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 938ac5c35..3e3f87751 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,324 +1,328 @@
/**
* @file cohesive_element_inserter.cc
*
+ * @author Mathias Lebihain <mathias.lebihain@enpc.fr>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Wed Nov 11 2020
*
* @brief Cohesive element inserter functions
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "cohesive_element_inserter_helper.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "global_ids_updater.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <limits>
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh, const ID & id)
: Parsable(ParserType::_cohesive_inserter), id(id), mesh(mesh),
mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
this->registerParam("cohesive_surfaces", physical_surfaces, _pat_parsable,
"List of groups to consider for insertion");
this->registerParam("cohesive_zones", physical_zones, _pat_parsable,
"List of groups to consider for insertion");
this->registerParam("bounding_box", insertion_limits, _pat_parsable,
"Global limit for insertion");
UInt spatial_dimension = mesh.getSpatialDimension();
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * Real(-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() = default;
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::parseSection(const ParserSection & section) {
Parsable::parseSection(section);
if (is_extrinsic) {
limitCheckFacets(this->check_facets);
}
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
limitCheckFacets(this->check_facets);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(SpatialDirection axis, Real first_limit,
Real second_limit) {
AKANTU_DEBUG_ASSERT(
axis < mesh.getSpatialDimension(),
"You are trying to limit insertion in a direction that doesn't exist");
insertion_limits(axis, 0) = std::min(first_limit, second_limit);
insertion_limits(axis, 1) = std::max(first_limit, second_limit);
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertIntrinsicElements() {
limitCheckFacets(insertion_facets);
return insertElements();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets(
ElementTypeMapArray<bool> & check_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = true);
check_facets.set(true);
// remove the pure ghost elements
for_each_element(
mesh_facets,
[&](auto && facet) {
const auto & element_to_facet = mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
auto & left = element_to_facet[0];
auto & right = element_to_facet[1];
if (right == ElementNull ||
(left.ghost_type == _ghost && right.ghost_type == _ghost)) {
check_facets(facet) = false;
return;
}
#ifndef AKANTU_NDEBUG
if (left == ElementNull) {
AKANTU_DEBUG_WARNING("By convention element should not have "
"ElementNull on there first side: "
<< facet);
}
#endif
if (left.kind() == _ek_cohesive or right.kind() == _ek_cohesive) {
check_facets(facet) = false;
}
},
_spatial_dimension = spatial_dimension - 1);
auto tolerance = Math::getTolerance();
Vector<Real> bary_facet(spatial_dimension);
// set the limits to the bounding box
for_each_element(
mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet);
if (not need_check) {
return;
}
mesh_facets.getBarycenter(facet, bary_facet);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension and
bary_facet(coord_in_limit) >
(insertion_limits(coord_in_limit, 0) - tolerance) and
bary_facet(coord_in_limit) <
(insertion_limits(coord_in_limit, 1) + tolerance)) {
++coord_in_limit;
}
if (coord_in_limit != spatial_dimension) {
need_check = false;
}
},
_spatial_dimension = spatial_dimension - 1);
// remove the physical zones
if (mesh.hasData("physical_names") and not physical_zones.empty()) {
auto && physical_names = mesh.getData<std::string>("physical_names");
for_each_element(
mesh_facets,
[&](auto && facet) {
const auto & element_to_facet = mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
auto count = 0;
for (auto i : arange(2)) {
const auto & element = element_to_facet[i];
if (element == ElementNull) {
continue;
}
const auto & name = physical_names(element);
count += find(physical_zones.begin(), physical_zones.end(), name) !=
physical_zones.end();
}
if (count != 2) {
check_facets(facet) = false;
}
},
_spatial_dimension = spatial_dimension - 1);
}
if (physical_surfaces.empty()) {
AKANTU_DEBUG_OUT();
return;
}
if (not mesh_facets.hasData("physical_names")) {
AKANTU_DEBUG_ASSERT(
physical_surfaces.empty(),
"No physical names in the mesh but insertion limited to a group");
AKANTU_DEBUG_OUT();
return;
}
const auto & physical_ids =
mesh_facets.getData<std::string>("physical_names");
// set the limits to the physical surfaces
for_each_element(
mesh_facets,
[&](auto && facet) {
auto & need_check = check_facets(facet, 0);
if (not need_check) {
return;
}
const auto & physical_id = physical_ids(facet);
auto it = find(physical_surfaces.begin(), physical_surfaces.end(),
physical_id);
need_check = (it != physical_surfaces.end());
},
_spatial_dimension = spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertElements(bool only_double_facets) {
CohesiveNewNodesEvent node_event(AKANTU_CURRENT_FUNCTION);
NewElementsEvent element_event(AKANTU_CURRENT_FUNCTION);
if (mesh_facets.isDistributed()) {
mesh_facets.getElementSynchronizer().synchronizeOnce(
*this, SynchronizationTag::_ce_groups);
}
CohesiveElementInserterHelper cohesive_element_inserter_helper(
mesh, insertion_facets);
UInt nb_new_elements{0};
if (only_double_facets) {
nb_new_elements = cohesive_element_inserter_helper.insertFacetsOnly();
} else {
nb_new_elements = cohesive_element_inserter_helper.insertCohesiveElement();
element_event.getList().copy(
cohesive_element_inserter_helper.getNewElements());
}
auto && doubled_nodes = cohesive_element_inserter_helper.getDoubledNodes();
auto nb_new_nodes = doubled_nodes.size();
node_event.getList().reserve(nb_new_nodes);
node_event.getOldNodesList().reserve(nb_new_nodes);
for (auto && doubled_node : make_view(doubled_nodes, 2)) {
node_event.getList().push_back(doubled_node(1));
node_event.getOldNodesList().push_back(doubled_node(0));
}
if (nb_new_elements > 0) {
updateInsertionFacets();
}
MeshAccessor mesh_accessor(mesh);
std::tie(nb_new_nodes, nb_new_elements) =
mesh_accessor.updateGlobalData(node_event, element_event);
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (auto && facet_gt : ghost_types) {
for (auto && facet_type :
mesh_facets.elementTypes(spatial_dimension - 1, facet_gt)) {
auto & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the intrinsic case
if (not is_extrinsic) {
continue;
}
auto & f_check = check_facets(facet_type, facet_gt);
for (auto && pair : zip(ins_facets, f_check)) {
bool & ins = std::get<0>(pair);
bool & check = std::get<1>(pair);
if (ins) {
ins = check = false;
}
}
}
}
// resize for the newly added facets
insertion_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
// resize for the newly added facets
if (is_extrinsic) {
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = false);
} else {
insertion_facets.set(false);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index d29a1b757..0ec5aa80f 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,173 +1,175 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
- * @date last modification: Sun Feb 04 2018
+ * @date last modification: Tue Jul 21 2020
*
* @brief Cohesive element inserter
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh_utils.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COHESIVE_ELEMENT_INSERTER_HH_
#define AKANTU_COHESIVE_ELEMENT_INSERTER_HH_
namespace akantu {
class GlobalIdsUpdater;
class FacetSynchronizer;
class SolidMechanicsModeslCohesivel;
} // namespace akantu
namespace akantu {
class CohesiveElementInserter : public DataAccessor<Element>, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh,
const ID & id = "cohesive_element_inserter");
~CohesiveElementInserter() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpatialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
auto insertIntrinsicElements() -> UInt;
/// insert extrinsic cohesive elements (returns the number of new
/// cohesive elements)
UInt insertElements(bool only_double_facets = false);
/// limit check facets to match given insertion limits
void limitCheckFacets();
protected:
void parseSection(const ParserSection & section) override;
protected:
/// internal version of limitCheckFacets
void limitCheckFacets(ElementTypeMapArray<bool> & check_facets);
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(InsertionFacetsByElement, insertion_facets,
ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO(InsertionFacetsByElement, insertion_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InsertionFacets, insertion_facets, bool);
AKANTU_GET_MACRO(CheckFacets, check_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO(MeshFacets, mesh_facets, const Mesh &);
AKANTU_GET_MACRO_NOT_CONST(MeshFacets, mesh_facets, Mesh &);
AKANTU_SET_MACRO(IsExtrinsic, is_extrinsic, bool);
public:
friend class SolidMechanicsModelCohesive;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// object id
ID id;
/// main mesh where to insert cohesive elements
Mesh & mesh;
/// mesh containing facets
Mesh & mesh_facets;
/// list of facets where to insert elements
ElementTypeMapArray<bool> insertion_facets;
/// limits for element insertion
Matrix<Real> insertion_limits;
/// list of groups to consider for insertion, ignored if empty
std::set<ID> physical_surfaces;
/// list of groups in between which an inside which element are insterted
std::set<ID> physical_zones;
/// vector containing facets in which extrinsic cohesive elements can be
/// inserted
ElementTypeMapArray<bool> check_facets;
/// global connectivity ids updater
std::unique_ptr<GlobalIdsUpdater> global_ids_updater;
/// is this inserter used in extrinsic
bool is_extrinsic{false};
};
class CohesiveNewNodesEvent : public NewNodesEvent {
public:
CohesiveNewNodesEvent(const std::string & origin) : NewNodesEvent(origin) {}
~CohesiveNewNodesEvent() override = default;
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
private:
Array<UInt> old_nodes;
};
} // namespace akantu
#include "cohesive_element_inserter_inline_impl.hh"
#endif /* AKANTU_COHESIVE_ELEMENT_INSERTER_HH_ */
diff --git a/src/mesh_utils/cohesive_element_inserter_helper.cc b/src/mesh_utils/cohesive_element_inserter_helper.cc
index 01ad01b92..8c5ed9d99 100644
--- a/src/mesh_utils/cohesive_element_inserter_helper.cc
+++ b/src/mesh_utils/cohesive_element_inserter_helper.cc
@@ -1,949 +1,953 @@
/**
* @file cohesive_element_inserter_helper.cc
*
- * @author Nicolas Richart
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation jeu sep 03 2020
+ * @date creation: Tue Sep 08 2020
+ * @date last modification: Wed Dec 23 2020
+ *
+ * @brief An helper class to handle cohesive element insertion
*
- * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter_helper.hh"
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#include <queue>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
CohesiveElementInserterHelper::CohesiveElementInserterHelper(
Mesh & mesh, const ElementTypeMapArray<bool> & facet_insertion)
: doubled_nodes(0, 2, "doubled_nodes"), mesh(mesh),
mesh_facets(mesh.getMeshFacets()) {
auto spatial_dimension = mesh_facets.getSpatialDimension();
for (auto gt : ghost_types) {
for (auto type : mesh_facets.elementTypes(_ghost_type = gt)) {
nb_new_facets(type, gt) = mesh_facets.getNbElement(type, gt);
}
}
std::array<Int, 2> nb_facet_to_insert{0, 0};
// creates a vector of the facets to insert
std::vector<Element> potential_facets_to_double;
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
const auto & f_insertion = facet_insertion(type_facet, gt_facet);
auto & counter = nb_facet_to_insert[gt_facet == _not_ghost ? 0 : 1];
for (auto && data : enumerate(f_insertion)) {
if (std::get<1>(data)) {
UInt el = std::get<0>(data);
potential_facets_to_double.push_back({type_facet, el, gt_facet});
++counter;
}
}
}
}
// Defines a global order of insertion oof cohesive element to ensure node
// doubling appens in the smae order, this is necessary for the global node
// numbering
if (mesh_facets.isDistributed()) {
const auto & comm = mesh_facets.getCommunicator();
ElementTypeMapArray<Int> global_orderings;
global_orderings.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _default_value = -1);
auto starting_index = nb_facet_to_insert[0];
comm.exclusiveScan(starting_index);
// define the local numbers for facet to insert
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
for (auto data : zip(facet_insertion(type_facet, gt_facet),
global_orderings(type_facet, gt_facet))) {
if (std::get<0>(data)) {
std::get<1>(data) = starting_index;
++starting_index;
}
}
}
}
// retreives the oorder number from neighoring processors
auto && synchronizer = mesh_facets.getElementSynchronizer();
SimpleElementDataAccessor<Int> data_accessor(
global_orderings, SynchronizationTag::_ce_insertion_order);
synchronizer.synchronizeOnce(data_accessor,
SynchronizationTag::_ce_insertion_order);
// sort the facets to double based on this global ordering
std::sort(potential_facets_to_double.begin(),
potential_facets_to_double.end(),
[&global_orderings](auto && el1, auto && el2) {
return global_orderings(el1) < global_orderings(el2);
});
}
for (auto d : arange(spatial_dimension)) {
facets_to_double_by_dim[d] = std::make_unique<Array<Element>>(
0, 2, "facets_to_double_" + std::to_string(d));
}
auto & facets_to_double = *facets_to_double_by_dim[spatial_dimension - 1];
MeshAccessor mesh_accessor(mesh_facets);
auto & elements_to_subelements = mesh_accessor.getElementToSubelement();
for (auto && facet_to_double : potential_facets_to_double) {
auto gt_facet = facet_to_double.ghost_type;
auto type_facet = facet_to_double.type;
auto & elements_to_facets = elements_to_subelements(type_facet, gt_facet);
auto & elements_to_facet = elements_to_facets(facet_to_double.element);
if (elements_to_facet[1].type == _not_defined
#if defined(AKANTU_COHESIVE_ELEMENT)
|| elements_to_facet[1].kind() == _ek_cohesive
#endif
) {
AKANTU_DEBUG_WARNING("attempt to double a facet on the boundary");
continue;
}
auto new_facet = nb_new_facets(type_facet, gt_facet)++;
facets_to_double.push_back(Vector<Element>{
facet_to_double, Element{type_facet, new_facet, gt_facet}});
/// update facet_to_element vector
auto & element_to_update = elements_to_facet[1];
auto el = element_to_update.element;
const auto & facets_to_elements = mesh_facets.getSubelementToElement(
element_to_update.type, element_to_update.ghost_type);
auto facets_to_element = Vector<Element>(
make_view(facets_to_elements, facets_to_elements.getNbComponent())
.begin()[el]);
auto facet_to_update = std::find(facets_to_element.begin(),
facets_to_element.end(), facet_to_double);
AKANTU_DEBUG_ASSERT(facet_to_update != facets_to_element.end(),
"Facet not found");
facet_to_update->element = new_facet;
/// update elements connected to facet
const auto & first_facet_list = elements_to_facet;
elements_to_facets.push_back(first_facet_list);
/// set new and original facets as boundary facets
elements_to_facets(new_facet)[0] = elements_to_facets(new_facet)[1];
elements_to_facets(new_facet)[1] = ElementNull;
elements_to_facets(facet_to_double.element)[1] = ElementNull;
}
}
/* -------------------------------------------------------------------------- */
inline auto
CohesiveElementInserterHelper::hasElement(const Vector<UInt> & nodes_element,
const Vector<UInt> & nodes) -> bool {
// if one of the nodes of "nodes" is not in "nodes_element" it stops
auto it = std::mismatch(nodes.begin(), nodes.end(), nodes_element.begin(),
[&](auto && node, auto && /*node2*/) -> bool {
auto it = std::find(nodes_element.begin(),
nodes_element.end(), node);
return (it != nodes_element.end());
});
// true if all "nodes" where found in "nodes_element"
return (it.first == nodes.end());
}
/* -------------------------------------------------------------------------- */
inline auto CohesiveElementInserterHelper::removeElementsInVector(
const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list) -> bool {
if (elem_list.size() <= elem_to_remove.size()) {
return true;
}
auto el_it = elem_to_remove.begin();
auto el_last = elem_to_remove.end();
std::vector<Element>::iterator el_del;
UInt deletions = 0;
for (; el_it != el_last; ++el_it) {
el_del = std::find(elem_list.begin(), elem_list.end(), *el_it);
if (el_del != elem_list.end()) {
elem_list.erase(el_del);
++deletions;
}
}
AKANTU_DEBUG_ASSERT(deletions == 0 || deletions == elem_to_remove.size(),
"Not all elements have been erased");
return deletions == 0;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> * facet_list) {
AKANTU_DEBUG_IN();
for (const auto & element : element_list) {
if (element.type == _not_defined) {
continue;
}
Vector<UInt> connectivity = mesh.getConnectivity(element);
if (element.kind() == _ek_cohesive) {
AKANTU_DEBUG_ASSERT(
facet_list != nullptr,
"Provide a facet list in order to update cohesive elements");
const Vector<Element> facets =
mesh_facets.getSubelementToElement(element);
auto facet_nb_nodes = connectivity.size() / 2;
/// loop over cohesive element's facets
for (const auto & facet : enumerate(facets)) {
/// skip facets if not present in the list
if (std::find(facet_list->begin(), facet_list->end(),
std::get<1>(facet)) == facet_list->end()) {
continue;
}
auto n = std::get<0>(facet);
auto begin =
connectivity.begin() + static_cast<UInt>(n * facet_nb_nodes);
auto end = begin + facet_nb_nodes;
auto it = std::find(begin, end, old_node);
AKANTU_DEBUG_ASSERT(it != end, "Node not found in current element");
*it = new_node;
}
} else {
auto it = std::find(connectivity.begin(), connectivity.end(), old_node);
AKANTU_DEBUG_ASSERT(it != connectivity.end(),
"Node not found in current element");
/// update connectivity
*it = new_node;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::updateSubelementToElement(UInt dim,
bool facet_mode) {
auto & facets_to_double = *facets_to_double_by_dim[dim];
auto & facets_to_subfacets = elementsOfDimToElementsOfDim(
dim + static_cast<decltype(dim)>(facet_mode), dim);
for (auto && data :
zip(make_view(facets_to_double, 2), facets_to_subfacets)) {
const auto & old_subfacet = std::get<0>(data)[0];
const auto & new_subfacet = std::get<0>(data)[1];
auto & facet_to_subfacets = std::get<1>(data);
MeshAccessor mesh_accessor(mesh_facets);
for (auto & facet : facet_to_subfacets) {
Vector<Element> subfacets = mesh_accessor.getSubelementToElement(facet);
auto && subfacet_to_update_it =
std::find(subfacets.begin(), subfacets.end(), old_subfacet);
AKANTU_DEBUG_ASSERT(subfacet_to_update_it != subfacets.end(),
"Subfacet not found");
*subfacet_to_update_it = new_subfacet;
}
}
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::updateElementToSubelement(UInt dim,
bool facet_mode) {
auto & facets_to_double = *facets_to_double_by_dim[dim];
auto & facets_to_subfacets = elementsOfDimToElementsOfDim(
dim + static_cast<decltype(dim)>(facet_mode), dim);
MeshAccessor mesh_accessor(mesh_facets);
// resize the arrays
mesh_accessor.getElementToSubelement().initialize(
mesh_facets, _spatial_dimension = dim, _with_nb_element = true);
for (auto && data :
zip(make_view(facets_to_double, 2), facets_to_subfacets)) {
const auto & new_facet = std::get<0>(data)[1];
mesh_accessor.getElementToSubelement(new_facet) = std::get<1>(data);
}
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::updateQuadraticSegments(UInt dim) {
AKANTU_DEBUG_IN();
auto spatial_dimension = mesh.getSpatialDimension();
auto & facets_to_double = *facets_to_double_by_dim[dim];
MeshAccessor mesh_accessor(mesh_facets);
auto & connectivities = mesh_accessor.getConnectivities();
/// this ones matter only for segments in 3D
Array<std::vector<Element>> * element_to_subfacet_double = nullptr;
Array<std::vector<Element>> * facet_to_subfacet_double = nullptr;
if (dim == spatial_dimension - 2) {
element_to_subfacet_double = &elementsOfDimToElementsOfDim(dim + 2, dim);
facet_to_subfacet_double = &elementsOfDimToElementsOfDim(dim + 1, dim);
}
const auto & element_to_subelement = mesh_facets.getElementToSubelement();
std::vector<UInt> middle_nodes;
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto & old_facet = facet_to_double[0];
if (old_facet.type != _segment_3) {
continue;
}
auto node = connectivities(old_facet, 2);
if (not mesh.isPureGhostNode(node)) {
middle_nodes.push_back(node);
}
}
auto n = doubled_nodes.size();
doubleNodes(middle_nodes);
for (auto && data : enumerate(make_view(facets_to_double, 2))) {
auto facet = std::get<0>(data);
auto & old_facet = std::get<1>(data)[0];
if (old_facet.type != _segment_3) {
continue;
}
auto old_node = connectivities(old_facet, 2);
if (mesh.isPureGhostNode(old_node)) {
continue;
}
auto new_node = doubled_nodes(n, 1);
auto & new_facet = std::get<1>(data)[1];
connectivities(new_facet, 2) = new_node;
if (dim == spatial_dimension - 2) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
element_to_subelement(new_facet, 0));
updateElementalConnectivity(mesh, old_node, new_node,
(*element_to_subfacet_double)(facet),
&(*facet_to_subfacet_double)(facet));
} else {
updateElementalConnectivity(mesh, old_node, new_node,
element_to_subelement(new_facet, 0));
}
++n;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserterHelper::insertCohesiveElement() {
auto nb_new_facets = insertFacetsOnly();
if (nb_new_facets == 0) {
return 0;
}
updateCohesiveData();
return nb_new_facets;
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserterHelper::insertFacetsOnly() {
UInt spatial_dimension = mesh.getSpatialDimension();
if (facets_to_double_by_dim[spatial_dimension - 1]->empty()) {
return 0;
}
if (spatial_dimension == 1) {
doublePointFacet();
} else if (spatial_dimension == 2) {
doubleFacets<1>();
findSubfacetToDouble<1>();
doubleSubfacet<2>();
} else if (spatial_dimension == 3) {
doubleFacets<2>();
findSubfacetToDouble<2>();
doubleFacets<1>();
findSubfacetToDouble<1>();
doubleSubfacet<3>();
}
return facets_to_double_by_dim[spatial_dimension - 1]->size();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void CohesiveElementInserterHelper::doubleFacets() {
AKANTU_DEBUG_IN();
NewElementsEvent new_facets;
auto spatial_dimension = mesh_facets.getSpatialDimension();
auto & facets_to_double = *facets_to_double_by_dim[dim];
MeshAccessor mesh_accessor(mesh_facets);
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto && old_facet = facet_to_double[0];
auto && new_facet = facet_to_double[1];
auto & facets_connectivities =
mesh_accessor.getConnectivity(old_facet.type, old_facet.ghost_type);
facets_connectivities.resize(
nb_new_facets(old_facet.type, old_facet.ghost_type));
auto facets_connectivities_begin =
make_view(facets_connectivities, facets_connectivities.getNbComponent())
.begin();
// copy the connectivities
Vector<UInt> new_conn(facets_connectivities_begin[new_facet.element]);
Vector<UInt> old_conn(facets_connectivities_begin[old_facet.element]);
new_conn = old_conn;
// this will fail if multiple facet types exists for a given element type
// \TODO handle multiple sub-facet types
auto nb_subfacet_per_facet = Mesh::getNbFacetsPerElement(old_facet.type);
auto & subfacets_to_facets = mesh_accessor.getSubelementToElementNC(
old_facet.type, old_facet.ghost_type);
subfacets_to_facets.resize(
nb_new_facets(old_facet.type, old_facet.ghost_type), ElementNull);
auto subfacets_to_facets_begin =
make_view(subfacets_to_facets, nb_subfacet_per_facet).begin();
// copy the subfacet to facets information
Vector<Element> old_subfacets_to_facet(
subfacets_to_facets_begin[old_facet.element]);
Vector<Element> new_subfacet_to_facet(
subfacets_to_facets_begin[new_facet.element]);
new_subfacet_to_facet = old_subfacets_to_facet;
for (auto & subfacet : old_subfacets_to_facet) {
if (subfacet == ElementNull) {
continue;
}
/// update facet_to_subfacet array
mesh_accessor.getElementToSubelement(subfacet).push_back(new_facet);
}
new_facets.getList().push_back(new_facet);
}
/// update facet_to_subfacet and _segment_3 facets if any
if (dim != spatial_dimension - 1) {
updateSubelementToElement(dim, true);
updateElementToSubelement(dim, true);
updateQuadraticSegments(dim);
} else {
updateQuadraticSegments(dim);
}
mesh_facets.sendEvent(new_facets);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void CohesiveElementInserterHelper::findSubfacetToDouble() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
MeshAccessor mesh_accessor(mesh_facets);
auto & facets_to_double = *facets_to_double_by_dim[spatial_dimension - 1];
auto & subfacets_to_facets = mesh_facets.getSubelementToElement();
auto & elements_to_facets = mesh_accessor.getElementToSubelement();
/// loop on every facet
for (auto f : arange(2)) {
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto old_facet = facet_to_double[f];
auto new_facet = facet_to_double[1 - f];
const auto & starting_element = elements_to_facets(new_facet, 0)[0];
auto current_facet = old_facet;
Vector<Element> subfacets_to_facet = subfacets_to_facets.get(old_facet);
/// loop on every subfacet
for (auto & subfacet : subfacets_to_facet) {
if (subfacet == ElementNull) {
continue;
}
if (dim == spatial_dimension - 2) {
Vector<Element> subsubfacets_to_subfacet =
subfacets_to_facets.get(subfacet);
/// loop on every subsubfacet
for (auto & subsubfacet : subsubfacets_to_subfacet) {
if (subsubfacet == ElementNull) {
continue;
}
Vector<UInt> subsubfacet_connectivity =
mesh_facets.getConnectivity(subsubfacet);
std::vector<Element> element_list;
std::vector<Element> facet_list;
std::vector<Element> subfacet_list;
/// check if subsubfacet is to be doubled
if (findElementsAroundSubfacet(
starting_element, current_facet, subsubfacet_connectivity,
element_list, facet_list, &subfacet_list) == false and
removeElementsInVector(
subfacet_list, elements_to_facets(subsubfacet)) == false) {
Element new_subsubfacet{
subsubfacet.type,
nb_new_facets(subsubfacet.type, subsubfacet.ghost_type)++,
subsubfacet.ghost_type};
facets_to_double_by_dim[dim - 1]->push_back(
Vector<Element>{subsubfacet, new_subsubfacet});
elementsOfDimToElementsOfDim(dim - 1, dim - 1)
.push_back(subfacet_list);
elementsOfDimToElementsOfDim(dim, dim - 1)
.push_back(facet_list);
elementsOfDimToElementsOfDim(dim + 1, dim - 1)
.push_back(element_list);
}
}
} else {
std::vector<Element> element_list;
std::vector<Element> facet_list;
Vector<UInt> subfacet_connectivity =
mesh_facets.getConnectivity(subfacet);
/// check if subfacet is to be doubled
if (findElementsAroundSubfacet(starting_element, current_facet,
subfacet_connectivity, element_list,
facet_list) == false and
removeElementsInVector(facet_list,
elements_to_facets(subfacet)) == false) {
Element new_subfacet{
subfacet.type,
nb_new_facets(subfacet.type, subfacet.ghost_type)++,
subfacet.ghost_type};
facets_to_double_by_dim[dim - 1]->push_back(
Vector<Element>{subfacet, new_subfacet});
elementsOfDimToElementsOfDim(dim, dim - 1).push_back(facet_list);
elementsOfDimToElementsOfDim(dim + 1, dim - 1)
.push_back(element_list);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::doubleNodes(
const std::vector<UInt> & old_nodes) {
auto & position = mesh.getNodes();
auto spatial_dimension = mesh.getSpatialDimension();
auto old_nb_nodes = position.size();
position.reserve(old_nb_nodes + old_nodes.size());
doubled_nodes.reserve(doubled_nodes.size() + old_nodes.size());
auto position_begin = position.begin(spatial_dimension);
for (auto && data : enumerate(old_nodes)) {
auto n = std::get<0>(data);
auto old_node = std::get<1>(data);
decltype(old_node) new_node = old_nb_nodes + n;
/// store doubled nodes
doubled_nodes.push_back(Vector<UInt>{old_node, new_node});
/// update position
Vector<Real> coords = Vector<Real>(position_begin[old_node]);
position.push_back(coords);
}
}
/* -------------------------------------------------------------------------- */
bool CohesiveElementInserterHelper::findElementsAroundSubfacet(
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & element_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list) {
bool facet_matched = false;
element_list.push_back(starting_element);
std::queue<Element> elements_to_check;
elements_to_check.push(starting_element);
/// keep going as long as there are elements to check
while (not elements_to_check.empty()) {
/// check current element
Element & current_element = elements_to_check.front();
const Vector<Element> facets_to_element =
mesh_facets.getSubelementToElement(current_element);
// for every facet of the element
for (auto & current_facet : facets_to_element) {
if (current_facet == ElementNull) {
continue;
}
if (current_facet == end_facet) {
facet_matched = true;
}
auto find_facet =
std::find(facet_list.begin(), facet_list.end(), current_facet);
// facet already listed or subfacet_connectivity is not in the
// connectivity of current_facet;
if ((find_facet != facet_list.end()) or
not hasElement(mesh_facets.getConnectivity(current_facet),
subfacet_connectivity)) {
continue;
}
facet_list.push_back(current_facet);
if (subfacet_list != nullptr) {
const Vector<Element> subfacets_of_facet =
mesh_facets.getSubelementToElement(current_facet);
/// check subfacets
for (const auto & current_subfacet : subfacets_of_facet) {
if (current_subfacet == ElementNull) {
continue;
}
auto find_subfacet = std::find(
subfacet_list->begin(), subfacet_list->end(), current_subfacet);
if ((find_subfacet != subfacet_list->end()) or
not hasElement(mesh_facets.getConnectivity(current_subfacet),
subfacet_connectivity)) {
continue;
}
subfacet_list->push_back(current_subfacet);
}
}
/// consider opposing element
const auto & elements_to_facet =
mesh_facets.getElementToSubelement(current_facet);
UInt opposing = 0;
if (elements_to_facet[0] == current_element) {
opposing = 1;
}
auto & opposing_element = elements_to_facet[opposing];
/// skip null elements since they are on a boundary
if (opposing_element == ElementNull) {
continue;
}
/// skip this element if already added
if (std::find(element_list.begin(), element_list.end(),
opposing_element) != element_list.end()) {
continue;
}
/// only regular elements have to be checked
if (opposing_element.kind() == _ek_regular) {
elements_to_check.push(opposing_element);
}
element_list.push_back(opposing_element);
AKANTU_DEBUG_ASSERT(hasElement(mesh.getConnectivity(opposing_element),
subfacet_connectivity),
"Subfacet doesn't belong to this element");
}
/// erased checked element from the list
elements_to_check.pop();
}
return facet_matched;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::updateCohesiveData() {
UInt spatial_dimension = mesh.getSpatialDimension();
bool third_dimension = spatial_dimension == 3;
MeshAccessor mesh_accessor(mesh);
MeshAccessor mesh_facets_accessor(mesh_facets);
for (auto ghost_type : ghost_types) {
for (auto cohesive_type : mesh.elementTypes(_element_kind = _ek_cohesive)) {
auto nb_cohesive_elements = mesh.getNbElement(cohesive_type, ghost_type);
nb_new_facets(cohesive_type, ghost_type) = nb_cohesive_elements;
mesh_facets_accessor.getSubelementToElement(cohesive_type, ghost_type);
}
}
auto & facets_to_double = *facets_to_double_by_dim[spatial_dimension - 1];
new_elements.reserve(new_elements.size() + facets_to_double.size());
std::array<Element, 2> facets;
auto & element_to_facet = mesh_facets_accessor.getElementToSubelement();
auto & facets_to_cohesive_elements =
mesh_facets_accessor.getSubelementToElement();
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto & old_facet = facet_to_double[0];
/// (in 3D cohesive elements connectivity is inverted)
facets[third_dimension ? 1 : 0] = old_facet;
facets[third_dimension ? 0 : 1] = facet_to_double[1];
auto type_cohesive = FEEngine::getCohesiveElementType(old_facet.type);
auto & facet_connectivities =
mesh_facets.getConnectivity(old_facet.type, old_facet.ghost_type);
auto facet_connectivity_it =
facet_connectivities.begin(facet_connectivities.getNbComponent());
auto cohesive_element = Element{
type_cohesive, nb_new_facets(type_cohesive, old_facet.ghost_type)++,
old_facet.ghost_type};
auto & cohesives_connectivities =
mesh_accessor.getConnectivity(type_cohesive, old_facet.ghost_type);
Matrix<UInt> connectivity(facet_connectivities.getNbComponent(), 2);
Vector<Element> facets_to_cohesive_element(2);
for (auto s : arange(2)) {
/// store doubled facets
facets_to_cohesive_element[s] = facets[s];
// update connectivities
connectivity(s) = Vector<UInt>(facet_connectivity_it[facets[s].element]);
/// update element_to_facet vectors
element_to_facet(facets[s], 0)[1] = cohesive_element;
}
cohesives_connectivities.push_back(connectivity);
facets_to_cohesive_elements(type_cohesive, old_facet.ghost_type)
.push_back(facets_to_cohesive_element);
/// add cohesive element to the element event list
new_elements.push_back(cohesive_element);
}
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserterHelper::doublePointFacet() {
UInt spatial_dimension = mesh.getSpatialDimension();
if (spatial_dimension != 1) {
return;
}
NewElementsEvent new_facets_event;
auto & facets_to_double = *facets_to_double_by_dim[spatial_dimension - 1];
const auto & element_to_facet = mesh_facets.getElementToSubelement();
auto & position = mesh.getNodes();
MeshAccessor mesh_accessor(mesh_facets);
for (auto ghost_type : ghost_types) {
for (auto facet_type : nb_new_facets.elementTypes(
spatial_dimension - 1, ghost_type, _ek_regular)) {
auto nb_new_element = nb_new_facets(facet_type, ghost_type);
auto & connectivities =
mesh_accessor.getConnectivity(facet_type, ghost_type);
connectivities.resize(nb_new_element);
}
}
position.reserve(position.size() + facets_to_double.size());
for (auto facet_to_double : make_view(facets_to_double, 2)) {
auto & old_facet = facet_to_double[0];
auto & new_facet = facet_to_double[1];
auto element = element_to_facet(new_facet)[0];
auto & facet_connectivities =
mesh_accessor.getConnectivity(old_facet.type, old_facet.ghost_type);
auto old_node = facet_connectivities(old_facet.element);
auto new_node = position.size();
/// update position
position.push_back(position(old_node));
facet_connectivities(new_facet.element) = new_node;
Vector<UInt> segment_conectivity = mesh.getConnectivity(element);
/// update facet connectivity
auto it = std::find(segment_conectivity.begin(), segment_conectivity.end(),
old_node);
*it = new_node;
doubled_nodes.push_back(Vector<UInt>{old_node, new_node});
new_facets_event.getList().push_back(new_facet);
}
mesh_facets.sendEvent(new_facets_event);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void CohesiveElementInserterHelper::doubleSubfacet() {
if (spatial_dimension == 1) {
return;
}
NewElementsEvent new_facets_event;
std::vector<UInt> nodes_to_double;
MeshAccessor mesh_accessor(mesh_facets);
auto & connectivities = mesh_accessor.getConnectivities();
auto & facets_to_double = *facets_to_double_by_dim[0];
ElementTypeMap<Int> nb_new_elements;
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto && old_element = facet_to_double[0];
nb_new_elements(old_element.type, old_element.ghost_type) = 0;
}
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto && old_element = facet_to_double[0];
++nb_new_elements(old_element.type, old_element.ghost_type);
}
for (auto ghost_type : ghost_types) {
for (auto facet_type :
nb_new_elements.elementTypes(0, ghost_type, _ek_regular)) {
auto & connectivities =
mesh_accessor.getConnectivity(facet_type, ghost_type);
connectivities.resize(connectivities.size() +
nb_new_elements(facet_type, ghost_type));
}
}
for (auto && facet_to_double : make_view(facets_to_double, 2)) {
auto & old_facet = facet_to_double(0);
// auto & new_facet = facet_to_double(1);
AKANTU_DEBUG_ASSERT(
old_facet.type == _point_1,
"Only _point_1 subfacet doubling is supported at the moment");
/// list nodes double
nodes_to_double.push_back(connectivities(old_facet));
}
auto old_nb_doubled_nodes = doubled_nodes.size();
doubleNodes(nodes_to_double);
auto double_nodes_view = make_view(doubled_nodes, 2);
for (auto && data :
zip(make_view(facets_to_double, 2),
range(double_nodes_view.begin() + old_nb_doubled_nodes,
double_nodes_view.end()),
arange(facets_to_double.size()))) {
// auto & old_facet = std::get<0>(data)[0];
auto & new_facet = std::get<0>(data)[1];
new_facets_event.getList().push_back(new_facet);
auto & nodes = std::get<1>(data);
auto old_node = nodes(0);
auto new_node = nodes(1);
auto f = std::get<2>(data);
/// add new nodes in connectivity
connectivities(new_facet) = new_node;
updateElementalConnectivity(mesh, old_node, new_node,
elementsOfDimToElementsOfDim(2, 0)(f),
&elementsOfDimToElementsOfDim(1, 0)(f));
updateElementalConnectivity(mesh_facets, old_node, new_node,
elementsOfDimToElementsOfDim(1, 0)(f));
if (spatial_dimension == 3) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
elementsOfDimToElementsOfDim(0, 0)(f));
}
}
updateSubelementToElement(0, spatial_dimension == 2);
updateElementToSubelement(0, spatial_dimension == 2);
mesh_facets.sendEvent(new_facets_event);
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter_helper.hh b/src/mesh_utils/cohesive_element_inserter_helper.hh
index dbc9ddf8f..3bdac0a3a 100644
--- a/src/mesh_utils/cohesive_element_inserter_helper.hh
+++ b/src/mesh_utils/cohesive_element_inserter_helper.hh
@@ -1,116 +1,118 @@
/**
* @file cohesive_element_inserter_helper.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation jeu sep 03 2020
+ * @date creation: Tue Sep 08 2020
+ * @date last modification: Wed Nov 11 2020
+ *
+ * @brief An helper class to handle cohesive element insertion
*
- * @brief A Documented file.
*
* @section LICENSE
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HELPER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HELPER_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class CohesiveElementInserterHelper {
public:
CohesiveElementInserterHelper(
Mesh & mesh, const ElementTypeMapArray<bool> & facet_insertion);
UInt insertCohesiveElement();
UInt insertFacetsOnly();
private:
template <UInt dim> UInt insertFacetsOnlyImpl();
template <UInt dim> void doubleFacets();
template <UInt dim> void findSubfacetToDouble();
void doubleNodes(const std::vector<UInt> & old_nodes);
bool findElementsAroundSubfacet(
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & element_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list = nullptr);
static inline bool hasElement(const Vector<UInt> & nodes_element,
const Vector<UInt> & nodes);
static inline bool
removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list);
void updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> * facet_list = nullptr);
// update functions
void updateElementToSubelement(UInt dim, bool facet_mode);
void updateSubelementToElement(UInt dim, bool facet_mode);
void updateQuadraticSegments(UInt dim);
void updateCohesiveData();
void doublePointFacet();
template <UInt spatial_dimension> void doubleSubfacet();
decltype(auto) elementsOfDimToElementsOfDim(Int dim1, Int dim2) {
AKANTU_DEBUG_ASSERT(dim1 >= 0 and dim1 <= 3,
"dimension of target element out of range");
AKANTU_DEBUG_ASSERT(dim2 >= 0 and dim2 <= 3,
"dimension of source element out of range");
auto & array = dimelements_to_dimelements[dim1][dim2];
if (not array) {
array = std::make_unique<Array<std::vector<Element>>>();
}
return (*array);
}
public:
decltype(auto) getNewElements() const { return (new_elements); }
decltype(auto) getDoubledNodes() const { return (doubled_nodes); }
private:
std::array<std::unique_ptr<Array<Element>>, 3> facets_to_double_by_dim;
std::array<std::array<std::unique_ptr<Array<std::vector<Element>>>, 2>, 4>
dimelements_to_dimelements;
Array<UInt> doubled_nodes;
Array<Element> new_elements;
Mesh & mesh;
Mesh & mesh_facets;
ElementTypeMap<UInt> nb_new_facets;
};
} // namespace akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HELPER_HH__ */
diff --git a/src/mesh_utils/cohesive_element_inserter_inline_impl.hh b/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
index 59540edb7..7a41290be 100644
--- a/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
+++ b/src/mesh_utils/cohesive_element_inserter_inline_impl.hh
@@ -1,88 +1,91 @@
/**
* @file cohesive_element_inserter_inline_impl.hh
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Fri Dec 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 11 2020
*
* @brief Cohesive element inserter inline functions
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_
#define AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
CohesiveElementInserter::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == SynchronizationTag::_ce_groups) {
size = elements.size() * sizeof(bool);
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_ce_groups) {
for (const auto & el : elements) {
const bool & data = insertion_facets(el);
buffer << data;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
CohesiveElementInserter::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_ce_groups) {
for (const auto & el : elements) {
bool & data = insertion_facets(el);
buffer >> data;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/cohesive_element_inserter_parallel.cc b/src/mesh_utils/cohesive_element_inserter_parallel.cc
index b679d2e29..9c72e265c 100644
--- a/src/mesh_utils/cohesive_element_inserter_parallel.cc
+++ b/src/mesh_utils/cohesive_element_inserter_parallel.cc
@@ -1,36 +1,38 @@
/**
* @file cohesive_element_inserter_parallel.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Fri Dec 08 2017
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Oct 11 2017
*
* @brief Parallel functions for the cohesive element inserter
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "global_ids_updater.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
diff --git a/src/mesh_utils/global_ids_updater.cc b/src/mesh_utils/global_ids_updater.cc
index 316c22d93..f4bef39f6 100644
--- a/src/mesh_utils/global_ids_updater.cc
+++ b/src/mesh_utils/global_ids_updater.cc
@@ -1,140 +1,143 @@
/**
* @file global_ids_updater.cc
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Tue Sep 08 2020
*
* @brief Functions of the GlobalIdsUpdater
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "global_ids_updater.hh"
#include "element_synchronizer.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
UInt GlobalIdsUpdater::updateGlobalIDs(UInt local_nb_new_nodes) {
if (mesh.getCommunicator().getNbProc() == 1) {
return local_nb_new_nodes;
}
UInt total_nb_new_nodes = this->updateGlobalIDsLocally(local_nb_new_nodes);
if (mesh.isDistributed()) {
this->synchronizeGlobalIDs();
}
return total_nb_new_nodes;
}
UInt GlobalIdsUpdater::updateGlobalIDsLocally(UInt local_nb_new_nodes) {
const auto & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
if (nb_proc == 1) {
return local_nb_new_nodes;
}
/// resize global ids array
MeshAccessor mesh_accessor(mesh);
auto && nodes_global_ids = mesh_accessor.getNodesGlobalIds();
UInt old_nb_nodes = mesh.getNbNodes() - local_nb_new_nodes;
nodes_global_ids.resize(mesh.getNbNodes(), -1);
auto && local_or_master_pred = [this](auto && n) {
return this->mesh.isLocalOrMasterNode(n);
};
Vector<UInt> local_master_nodes(2, 0);
/// compute the number of global nodes based on the number of old nodes
auto range_old = arange(old_nb_nodes);
local_master_nodes(0) =
std::count_if(range_old.begin(), range_old.end(), local_or_master_pred);
/// compute amount of local or master doubled nodes
auto range_new = arange(old_nb_nodes, mesh.getNbNodes());
local_master_nodes(1) =
std::count_if(range_new.begin(), range_new.end(), local_or_master_pred);
auto starting_index = local_master_nodes(1);
comm.allReduce(local_master_nodes);
UInt old_global_nodes = local_master_nodes(0);
UInt total_nb_new_nodes = local_master_nodes(1);
if (total_nb_new_nodes == 0) {
return 0;
}
/// set global ids of local and master nodes
comm.exclusiveScan(starting_index);
starting_index += old_global_nodes;
for (auto n : range_new) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
}
}
mesh_accessor.setNbGlobalNodes(old_global_nodes + total_nb_new_nodes);
return total_nb_new_nodes;
}
void GlobalIdsUpdater::synchronizeGlobalIDs() {
this->reduce = true;
this->synchronizer.slaveReductionOnce(*this,
SynchronizationTag::_giu_global_conn);
#ifndef AKANTU_NDEBUG
for (auto node : nodes_flags) {
auto node_flag = mesh.getNodeFlag(node.first);
if (node_flag != NodeFlag::_pure_ghost) {
continue;
}
auto n = 0U;
for (auto & pair : node.second) {
if (std::get<1>(pair) == NodeFlag::_pure_ghost) {
++n;
}
}
if (n == node.second.size()) {
AKANTU_DEBUG_WARNING(
"The node " << n << "is ghost on all the neighboring processors");
}
}
#endif
this->reduce = false;
this->synchronizer.synchronizeOnce(*this,
SynchronizationTag::_giu_global_conn);
}
} // namespace akantu
diff --git a/src/mesh_utils/global_ids_updater.hh b/src/mesh_utils/global_ids_updater.hh
index 21ae2dea4..8d7f3b2ac 100644
--- a/src/mesh_utils/global_ids_updater.hh
+++ b/src/mesh_utils/global_ids_updater.hh
@@ -1,106 +1,108 @@
/**
* @file global_ids_updater.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Class that updates the global ids of new nodes that are
* inserted in the mesh. The functions in this class must be called
* after updating the node types
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GLOBAL_IDS_UPDATER_HH_
#define AKANTU_GLOBAL_IDS_UPDATER_HH_
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
class GlobalIdsUpdater : public DataAccessor<Element> {
public:
GlobalIdsUpdater(Mesh & mesh, ElementSynchronizer & synchronizer)
: mesh(mesh), synchronizer(synchronizer) {}
/// function to update and synchronize the global connectivity of
/// new inserted nodes. It must be called after updating the node
/// types. (It calls in sequence the functions
/// updateGlobalIDsLocally and synchronizeGlobalIDs)
UInt updateGlobalIDs(UInt local_nb_new_nodes);
/// function to update the global connectivity (only locally) of new
/// inserted nodes. It must be called after updating the node types.
UInt updateGlobalIDsLocally(UInt local_nb_new_nodes);
/// function to synchronize the global connectivity of new inserted
/// nodes among the processors. It must be called after updating the
/// node types.
void synchronizeGlobalIDs();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// Reference to the mesh to update
Mesh & mesh;
/// distributed synchronizer to communicate the connectivity
ElementSynchronizer & synchronizer;
/// Tells if a reduction is taking place or not
bool reduce{false};
std::unordered_map<UInt, std::vector<std::pair<UInt, NodeFlag>>> nodes_flags;
};
} // namespace akantu
#include "global_ids_updater_inline_impl.hh"
#endif /* AKANTU_GLOBAL_IDS_UPDATER_HH_ */
diff --git a/src/mesh_utils/global_ids_updater_inline_impl.hh b/src/mesh_utils/global_ids_updater_inline_impl.hh
index 2c3b954c1..63cc4d022 100644
--- a/src/mesh_utils/global_ids_updater_inline_impl.hh
+++ b/src/mesh_utils/global_ids_updater_inline_impl.hh
@@ -1,139 +1,157 @@
/**
* @file global_ids_updater_inline_impl.hh
*
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Tue Sep 08 2020
*
* @brief Implementation of the inline functions of GlobalIdsUpdater
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
- * You should have received a copy of the GNU Lesser General Public License
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "global_ids_updater.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_
#define AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt GlobalIdsUpdater::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
if (tag == SynchronizationTag::_giu_global_conn) {
- size +=
- Mesh::getNbNodesPerElementList(elements) * sizeof(UInt) + sizeof(int);
+ size += Mesh::getNbNodesPerElementList(elements) *
+ (sizeof(UInt) + sizeof(Int)) +
+ sizeof(int);
#ifndef AKANTU_NDEBUG
size += sizeof(NodeFlag) * Mesh::getNbNodesPerElementList(elements);
#endif
}
return size;
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag != SynchronizationTag::_giu_global_conn) {
return;
}
int prank = mesh.getCommunicator().whoAmI();
- auto & global_nodes_ids = mesh.getGlobalNodesIds();
+ const auto & global_nodes_ids = mesh.getGlobalNodesIds();
buffer << prank;
for (const auto & element : elements) {
/// get element connectivity
const Vector<UInt> current_conn =
const_cast<const Mesh &>(mesh).getConnectivity(element);
/// loop on all connectivity nodes
for (auto node : current_conn) {
UInt index = -1;
if ((this->reduce and mesh.isLocalOrMasterNode(node)) or
(not this->reduce and not mesh.isPureGhostNode(node))) {
index = global_nodes_ids(node);
}
buffer << index;
+ buffer << (mesh.isLocalOrMasterNode(node) ? prank
+ : mesh.getNodePrank(node));
#ifndef AKANTU_NDEBUG
- buffer << mesh.getNodeFlag(node);
+ auto node_flag = mesh.getNodeFlag(node);
+ buffer << node_flag;
#endif
}
}
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag != SynchronizationTag::_giu_global_conn) {
return;
}
MeshAccessor mesh_accessor(mesh);
auto & global_nodes_ids = mesh_accessor.getNodesGlobalIds();
int proc;
buffer >> proc;
for (const auto & element : elements) {
/// get element connectivity
Vector<UInt> current_conn =
const_cast<const Mesh &>(mesh).getConnectivity(element);
/// loop on all connectivity nodes
for (auto node : current_conn) {
UInt index;
+ Int node_prank;
buffer >> index;
+ buffer >> node_prank;
#ifndef AKANTU_NDEBUG
NodeFlag node_flag;
buffer >> node_flag;
if (reduce) {
nodes_flags[node].push_back(std::make_pair(proc, node_flag));
}
#endif
if (index == UInt(-1)) {
continue;
}
if (mesh.isSlaveNode(node)) {
auto & gid = global_nodes_ids(node);
AKANTU_DEBUG_ASSERT(gid == UInt(-1) or gid == index,
"The node already has a global id, from proc "
<< proc << ", different from the one received "
<< gid << " " << index);
gid = index;
- mesh_accessor.setNodePrank(node, proc);
+#ifndef AKANTU_NDEBUG
+ auto current_proc = mesh.getNodePrank(node);
+ AKANTU_DEBUG_ASSERT(
+ current_proc == -1 or current_proc == node_prank,
+ "The node "
+ << index << " already has a prank: " << current_proc
+ << ", that is different from the one we are trying to set "
+ << node_prank << " " << node_flag);
+#endif
+ mesh_accessor.setNodePrank(node, node_prank);
}
}
}
}
} // namespace akantu
#endif /* AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/mesh_partition.cc b/src/mesh_utils/mesh_partition.cc
index 38a560665..64f8d599b 100644
--- a/src/mesh_utils/mesh_partition.cc
+++ b/src/mesh_utils/mesh_partition.cc
@@ -1,403 +1,406 @@
/**
* @file mesh_partition.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 17 2010
- * @date last modification: Wed Jan 24 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of common part of all partitioner
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_partition.hh"
#include "aka_iterators.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartition::MeshPartition(Mesh & mesh, UInt spatial_dimension, const ID & id)
: mesh(mesh), spatial_dimension(spatial_dimension),
partitions("partition", id), ghost_partitions("ghost_partition", id),
ghost_partitions_offset("ghost_partition_offset", id),
saved_connectivity("saved_connectivity", id) {
AKANTU_DEBUG_IN();
UInt nb_total_element = 0;
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
linearized_offsets.emplace_back(type, nb_total_element);
nb_total_element += mesh.getConnectivity(type).size();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartition::~MeshPartition() = default;
/* -------------------------------------------------------------------------- */
UInt MeshPartition::linearized(const Element & element) {
auto it =
std::find_if(linearized_offsets.begin(), linearized_offsets.end(),
[&element](auto & a) { return a.first == element.type; });
AKANTU_DEBUG_ASSERT(it != linearized_offsets.end(),
"A bug might be crawling around this corner...");
return (it->second + element.element);
}
/* -------------------------------------------------------------------------- */
Element MeshPartition::unlinearized(UInt lin_element) {
ElementType type{_not_defined};
UInt offset{0};
for (auto & pair : linearized_offsets) {
if (lin_element < pair.second) {
continue;
}
std::tie(type, offset) = pair;
}
return Element{type, lin_element - offset, _not_ghost};
}
/* -------------------------------------------------------------------------- */
/**
* conversion in c++ of the METIS_MeshToDual (mesh.c) function wrote by George
* in Metis (University of Minnesota)
*/
void MeshPartition::buildDualGraph(
Array<Int> & dxadj, Array<Int> & dadjncy, Array<Int> & edge_loads,
const std::function<Int(const Element &, const Element &)> & edge_load_func,
Array<Int> & vertex_loads,
const std::function<Int(const Element &)> & vertex_load_func) {
CSR<Element> nodes_to_elements;
MeshUtils::buildNode2Elements(mesh, nodes_to_elements);
std::unordered_map<UInt, std::vector<UInt>> adjacent_elements;
// for each elements look for its connected elements
for_each_element(
mesh,
[&](auto && element) {
const auto & conn =
const_cast<const Mesh &>(mesh).getConnectivity(element);
std::map<Element, UInt> hits;
// count the number of nodes shared with a given element
for (auto && node : conn) {
for (auto && connected_element : nodes_to_elements.getRow(node)) {
++hits[connected_element];
}
}
// define a minumum number of nodes to share to be considered as a
// ajacent element
UInt magic_number{conn.size()};
for (auto n : arange(mesh.getNbFacetTypes(element.type))) {
magic_number = std::min(
mesh.getNbNodesPerElement(mesh.getFacetType(element.type, n)),
magic_number);
}
// check all neighbors to see which ones are "adjacent"
for (auto && data : hits) {
const auto & adjacent_element = data.first;
// not adjacent to miself
if (adjacent_element == element) {
continue;
}
// not enough shared nodes
if (data.second < magic_number) {
continue;
}
/// Patch in order to prevent neighboring cohesive elements
/// from detecting each other
#if defined(AKANTU_COHESIVE_ELEMENT)
auto element_kind = element.kind();
auto adjacent_element_kind = adjacent_element.kind();
if (element_kind == adjacent_element_kind &&
element_kind == _ek_cohesive) {
continue;
}
#endif
adjacent_elements[this->linearized(element)].push_back(
this->linearized(adjacent_element));
}
},
_spatial_dimension = mesh.getSpatialDimension(),
_element_kind = _ek_not_defined);
// prepare the arrays
auto nb_elements{adjacent_elements.size()};
dxadj.resize(nb_elements + 1);
vertex_loads.resize(nb_elements);
for (auto && data : adjacent_elements) {
const auto & element{data.first};
const auto & neighbors{data.second};
dxadj[element] = neighbors.size();
}
/// convert the dxadj array of sizes in a csr one of offsets
for (UInt i = 1; i < nb_elements; ++i) {
dxadj(i) += dxadj(i - 1);
}
for (UInt i = nb_elements; i > 0; --i) {
dxadj(i) = dxadj(i - 1);
}
dxadj(0) = 0;
dadjncy.resize(dxadj(nb_elements));
edge_loads.resize(dadjncy.size());
// fill the different arrays
for (auto && data : adjacent_elements) {
const auto & element{data.first};
const auto & neighbors{data.second};
auto unlinearized_element = unlinearized(element);
vertex_loads(element) = vertex_load_func(unlinearized_element);
auto pos = dxadj(element);
for (auto && neighbor : neighbors) {
dadjncy(pos) = neighbor;
edge_loads(pos) =
edge_load_func(unlinearized_element, unlinearized(neighbor));
++pos;
}
}
}
/* -------------------------------------------------------------------------- */
void MeshPartition::fillPartitionInformation(
const Mesh & mesh, const Int * linearized_partitions) {
AKANTU_DEBUG_IN();
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
UInt linearized_el = 0;
for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
auto & ghost_partition_offset =
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt part = linearized_partitions[linearized_el];
partition(el) = part;
std::list<UInt> list_adj_part;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
auto conn = Vector<UInt>(*(conn_it + el));
UInt node = conn(n);
for (const auto & adj_element : node_to_elem.getRow(node)) {
UInt adj_el = linearized(adj_element);
UInt adj_part = linearized_partitions[adj_el];
if (part != adj_part) {
list_adj_part.push_back(adj_part);
}
}
}
list_adj_part.sort();
list_adj_part.unique();
for (auto & adj_part : list_adj_part) {
ghost_part_csr.getRows().push_back(adj_part);
ghost_part_csr.rowOffset(el)++;
ghost_partition.push_back(adj_part);
ghost_partition_offset(el)++;
}
}
ghost_part_csr.countToCSR();
/// convert the ghost_partitions_offset array in an offset array
auto & ghost_partitions_offset_ptr = ghost_partitions_offset(type, _ghost);
for (UInt i = 1; i < nb_element; ++i) {
ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
}
for (UInt i = nb_element; i > 0; --i) {
ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
}
ghost_partitions_offset_ptr(0) = 0;
}
// All Facets
for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
for (const auto & type :
mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type);
auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
AKANTU_DEBUG_INFO("Allocating partitions for " << type);
auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
auto & ghost_partition_offset =
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);
AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
const Array<std::vector<Element>> & elem_to_subelem =
mesh.getElementToSubelement(type, _not_ghost);
// Facet loop
for (UInt i(0); i < mesh.getNbElement(type, _not_ghost); ++i) {
const auto & adjacent_elems = elem_to_subelem(i);
if (adjacent_elems.empty()) {
partition(i) = 0;
continue;
}
Element min_elem{_max_element_type, std::numeric_limits<UInt>::max(),
*(ghost_type_t{}.end())};
UInt min_part(std::numeric_limits<UInt>::max());
std::set<UInt> adjacent_parts;
for (auto adj_elem : adjacent_elems) {
if (adj_elem == ElementNull) { // case of boundary elements
continue;
}
auto adjacent_elem_part = partitions(adj_elem);
if (adjacent_elem_part < min_part) {
min_part = adjacent_elem_part;
min_elem = adj_elem;
}
adjacent_parts.insert(adjacent_elem_part);
}
partition(i) = min_part;
auto git = ghost_partitions_csr(min_elem.type, _not_ghost)
.begin(min_elem.element);
auto gend = ghost_partitions_csr(min_elem.type, _not_ghost)
.end(min_elem.element);
for (; git != gend; ++git) {
adjacent_parts.insert(*git);
}
adjacent_parts.erase(min_part);
for (const auto & part : adjacent_parts) {
ghost_part_csr.getRows().push_back(part);
ghost_part_csr.rowOffset(i)++;
ghost_partition.push_back(part);
}
ghost_partition_offset(i + 1) =
ghost_partition_offset(i + 1) + adjacent_elems.size();
}
ghost_part_csr.countToCSR();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::tweakConnectivity() {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
auto & connectivity = mesh_accessor.getConnectivity(type, _not_ghost);
auto & saved_conn = saved_connectivity.alloc(
connectivity.size(), connectivity.getNbComponent(), type, _not_ghost);
saved_conn.copy(connectivity);
for (auto && conn :
make_view(connectivity, connectivity.getNbComponent())) {
for (auto && node : conn) {
if (mesh.isPeriodicSlave(node)) {
node = mesh.getPeriodicMaster(node);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::restoreConnectivity() {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
for (auto && type : saved_connectivity.elementTypes(
spatial_dimension, _not_ghost, _ek_not_defined)) {
auto & conn = mesh_accessor.getConnectivity(type, _not_ghost);
auto & saved_conn = saved_connectivity(type, _not_ghost);
conn.copy(saved_conn);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
bool MeshPartition::hasPartitions(ElementType type, GhostType ghost_type) {
return partitions.exists(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
void MeshPartition::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "MeshPartition ["
<< "\n";
stream << space << " + id : " << id << "\n";
stream << space << " + nb partitions: " << nb_partitions << "\n";
stream << space << " + partitions [ "
<< "\n";
partitions.printself(stream, indent + 2);
stream << space << " ]"
<< "\n";
stream << space << "]"
<< "\n";
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index ab85a9c20..d3d99167d 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,150 +1,153 @@
/**
* @file mesh_partition.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Jan 23 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief tools to partitionate a mesh
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_PARTITION_HH_
#define AKANTU_MESH_PARTITION_HH_
namespace akantu {
class MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartition(Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitioner");
virtual ~MeshPartition();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// define a partition of the mesh
virtual void partitionate(
UInt nb_part,
const std::function<Int(const Element &, const Element &)> &
edge_load_func =
[](auto && /*unused*/, auto && /*unused*/) { return 1; },
const std::function<Int(const Element &)> & vertex_load_func =
[](auto && /*unused*/) { return 1; }) = 0;
/// reorder the nodes to reduce the filling during the factorization of a
/// matrix that has a profil based on the connectivity of the mesh
virtual void reorder() = 0;
/// fill the partitions array with a given linearized partition information
void fillPartitionInformation(const Mesh & mesh,
const Int * linearized_partitions);
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// build the dual graph of the mesh, for all element of spatial_dimension
void
buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const std::function<Int(const Element &, const Element &)> &
edge_load_func,
Array<Int> & vertex_loads,
const std::function<Int(const Element &)> & vertex_load_func);
/// tweak the mesh to handle the PBC pairs
void tweakConnectivity();
/// restore the mesh that has been tweaked
void restoreConnectivity();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
bool hasPartitions(ElementType type, GhostType ghost_type);
AKANTU_GET_MACRO(Partitions, partitions, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Partition, partitions, UInt);
AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr,
const ElementTypeMap<CSR<UInt>> &);
AKANTU_GET_MACRO(NbPartition, nb_partitions, UInt);
AKANTU_SET_MACRO(NbPartition, nb_partitions, UInt);
protected:
UInt linearized(const Element & element);
Element unlinearized(UInt lin_element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id
ID id;
/// the mesh to partition
Mesh & mesh;
/// dimension of the elements to consider in the mesh
UInt spatial_dimension;
/// number of partitions
UInt nb_partitions;
/// partition numbers
ElementTypeMapArray<UInt> partitions;
ElementTypeMap<CSR<UInt>> ghost_partitions_csr;
ElementTypeMapArray<UInt> ghost_partitions;
ElementTypeMapArray<UInt> ghost_partitions_offset;
Array<UInt> * permutation;
ElementTypeMapArray<UInt> saved_connectivity;
// vector of pair to ensure the iteration order
std::vector<std::pair<ElementType, UInt>> linearized_offsets;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const MeshPartition & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#ifdef AKANTU_USE_SCOTCH
#include "mesh_partition_scotch.hh"
#endif
#endif /* AKANTU_MESH_PARTITION_HH_ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
index 5572fc5e8..8aa2b514c 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
@@ -1,139 +1,141 @@
/**
* @file mesh_partition_mesh_data.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of the MeshPartitionMeshData class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "mesh_partition_mesh_data.hh"
#if !defined(AKANTU_NDEBUG)
#include <set>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(Mesh & mesh,
UInt spatial_dimension,
const ID & id)
: MeshPartition(mesh, spatial_dimension, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(
Mesh & mesh, const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension, const ID & id)
: MeshPartition(mesh, spatial_dimension, id),
partition_mapping(&mapping) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::partitionate(
UInt nb_part,
const std::function<Int(const Element &, const Element &)> &/*edge_load_func*/,
const std::function<Int(const Element &)> &/*vertex_load_func*/) {
AKANTU_DEBUG_IN();
if (mesh.isPeriodic()) {
tweakConnectivity();
}
nb_partitions = nb_part;
auto ghost_type = _not_ghost;
auto spatial_dimension = mesh.getSpatialDimension();
UInt linearized_el = 0;
auto nb_elements = mesh.getNbElement(mesh.getSpatialDimension(), ghost_type);
auto *partition_list = new Int[nb_elements];
#if !defined(AKANTU_NDEBUG)
std::set<UInt> partitions;
#endif
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
const auto & partition_array = (*partition_mapping)(type, ghost_type);
AKANTU_DEBUG_ASSERT(partition_array.size() ==
mesh.getNbElement(type, ghost_type),
"The partition mapping does not have the right number "
<< "of entries for type " << type
<< " and ghost type " << ghost_type << "."
<< " Tags=" << partition_array.size()
<< " Mesh=" << mesh.getNbElement(type, ghost_type));
for (auto && part : partition_array) {
partition_list[linearized_el] = part;
#if !defined(AKANTU_NDEBUG)
partitions.insert(part);
#endif
++linearized_el;
}
}
#if !defined(AKANTU_NDEBUG)
AKANTU_DEBUG_ASSERT(partitions.size() == nb_part,
"The number of real partitions does not match with the "
"number of asked partitions");
#endif
fillPartitionInformation(mesh, partition_list);
delete[] partition_list;
if (mesh.isPeriodic()) {
restoreConnectivity();
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::reorder() { AKANTU_TO_IMPLEMENT(); }
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMapping(
const ElementTypeMapArray<UInt> & mapping) {
partition_mapping = &mapping;
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMappingFromMeshData(
const std::string & data_name) {
partition_mapping = &(mesh.getData<UInt>(data_name));
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
index ea386a223..10e73281d 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
@@ -1,93 +1,95 @@
/**
* @file mesh_partition_mesh_data.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief mesh partitioning based on data provided in the mesh
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_PARTITION_MESH_DATA_HH_
#define AKANTU_MESH_PARTITION_MESH_DATA_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionMeshData : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionMeshData(Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData"
);
MeshPartitionMeshData(Mesh & mesh,
const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void partitionate(
UInt nb_part,
const std::function<Int(const Element &, const Element &)> &edge_load_func =
[](auto && /*unused*/, auto && /*unused*/) { return 1; },
const std::function<Int(const Element &)> &vertex_load_func =
[](auto && /*unused*/) { return 1; }) override;
void reorder() override;
void setPartitionMapping(const ElementTypeMapArray<UInt> & mapping);
void setPartitionMappingFromMeshData(const std::string & data_name);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const ElementTypeMapArray<UInt> * partition_mapping;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_MESH_PARTITION_MESH_DATA_HH_ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
index d1c33da68..638375a22 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
@@ -1,471 +1,473 @@
/**
* @file mesh_partition_scotch.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of the MeshPartitionScotch class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_partition_scotch.hh"
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "aka_static_if.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <cstdio>
#include <fstream>
/* -------------------------------------------------------------------------- */
#if !defined(AKANTU_USE_PTSCOTCH)
#ifndef AKANTU_SCOTCH_NO_EXTERN
extern "C" {
#endif // AKANTU_SCOTCH_NO_EXTERN
#include <scotch.h>
#ifndef AKANTU_SCOTCH_NO_EXTERN
}
#endif // AKANTU_SCOTCH_NO_EXTERN
#else // AKANTU_USE_PTSCOTCH
#include <ptscotch.h>
#endif // AKANTU_USE_PTSCOTCH
namespace akantu {
namespace {
constexpr int scotch_version = int(SCOTCH_VERSION);
}
/* -------------------------------------------------------------------------- */
MeshPartitionScotch::MeshPartitionScotch(Mesh & mesh, UInt spatial_dimension,
const ID & id)
: MeshPartition(mesh, spatial_dimension, id) {
AKANTU_DEBUG_IN();
// check if the akantu types and Scotch one are consistent
static_assert(
sizeof(Int) == sizeof(SCOTCH_Num),
"The integer type of Akantu does not match the one from Scotch");
static_if(aka::bool_constant<scotch_version >= 6>{})
.then([](auto && y) { SCOTCH_randomSeed(y); })
.else_([](auto && y) { srandom(y); })(
std::forward<UInt>(RandomGenerator<UInt>::seed()));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
static SCOTCH_Mesh * createMesh(const Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes = mesh.getNbNodes();
UInt total_nb_element = 0;
UInt nb_edge = 0;
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
total_nb_element += nb_element;
nb_edge += nb_element * nb_nodes_per_element;
}
SCOTCH_Num vnodbas = 0;
SCOTCH_Num vnodnbr = nb_nodes;
SCOTCH_Num velmbas = vnodnbr;
SCOTCH_Num velmnbr = total_nb_element;
auto * verttab = new SCOTCH_Num[vnodnbr + velmnbr + 1];
SCOTCH_Num * vendtab = verttab + 1;
SCOTCH_Num * velotab = nullptr;
SCOTCH_Num * vnlotab = nullptr;
SCOTCH_Num * vlbltab = nullptr;
memset(verttab, 0, (vnodnbr + velmnbr + 1) * sizeof(SCOTCH_Num));
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
if (Mesh::getSpatialDimension(type) != spatial_dimension) {
continue;
}
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
/// count number of occurrence of each node
for (UInt el = 0; el < nb_element; ++el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
verttab[*(conn_val++)]++;
}
}
}
/// convert the occurrence array in a csr one
for (UInt i = 1; i < nb_nodes; ++i) {
verttab[i] += verttab[i - 1];
}
for (UInt i = nb_nodes; i > 0; --i) {
verttab[i] = verttab[i - 1];
}
verttab[0] = 0;
/// rearrange element to get the node-element list
SCOTCH_Num edgenbr = verttab[vnodnbr] + nb_edge;
auto * edgetab = new SCOTCH_Num[edgenbr];
UInt linearized_el = 0;
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
for (auto c : conn) {
edgetab[verttab[c]++] = linearized_el + velmbas;
}
++linearized_el;
}
}
for (UInt i = nb_nodes; i > 0; --i) {
verttab[i] = verttab[i - 1];
}
verttab[0] = 0;
SCOTCH_Num * verttab_tmp = verttab + vnodnbr + 1;
SCOTCH_Num * edgetab_tmp = edgetab + verttab[vnodnbr];
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
*verttab_tmp = *(verttab_tmp - 1) + nb_nodes_per_element;
verttab_tmp++;
for (auto c : conn) {
*(edgetab_tmp++) = c + vnodbas;
}
}
}
auto * meshptr = new SCOTCH_Mesh;
SCOTCH_meshInit(meshptr);
SCOTCH_meshBuild(meshptr, velmbas, vnodbas, velmnbr, vnodnbr, verttab,
vendtab, velotab, vnlotab, vlbltab, edgenbr, edgetab);
/// Check the mesh
AKANTU_DEBUG_ASSERT(SCOTCH_meshCheck(meshptr) == 0,
"Scotch mesh is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fmesh = fopen("ScotchMesh.msh", "w");
SCOTCH_meshSave(meshptr, fmesh);
fclose(fmesh);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("ScotchMesh.xyz");
fgeominit << spatial_dimension << std::endl << nb_nodes << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Real * nodes_val = nodes.storage();
for (UInt i = 0; i < nb_nodes; ++i) {
fgeominit << i << " ";
for (UInt s = 0; s < spatial_dimension; ++s) {
fgeominit << *(nodes_val++) << " ";
}
fgeominit << std::endl;
;
}
fgeominit.close();
}
#endif
AKANTU_DEBUG_OUT();
return meshptr;
}
/* -------------------------------------------------------------------------- */
static void destroyMesh(SCOTCH_Mesh * meshptr) {
AKANTU_DEBUG_IN();
SCOTCH_Num velmbas;
SCOTCH_Num vnodbas;
SCOTCH_Num vnodnbr;
SCOTCH_Num velmnbr;
SCOTCH_Num * verttab;
SCOTCH_Num * vendtab;
SCOTCH_Num * velotab;
SCOTCH_Num * vnlotab;
SCOTCH_Num * vlbltab;
SCOTCH_Num edgenbr;
SCOTCH_Num * edgetab;
SCOTCH_Num degrptr;
SCOTCH_meshData(meshptr, &velmbas, &vnodbas, &velmnbr, &vnodnbr, &verttab,
&vendtab, &velotab, &vnlotab, &vlbltab, &edgenbr, &edgetab,
&degrptr);
delete[] verttab;
delete[] edgetab;
SCOTCH_meshExit(meshptr);
delete meshptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::partitionate(
UInt nb_part,
const std::function<Int(const Element &, const Element &)> & edge_load_func,
const std::function<Int(const Element &)> & vertex_load_func) {
AKANTU_DEBUG_IN();
nb_partitions = nb_part;
if (mesh.isPeriodic()) {
tweakConnectivity();
}
AKANTU_DEBUG_INFO("Partitioning the mesh " << mesh.getID() << " in "
<< nb_part << " parts.");
Array<Int> dxadj;
Array<Int> dadjncy;
Array<Int> edge_loads;
Array<Int> vertex_loads;
buildDualGraph(dxadj, dadjncy, edge_loads, edge_load_func, vertex_loads,
vertex_load_func);
/// variables that will hold our structures in scotch format
SCOTCH_Graph scotch_graph;
SCOTCH_Strat scotch_strat;
/// description number and arrays for struct mesh for scotch
SCOTCH_Num baseval = 0; // base numbering for element and
// nodes (0 -> C , 1 -> fortran)
SCOTCH_Num vertnbr = dxadj.size() - 1; // number of vertexes
SCOTCH_Num * parttab; // array of partitions
SCOTCH_Num edgenbr = dxadj(vertnbr); // twice the number of "edges"
//(an "edge" bounds two nodes)
SCOTCH_Num * verttab = dxadj.storage(); // array of start indices in edgetab
SCOTCH_Num * vendtab = nullptr; // array of after-last indices in edgetab
SCOTCH_Num * velotab =
vertex_loads.storage(); // integer load associated with
// every vertex ( optional )
SCOTCH_Num * edlotab = edge_loads.storage(); // integer load associated with
// every edge ( optional )
SCOTCH_Num * edgetab = dadjncy.storage(); // adjacency array of every vertex
SCOTCH_Num * vlbltab = nullptr; // vertex label array (optional)
/// Allocate space for Scotch arrays
parttab = new SCOTCH_Num[vertnbr];
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
/// Initialize the graph structure
SCOTCH_graphInit(&scotch_graph);
/// Build the graph from the adjacency arrays
SCOTCH_graphBuild(&scotch_graph, baseval, vertnbr, verttab, vendtab, velotab,
vlbltab, edgenbr, edgetab, edlotab);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fgraphinit = fopen("GraphIniFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("GeomIniFile.xyz");
fgeominit << spatial_dimension << std::endl << vertnbr << std::endl;
const Array<Real> & nodes = mesh.getNodes();
auto nodes_it = nodes.begin(spatial_dimension);
UInt out_linerized_el = 0;
for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> mid(spatial_dimension);
for (auto && conn : make_view(connectivity, nb_nodes_per_element)) {
mid.set(0.);
for (auto node : conn) {
mid += Vector<Real>(nodes_it[node]);
}
mid /= nb_nodes_per_element;
fgeominit << out_linerized_el++ << " ";
for (UInt s = 0; s < spatial_dimension; ++s) {
fgeominit << mid[s] << " ";
}
fgeominit << std::endl;
;
}
}
fgeominit.close();
}
#endif
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Graph to partition is not consistent");
/// Partition the mesh
SCOTCH_graphPart(&scotch_graph, nb_part, &scotch_strat, parttab);
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Partitioned graph is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save the partitioned graph
FILE * fgraph = fopen("GraphFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraph);
fclose(fgraph);
/// save the partition map
std::ofstream fmap;
fmap.open("MapFile.map");
fmap << vertnbr << std::endl;
for (Int i = 0; i < vertnbr; i++) {
fmap << i << " " << parttab[i] << std::endl;
}
fmap.close();
}
#endif
/// free the scotch data structures
SCOTCH_stratExit(&scotch_strat);
SCOTCH_graphFree(&scotch_graph);
SCOTCH_graphExit(&scotch_graph);
fillPartitionInformation(mesh, parttab);
delete[] parttab;
if (mesh.isPeriodic()) {
restoreConnectivity();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::reorder() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Reordering the mesh " << mesh.getID());
SCOTCH_Mesh * scotch_mesh = createMesh(mesh);
UInt nb_nodes = mesh.getNbNodes();
SCOTCH_Strat scotch_strat;
// SCOTCH_Ordering scotch_order;
auto * permtab = new SCOTCH_Num[nb_nodes];
SCOTCH_Num * peritab = nullptr;
SCOTCH_Num cblknbr = 0;
SCOTCH_Num * rangtab = nullptr;
SCOTCH_Num * treetab = nullptr;
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
SCOTCH_Graph scotch_graph;
SCOTCH_graphInit(&scotch_graph);
SCOTCH_meshGraph(scotch_mesh, &scotch_graph);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
FILE * fgraphinit = fopen("ScotchMesh.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
}
#endif
/// Check the graph
// AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
// "Mesh to Graph is not consistent");
SCOTCH_graphOrder(&scotch_graph, &scotch_strat, permtab, peritab, &cblknbr,
rangtab, treetab);
SCOTCH_graphExit(&scotch_graph);
SCOTCH_stratExit(&scotch_strat);
destroyMesh(scotch_mesh);
/// Renumbering
UInt spatial_dimension = mesh.getSpatialDimension();
MeshAccessor mesh_accessor(mesh);
for (auto gt : ghost_types) {
for (const auto & type : mesh.elementTypes(_ghost_type = gt)) {
auto & connectivity = mesh_accessor.getConnectivity(type, gt);
for (auto && c : make_view(connectivity)) {
c = permtab[c];
}
}
}
/// \todo think of a in-place way to do it
auto * new_coordinates = new Real[spatial_dimension * nb_nodes];
Real * old_coordinates = mesh.getNodes().storage();
for (UInt i = 0; i < nb_nodes; ++i) {
memcpy(new_coordinates + permtab[i] * spatial_dimension,
old_coordinates + i * spatial_dimension,
spatial_dimension * sizeof(Real));
}
memcpy(old_coordinates, new_coordinates,
nb_nodes * spatial_dimension * sizeof(Real));
delete[] new_coordinates;
delete[] permtab;
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
index 4e51d4fe6..f7e3e2e4e 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
@@ -1,75 +1,78 @@
/**
* @file mesh_partition_scotch.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief mesh partitioning based on libScotch
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_PARTITION_SCOTCH_HH_
#define AKANTU_MESH_PARTITION_SCOTCH_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionScotch : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionScotch(Mesh & mesh, UInt spatial_dimension,
const ID & id = "mesh_partition_scotch");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void partitionate(
UInt nb_part,
const std::function<Int(const Element &, const Element &)> &
edge_load_func =
[](auto && /*unused*/, auto && /*unused*/) { return 1; },
const std::function<Int(const Element &)> & vertex_load_func =
[](auto && /*unused*/) { return 1; }) override;
void reorder() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#endif /* AKANTU_MESH_PARTITION_SCOTCH_HH_ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index b1a88f4dd..f2683399c 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,808 +1,812 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Jan 14 2021
*
* @brief All mesh utils necessary for various tasks
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <numeric>
#include <queue>
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<Element> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
if (spatial_dimension == _all_dimensions) {
spatial_dimension = mesh.getSpatialDimension();
}
/// count number of occurrence of each node
UInt nb_nodes = mesh.getNbNodes();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
for_each_element(
mesh,
[&](auto && element) {
Vector<UInt> conn = mesh.getConnectivity(element);
for (auto && node : conn) {
++node_to_elem.rowOffset(node);
}
},
_spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);
node_to_elem.countToCSR();
node_to_elem.resizeCols();
/// rearrange element to get the node-element list
// Element e;
node_to_elem.beginInsertions();
for_each_element(
mesh,
[&](auto && element) {
Vector<UInt> conn = mesh.getConnectivity(element);
for (auto && node : conn) {
node_to_elem.insertInRow(node, element);
}
},
_spatial_dimension = spatial_dimension, _element_kind = _ek_not_defined);
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
CSR<UInt> & node_to_elem,
ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_elements = mesh.getConnectivity(type, ghost_type).size();
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
/// count number of occurrence of each node
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
++node_to_elem.rowOffset(conn_val[el_offset + n]);
}
}
/// convert the occurrence array in a csr one
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// save the element index in the node-element list
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
node_to_elem.insertInRow(conn_val[el_offset + n], el);
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacets(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (auto ghost_type : ghost_types) {
for (const auto & type :
mesh.elementTypes(spatial_dimension - 1, ghost_type)) {
mesh.getConnectivity(type, ghost_type).resize(0);
// \todo inform the mesh event handler
}
}
buildFacetsDimension(mesh, mesh, true, spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension) {
AKANTU_DEBUG_IN();
to_dimension = std::max(to_dimension, UInt(0));
AKANTU_DEBUG_ASSERT(
mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension);
/// sort facets and generate sub-facets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets, mesh_facets, false, i);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension) {
AKANTU_DEBUG_IN();
// save the current parent of mesh_facets and set it temporarly to mesh since
// mesh is the one containing the elements for which mesh_facets has the
// sub-elements
// example: if the function is called with mesh = mesh_facets
const Mesh * mesh_facets_parent = nullptr;
try {
mesh_facets_parent = &mesh_facets.getMeshParent();
} catch (...) {
}
mesh_facets.defineMeshParent(mesh);
MeshAccessor mesh_accessor(mesh_facets);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const auto mesh_facets_nodes_it = mesh_facets_nodes.begin(spatial_dimension);
CSR<Element> node_to_elem;
buildNode2Elements(mesh, node_to_elem, dimension);
Array<UInt> counter;
std::vector<Element> connected_elements;
NewElementsEvent event(AKANTU_CURRENT_FUNCTION);
// init the SubelementToElement data to improve performance
for (auto && ghost_type : ghost_types) {
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
auto & subelement_to_element =
mesh_accessor.getSubelementToElement(type, ghost_type);
subelement_to_element.resize(mesh.getNbElement(type, ghost_type),
ElementNull);
auto facet_types = mesh.getAllFacetTypes(type);
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
const ElementSynchronizer * synchronizer = nullptr;
if (mesh.isDistributed()) {
synchronizer = &(mesh.getElementSynchronizer());
}
Element current_element;
for (auto && ghost_type : ghost_types) {
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
auto facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto && element_to_subelement =
&mesh_accessor.getElementToSubelementNC(facet_type, ghost_type);
auto && connectivity_facets =
&mesh_accessor.getConnectivity(facet_type, ghost_type);
auto nb_nodes_per_facet = connectivity_facets->getNbComponent();
// Vector<UInt> facet(nb_nodes_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
current_element.element = el;
auto && facets =
mesh.getFacetConnectivity(current_element, ft).transpose();
for (auto facet : facets) {
// facet = facets(f);
UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
counter.resize(first_node_nb_elements);
counter.zero();
// loop over the other nodes to search intersecting elements,
// which are the elements that share another node with the
// starting element after first_node
for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {
auto && local_el = std::get<0>(data);
auto && first_node = std::get<1>(data);
for (auto n : arange(1, nb_nodes_per_facet)) {
auto && node_elements = node_to_elem.getRow(facet(n));
counter(local_el) += std::count(
node_elements.begin(), node_elements.end(), first_node);
}
}
// counting the number of elements connected to the facets and
// taking the minimum element number, because the facet should
// be inserted just once
UInt nb_element_connected_to_facet = 0;
Element minimum_el = ElementNull;
connected_elements.clear();
for (auto && data : enumerate(node_to_elem.getRow(facet(0)))) {
if (not(counter(std::get<0>(data)) == nb_nodes_per_facet - 1)) {
continue;
}
auto && real_el = std::get<1>(data);
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
if (minimum_el != current_element) {
continue;
}
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet and mesh.isPureGhostNode(facet(n))) {
++n;
}
if (n == nb_nodes_per_facet) {
full_ghost_facet = true;
}
if (full_ghost_facet) {
continue;
}
if (boundary_only and nb_element_connected_to_facet != 1) {
continue;
}
std::vector<Element> elements;
// build elements_on_facets: linearized_el must come first
// in order to store the facet in the correct direction
// and avoid to invert the sign in the normal computation
elements.reserve(elements.size() + connected_elements.size());
for (auto && connected_element : connected_elements) {
elements.push_back(connected_element);
}
if (nb_element_connected_to_facet == 1) { /// boundary facet
elements.push_back(ElementNull);
} else if (nb_element_connected_to_facet == 2) { /// internal facet
/// check if facet is in between ghost and normal
/// elements: if it's the case, the facet is either
/// ghost or not ghost. The criterion to decide this
/// is arbitrary. It was chosen to check the processor
/// id (prank) of the two neighboring elements. If
/// prank of the ghost element is lower than prank of
/// the normal one, the facet is not ghost, otherwise
/// it's ghost
GhostType gt[2] = {_not_ghost, _not_ghost};
for (UInt el = 0; el < connected_elements.size(); ++el) {
gt[el] = connected_elements[el].ghost_type;
}
if ((gt[0] == _not_ghost) xor (gt[1] == _not_ghost)) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
prank[el] = synchronizer->getRank(connected_elements[el]);
}
// ugly trick from Marco detected :P
bool ghost_one = (gt[0] != _ghost);
if (prank[ghost_one] > prank[!ghost_one]) {
facet_ghost_type = _not_ghost;
} else {
facet_ghost_type = _ghost;
}
connectivity_facets = &mesh_accessor.getConnectivity(
facet_type, facet_ghost_type);
element_to_subelement = &mesh_accessor.getElementToSubelementNC(
facet_type, facet_ghost_type);
}
}
element_to_subelement->push_back(elements);
connectivity_facets->push_back(facet);
/// current facet index
UInt current_facet = connectivity_facets->size() - 1;
Element facet_element{facet_type, current_facet, facet_ghost_type};
event.getList().push_back(facet_element);
/// loop on every element connected to current facet and
/// insert current facet in the first free spot of the
/// subelement_to_element vector
for (auto & loc_el : elements) {
if (loc_el == ElementNull) {
continue;
}
auto && subelements =
mesh_accessor.getSubelementToElement(loc_el);
for (auto & el : subelements) {
if (el != ElementNull) {
continue;
}
el = facet_element;
break;
}
}
/// reset connectivity in case a facet was found in
/// between ghost and normal elements
if (facet_ghost_type != ghost_type) {
facet_ghost_type = ghost_type;
connectivity_facets =
&mesh_accessor.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_accessor.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
}
}
}
}
mesh_facets.sendEvent(event);
// restore the parent of mesh_facet
if (mesh_facets_parent != nullptr) {
mesh_facets.defineMeshParent(*mesh_facets_parent);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes_numbers) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
std::map<UInt, UInt> renumbering_map;
for (UInt i = 0; i < old_nodes_numbers.size(); ++i) {
renumbering_map[old_nodes_numbers(i)] = i;
}
/// renumber the nodes
renumberNodesInConnectivity(local_connectivities,
(nb_local_element + nb_ghost_element) *
nb_nodes_per_element,
renumbering_map);
old_nodes_numbers.resize(renumbering_map.size());
for (auto & renumber_pair : renumbering_map) {
old_nodes_numbers(renumber_pair.second) = renumber_pair.first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
auto & local_conn = mesh_accessor.getConnectivity(type);
local_conn.resize(nb_local_element);
if (nb_local_element > 0) {
memcpy(local_conn.storage(), local_connectivities.storage(),
nb_local_element * nb_nodes_per_element * sizeof(UInt));
}
auto & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
if (nb_ghost_element > 0) {
std::memcpy(ghost_conn.storage(),
local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
}
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
ghost_counter.resize(nb_ghost_element, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(
Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes.storage();
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
auto it = renumbering_map.find(node);
if (it == renumbering_map.end()) {
UInt old_node = node;
renumbering_map[old_node] = new_node_num;
node = new_node_num;
++new_node_num;
} else {
node = it->second;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::purifyMesh(Mesh & mesh) {
AKANTU_DEBUG_IN();
std::map<UInt, UInt> renumbering_map;
RemovedNodesEvent remove_nodes(mesh, AKANTU_CURRENT_FUNCTION);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (auto ghost_type : ghost_types) {
for (auto type :
mesh.elementTypes(_all_dimensions, ghost_type, _ek_not_defined)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity.size());
renumberNodesInConnectivity(
connectivity, nb_element * nb_nodes_per_element, renumbering_map);
}
}
Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));
for (auto && pair : renumbering_map) {
new_numbering(std::get<0>(pair)) = std::get<1>(pair);
}
for (UInt i = 0; i < new_numbering.size(); ++i) {
if (new_numbering(i) == UInt(-1)) {
nodes_removed.push_back(i);
}
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::flipFacets(
Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & remote_global_connectivities,
GhostType gt_facet) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
/// get global connectivity for local mesh
ElementTypeMapArray<UInt> local_global_connectivities(
"local_global_connectivity", mesh_facets.getID());
local_global_connectivities.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_ghost_type = gt_facet, _with_nb_nodes_per_element = true,
_with_nb_element = true);
mesh_facets.getGlobalConnectivity(local_global_connectivities);
MeshAccessor mesh_accessor(mesh_facets);
/// loop on every facet
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & connectivity = mesh_accessor.getConnectivity(type_facet, gt_facet);
auto & local_global_connectivity =
local_global_connectivities(type_facet, gt_facet);
const auto & remote_global_connectivity =
remote_global_connectivities(type_facet, gt_facet);
auto & element_per_facet =
mesh_accessor.getElementToSubelementNC(type_facet, gt_facet);
auto & subfacet_to_facet =
mesh_accessor.getSubelementToElementNC(type_facet, gt_facet);
auto nb_nodes_per_facet = connectivity.getNbComponent();
auto nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
for (auto && data :
zip(make_view(connectivity, nb_nodes_per_facet),
make_view(local_global_connectivity, nb_nodes_per_facet),
make_view(remote_global_connectivity, nb_nodes_per_facet),
make_view(subfacet_to_facet, subfacet_to_facet.getNbComponent()),
make_view(element_per_facet))) {
auto & conn = std::get<0>(data);
auto & local_gconn = std::get<1>(data);
const auto & remote_gconn = std::get<2>(data);
/// skip facet if connectivities are the same
if (local_gconn == remote_gconn) {
continue;
}
/// re-arrange connectivity
auto conn_tmp = conn;
auto begin = local_gconn.begin();
auto end = local_gconn.end();
AKANTU_DEBUG_ASSERT(std::is_permutation(begin, end, remote_gconn.begin()),
"This facets are not just permutation of each other, "
<< local_gconn << " and " << remote_gconn);
for (auto && data : enumerate(remote_gconn)) {
auto it = std::find(begin, end, std::get<1>(data));
AKANTU_DEBUG_ASSERT(it != end, "Node not found");
UInt new_position = it - begin;
conn(new_position) = conn_tmp(std::get<0>(data));
;
}
// std::transform(remote_gconn.begin(), remote_gconn.end(), conn.begin(),
// [&](auto && gnode) {
// auto it = std::find(begin, end, gnode);
// AKANTU_DEBUG_ASSERT(it != end, "Node not found");
// return conn_tmp(it - begin);
// });
/// if 3D, check if facets are just rotated
if (spatial_dimension == 3) {
auto begin = remote_gconn.begin();
/// find first node
auto it = std::find(begin, remote_gconn.end(), local_gconn(0));
UInt n;
UInt start = it - begin;
/// count how many nodes in the received connectivity follow
/// the same order of those in the local connectivity
for (n = 1; n < nb_nodes_per_P1_facet &&
local_gconn(n) ==
remote_gconn((start + n) % nb_nodes_per_P1_facet);
++n) {
;
}
/// skip the facet inversion if facet is just rotated
if (n == nb_nodes_per_P1_facet) {
continue;
}
}
/// update data to invert facet
auto & element_per_facet = std::get<4>(data);
if (element_per_facet[1] !=
ElementNull) { // by convention the first facet
// cannot be a ElementNull
std::swap(element_per_facet[0], element_per_facet[1]);
}
auto & subfacets_of_facet = std::get<3>(data);
std::swap(subfacets_of_facet(0), subfacets_of_facet(1));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::fillElementToSubElementsData(Mesh & mesh) {
AKANTU_DEBUG_IN();
if (mesh.getNbElement(mesh.getSpatialDimension() - 1) == 0) {
AKANTU_DEBUG_INFO("There are not facets, add them in the mesh file or call "
"the buildFacet method.");
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<Real> barycenters("barycenter_tmp", mesh.getID());
barycenters.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = _all_dimensions);
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (const auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> & barycenters_arr = barycenters(type, ghost_type);
barycenters_arr.resize(nb_element);
auto bary = barycenters_arr.begin(spatial_dimension);
auto bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
element.element = el;
mesh.getBarycenter(element, *bary);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
if (mesh.getNbElement(sp) == 0) {
continue;
}
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(sp, ghost_type)) {
auto & subelement_to_element =
mesh_accessor.getSubelementToElement(type, ghost_type);
subelement_to_element.resize(mesh.getNbElement(type, ghost_type));
subelement_to_element.set(ElementNull);
}
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
auto & element_to_subelement =
mesh_accessor.getElementToSubelement(type, ghost_type);
element_to_subelement.resize(mesh.getNbElement(type, ghost_type));
element_to_subelement.clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (auto ghost_type : ghost_types) {
facet_element.ghost_type = ghost_type;
for (const auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
facet_element.type = type;
auto & element_to_subelement =
mesh_accessor.getElementToSubelement(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
//element_to_subelement.resize(connectivity.size());
for (auto && data : enumerate(
make_view(connectivity, mesh.getNbNodesPerElement(type)))) {
const auto & facet = std::get<1>(data);
facet_element.element = std::get<0>(data);
std::map<Element, UInt> element_seen_counter;
auto nb_nodes_per_facet =
mesh.getNbNodesPerElement(Mesh::getP1ElementType(type));
// count the number of node in common between the facet and the
// other element connected to the nodes of the facet
for (auto node : arange(nb_nodes_per_facet)) {
for (auto & elem : nodes_to_elements.getRow(facet(node))) {
auto cit = element_seen_counter.find(elem);
if (cit != element_seen_counter.end()) {
cit->second++;
} else {
element_seen_counter[elem] = 1;
}
}
}
// check which are the connected elements
std::vector<Element> connected_elements;
for (auto && cit : element_seen_counter) {
if (cit.second == nb_nodes_per_facet) {
connected_elements.push_back(cit.first);
}
}
// add the connected elements as sub-elements
for (auto & connected_element : connected_elements) {
element_to_subelement(facet_element.element)
.push_back(connected_element);
}
// add the element as sub-element to the connected elements
for (auto & connected_element : connected_elements) {
Vector<Element> subelements_to_element =
mesh.getSubelementToElement(connected_element);
// find the position where to insert the element
auto it = std::find(subelements_to_element.begin(),
subelements_to_element.end(), ElementNull);
AKANTU_DEBUG_ASSERT(
it != subelements_to_element.end(),
"The element "
<< connected_element << " seems to have too many facets!! ("
<< (it - subelements_to_element.begin()) << " < "
<< mesh.getNbFacetsPerElement(connected_element.type)
<< ")");
*it = facet_element;
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index 23ba3c294..cbcb22468 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,138 +1,140 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Jan 14 2021
*
* @brief All mesh utils necessary for various tasks
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_UTILS_HH_
#define AKANTU_MESH_UTILS_HH_
namespace akantu {
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<Element> that contains for each node the list of connected
/// elements of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh, CSR<Element> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<UInt> that contains for each node the number of
/// the connected elements of a given ElementType
static void
buildNode2ElementsElementTypeMap(const Mesh & mesh, CSR<UInt> & node_to_elem,
ElementType type,
GhostType ghost_type = _not_ghost);
/// build the facets elements on the boundaries of a mesh
static void buildFacets(Mesh & mesh);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets for element of dimension from_dimension to to_dimension
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension = 0);
/// build facets for a given spatial dimension
static void buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension);
/// take the local_connectivity array as the array of local and ghost
/// connectivity, renumber the nodes and set the connectivity of the mesh
static void renumberMeshNodes(Mesh & mesh, Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type, Array<UInt> & old_nodes);
/// compute pbc pair for a given direction
static void computePBCMap(const Mesh & mymesh, UInt dir,
std::map<UInt, UInt> & pbc_pair);
/// compute pbc pair for a surface pair
static void computePBCMap(const Mesh & mymesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair);
/// remove not connected nodes /!\ this functions renumbers the nodes.
static void purifyMesh(Mesh & mesh);
/// fill the subelement to element and the elements to subelements data
static void fillElementToSubElementsData(Mesh & mesh);
/// flip facets based on global connectivity
static void
flipFacets(Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & remote_global_connectivities,
GhostType gt_facet);
private:
/// match pairs that are on the associated pbc's
static void matchPBCPairs(const Mesh & mymesh, UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair);
/// function used by all the renumbering functions
static void
renumberNodesInConnectivity(Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "mesh_utils_inline_impl.hh"
#endif /* AKANTU_MESH_UTILS_HH_ */
diff --git a/src/mesh_utils/mesh_utils_distribution.cc b/src/mesh_utils/mesh_utils_distribution.cc
index b9e7ad2ad..81d184f48 100644
--- a/src/mesh_utils/mesh_utils_distribution.cc
+++ b/src/mesh_utils/mesh_utils_distribution.cc
@@ -1,162 +1,164 @@
/**
* @file mesh_utils_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue Nov 08 2016
- * @date last modification: Tue Nov 07 2017
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Wed Mar 04 2020
*
* @brief Implementation of the methods of mesh utils distribute
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils_distribution.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_partition.hh"
#include "mesh_utils.hh"
#include "node_info_per_processor.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace MeshUtilsDistribution {
/* ------------------------------------------------------------------------ */
void distributeMeshCentralized(Mesh & mesh, UInt /*unused*/,
const MeshPartition & partition) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
auto & gids = mesh_accessor.getNodesGlobalIds();
if (nb_proc == 1) {
return;
}
gids.resize(0);
mesh.synchronizeGroupNames();
AKANTU_DEBUG_ASSERT(
partition.getNbPartition() == nb_proc,
"The number of partition does not match the number of processors: "
<< partition.getNbPartition() << " != " << nb_proc);
/**
* connectivity and communications scheme construction
*/
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
try {
partition.getPartition(type, _not_ghost);
} catch (...) {
continue;
}
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
type, partition);
proc_infos.synchronize();
++count;
}
{ /// Ending the synchronization of elements by sending a stop message
MasterElementInfoPerProc proc_infos(element_synchronizer, count, my_rank,
_not_defined, partition);
proc_infos.synchronize();
++count;
}
/**
* Nodes synchronization
*/
MasterNodeInfoPerProc node_proc_infos(node_synchronizer, count, my_rank);
node_proc_infos.synchronize();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------ */
void distributeMeshCentralized(Mesh & mesh, UInt root) {
MeshAccessor mesh_accessor(mesh);
ElementSynchronizer & element_synchronizer =
mesh_accessor.getElementSynchronizer();
NodeSynchronizer & node_synchronizer = mesh_accessor.getNodeSynchronizer();
const Communicator & comm = element_synchronizer.getCommunicator();
UInt nb_proc = comm.getNbProc();
mesh_accessor.getNodesGlobalIds().resize(0);
if (nb_proc == 1) {
return;
}
mesh.synchronizeGroupNames();
/**
* connectivity and communications scheme construction on distant
* processors
*/
UInt count = 0;
bool need_synchronize = true;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
SlaveElementInfoPerProc proc_infos(element_synchronizer, count, root);
need_synchronize = proc_infos.synchronize();
++count;
} while (need_synchronize);
/**
* Nodes synchronization
*/
SlaveNodeInfoPerProc node_proc_infos(node_synchronizer, count, root);
node_proc_infos.synchronize();
MeshUtils::fillElementToSubElementsData(mesh);
mesh_accessor.setDistributed();
}
} // namespace MeshUtilsDistribution
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils_distribution.hh b/src/mesh_utils/mesh_utils_distribution.hh
index f8c768f12..e9adb97b9 100644
--- a/src/mesh_utils/mesh_utils_distribution.hh
+++ b/src/mesh_utils/mesh_utils_distribution.hh
@@ -1,54 +1,56 @@
/**
* @file mesh_utils_distribution.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sat Apr 01 2017
*
* @brief Mesh utils to distribute a mesh
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_UTILS_DISTRIBUTION_HH_
#define AKANTU_MESH_UTILS_DISTRIBUTION_HH_
namespace akantu {
class Mesh;
class MeshPartition;
} // namespace akantu
namespace akantu {
namespace MeshUtilsDistribution {
/// Master call to distribute a mesh in a centralized manner (the UInt is just
/// to avoid some shitty access from the slave...)
void distributeMeshCentralized(Mesh & mesh, UInt /*unused*/,
const MeshPartition & partition);
/// Slave call to distribute a mesh in a centralized manner
void distributeMeshCentralized(Mesh & mesh, UInt root);
} // namespace MeshUtilsDistribution
} // namespace akantu
#endif /* AKANTU_MESH_UTILS_DISTRIBUTION_HH_ */
diff --git a/src/mesh_utils/mesh_utils_inline_impl.hh b/src/mesh_utils/mesh_utils_inline_impl.hh
index 2c58e450e..19663c824 100644
--- a/src/mesh_utils/mesh_utils_inline_impl.hh
+++ b/src/mesh_utils/mesh_utils_inline_impl.hh
@@ -1,42 +1,45 @@
/**
* @file mesh_utils_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Sep 08 2020
*
* @brief Mesh utils inline functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MESH_UTILS_INLINE_IMPL_HH_
#define AKANTU_MESH_UTILS_INLINE_IMPL_HH_
namespace akantu {
} // namespace akantu
#endif /* AKANTU_MESH_UTILS_INLINE_IMPL_HH_ */
diff --git a/src/mesh_utils/mesh_utils_pbc.cc b/src/mesh_utils/mesh_utils_pbc.cc
index b491caba8..8a44625af 100644
--- a/src/mesh_utils/mesh_utils_pbc.cc
+++ b/src/mesh_utils/mesh_utils_pbc.cc
@@ -1,309 +1,311 @@
/**
* @file mesh_utils_pbc.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Wed Feb 09 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Mar 04 2020
*
* @brief periodic boundary condition connectivity tweak
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/// class that sorts a set of nodes of same coordinates in 'dir' direction
class CoordinatesComparison {
public:
CoordinatesComparison(const UInt dimension, const UInt dir_1,
const UInt dir_2, Real normalization, Real tolerance,
const Array<Real> & coords)
: dim(dimension), dir_1(dir_1), dir_2(dir_2),
normalization(normalization), tolerance(tolerance),
coords_it(coords.begin(dim)) {}
// answers the question whether n2 is larger or equal to n1
bool operator()(const UInt n1, const UInt n2) {
Vector<Real> coords_n1 = coords_it[n1];
Vector<Real> coords_n2 = coords_it[n2];
return this->operator()(coords_n1, coords_n2);
}
bool operator()(const Vector<Real> & coords_n1,
const Vector<Real> & coords_n2) const {
Real diff = coords_n1(dir_1) - coords_n2(dir_1);
;
if (dim == 2 || std::abs(diff) / normalization > tolerance) {
return (diff <= 0.);
}
if (dim > 2) {
diff = coords_n1(dir_2) - coords_n2(dir_2);
return (diff <= 0);
}
return true;
}
private:
UInt dim;
UInt dir_1;
UInt dir_2;
Real normalization;
Real tolerance;
const Array<Real>::const_vector_iterator coords_it;
};
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_left;
Array<UInt> selected_right;
const UInt dim = mesh.getSpatialDimension();
auto it = mesh.getNodes().begin(dim);
auto end = mesh.getNodes().end(dim);
if (dim <= dir) {
return;
}
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_INFO("min " << lower_bounds(dir));
AKANTU_DEBUG_INFO("max " << upper_bounds(dir));
for (UInt node = 0; it != end; ++it, ++node) {
const Vector<Real> & coords = *it;
AKANTU_DEBUG_TRACE("treating " << coords(dir));
if (Math::are_float_equal(coords(dir), lower_bounds(dir))) {
AKANTU_DEBUG_TRACE("pushing node " << node << " on the left side");
selected_left.push_back(node);
} else if (Math::are_float_equal(coords(dir), upper_bounds(dir))) {
selected_right.push_back(node);
AKANTU_DEBUG_TRACE("pushing node " << node << " on the right side");
}
}
AKANTU_DEBUG_INFO("found "
<< selected_left.size() << " and " << selected_right.size()
<< " nodes at each boundary for direction " << dir);
// match pairs
MeshUtils::matchPBCPairs(mesh, dir, selected_left, selected_right, pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh,
const std::pair<ID, ID> & surface_pair,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_first;
Array<UInt> selected_second;
// find nodes on surfaces
const ElementGroup & first_surf = mesh.getElementGroup(surface_pair.first);
const ElementGroup & second_surf = mesh.getElementGroup(surface_pair.second);
// if this surface pair is not on this proc
if (first_surf.getNbNodes() == 0 || second_surf.getNbNodes() == 0) {
AKANTU_DEBUG_WARNING("computePBCMap has at least one surface without any "
"nodes. I will ignore it.");
return;
}
// copy nodes from element group
selected_first.copy(first_surf.getNodeGroup().getNodes());
selected_second.copy(second_surf.getNodeGroup().getNodes());
// coordinates
const Array<Real> & coords = mesh.getNodes();
const UInt dim = mesh.getSpatialDimension();
// variables to find min and max of surfaces
Real first_max[3];
Real first_min[3];
Real second_max[3];
Real second_min[3];
for (UInt i = 0; i < dim; ++i) {
first_min[i] = std::numeric_limits<Real>::max();
second_min[i] = std::numeric_limits<Real>::max();
first_max[i] = -std::numeric_limits<Real>::max();
second_max[i] = -std::numeric_limits<Real>::max();
}
// find min and max of surface nodes
for (auto it = selected_first.begin(); it != selected_first.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (first_min[i] > coords(*it, i)) {
first_min[i] = coords(*it, i);
}
if (first_max[i] < coords(*it, i)) {
first_max[i] = coords(*it, i);
}
}
}
for (auto it = selected_second.begin(); it != selected_second.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (second_min[i] > coords(*it, i)) {
second_min[i] = coords(*it, i);
}
if (second_max[i] < coords(*it, i)) {
second_max[i] = coords(*it, i);
}
}
}
// find direction of pbc
Int first_dir = -1;
#ifndef AKANTU_NDEBUG
Int second_dir = -2;
#endif
for (UInt i = 0; i < dim; ++i) {
if (Math::are_float_equal(first_min[i], first_max[i])) {
first_dir = i;
}
#ifndef AKANTU_NDEBUG
if (Math::are_float_equal(second_min[i], second_max[i])) {
second_dir = i;
}
#endif
}
AKANTU_DEBUG_ASSERT(first_dir == second_dir,
"Surface pair has not same direction. Surface "
<< surface_pair.first << " dir=" << first_dir
<< " ; Surface " << surface_pair.second
<< " dir=" << second_dir);
UInt dir = first_dir;
// match pairs
if (first_min[dir] < second_min[dir]) {
MeshUtils::matchPBCPairs(mesh, dir, selected_first, selected_second,
pbc_pair);
} else {
MeshUtils::matchPBCPairs(mesh, dir, selected_second, selected_first,
pbc_pair);
}
}
/* -------------------------------------------------------------------------- */
void MeshUtils::matchPBCPairs(const Mesh & mesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair) {
// tolerance is that large because most meshers generate points coordinates
// with single precision only (it is the case of GMSH for instance)
Real tolerance = 1e-7;
const UInt dim = mesh.getSpatialDimension();
Real normalization = mesh.getUpperBounds()(dir) - mesh.getLowerBounds()(dir);
AKANTU_DEBUG_ASSERT(std::abs(normalization) > Math::getTolerance(),
"In matchPBCPairs: The normalization is zero. "
<< "Did you compute the bounding box of the mesh?");
auto odir_1 = UInt(-1);
auto odir_2 = UInt(-1);
if (dim == 3) {
if (dir == _x) {
odir_1 = _y;
odir_2 = _z;
} else if (dir == _y) {
odir_1 = _x;
odir_2 = _z;
} else if (dir == _z) {
odir_1 = _x;
odir_2 = _y;
}
} else if (dim == 2) {
if (dir == _x) {
odir_1 = _y;
} else if (dir == _y) {
odir_1 = _x;
}
}
CoordinatesComparison compare_nodes(dim, odir_1, odir_2, normalization,
tolerance, mesh.getNodes());
std::sort(selected_left.begin(), selected_left.end(), compare_nodes);
std::sort(selected_right.begin(), selected_right.end(), compare_nodes);
auto it_left = selected_left.begin();
auto end_left = selected_left.end();
auto it_right = selected_right.begin();
auto end_right = selected_right.end();
auto nit = mesh.getNodes().begin(dim);
while ((it_left != end_left) && (it_right != end_right)) {
UInt i1 = *it_left;
UInt i2 = *it_right;
Vector<Real> coords1 = nit[i1];
Vector<Real> coords2 = nit[i2];
AKANTU_DEBUG_TRACE("do I pair? " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
Real dx = 0.0;
Real dy = 0.0;
if (dim >= 2) {
dx = coords1(odir_1) - coords2(odir_1);
}
if (dim == 3) {
dy = coords1(odir_2) - coords2(odir_2);
}
if (std::abs(dx * dx + dy * dy) / normalization < tolerance) {
// then i match these pairs
if (pbc_pair.count(i2) != 0U) {
i2 = pbc_pair[i2];
}
pbc_pair[i1] = i2;
AKANTU_DEBUG_TRACE("pairing " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
++it_left;
++it_right;
} else if (compare_nodes(coords1, coords2)) {
++it_left;
} else {
++it_right;
}
}
AKANTU_DEBUG_INFO("found " << pbc_pair.size() << " pairs for direction "
<< dir);
}
} // namespace akantu
diff --git a/src/model/common/boundary_condition/boundary_condition.hh b/src/model/common/boundary_condition/boundary_condition.hh
index c51a09c6f..4a08f2267 100644
--- a/src/model/common/boundary_condition/boundary_condition.hh
+++ b/src/model/common/boundary_condition/boundary_condition.hh
@@ -1,99 +1,101 @@
/**
* @file boundary_condition.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief XXX
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BOUNDARY_CONDITION_HH_
#define AKANTU_BOUNDARY_CONDITION_HH_
#include "aka_common.hh"
#include "boundary_condition_functor.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class ModelType> class BoundaryCondition {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
/* ------------------------------------------------------------------------ */
/* Constructors / Destructors / Initializers */
/* ------------------------------------------------------------------------ */
public:
BoundaryCondition() : model(nullptr) {}
/// Initialize the boundary conditions
void initBC(ModelType & model, Array<Real> & primal, Array<Real> & dual);
void initBC(ModelType & model, Array<Real> & primal,
Array<Real> & primal_increment, Array<Real> & dual);
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// Apply the boundary conditions
template <typename FunctorType>
inline void applyBC(const FunctorType & func);
template <class FunctorType>
inline void applyBC(const FunctorType & func, const std::string & group_name);
template <class FunctorType>
inline void applyBC(const FunctorType & func,
const ElementGroup & element_group);
AKANTU_GET_MACRO_NOT_CONST(Model, *model, ModelType &);
AKANTU_GET_MACRO_NOT_CONST(Primal, *primal, Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Dual, *dual, Array<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
template <class FunctorType, BC::Functor::Type type = FunctorType::type>
struct TemplateFunctionWrapper;
private:
ModelType * model;
Array<Real> * primal{nullptr};
Array<Real> * dual{nullptr};
Array<Real> * primal_increment{nullptr};
};
} // namespace akantu
#include "boundary_condition_tmpl.hh"
#endif /* AKANTU_BOUNDARY_CONDITION_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_functor.hh b/src/model/common/boundary_condition/boundary_condition_functor.hh
index d793cb055..19138acbe 100644
--- a/src/model/common/boundary_condition/boundary_condition_functor.hh
+++ b/src/model/common/boundary_condition/boundary_condition_functor.hh
@@ -1,213 +1,215 @@
/**
* @file boundary_condition_functor.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Definitions of the functors to apply boundary conditions
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_
#define AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace BC {
using Axis = ::akantu::SpatialDirection;
/* ---------------------------------------------------------------------- */
struct Functor {
enum Type { _dirichlet, _neumann };
virtual ~Functor() = default;
};
/* ---------------------------------------------------------------------- */
namespace Dirichlet {
class DirichletFunctor : public Functor {
public:
DirichletFunctor() = default;
explicit DirichletFunctor(Axis ax) : axis(ax) {}
virtual void operator()(__attribute__((unused)) UInt node,
__attribute__((unused)) Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
AKANTU_TO_IMPLEMENT();
}
public:
static const Type type = _dirichlet;
protected:
Axis axis{_x};
};
/* ---------------------------------------------------------------------- */
class FlagOnly : public DirichletFunctor {
public:
explicit FlagOnly(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const override;
};
/* ---------------------------------------------------------------------- */
// class FreeBoundary : public DirichletFunctor {
// public:
// explicit FreeBoundary(Axis ax = _x) : DirichletFunctor(ax) {}
// public:
// inline void operator()(UInt node, Vector<bool> & flags,
// Vector<Real> & primal,
// const Vector<Real> & coord) const;
// };
/* ---------------------------------------------------------------------- */
class FixedValue : public DirichletFunctor {
public:
FixedValue(Real val, Axis ax = _x) : DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const override;
protected:
Real value;
};
/* ---------------------------------------------------------------------- */
class IncrementValue : public DirichletFunctor {
public:
IncrementValue(Real val, Axis ax = _x)
: DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const override;
inline void setIncrement(Real val) { this->value = val; }
protected:
Real value;
};
/* ---------------------------------------------------------------------- */
class Increment : public DirichletFunctor {
public:
explicit Increment(const Vector<Real> & val)
: DirichletFunctor(_x), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const override;
inline void setIncrement(const Vector<Real> & val) { this->value = val; }
protected:
Vector<Real> value;
};
} // namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
class NeumannFunctor : public Functor {
protected:
NeumannFunctor() = default;
public:
virtual void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const = 0;
~NeumannFunctor() override = default;
public:
static const Type type = _neumann;
};
/* ---------------------------------------------------------------------- */
class FromHigherDim : public NeumannFunctor {
public:
explicit FromHigherDim(const Matrix<Real> & mat) : bc_data(mat) {}
~FromHigherDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
explicit FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
~FromSameDim() override = default;
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
protected:
Vector<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public NeumannFunctor {
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const override;
};
} // namespace Neumann
} // namespace BC
} // namespace akantu
#include "boundary_condition_functor_inline_impl.hh"
#endif /* AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh b/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
index e7ec81c3d..d19c4aa3a 100644
--- a/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
+++ b/src/model/common/boundary_condition/boundary_condition_functor_inline_impl.hh
@@ -1,146 +1,148 @@
/**
* @file boundary_condition_functor_inline_impl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Sat Dec 22 2018
*
* @brief implementation of the BC::Functors
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_
#define AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
#define DIRICHLET_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
primal.size() <= flags.size(), \
"The primal vector and flags vectors given" \
<< " to the boundary condition functor have different sizes!");
#define NEUMANN_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= normals.size(), \
"The coordinates and normals vectors given to the" \
<< " boundary condition functor have different sizes!"); \
namespace akantu {
namespace BC {
/* ---------------------------------------------------------------------- */
namespace Dirichlet {
inline void FlagOnly::
operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
}
/* ---------------------------------------------------------------------- */
// inline void FreeBoundary::
// operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
// __attribute__((unused)) Vector<Real> & primal,
// __attribute__((unused)) const Vector<Real> & coord) const {
// DIRICHLET_SANITY_CHECK;
// flags(this->axis) = false;
// }
/* ---------------------------------------------------------------------- */
inline void FixedValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) = value;
}
/* ---------------------------------------------------------------------- */
inline void IncrementValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) += value;
}
/* ---------------------------------------------------------------------- */
inline void Increment::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags.set(true);
primal += value;
}
} // namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
inline void FreeBoundary::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
for (UInt i(0); i < dual.size(); ++i) {
dual(i) = 0.0;
}
}
/* ---------------------------------------------------------------------- */
inline void FromHigherDim::operator()(__attribute__((unused))
const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused))
const Vector<Real> & coord,
const Vector<Real> & normals) const {
dual.mul<false>(this->bc_data, normals);
}
/* ---------------------------------------------------------------------- */
inline void FromSameDim::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
dual = this->bc_data;
}
} // namespace Neumann
} // namespace BC
} // namespace akantu
#endif /* AKANTU_BOUNDARY_CONDITION_FUNCTOR_INLINE_IMPL_HH_ */
diff --git a/src/model/common/boundary_condition/boundary_condition_tmpl.hh b/src/model/common/boundary_condition/boundary_condition_tmpl.hh
index 5d825594b..d98a09e01 100644
--- a/src/model/common/boundary_condition/boundary_condition_tmpl.hh
+++ b/src/model/common/boundary_condition/boundary_condition_tmpl.hh
@@ -1,231 +1,233 @@
/**
* @file boundary_condition_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Mon Oct 28 2019
*
* @brief implementation of the applyBC
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BOUNDARY_CONDITION_TMPL_HH_
#define AKANTU_BOUNDARY_CONDITION_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & dual) {
this->model = &model;
this->primal = &primal;
this->dual = &dual;
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & primal_increment,
Array<Real> & dual) {
this->initBC(model, primal, dual);
this->primal_increment = &primal_increment;
}
/* -------------------------------------------------------------------------- */
/* Partial specialization for DIRICHLET functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_dirichlet> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
auto & model = bc_instance.getModel();
auto & primal = bc_instance.getPrimal();
const auto & coords = model.getMesh().getNodes();
auto & boundary_flags = model.getBlockedDOFs();
UInt dim = model.getMesh().getSpatialDimension();
auto primal_iter = primal.begin(primal.getNbComponent());
auto coords_iter = coords.begin(dim);
auto flags_iter = boundary_flags.begin(boundary_flags.getNbComponent());
for (auto n : group.getNodeGroup()) {
Vector<bool> flag(flags_iter[n]);
Vector<Real> primal(primal_iter[n]);
Vector<Real> coords(coords_iter[n]);
func(n, flag, primal, coords);
}
}
};
/* -------------------------------------------------------------------------- */
/* Partial specialization for NEUMANN functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_neumann> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
UInt dim = bc_instance.getModel().getSpatialDimension();
switch (dim) {
case 1: {
AKANTU_TO_IMPLEMENT();
break;
}
case 2:
case 3: {
applyBC(func, group, bc_instance, _not_ghost);
applyBC(func, group, bc_instance, _ghost);
break;
}
}
}
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance,
GhostType ghost_type) {
auto & model = bc_instance.getModel();
auto & dual = bc_instance.getDual();
const auto & mesh = model.getMesh();
const auto & nodes_coords = mesh.getNodes();
const auto & fem_boundary = model.getFEEngineBoundary();
UInt dim = model.getSpatialDimension();
UInt nb_degree_of_freedom = dual.getNbComponent();
IntegrationPoint quad_point;
quad_point.ghost_type = ghost_type;
// Loop over the boundary element types
for (auto && type : group.elementTypes(dim - 1, ghost_type)) {
const auto & element_ids = group.getElements(type, ghost_type);
UInt nb_quad_points =
fem_boundary.getNbIntegrationPoints(type, ghost_type);
UInt nb_elements = element_ids.size();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> dual_before_integ(nb_elements * nb_quad_points,
nb_degree_of_freedom, 0.);
Array<Real> quad_coords(nb_elements * nb_quad_points, dim);
const auto & normals_on_quad =
fem_boundary.getNormalsOnIntegrationPoints(type, ghost_type);
fem_boundary.interpolateOnIntegrationPoints(
nodes_coords, quad_coords, dim, type, ghost_type, element_ids);
auto normals_begin = normals_on_quad.begin(dim);
decltype(normals_begin) normals_iter;
auto quad_coords_iter = quad_coords.begin(dim);
auto dual_iter = dual_before_integ.begin(nb_degree_of_freedom);
quad_point.type = type;
for (auto el : element_ids) {
quad_point.element = el;
normals_iter = normals_begin + el * nb_quad_points;
for (auto q : arange(nb_quad_points)) {
quad_point.num_point = q;
func(quad_point, *dual_iter, *quad_coords_iter, *normals_iter);
++dual_iter;
++quad_coords_iter;
++normals_iter;
}
}
Array<Real> dual_by_shapes(nb_elements * nb_quad_points,
nb_degree_of_freedom * nb_nodes_per_element);
fem_boundary.computeNtb(dual_before_integ, dual_by_shapes, type,
ghost_type, element_ids);
Array<Real> dual_by_shapes_integ(nb_elements, nb_degree_of_freedom *
nb_nodes_per_element);
fem_boundary.integrate(dual_by_shapes, dual_by_shapes_integ,
nb_degree_of_freedom * nb_nodes_per_element, type,
ghost_type, element_ids);
// assemble the result into force vector
model.getDOFManager().assembleElementalArrayLocalArray(
dual_by_shapes_integ, dual, type, ghost_type, 1., element_ids);
}
}
};
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void BoundaryCondition<ModelType>::applyBC(const FunctorType & func) {
auto bit = model->getMesh().getGroupManager().element_group_begin();
auto bend = model->getMesh().getGroupManager().element_group_end();
for (; bit != bend; ++bit) {
applyBC(func, *bit);
}
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const std::string & group_name) {
try {
const ElementGroup & element_group =
model->getMesh().getElementGroup(group_name);
applyBC(func, element_group);
} catch (akantu::debug::Exception & e) {
AKANTU_EXCEPTION("Error applying a boundary condition onto \""
<< group_name << "\"! [" << e.what() << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const ElementGroup & element_group) {
#if !defined(AKANTU_NDEBUG)
if (element_group.getDimension() != model->getSpatialDimension() - 1) {
AKANTU_DEBUG_WARNING("The group "
<< element_group.getName()
<< " does not contain only boundaries elements");
}
#endif
TemplateFunctionWrapper<FunctorType>::applyBC(func, element_group, *this);
}
#endif /* AKANTU_BOUNDARY_CONDITION_TMPL_HH_ */
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager.cc b/src/model/common/dof_manager/dof_manager.cc
index ac135f4bb..5c0918248 100644
--- a/src/model/common/dof_manager/dof_manager.cc
+++ b/src/model/common/dof_manager/dof_manager.cc
@@ -1,1015 +1,1017 @@
/**
* @file dof_manager.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Sat Mar 06 2021
*
* @brief Implementation of the common parts of the DOFManagers
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "communicator.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
#include "non_linear_solver.hh"
#include "periodic_node_synchronizer.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(const ID & id)
: id(id), dofs_flag(0, 1, std::string(id + ":dofs_type")),
global_equation_number(0, 1, "global_equation_number"),
communicator(Communicator::getStaticCommunicator()) {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(Mesh & mesh, const ID & id)
: id(id), mesh(&mesh), dofs_flag(0, 1, std::string(id + ":dofs_type")),
global_equation_number(0, 1, "global_equation_number"),
communicator(mesh.getCommunicator()) {
this->mesh->registerEventHandler(*this, _ehp_dof_manager);
}
/* -------------------------------------------------------------------------- */
DOFManager::~DOFManager() = default;
/* -------------------------------------------------------------------------- */
std::vector<ID> DOFManager::getDOFIDs() const {
std::vector<ID> keys;
for (const auto & dof_data : this->dofs) {
keys.push_back(dof_data.first);
}
return keys;
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
ElementType type, GhostType ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
AKANTU_DEBUG_ASSERT(elementary_vect.size() == nb_element,
"The vector elementary_vect("
<< elementary_vect.getID()
<< ") has not the good size.");
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
Array<Real>::const_matrix_iterator elem_it =
elementary_vect.begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++elem_it) {
UInt element = el;
if (filter_it != nullptr) {
// conn_it = conn_begin + *filter_it;
element = *filter_it;
}
// const Vector<UInt> & conn = *conn_it;
const Matrix<Real> & elemental_val = *elem_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_node = connectivity(element, n) * nb_degree_of_freedom;
Vector<Real> assemble(array_assembeled.storage() + offset_node,
nb_degree_of_freedom);
Vector<Real> elem_val = elemental_val(n);
assemble.aXplusY(elem_val, scale_factor);
}
if (filter_it != nullptr) {
++filter_it;
}
// else
// ++conn_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect, ElementType type,
GhostType ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.zero();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToResidual(dof_id, array_localy_assembeled, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, ElementType type, GhostType ghost_type,
Real scale_factor, const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.zero();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToLumpedMatrix(dof_id, array_localy_assembeled, lumped_mtx, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = *pair.second;
this->assembleMatMulVectToResidual(dof_id, A_id, *dof_data.dof,
scale_factor);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::splitSolutionPerDOFs() {
for (auto && data : this->dofs) {
auto & dof_data = *data.second;
dof_data.solution.resize(dof_data.dof->size() *
dof_data.dof->getNbComponent());
this->getSolutionPerDOFs(data.first, dof_data.solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getSolution(), solution_array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::getLumpedMatrixPerDOFs(const ID & dof_id,
const ID & lumped_mtx,
Array<Real> & lumped) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getLumpedMatrix(lumped_mtx), lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
// this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
this->assembleToGlobalArray(dof_id, array_to_assemble, this->getResidual(),
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor) {
AKANTU_DEBUG_IN();
// this->makeConsistentForPeriodicity(dof_id, array_to_assemble);
auto & lumped = this->getLumpedMatrix(lumped_mtx);
this->assembleToGlobalArray(dof_id, array_to_assemble, lumped, scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::DOFData(const ID & dof_id)
: support_type(_dst_generic), group_support("__mesh__"),
solution(0, 1, dof_id + ":solution"),
local_equation_number(0, 1, dof_id + ":local_equation_number"),
associated_nodes(0, 1, dof_id + "associated_nodes") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::~DOFData() = default;
/* -------------------------------------------------------------------------- */
template <typename Func>
auto DOFManager::countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
Func && getNode) {
auto nb_local_dofs = nb_nodes;
decltype(nb_local_dofs) nb_pure_local = 0;
for (auto n : arange(nb_nodes)) {
UInt node = getNode(n);
// http://www.open-std.org/jtc1/sc22/open/n2356/conv.html
// bool are by convention casted to 0 and 1 when promoted to int
nb_pure_local += this->mesh->isLocalOrMasterNode(node);
nb_local_dofs -= this->mesh->isPeriodicSlave(node);
}
const auto & dofs_array = *dof_data.dof;
nb_pure_local *= dofs_array.getNbComponent();
nb_local_dofs *= dofs_array.getNbComponent();
return std::make_pair(nb_local_dofs, nb_pure_local);
}
/* -------------------------------------------------------------------------- */
auto DOFManager::getNewDOFDataInternal(const ID & dof_id) -> DOFData & {
auto it = this->dofs.find(dof_id);
if (it != this->dofs.end()) {
AKANTU_EXCEPTION("This dof array has already been registered");
}
std::unique_ptr<DOFData> dof_data_ptr = this->getNewDOFData(dof_id);
DOFData & dof_data = *dof_data_ptr;
this->dofs[dof_id] = std::move(dof_data_ptr);
return dof_data;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) {
auto & dofs_storage = this->getNewDOFDataInternal(dof_id);
dofs_storage.support_type = support_type;
this->registerDOFsInternal(dof_id, dofs_array);
resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group) {
auto & dofs_storage = this->getNewDOFDataInternal(dof_id);
dofs_storage.support_type = _dst_nodal;
dofs_storage.group_support = support_group;
this->registerDOFsInternal(dof_id, dofs_array);
resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManager::registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) {
DOFData & dof_data = this->getDOFData(dof_id);
dof_data.dof = &dofs_array;
UInt nb_local_dofs = 0;
UInt nb_pure_local = 0;
const auto & support_type = dof_data.support_type;
switch (support_type) {
case _dst_nodal: {
const auto & group = dof_data.group_support;
std::function<UInt(UInt)> getNode;
if (group == "__mesh__") {
AKANTU_DEBUG_ASSERT(
dofs_array.size() == this->mesh->getNbNodes(),
"The array of dof is too short to be associated to nodes.");
std::tie(nb_local_dofs, nb_pure_local) = countDOFsForNodes(
dof_data, this->mesh->getNbNodes(), [](auto && n) { return n; });
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
AKANTU_DEBUG_ASSERT(
dofs_array.size() == node_group.size(),
"The array of dof is too shot to be associated to nodes.");
std::tie(nb_local_dofs, nb_pure_local) =
countDOFsForNodes(dof_data, node_group.size(),
[&node_group](auto && n) { return node_group(n); });
}
break;
}
case _dst_generic: {
nb_local_dofs = nb_pure_local =
dofs_array.size() * dofs_array.getNbComponent();
break;
}
default: {
AKANTU_EXCEPTION("This type of dofs is not handled yet.");
}
}
dof_data.local_nb_dofs = nb_local_dofs;
dof_data.pure_local_nb_dofs = nb_pure_local;
dof_data.ghosts_nb_dofs = nb_local_dofs - nb_pure_local;
this->pure_local_system_size += nb_pure_local;
this->local_system_size += nb_local_dofs;
auto nb_total_pure_local = nb_pure_local;
communicator.allReduce(nb_total_pure_local, SynchronizerOperation::_sum);
this->system_size += nb_total_pure_local;
// updating the dofs data after counting is finished
switch (support_type) {
case _dst_nodal: {
const auto & group = dof_data.group_support;
if (group != "__mesh__") {
auto & support_nodes =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
this->updateDOFsData(
dof_data, nb_local_dofs, nb_pure_local, support_nodes.size(),
[&support_nodes](UInt node) -> UInt { return support_nodes[node]; });
} else {
this->updateDOFsData(dof_data, nb_local_dofs, nb_pure_local,
mesh->getNbNodes(),
[](UInt node) -> UInt { return node; });
}
break;
}
case _dst_generic: {
this->updateDOFsData(dof_data, nb_local_dofs, nb_pure_local);
break;
}
}
return std::make_tuple(nb_local_dofs, nb_pure_local, nb_total_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.previous != nullptr) {
AKANTU_EXCEPTION("The previous dofs array for "
<< dof_id << " has already been registered");
}
dof.previous = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsIncrement(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.increment != nullptr) {
AKANTU_EXCEPTION("The dofs increment array for "
<< dof_id << " has already been registered");
}
dof.increment = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative) {
DOFData & dof = this->getDOFData(dof_id);
std::vector<Array<Real> *> & derivatives = dof.dof_derivatives;
if (derivatives.size() < order) {
derivatives.resize(order, nullptr);
} else {
if (derivatives[order - 1] != nullptr) {
AKANTU_EXCEPTION("The dof derivatives of order "
<< order << " already been registered for this dof ("
<< dof_id << ")");
}
}
derivatives[order - 1] = &dofs_derivative;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs) {
DOFData & dof = this->getDOFData(dof_id);
if (dof.blocked_dofs != nullptr) {
AKANTU_EXCEPTION("The blocked dofs array for "
<< dof_id << " has already been registered");
}
dof.blocked_dofs = &blocked_dofs;
}
/* -------------------------------------------------------------------------- */
SparseMatrix &
DOFManager::registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix) {
auto it = this->matrices.find(matrix_id);
if (it != this->matrices.end()) {
AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
<< this->id);
}
auto & ret = *matrix;
this->matrices[matrix_id] = std::move(matrix);
return ret;
}
/* -------------------------------------------------------------------------- */
/// Get an instance of a new SparseMatrix
SolverVector &
DOFManager::registerLumpedMatrix(const ID & matrix_id,
std::unique_ptr<SolverVector> & matrix) {
auto it = this->lumped_matrices.find(matrix_id);
if (it != this->lumped_matrices.end()) {
AKANTU_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
<< this->id);
}
auto & ret = *matrix;
this->lumped_matrices[matrix_id] = std::move(matrix);
ret.resize();
return ret;
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::registerNonLinearSolver(
const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver) {
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it != this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " already exists in "
<< this->id);
}
NonLinearSolver & ret = *non_linear_solver;
this->non_linear_solvers[non_linear_solver_id] = std::move(non_linear_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::registerTimeStepSolver(
const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver) {
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it != this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " already exists in "
<< this->id);
}
TimeStepSolver & ret = *time_step_solver;
this->time_step_solvers[time_step_solver_id] = std::move(time_step_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManager::getMatrix(const ID & id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it == this->matrices.end()) {
AKANTU_SILENT_EXCEPTION("The matrix " << matrix_id << " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasMatrix(const ID & id) const {
ID mtx_id = this->id + ":mtx:" + id;
auto it = this->matrices.find(mtx_id);
return it != this->matrices.end();
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManager::getLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const SolverVector & DOFManager::getLumpedMatrix(const ID & id) const {
ID matrix_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasLumpedMatrix(const ID & id) const {
ID mtx_id = this->id + ":lumped_mtx:" + id;
auto it = this->lumped_matrices.find(mtx_id);
return it != this->lumped_matrices.end();
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::getNonLinearSolver(const ID & id) {
ID non_linear_solver_id = this->id + ":nls:" + id;
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it == this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasNonLinearSolver(const ID & id) const {
ID solver_id = this->id + ":nls:" + id;
auto it = this->non_linear_solvers.find(solver_id);
return it != this->non_linear_solvers.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::getTimeStepSolver(const ID & id) {
ID time_step_solver_id = this->id + ":tss:" + id;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it == this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasTimeStepSolver(const ID & solver_id) const {
ID time_step_solver_id = this->id + ":tss:" + solver_id;
auto it = this->time_step_solvers.find(time_step_solver_id);
return it != this->time_step_solvers.end();
}
/* -------------------------------------------------------------------------- */
void DOFManager::savePreviousDOFs(const ID & dofs_id) {
this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
}
/* -------------------------------------------------------------------------- */
void DOFManager::zeroResidual() { this->residual->zero(); }
/* -------------------------------------------------------------------------- */
void DOFManager::zeroMatrix(const ID & mtx) { this->getMatrix(mtx).zero(); }
/* -------------------------------------------------------------------------- */
void DOFManager::zeroLumpedMatrix(const ID & mtx) {
this->getLumpedMatrix(mtx).zero();
}
/* -------------------------------------------------------------------------- */
/* Mesh Events */
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManager::updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) {
auto & dof_data = this->getDOFData(dof_id);
UInt nb_new_local_dofs;
UInt nb_new_pure_local;
std::tie(nb_new_local_dofs, nb_new_pure_local) =
countDOFsForNodes(dof_data, nodes_list.size(),
[&nodes_list](auto && n) { return nodes_list(n); });
this->pure_local_system_size += nb_new_pure_local;
this->local_system_size += nb_new_local_dofs;
UInt nb_new_global = nb_new_pure_local;
communicator.allReduce(nb_new_global, SynchronizerOperation::_sum);
this->system_size += nb_new_global;
dof_data.solution.resize(local_system_size);
updateDOFsData(dof_data, nb_new_local_dofs, nb_new_pure_local,
nodes_list.size(),
[&nodes_list](UInt pos) -> UInt { return nodes_list[pos]; });
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::resizeGlobalArrays() {
// resize all relevant arrays
this->residual->resize();
this->solution->resize();
this->data_cache->resize();
for (auto & lumped_matrix : lumped_matrices) {
lumped_matrix.second->resize();
}
for (auto & matrix : matrices) {
matrix.second->clearProfile();
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & /*unused*/) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal) {
continue;
}
const auto & group = dof_data.group_support;
if (group == "__mesh__") {
this->updateNodalDOFs(dof_id, nodes_list);
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup();
Array<UInt> new_nodes_list;
for (const auto & node : nodes_list) {
if (node_group.find(node) != UInt(-1)) {
new_nodes_list.push_back(node);
}
}
this->updateNodalDOFs(dof_id, new_nodes_list);
}
}
this->resizeGlobalArrays();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class GlobalDOFInfoDataAccessor : public DataAccessor<UInt> {
public:
using size_type =
typename std::unordered_map<UInt, std::vector<UInt>>::size_type;
GlobalDOFInfoDataAccessor(DOFManager::DOFData & dof_data,
DOFManager & dof_manager)
: dof_data(dof_data), dof_manager(dof_manager) {
for (auto && pair :
zip(dof_data.local_equation_number, dof_data.associated_nodes)) {
UInt node;
Int dof;
std::tie(dof, node) = pair;
dofs_per_node[node].push_back(dof);
}
}
UInt getNbData(const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
return nodes.size() * dof_data.dof->getNbComponent() * sizeof(Int);
}
return 0;
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
for (const auto & node : nodes) {
const auto & dofs = dofs_per_node.at(node);
for (const auto & dof : dofs) {
buffer << dof_manager.global_equation_number(dof);
}
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_ask_nodes or
tag == SynchronizationTag::_giu_global_conn) {
for (const auto & node : nodes) {
const auto & dofs = dofs_per_node[node];
for (const auto & dof : dofs) {
Int global_dof;
buffer >> global_dof;
AKANTU_DEBUG_ASSERT(
(dof_manager.global_equation_number(dof) == -1 or
dof_manager.global_equation_number(dof) == global_dof),
"This dof already had a global_dof_id which is different from "
"the received one. "
<< dof_manager.global_equation_number(dof)
<< " != " << global_dof);
dof_manager.global_equation_number(dof) = global_dof;
dof_manager.global_to_local_mapping[global_dof] = dof;
}
}
}
}
protected:
std::unordered_map<UInt, std::vector<Int>> dofs_per_node;
DOFManager::DOFData & dof_data;
DOFManager & dof_manager;
};
/* -------------------------------------------------------------------------- */
auto DOFManager::computeFirstDOFIDs(UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
// determine the first local/global dof id to use
UInt offset = 0;
this->communicator.exclusiveScan(nb_new_pure_local, offset);
auto first_global_dof_id = this->first_global_dof_id + offset;
auto first_local_dof_id = this->local_system_size - nb_new_local_dofs;
offset = nb_new_pure_local;
this->communicator.allReduce(offset);
this->first_global_dof_id += offset;
return std::make_pair(first_local_dof_id, first_global_dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManager::updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_node,
const std::function<UInt(UInt)> & getNode) {
auto nb_local_dofs_added = nb_node * dof_data.dof->getNbComponent();
auto first_dof_pos = dof_data.local_equation_number.size();
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_local_dofs_added);
dof_data.associated_nodes.reserve(dof_data.associated_nodes.size() +
nb_local_dofs_added);
this->dofs_flag.resize(this->local_system_size, NodeFlag::_normal);
this->global_equation_number.resize(this->local_system_size, -1);
std::unordered_map<std::pair<UInt, UInt>, UInt> masters_dofs;
// update per dof info
UInt local_eq_num;
UInt first_global_dof_id;
std::tie(local_eq_num, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
for (auto d : arange(nb_local_dofs_added)) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof_flag = this->mesh->getNodeFlag(node);
dof_data.associated_nodes.push_back(node);
auto is_local_dof = this->mesh->isLocalOrMasterNode(node);
auto is_periodic_slave = this->mesh->isPeriodicSlave(node);
auto is_periodic_master = this->mesh->isPeriodicMaster(node);
if (is_periodic_slave) {
dof_data.local_equation_number.push_back(-1);
continue;
}
// update equation numbers
this->dofs_flag(local_eq_num) = dof_flag;
dof_data.local_equation_number.push_back(local_eq_num);
if (is_local_dof) {
this->global_equation_number(local_eq_num) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = local_eq_num;
++first_global_dof_id;
} else {
this->global_equation_number(local_eq_num) = -1;
}
if (is_periodic_master) {
auto node = getNode(d / dof_data.dof->getNbComponent());
auto dof = d % dof_data.dof->getNbComponent();
masters_dofs.insert(
std::make_pair(std::make_pair(node, dof), local_eq_num));
}
++local_eq_num;
}
// correct periodic slave equation numbers
if (this->mesh->isPeriodic()) {
auto assoc_begin = dof_data.associated_nodes.begin();
for (auto d : arange(nb_local_dofs_added)) {
auto node = dof_data.associated_nodes(first_dof_pos + d);
if (not this->mesh->isPeriodicSlave(node)) {
continue;
}
auto master_node = this->mesh->getPeriodicMaster(node);
auto dof = d % dof_data.dof->getNbComponent();
dof_data.local_equation_number(first_dof_pos + d) =
masters_dofs[std::make_pair(master_node, dof)];
}
}
// synchronize the global numbering for slaves nodes
if (this->mesh->isDistributed()) {
GlobalDOFInfoDataAccessor data_accessor(dof_data, *this);
if (this->mesh->isPeriodic()) {
mesh->getPeriodicNodeSynchronizer().synchronizeOnce(
data_accessor, SynchronizationTag::_giu_global_conn);
}
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronizeOnce(data_accessor,
SynchronizationTag::_ask_nodes);
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local) {
dof_data.local_equation_number.reserve(dof_data.local_equation_number.size() +
nb_new_local_dofs);
UInt first_local_dof_id;
UInt first_global_dof_id;
std::tie(first_local_dof_id, first_global_dof_id) =
computeFirstDOFIDs(nb_new_local_dofs, nb_new_pure_local);
this->dofs_flag.resize(this->local_system_size, NodeFlag::_normal);
this->global_equation_number.resize(this->local_system_size, -1);
// update per dof info
for (auto _ [[gnu::unused]] : arange(nb_new_local_dofs)) {
// update equation numbers
this->dofs_flag(first_local_dof_id) = NodeFlag::_normal;
dof_data.local_equation_number.push_back(first_local_dof_id);
this->global_equation_number(first_local_dof_id) = first_global_dof_id;
this->global_to_local_mapping[first_global_dof_id] = first_local_dof_id;
++first_global_dof_id;
++first_local_dof_id;
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesRemoved(const Array<UInt> & /*unused*/,
const Array<UInt> & /*unused*/,
const RemovedNodesEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsAdded(const Array<Element> & /*unused*/,
const NewElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const RemovedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsChanged(const Array<Element> & /*unused*/,
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) {}
/* -------------------------------------------------------------------------- */
void DOFManager::updateGlobalBlockedDofs() {
this->previous_global_blocked_dofs.copy(this->global_blocked_dofs);
this->global_blocked_dofs.reserve(this->local_system_size, 0);
this->previous_global_blocked_dofs_release =
this->global_blocked_dofs_release;
for (auto & pair : dofs) {
if (not this->hasBlockedDOFs(pair.first)) {
continue;
}
DOFData & dof_data = *pair.second;
for (auto && data : zip(dof_data.getLocalEquationsNumbers(),
make_view(*dof_data.blocked_dofs))) {
const auto & dof = std::get<0>(data);
const auto & is_blocked = std::get<1>(data);
if (is_blocked) {
this->global_blocked_dofs.push_back(dof);
}
}
}
std::sort(this->global_blocked_dofs.begin(), this->global_blocked_dofs.end());
auto last = std::unique(this->global_blocked_dofs.begin(),
this->global_blocked_dofs.end());
this->global_blocked_dofs.resize(last - this->global_blocked_dofs.begin());
auto are_equal =
global_blocked_dofs.size() == previous_global_blocked_dofs.size() and
std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
previous_global_blocked_dofs.begin());
if (not are_equal) {
++this->global_blocked_dofs_release;
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::applyBoundary(const ID & matrix_id) {
auto & J = this->getMatrix(matrix_id);
if (this->jacobian_release == J.getRelease()) {
if (this->hasBlockedDOFsChanged()) {
J.applyBoundary();
}
previous_global_blocked_dofs.copy(global_blocked_dofs);
} else {
J.applyBoundary();
}
this->jacobian_release = J.getRelease();
this->previous_global_blocked_dofs_release =
this->global_blocked_dofs_release;
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulVectToGlobalArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
SolverVector & array,
Real scale_factor) {
auto & A = this->getMatrix(A_id);
data_cache->resize();
data_cache->zero();
this->assembleToGlobalArray(dof_id, x, *data_cache, 1.);
A.matVecMul(*data_cache, array, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
assembleMatMulVectToGlobalArray(dof_id, A_id, x, *residual, scale_factor);
}
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager.hh b/src/model/common/dof_manager/dof_manager.hh
index 2014fb11b..2b3e6362a 100644
--- a/src/model/common/dof_manager/dof_manager.hh
+++ b/src/model/common/dof_manager/dof_manager.hh
@@ -1,721 +1,723 @@
/**
* @file dof_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Class handling the different types of dofs
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_MANAGER_HH_
#define AKANTU_DOF_MANAGER_HH_
namespace akantu {
class TermsToAssemble;
class NonLinearSolver;
class TimeStepSolver;
class SparseMatrix;
class SolverVector;
class SolverCallback;
} // namespace akantu
namespace akantu {
class DOFManager : protected MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
struct DOFData;
public:
DOFManager(const ID & id = "dof_manager");
DOFManager(Mesh & mesh, const ID & id = "dof_manager");
~DOFManager() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register an array of degree of freedom
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type);
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group);
/// register an array of previous values of the degree of freedom
virtual void registerDOFsPrevious(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of increment of degree of freedom
virtual void registerDOFsIncrement(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of derivatives for a particular dof array
virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative);
/// register array representing the blocked degree of freedoms
virtual void registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor = 1.);
/// Assemble an array to the global lumped matrix array
virtual void assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.);
/**
* Assemble elementary values to a local array of the size nb_nodes *
* nb_dof_per_node. The dof number is implicitly considered as
* conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
ElementType type, GhostType ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
ElementType type, GhostType ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to a global array corresponding to a lumped
* matrix
*/
virtual void assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, ElementType type,
GhostType ghost_type, Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, ElementType type,
GhostType ghost_type = _not_ghost,
const MatrixType & elemental_matrix_type = _symmetric,
const Array<UInt> & filter_elements = empty_filter) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor = 1) = 0;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// assemble coupling terms between to dofs
virtual void assemblePreassembledMatrix(const ID & dof_id_m,
const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1);
/// multiply the dofs by a matrix and assemble the result to the residual
virtual void assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor = 1);
/// updates the global blocked_dofs array
virtual void updateGlobalBlockedDofs();
/// sets the residual to 0
virtual void zeroResidual();
/// sets the matrix to 0
virtual void zeroMatrix(const ID & mtx);
/// sets the lumped matrix to 0
virtual void zeroLumpedMatrix(const ID & mtx);
virtual void applyBoundary(const ID & matrix_id = "J");
// virtual void applyBoundaryLumped(const ID & matrix_id = "J");
/// extract a lumped matrix part corresponding to a given dof
virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped);
/// splits the solution storage from a global view to the per dof storages
void splitSolutionPerDOFs();
private:
/// dispatch the creation of the dof data and register it
DOFData & getNewDOFDataInternal(const ID & dof_id);
protected:
/// common function to help registering dofs the return values are the add new
/// numbers of local dofs, pure local dofs, and system size
virtual std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);
/// minimum functionality to implement per derived version of the DOFManager
/// to allow the splitSolutionPerDOFs function to work
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array);
/// fill a Vector with the equation numbers corresponding to the given
/// connectivity
static inline void extractElementEquationNumber(
const Array<Int> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<Int> & element_equation_number);
/// Assemble a array to a global one
void assembleMatMulVectToGlobalArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
SolverVector & array,
Real scale_factor = 1.);
/// common function that can be called by derived class with proper matrice
/// types
template <typename Mat>
void assemblePreassembledMatrix_(Mat & A, const ID & dof_id_m,
const ID & dof_id_n,
const TermsToAssemble & terms);
template <typename Mat>
void assembleElementalMatricesToMatrix_(
Mat & A, const ID & dof_id, const Array<Real> & elementary_mat,
ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements);
template <typename Vec>
void assembleMatMulVectToArray_(const ID & dof_id, const ID & A_id,
const Array<Real> & x, Array<Real> & array,
Real scale_factor);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the location type of a given dof
inline bool isLocalOrMasterDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isSlaveDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isPureGhostDOF(UInt local_dof_num);
/// tells if the dof manager knows about a global dof
bool hasGlobalEquationNumber(Int global) const;
/// return the local index of the global equation number
inline Int globalToLocalEquationNumber(Int global) const;
/// converts local equation numbers to global equation numbers;
inline Int localToGlobalEquationNumber(Int local) const;
/// get the array of dof types (use only if you know what you do...)
inline NodeFlag getDOFFlag(Int local_id) const;
/// defines if the boundary changed
bool hasBlockedDOFsChanged() {
return this->global_blocked_dofs_release !=
this->previous_global_blocked_dofs_release;
}
/// Global number of dofs
AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);
/// Local number of dofs
AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);
/// Pure local number of dofs
AKANTU_GET_MACRO(PureLocalSystemSize, this->pure_local_system_size, UInt);
/// Retrieve all the registered DOFs
std::vector<ID> getDOFIDs() const;
/* ------------------------------------------------------------------------ */
/* DOFs and derivatives accessors */
/* ------------------------------------------------------------------------ */
/// Get a reference to the registered dof array for a given id
inline Array<Real> & getDOFs(const ID & dofs_id);
/// Get the support type of a given dof
inline DOFSupportType getSupportType(const ID & dofs_id) const;
/// are the dofs registered
inline bool hasDOFs(const ID & dof_id) const;
/// Get a reference to the registered dof derivatives array for a given id
inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);
/// Does the dof has derivatives
inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;
/// Get a reference to the blocked dofs array registered for the given id
inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;
/// Does the dof has a blocked array
inline bool hasBlockedDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof increment array for a given id
inline Array<Real> & getDOFsIncrement(const ID & dofs_id);
/// Does the dof has a increment array
inline bool hasDOFsIncrement(const ID & dofs_id) const;
/// Does the dof has a previous array
inline Array<Real> & getPreviousDOFs(const ID & dofs_id);
/// Get a reference to the registered dof array for previous step values a
/// given id
inline bool hasPreviousDOFs(const ID & dofs_id) const;
/// saves the values from dofs to previous dofs
virtual void savePreviousDOFs(const ID & dofs_id);
/// Get a reference to the solution array registered for the given id
inline const Array<Real> & getSolution(const ID & dofs_id) const;
/// Get a reference to the solution array registered for the given id
inline Array<Real> & getSolution(const ID & dofs_id);
/// Get the blocked dofs array
AKANTU_GET_MACRO(GlobalBlockedDOFs, global_blocked_dofs, const Array<Int> &);
/// Get the blocked dofs array
AKANTU_GET_MACRO(PreviousGlobalBlockedDOFs, previous_global_blocked_dofs,
const Array<Int> &);
/* ------------------------------------------------------------------------ */
/* Matrices accessors */
/* ------------------------------------------------------------------------ */
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) = 0;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) = 0;
/// Get the equation numbers corresponding to a dof_id. This might be used to
/// access the matrix.
inline const Array<Int> & getLocalEquationsNumbers(const ID & dof_id) const;
protected:
/// get the array of dof types (use only if you know what you do...)
inline const Array<UInt> & getDOFsAssociatedNodes(const ID & dof_id) const;
protected:
/* ------------------------------------------------------------------------ */
/// register a matrix
SparseMatrix & registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix);
/// register a lumped matrix (aka a Vector)
SolverVector & registerLumpedMatrix(const ID & matrix_id,
std::unique_ptr<SolverVector> & matrix);
/// register a non linear solver instantiated by a derived class
NonLinearSolver &
registerNonLinearSolver(const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver);
/// register a time step solver instantiated by a derived class
TimeStepSolver &
registerTimeStepSolver(const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver);
template <class NLSType, class DMType>
NonLinearSolver & registerNonLinearSolver(DMType & dm, const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls = std::make_unique<NLSType>(
dm, type, non_linear_solver_id);
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
template <class TSSType, class DMType>
TimeStepSolver & registerTimeStepSolver(DMType & dm, const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss =
std::make_unique<TSSType>(dm, type, non_linear_solver, solver_callback,
time_step_solver_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
template <class MatType, class DMType>
SparseMatrix & registerSparseMatrix(DMType & dm, const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(dm, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType>
SparseMatrix & registerSparseMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
auto & sm_to_copy =
aka::as_type<MatType>(this->getMatrix(matrix_to_copy_id));
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType, class DMType>
SolverVector & registerLumpedMatrix(DMType & dm, const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
std::unique_ptr<SolverVector> sm = std::make_unique<MatType>(dm, matrix_id);
return this->registerLumpedMatrix(matrix_id, sm);
}
protected:
virtual void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) = 0;
virtual void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) = 0;
public:
/// extract degrees of freedom (identified by ID) from a global solver array
virtual void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) = 0;
/// Get the reference of an existing matrix
SparseMatrix & getMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasMatrix(const ID & matrix_id) const;
/// Get an instance of a new lumped matrix
virtual SolverVector & getNewLumpedMatrix(const ID & matrix_id) = 0;
/// Get the lumped version of a given matrix
const SolverVector & getLumpedMatrix(const ID & matrix_id) const;
/// Get the lumped version of a given matrix
SolverVector & getLumpedMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasLumpedMatrix(const ID & matrix_id) const;
/* ------------------------------------------------------------------------ */
/* Non linear system solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
virtual NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) = 0;
/// get instance of a non linear solver
virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);
/// check if the given solver exists
bool hasNonLinearSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
virtual TimeStepSolver &
getNewTimeStepSolver(const ID & time_step_solver_id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) = 0;
/// get instance of a time step solver
virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);
/// check if the given solver exists
bool hasTimeStepSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
const Mesh & getMesh() {
if (mesh != nullptr) {
return *mesh;
}
AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Communicator, communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, communicator, auto &);
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Solution, *(solution.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Solution, *(solution.get()), auto &);
AKANTU_GET_MACRO(Residual, *(residual.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Residual, *(residual.get()), auto &);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
friend class GlobalDOFInfoDataAccessor;
/// helper function for the DOFManager::onNodesAdded method
virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list);
template <typename Func>
auto countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
Func && getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_nodes,
const std::function<UInt(UInt)> & getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local);
auto computeFirstDOFIDs(UInt nb_new_local_dofs, UInt nb_new_pure_local);
/// resize all the global information and takes the needed measure like
/// cleaning matrices profiles
virtual void resizeGlobalArrays();
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
protected:
inline DOFData & getDOFData(const ID & dof_id);
inline const DOFData & getDOFData(const ID & dof_id) const;
template <class DOFData_>
inline DOFData_ & getDOFDataTyped(const ID & dof_id);
template <class DOFData_>
inline const DOFData_ & getDOFDataTyped(const ID & dof_id) const;
virtual std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// dof representations in the dof manager
struct DOFData {
DOFData() = delete;
explicit DOFData(const ID & dof_id);
virtual ~DOFData();
/// DOF support type (nodal, general) this is needed to determine how the
/// dof are shared among processors
DOFSupportType support_type;
ID group_support;
/// Degree of freedom array
Array<Real> * dof{nullptr};
/// Blocked degree of freedoms array
Array<bool> * blocked_dofs{nullptr};
/// Degree of freedoms increment
Array<Real> * increment{nullptr};
/// Degree of freedoms at previous step
Array<Real> * previous{nullptr};
/// Solution associated to the dof
Array<Real> solution;
/* ---------------------------------------------------------------------- */
/* data for dynamic simulations */
/* ---------------------------------------------------------------------- */
/// Degree of freedom derivatives arrays
std::vector<Array<Real> *> dof_derivatives;
/* ---------------------------------------------------------------------- */
/// number of dofs to consider locally for this dof id
UInt local_nb_dofs{0};
/// Number of purely local dofs
UInt pure_local_nb_dofs{0};
/// number of ghost dofs
UInt ghosts_nb_dofs{0};
/// local numbering equation numbers
Array<Int> local_equation_number;
/// associated node for _dst_nodal dofs only
Array<UInt> associated_nodes;
virtual Array<Int> & getLocalEquationsNumbers() {
return local_equation_number;
}
};
/// type to store dofs information
using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;
/// type to store all the matrices
using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;
/// type to store all the lumped matrices
using LumpedMatricesMap = std::map<ID, std::unique_ptr<SolverVector>>;
/// type to store all the non linear solver
using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;
/// type to store all the time step solver
using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;
ID id;
/// store a reference to the dof arrays
DOFStorage dofs;
/// list of sparse matrices that where created
SparseMatricesMap matrices;
/// list of lumped matrices
LumpedMatricesMap lumped_matrices;
/// non linear solvers storage
NonLinearSolversMap non_linear_solvers;
/// time step solvers storage
TimeStepSolversMap time_step_solvers;
/// reference to the underlying mesh
Mesh * mesh{nullptr};
/// Total number of degrees of freedom (size with the ghosts)
UInt local_system_size{0};
/// Number of purely local dofs (size without the ghosts)
UInt pure_local_system_size{0};
/// Total number of degrees of freedom
UInt system_size{0};
/// rhs to the system of equation corresponding to the residual linked to the
/// different dofs
std::unique_ptr<SolverVector> residual;
/// solution of the system of equation corresponding to the different dofs
std::unique_ptr<SolverVector> solution;
/// a vector that helps internally to perform some tasks
std::unique_ptr<SolverVector> data_cache;
/// define the dofs type, local, shared, ghost
Array<NodeFlag> dofs_flag;
/// equation number in global numbering
Array<Int> global_equation_number;
using equation_numbers_map = std::unordered_map<Int, Int>;
/// dual information of global_equation_number
equation_numbers_map global_to_local_mapping;
/// Communicator used for this manager, should be the same as in the mesh if a
/// mesh is registered
Communicator & communicator;
/// accumulator to know what would be the next global id to use
UInt first_global_dof_id{0};
/// Release at last apply boundary on jacobian
UInt jacobian_release{0};
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<Int> global_blocked_dofs;
UInt global_blocked_dofs_release{0};
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<Int> previous_global_blocked_dofs;
UInt previous_global_blocked_dofs_release{0};
private:
/// This is for unit testing
friend class DOFManagerTester;
};
using DefaultDOFManagerFactory =
Factory<DOFManager, ID, const ID &>;
using DOFManagerFactory =
Factory<DOFManager, ID, Mesh &, const ID &>;
} // namespace akantu
#include "dof_manager_inline_impl.hh"
#endif /* AKANTU_DOF_MANAGER_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_default.cc b/src/model/common/dof_manager/dof_manager_default.cc
index 202de3108..feda05c7d 100644
--- a/src/model/common/dof_manager/dof_manager_default.cc
+++ b/src/model/common/dof_manager/dof_manager_default.cc
@@ -1,488 +1,491 @@
/**
* @file dof_manager_default.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Thu Feb 08 2018
+ * @date last modification: Tue Mar 30 2021
*
* @brief Implementation of the default DOFManager
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include "non_linear_solver_default.hh"
#include "periodic_node_synchronizer.hh"
#include "solver_vector_default.hh"
#include "solver_vector_distributed.hh"
#include "sparse_matrix_aij.hh"
#include "time_step_solver_default.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <memory>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(const ID & id)
: DOFManager(id), synchronizer(nullptr) {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":data_cache"));
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id)
: DOFManager(mesh, id), synchronizer(nullptr) {
if (this->mesh->isDistributed()) {
this->synchronizer = std::make_unique<DOFSynchronizer>(
*this, this->id + ":dof_synchronizer");
residual = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDistributed>(
*this, std::string(id + ":data_cache"));
} else {
residual = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":residual"));
solution = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":solution"));
data_cache = std::make_unique<SolverVectorDefault>(
*this, std::string(id + ":data_cache"));
}
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() = default;
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) {
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
if (dof_data.support_type != _dst_nodal) {
return;
}
if (not mesh->isPeriodic()) {
return;
}
this->mesh->getPeriodicNodeSynchronizer()
.reduceSynchronizeWithPBCSlaves<AddOperation>(
aka::as_type<SolverVectorDefault>(array).getVector());
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor) {
AKANTU_DEBUG_IN();
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.local_equation_number.size() ==
array_to_assemble.size() *
array_to_assemble.getNbComponent(),
"The array to assemble does not have a correct size."
<< " (" << array_to_assemble.getID() << ")");
if (dof_data.support_type == _dst_nodal and mesh->isPeriodic()) {
for (auto && data :
zip(dof_data.local_equation_number, dof_data.associated_nodes,
make_view(array_to_assemble))) {
auto && equ_num = std::get<0>(data);
// auto && node = std::get<1>(data);
auto && arr = std::get<2>(data);
// Guillaume to Nico:
// This filter of periodic slave should not be.
// Indeed you want to get the contribution even
// from periodic slaves and cumulate to the right
// equation number.
global_array(equ_num) += scale_factor * (arr);
// scale_factor * (arr) * (not this->mesh->isPeriodicSlave(node));
}
} else {
for (auto && data :
zip(dof_data.local_equation_number, make_view(array_to_assemble))) {
auto && equ_num = std::get<0>(data);
auto && arr = std::get<1>(data);
global_array(equ_num) += scale_factor * (arr);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<Real> & array_to_assemble,
SolverVector & global_array_v, Real scale_factor) {
assembleToGlobalArray(
dof_id, array_to_assemble,
aka::as_type<SolverVectorDefault>(global_array_v).getVector(),
scale_factor);
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
: DOFData(dof_id) {}
/* -------------------------------------------------------------------------- */
auto DOFManagerDefault::getNewDOFData(const ID & dof_id)
-> std::unique_ptr<DOFData> {
return std::make_unique<DOFDataDefault>(dof_id);
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManagerDefault::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);
// update the synchronizer if needed
if (this->synchronizer) {
this->synchronizer->registerDOFs(dof_id);
}
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
return this->registerSparseMatrix<SparseMatrixAIJ>(*this, id, matrix_type);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
return this->registerSparseMatrix<SparseMatrixAIJ>(id, matrix_to_copy_id);
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManagerDefault::getNewLumpedMatrix(const ID & id) {
return this->registerLumpedMatrix<SolverVectorDefault>(*this, id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
auto & matrix = DOFManager::getMatrix(id);
return aka::as_type<SparseMatrixAIJ>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
switch (type) {
#if defined(AKANTU_USE_MUMPS)
case NonLinearSolverType::_newton_raphson:
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case NonLinearSolverType::_newton_raphson_contact:
case NonLinearSolverType::_newton_raphson_modified: {
return this->registerNonLinearSolver<NonLinearSolverNewtonRaphson>(
*this, id, type);
}
case NonLinearSolverType::_linear: {
return this->registerNonLinearSolver<NonLinearSolverLinear>(*this, id,
type);
}
#endif
case NonLinearSolverType::_lumped: {
return this->registerNonLinearSolver<NonLinearSolverLumped>(*this, id,
type);
}
default:
AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
"this dof manager");
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManagerDefault::getNewTimeStepSolver(
const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & solver_callback) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(
*this, id, type, non_linear_solver, solver_callback);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const Array<T> & global_array,
Array<T> & local_array) const {
AKANTU_DEBUG_IN();
const Array<Int> & equation_number = this->getLocalEquationsNumbers(dof_id);
UInt nb_degree_of_freedoms = equation_number.size();
local_array.resize(nb_degree_of_freedoms / local_array.getNbComponent());
auto loc_it = local_array.begin_reinterpret(nb_degree_of_freedoms);
auto equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++loc_it, ++equ_it) {
(*loc_it) = global_array(*equ_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const SolverVector & global_array,
Array<Real> & local_array) {
getArrayPerDOFs(dof_id,
aka::as_type<SolverVectorDefault>(global_array).getVector(),
local_array);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleLumpedMatMulVectToResidual(
const ID & dof_id, const ID & A_id, const Array<Real> & x,
Real scale_factor) {
const Array<Real> & A = this->getLumpedMatrix(A_id);
auto & cache = aka::as_type<SolverVectorArray>(*this->data_cache);
cache.zero();
this->assembleToGlobalArray(dof_id, x, cache.getVector(), scale_factor);
for (auto && data : zip(make_view(A), make_view(cache.getVector()),
make_view(this->getResidualArray()))) {
const auto & A = std::get<0>(data);
const auto & x = std::get<1>(data);
auto & r = std::get<2>(data);
r += A * x;
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
this->addToProfile(matrix_id, dof_id, type, ghost_type);
auto & A = getMatrix(matrix_id);
DOFManager::assembleElementalMatricesToMatrix_(
A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
auto & A = getMatrix(matrix_id);
DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
if (mesh->isDistributed()) {
DOFManager::assembleMatMulVectToArray_<SolverVectorDistributed>(
dof_id, A_id, x, array, scale_factor);
} else {
DOFManager::assembleMatMulVectToArray_<SolverVectorDefault>(
dof_id, A_id, x, array, scale_factor);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
const auto & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal) {
return;
}
auto mat_dof = std::make_pair(matrix_id, dof_id);
auto type_pair = std::make_pair(type, ghost_type);
auto prof_it = this->matrix_profiled_dofs.find(mat_dof);
if (prof_it != this->matrix_profiled_dofs.end() &&
std::find(prof_it->second.begin(), prof_it->second.end(), type_pair) !=
prof_it->second.end()) {
return;
}
auto nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();
const auto & equation_number = this->getLocalEquationsNumbers(dof_id);
auto & A = this->getMatrix(matrix_id);
A.resize(system_size);
auto size = A.size();
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = this->mesh->getConnectivity(type, ghost_type);
auto cbegin = connectivity.begin(nb_nodes_per_element);
auto cit = cbegin;
auto nb_elements = connectivity.size();
UInt * ge_it = nullptr;
if (dof_data.group_support != "__mesh__") {
const auto & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
ge_it = group_elements.storage();
nb_elements = group_elements.size();
}
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom_per_node;
Vector<Int> element_eq_nb(size_mat);
for (UInt e = 0; e < nb_elements; ++e) {
if (ge_it != nullptr) {
cit = cbegin + *ge_it;
}
this->extractElementEquationNumber(
equation_number, *cit, nb_degree_of_freedom_per_node, element_eq_nb);
std::transform(
element_eq_nb.storage(), element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(),
[&](auto & local) { return this->localToGlobalEquationNumber(local); });
if (ge_it != nullptr) {
++ge_it;
} else {
++cit;
}
for (UInt i = 0; i < size_mat; ++i) {
UInt c_irn = element_eq_nb(i);
if (c_irn < size) {
for (UInt j = 0; j < size_mat; ++j) {
UInt c_jcn = element_eq_nb(j);
if (c_jcn < size) {
A.add(c_irn, c_jcn);
}
}
}
}
}
this->matrix_profiled_dofs[mat_dof].push_back(type_pair);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManagerDefault::getSolutionArray() {
return dynamic_cast<SolverVectorDefault *>(this->solution.get())->getVector();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getResidualArray() const {
return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManagerDefault::getResidualArray() {
return dynamic_cast<SolverVectorDefault *>(this->residual.get())->getVector();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
DOFManager::onNodesAdded(nodes_list, event);
if (this->synchronizer) {
this->synchronizer->onNodesAdded(nodes_list);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::resizeGlobalArrays() {
DOFManager::resizeGlobalArrays();
this->global_blocked_dofs.resize(this->local_system_size, 1);
this->previous_global_blocked_dofs.resize(this->local_system_size, 1);
matrix_profiled_dofs.clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateGlobalBlockedDofs() {
DOFManager::updateGlobalBlockedDofs();
if (this->global_blocked_dofs_release ==
this->previous_global_blocked_dofs_release) {
return;
}
global_blocked_dofs_uint.resize(local_system_size);
global_blocked_dofs_uint.set(false);
for (const auto & dof : global_blocked_dofs) {
global_blocked_dofs_uint[dof] = true;
}
}
/* -------------------------------------------------------------------------- */
Array<bool> & DOFManagerDefault::getBlockedDOFs() {
return global_blocked_dofs_uint;
}
/* -------------------------------------------------------------------------- */
const Array<bool> & DOFManagerDefault::getBlockedDOFs() const {
return global_blocked_dofs_uint;
}
/* -------------------------------------------------------------------------- */
static bool dof_manager_is_registered [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"default",
[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(mesh, id);
});
static bool dof_manager_is_registered_mumps [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"mumps",
[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerDefault>(mesh, id);
});
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager_default.hh b/src/model/common/dof_manager/dof_manager_default.hh
index 4cebb4b6c..f12072ff8 100644
--- a/src/model/common/dof_manager/dof_manager_default.hh
+++ b/src/model/common/dof_manager/dof_manager_default.hh
@@ -1,253 +1,255 @@
/**
* @file dof_manager_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Default implementation of the dof manager
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_MANAGER_DEFAULT_HH_
#define AKANTU_DOF_MANAGER_DEFAULT_HH_
namespace akantu {
class SparseMatrixAIJ;
class NonLinearSolverDefault;
class TimeStepSolverDefault;
class DOFSynchronizer;
} // namespace akantu
namespace akantu {
class DOFManagerDefault : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerDefault(const ID & id = "dof_manager_default");
DOFManagerDefault(Mesh & mesh, const ID & id = "dof_manager_default");
~DOFManagerDefault() override;
protected:
struct DOFDataDefault : public DOFData {
explicit DOFDataDefault(const ID & dof_id);
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// /// register an array of degree of freedom
// void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
// const DOFSupportType & support_type) override;
// /// the dof as an implied type of _dst_nodal and is defined only on a
// subset
// /// of nodes
// void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
// const ID & group_support) override;
/**
* Assemble elementary values to the global matrix. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, ElementType type,
GhostType ghost_type, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) override;
void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x, Array<Real> & array,
Real scale_factor = 1.) override;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
void assembleLumpedMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// assemble coupling terms between to dofs
void assemblePreassembledMatrix(const ID & dof_id_m, const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) override;
protected:
void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) override;
template <typename T>
void assembleToGlobalArray(const ID & dof_id,
const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor);
void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) override;
template <typename T>
void getArrayPerDOFs(const ID & dof_id, const Array<T> & global_array,
Array<T> & local_array) const;
void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) override;
public:
/// update the global dofs vector
void updateGlobalBlockedDofs() override;
// /// apply boundary conditions to jacobian matrix
// void applyBoundary(const ID & matrix_id = "J") override;
private:
/// Add a symmetric matrices to a symmetric sparse matrix
void addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers, UInt max_size);
/// Add a unsymmetric matrices to a symmetric sparse matrix (i.e. cohesive
/// elements)
void addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers, UInt max_size);
/// Add a matrices to a unsymmetric sparse matrix
void addElementalMatrixToUnsymmetric(SparseMatrixAIJ & matrix,
const Matrix<Real> & element_mat,
const Vector<Int> & equation_numbers,
UInt max_size);
void addToProfile(const ID & matrix_id, const ID & dof_id,
ElementType type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) override;
// std::pair<UInt, UInt>
// updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list)
// override;
void resizeGlobalArrays() override;
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixAIJ & getMatrix(const ID & matrix_id);
/// Get an instance of a new lumped matrix
SolverVector & getNewLumpedMatrix(const ID & matrix_id) override;
/* ------------------------------------------------------------------------ */
/* Non Linear Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) override;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
private:
/// Get the solution array
Array<Real> & getSolutionArray();
/// Get the residual array
const Array<Real> & getResidualArray() const;
/// Get the residual array
Array<Real> & getResidualArray();
public:
/// access the internal dof_synchronizer
AKANTU_GET_MACRO_NOT_CONST(Synchronizer, *synchronizer, DOFSynchronizer &);
/// access the internal dof_synchronizer
bool hasSynchronizer() const { return synchronizer != nullptr; }
Array<bool> & getBlockedDOFs();
const Array<bool> & getBlockedDOFs() const;
protected:
std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using DOFToMatrixProfile =
std::map<std::pair<ID, ID>,
std::vector<std::pair<ElementType, GhostType>>>;
/// contains the the dofs that where added to the profile of a given matrix.
DOFToMatrixProfile matrix_profiled_dofs;
/// synchronizer to maintain coherency in dof fields
std::unique_ptr<DOFSynchronizer> synchronizer;
friend class DOFSynchronizer;
/// Array containing the true or false if the node is in global_blocked_dofs
Array<bool> global_blocked_dofs_uint;
};
} // namespace akantu
#include "dof_manager_default_inline_impl.hh"
#endif /* AKANTU_DOF_MANAGER_DEFAULT_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_default_inline_impl.hh b/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
index d473c1f68..862af9ba9 100644
--- a/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
+++ b/src/model/common/dof_manager/dof_manager_default_inline_impl.hh
@@ -1,39 +1,41 @@
/**
* @file dof_manager_default_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 13 2019
*
* @brief Implementation of the DOFManagerDefault inline functions
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_
#define AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_
namespace akantu {} // namespace akantu
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_inline_impl.hh b/src/model/common/dof_manager/dof_manager_inline_impl.hh
index 22713a58d..1fc5bb2b5 100644
--- a/src/model/common/dof_manager/dof_manager_inline_impl.hh
+++ b/src/model/common/dof_manager/dof_manager_inline_impl.hh
@@ -1,335 +1,337 @@
/**
* @file dof_manager_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief inline functions of the dof manager
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "element_group.hh"
#include "solver_vector.hh"
#include "sparse_matrix.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_MANAGER_INLINE_IMPL_HH_
#define AKANTU_DOF_MANAGER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFs(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
return it != this->dofs.end();
}
/* -------------------------------------------------------------------------- */
inline DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) const {
auto it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
inline void DOFManager::extractElementEquationNumber(
const Array<Int> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<Int> & element_equation_number) {
for (UInt i = 0, ld = 0; i < connectivity.size(); ++i) {
UInt n = connectivity(i);
for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
element_equation_number(ld) =
equation_numbers(n * nb_degree_of_freedom + d);
}
}
}
/* -------------------------------------------------------------------------- */
template <class DOFData_>
inline DOFData_ & DOFManager::getDOFDataTyped(const ID & dof_id) {
return aka::as_type<DOFData_>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
template <class DOFData_>
inline const DOFData_ & DOFManager::getDOFDataTyped(const ID & dof_id) const {
return aka::as_type<DOFData_>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).dof);
}
/* -------------------------------------------------------------------------- */
inline DOFSupportType DOFManager::getSupportType(const ID & dofs_id) const {
return this->getDOFData(dofs_id).support_type;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getPreviousDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).previous);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasPreviousDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).previous != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsIncrement(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).increment);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsIncrement(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).increment != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsDerivatives(const ID & dofs_id,
UInt order) {
if (order == 0) {
return getDOFs(dofs_id);
}
std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
if ((order > derivatives.size()) || (derivatives[order - 1] == nullptr)) {
AKANTU_EXCEPTION("No derivatives of order " << order << " present in "
<< this->id << " for dof "
<< dofs_id);
}
return *derivatives[order - 1];
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsDerivatives(const ID & dofs_id,
UInt order) const {
const std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
return ((order < derivatives.size()) && (derivatives[order - 1] != nullptr));
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> & DOFManager::getSolution(const ID & dofs_id) const {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getSolution(const ID & dofs_id) {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline const Array<bool> &
DOFManager::getBlockedDOFs(const ID & dofs_id) const {
return *(this->getDOFData(dofs_id).blocked_dofs);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasBlockedDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).blocked_dofs != nullptr);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isLocalOrMasterDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_local_master_mask) == NodeFlag::_normal;
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isSlaveDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_shared_mask) == NodeFlag::_slave;
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::isPureGhostDOF(UInt dof_num) {
auto dof_flag = this->dofs_flag(dof_num);
return (dof_flag & NodeFlag::_shared_mask) == NodeFlag::_pure_ghost;
}
/* -------------------------------------------------------------------------- */
inline Int DOFManager::localToGlobalEquationNumber(Int local) const {
return this->global_equation_number(local);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasGlobalEquationNumber(Int global) const {
auto it = this->global_to_local_mapping.find(global);
return (it != this->global_to_local_mapping.end());
}
/* -------------------------------------------------------------------------- */
inline Int DOFManager::globalToLocalEquationNumber(Int global) const {
auto it = this->global_to_local_mapping.find(global);
AKANTU_DEBUG_ASSERT(it != this->global_to_local_mapping.end(),
"This global equation number "
<< global << " does not exists in " << this->id);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline NodeFlag DOFManager::getDOFFlag(Int local_id) const {
return this->dofs_flag(local_id);
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
DOFManager::getDOFsAssociatedNodes(const ID & dof_id) const {
const auto & dof_data = this->getDOFData(dof_id);
return dof_data.associated_nodes;
}
/* -------------------------------------------------------------------------- */
const Array<Int> &
DOFManager::getLocalEquationsNumbers(const ID & dof_id) const {
return getDOFData(dof_id).local_equation_number;
}
/* -------------------------------------------------------------------------- */
template <typename Vec>
void DOFManager::assembleMatMulVectToArray_(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
Vec tmp_array(aka::as_type<Vec>(*data_cache), this->id + ":tmp_array");
tmp_array.zero();
assembleMatMulVectToGlobalArray(dof_id, A_id, x, tmp_array, scale_factor);
getArrayPerDOFs(dof_id, tmp_array, array);
}
/* -------------------------------------------------------------------------- */
template <typename Mat>
void DOFManager::assembleElementalMatricesToMatrix_(
Mat & A, const ID & dof_id, const Array<Real> & elementary_mat,
ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
auto & dof_data = this->getDOFData(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.support_type == _dst_nodal,
"This function applies only on Nodal dofs");
const auto & equation_number = this->getLocalEquationsNumbers(dof_id);
UInt nb_element;
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
if (dof_data.group_support != "__mesh__") {
const auto & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
nb_element = group_elements.size();
filter_it = group_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
}
AKANTU_DEBUG_ASSERT(elementary_mat.size() == nb_element,
"The vector elementary_mat("
<< elementary_mat.getID()
<< ") has not the good size.");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = dof_data.dof->getNbComponent();
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
auto conn_begin = connectivity.begin(nb_nodes_per_element);
auto conn_it = conn_begin;
auto size_mat = nb_nodes_per_element * nb_degree_of_freedom;
Vector<Int> element_eq_nb(nb_degree_of_freedom * nb_nodes_per_element);
auto el_mat_it = elementary_mat.begin(size_mat, size_mat);
for (UInt e = 0; e < nb_element; ++e, ++el_mat_it) {
if (filter_it) {
conn_it = conn_begin + *filter_it;
}
this->extractElementEquationNumber(equation_number, *conn_it,
nb_degree_of_freedom, element_eq_nb);
std::transform(element_eq_nb.begin(), element_eq_nb.end(),
element_eq_nb.begin(), [&](auto && local) {
return this->localToGlobalEquationNumber(local);
});
if (filter_it) {
++filter_it;
} else {
++conn_it;
}
A.addValues(element_eq_nb, element_eq_nb, *el_mat_it,
elemental_matrix_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Mat>
void DOFManager::assemblePreassembledMatrix_(Mat & A, const ID & dof_id_m,
const ID & dof_id_n,
const TermsToAssemble & terms) {
const auto & equation_number_m = this->getLocalEquationsNumbers(dof_id_m);
const auto & equation_number_n = this->getLocalEquationsNumbers(dof_id_n);
for (const auto & term : terms) {
auto gi = this->localToGlobalEquationNumber(equation_number_m(term.i()));
auto gj = this->localToGlobalEquationNumber(equation_number_n(term.j()));
A.add(gi, gj, term);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_DOF_MANAGER_INLINE_IMPL_HH_ */
diff --git a/src/model/common/dof_manager/dof_manager_petsc.cc b/src/model/common/dof_manager/dof_manager_petsc.cc
index 9980ed3d6..32a0e5568 100644
--- a/src/model/common/dof_manager/dof_manager_petsc.cc
+++ b/src/model/common/dof_manager/dof_manager_petsc.cc
@@ -1,303 +1,305 @@
/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief DOFManaterPETSc is the PETSc implementation of the DOFManager
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "cppargparse.hh"
#include "non_linear_solver_petsc.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
#include "time_step_solver_default.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscis.h>
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class PETScSingleton {
private:
PETScSingleton() {
PETSc_call(PetscInitialized, &is_initialized);
if (is_initialized == 0U) {
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
PETSc_call(PetscInitialize, &argc, &argv, nullptr, nullptr);
PETSc_call(
PetscPopErrorHandler); // remove the default PETSc signal handler
PETSc_call(PetscPushErrorHandler, PetscIgnoreErrorHandler, nullptr);
}
}
public:
PETScSingleton(const PETScSingleton &) = delete;
PETScSingleton & operator=(const PETScSingleton &) = delete;
~PETScSingleton() {
if (is_initialized == 0U) {
PetscFinalize();
}
}
static PETScSingleton & getInstance() {
static PETScSingleton instance;
return instance;
}
private:
PetscBool is_initialized;
};
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFDataPETSc::DOFDataPETSc(const ID & dof_id)
: DOFData(dof_id) {}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id)
: DOFManager(id) {
init();
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(Mesh & mesh, const ID & id)
: DOFManager(mesh, id) {
init();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::init() {
// check if the akantu types and PETSc one are consistant
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#if defined(AKANTU_USE_MPI)
const auto & mpi_data =
aka::as_type<MPICommunicatorData>(communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mpi_communicator = mpi_comm;
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
PETScSingleton & instance [[gnu::unused]] = PETScSingleton::getInstance();
}
/* -------------------------------------------------------------------------- */
auto DOFManagerPETSc::getNewDOFData(const ID & dof_id)
-> std::unique_ptr<DOFData> {
return std::make_unique<DOFDataPETSc>(dof_id);
}
/* -------------------------------------------------------------------------- */
std::tuple<UInt, UInt, UInt>
DOFManagerPETSc::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
dofs_ids.push_back(dof_id);
auto ret = DOFManager::registerDOFsInternal(dof_id, dofs_array);
UInt nb_dofs;
UInt nb_pure_local_dofs;
std::tie(nb_dofs, nb_pure_local_dofs, std::ignore) = ret;
auto && vector = std::make_unique<SolverVectorPETSc>(*this, id + ":solution");
auto *x = vector->getVec();
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
// redoing the indexes based on the petsc numbering
for (auto & dof_id : dofs_ids) {
auto & dof_data = this->getDOFDataTyped<DOFDataPETSc>(dof_id);
Array<PetscInt> gidx(dof_data.local_equation_number.size());
for (auto && data : zip(dof_data.local_equation_number, gidx)) {
std::get<1>(data) = localToGlobalEquationNumber(std::get<0>(data));
}
auto & lidx = dof_data.local_equation_number_petsc;
if (is_ltog_map != nullptr) {
lidx.resize(gidx.size());
PetscInt n;
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
gidx.size(), gidx.storage(), &n, lidx.storage());
}
}
residual = std::make_unique<SolverVectorPETSc>(*vector, id + ":residual");
data_cache = std::make_unique<SolverVectorPETSc>(*vector, id + ":data_cache");
solution = std::move(vector);
for (auto & mat : matrices) {
auto & A = this->getMatrix(mat.first);
A.resize();
}
return ret;
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleToGlobalArray(
const ID & dof_id, const Array<Real> & array_to_assemble,
SolverVector & global_array, Real scale_factor) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
auto & g = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(array_to_assemble.size() *
array_to_assemble.getNbComponent() ==
dof_data.local_nb_dofs,
"The array to assemble does not have the proper size");
g.addValuesLocal(dof_data.local_equation_number_petsc, array_to_assemble,
scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::getArrayPerDOFs(const ID & dof_id,
const SolverVector & global_array,
Array<Real> & local) {
const auto & dof_data = getDOFDataTyped<DOFDataPETSc>(dof_id);
const auto & petsc_vector = aka::as_type<SolverVectorPETSc>(global_array);
AKANTU_DEBUG_ASSERT(
local.size() * local.getNbComponent() == dof_data.local_nb_dofs,
"The array to get the values does not have the proper size");
petsc_vector.getValuesLocal(dof_data.local_equation_number_petsc, local);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
ElementType type, GhostType ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
auto & A = getMatrix(matrix_id);
DOFManager::assembleElementalMatricesToMatrix_(
A, dof_id, elementary_mat, type, ghost_type, elemental_matrix_type,
filter_elements);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
auto & A = getMatrix(matrix_id);
DOFManager::assemblePreassembledMatrix_(A, dof_id_m, dof_id_n, terms);
A.applyModifications();
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::assembleMatMulVectToArray(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor) {
DOFManager::assembleMatMulVectToArray_<SolverVectorPETSc>(
dof_id, A_id, x, array, scale_factor);
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::makeConsistentForPeriodicity(const ID & /*dof_id*/,
SolverVector & /*array*/) {}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerPETSc::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
return this->registerNonLinearSolver<NonLinearSolverPETSc>(*this, id, type);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManagerPETSc::getNewTimeStepSolver(
const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & callback) {
return this->registerTimeStepSolver<TimeStepSolverDefault>(
*this, id, type, non_linear_solver, callback);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
return this->registerSparseMatrix<SparseMatrixPETSc>(*this, id, matrix_type);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerPETSc::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
return this->registerSparseMatrix<SparseMatrixPETSc>(id, matrix_to_copy_id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc & DOFManagerPETSc::getMatrix(const ID & id) {
auto & matrix = DOFManager::getMatrix(id);
return aka::as_type<SparseMatrixPETSc>(matrix);
}
/* -------------------------------------------------------------------------- */
SolverVector & DOFManagerPETSc::getNewLumpedMatrix(const ID & id) {
return this->registerLumpedMatrix<SolverVectorPETSc>(*this, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & DOFManagerPETSc::getSolution() {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
const SolverVectorPETSc & DOFManagerPETSc::getSolution() const {
return aka::as_type<SolverVectorPETSc>(*this->solution);
}
SolverVectorPETSc & DOFManagerPETSc::getResidual() {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
const SolverVectorPETSc & DOFManagerPETSc::getResidual() const {
return aka::as_type<SolverVectorPETSc>(*this->residual);
}
/* -------------------------------------------------------------------------- */
static bool dof_manager_is_registered [[gnu::unused]] =
DOFManagerFactory::getInstance().registerAllocator(
"petsc",
[](Mesh & mesh, const ID & id) -> std::unique_ptr<DOFManager> {
return std::make_unique<DOFManagerPETSc>(mesh, id);
});
} // namespace akantu
diff --git a/src/model/common/dof_manager/dof_manager_petsc.hh b/src/model/common/dof_manager/dof_manager_petsc.hh
index d0f441c87..eb138f6bc 100644
--- a/src/model/common/dof_manager/dof_manager_petsc.hh
+++ b/src/model/common/dof_manager/dof_manager_petsc.hh
@@ -1,216 +1,219 @@
/**
* @file dof_manager_petsc.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief PETSc implementation of the dof manager
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <petscis.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_MANAGER_PETSC_HH_
#define AKANTU_DOF_MANAGER_PETSC_HH_
#define PETSc_call(func, ...) \
do { \
auto ierr = func(__VA_ARGS__); \
if (PetscUnlikely(ierr != 0)) { \
const char * desc; \
PetscErrorMessage(ierr, &desc, nullptr); \
AKANTU_EXCEPTION("Error in PETSc call to \'" << #func \
<< "\': " << desc); \
} \
} while (false)
namespace akantu {
namespace detail {
template <typename T> void PETScSetName(T t, const ID & id) {
PETSc_call(PetscObjectSetName, reinterpret_cast<PetscObject>(t),
id.c_str());
}
} // namespace detail
} // namespace akantu
namespace akantu {
class SparseMatrixPETSc;
class SolverVectorPETSc;
} // namespace akantu
namespace akantu {
class DOFManagerPETSc : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerPETSc(const ID & id = "dof_manager_petsc");
DOFManagerPETSc(Mesh & mesh, const ID & id = "dof_manager_petsc");
~DOFManagerPETSc() override = default;
protected:
void init();
struct DOFDataPETSc : public DOFData {
explicit DOFDataPETSc(const ID & dof_id);
/// petsc compressed version of local_equation_number
Array<PetscInt> local_equation_number_petsc;
Array<Int> & getLocalEquationsNumbers() override {
return local_equation_number_petsc;
}
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void assembleToLumpedMatrix(const ID & /*dof_id*/,
Array<Real> & /*array_to_assemble*/,
const ID & /*lumped_mtx*/,
Real /*scale_factor*/ = 1.) override {
AKANTU_TO_IMPLEMENT();
}
void assembleElementalMatricesToMatrix(
const ID & /*matrix_id*/, const ID & /*dof_id*/,
const Array<Real> & /*elementary_mat*/, ElementType /*type*/,
GhostType /*ghost_type*/,
const MatrixType & /*elemental_matrix_type*/,
const Array<UInt> & /*filter_elements*/) override;
void assembleMatMulVectToArray(const ID & /*dof_id*/, const ID & /*A_id*/,
const Array<Real> & /*x*/,
Array<Real> & /*array*/,
Real /*scale_factor*/ = 1.) override;
void assembleLumpedMatMulVectToResidual(const ID & /*dof_id*/,
const ID & /*A_id*/,
const Array<Real> & /*x*/,
Real /*scale_factor*/ = 1) override {
AKANTU_TO_IMPLEMENT();
}
void assemblePreassembledMatrix(const ID & /* dof_id_m*/,
const ID & /*dof_id_n*/,
const ID & /*matrix_id*/,
const TermsToAssemble & /*terms*/) override;
protected:
void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) override;
void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) override;
void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) override;
std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) override;
std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array) override;
void updateDOFsData(DOFDataPETSc & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_node,
const std::function<UInt(UInt)> & getNode);
protected:
void getLumpedMatrixPerDOFs(const ID & /*dof_id*/, const ID & /*lumped_mtx*/,
Array<Real> & /*lumped*/) override {}
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & non_linear_solver_type) override;
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixPETSc & getMatrix(const ID & matrix_id);
/// Get an instance of a new lumped matrix
SolverVector & getNewLumpedMatrix(const ID & matrix_id) override;
/// Get the blocked dofs array
// AKANTU_GET_MACRO(BlockedDOFs, blocked_dofs, const Array<bool> &);
AKANTU_GET_MACRO(MPIComm, mpi_communicator, MPI_Comm);
AKANTU_GET_MACRO_NOT_CONST(ISLocalToGlobalMapping, is_ltog_map,
ISLocalToGlobalMapping &);
SolverVectorPETSc & getSolution();
const SolverVectorPETSc & getSolution() const;
SolverVectorPETSc & getResidual();
const SolverVectorPETSc & getResidual() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using PETScMatrixMap = std::map<ID, SparseMatrixPETSc *>;
using PETScLumpedMatrixMap = std::map<ID, SolverVectorPETSc *>;
/// list of matrices registered to the dof manager
PETScMatrixMap petsc_matrices;
/// list of lumped matrices registered
PETScLumpedMatrixMap petsc_lumped_matrices;
/// PETSc local to global mapping of dofs
ISLocalToGlobalMapping is_ltog_map{nullptr};
/// Communicator associated to PETSc
MPI_Comm mpi_communicator;
/// list of the dof ids to be able to always iterate in the same order
std::vector<ID> dofs_ids;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_DOF_MANAGER_PETSC_HH_ */
diff --git a/src/model/common/integration_scheme/generalized_trapezoidal.cc b/src/model/common/integration_scheme/generalized_trapezoidal.cc
index 906f9322e..4ca0d930d 100644
--- a/src/model/common/integration_scheme/generalized_trapezoidal.cc
+++ b/src/model/common/integration_scheme/generalized_trapezoidal.cc
@@ -1,195 +1,197 @@
/**
* @file generalized_trapezoidal.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 23 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 27 2019
*
* @brief implementation of inline functions
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "generalized_trapezoidal.hh"
#include "aka_array.hh"
#include "dof_manager.hh"
#include "mesh.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GeneralizedTrapezoidal::GeneralizedTrapezoidal(DOFManager & dof_manager,
const ID & dof_id, Real alpha)
: IntegrationScheme1stOrder(dof_manager, dof_id), alpha(alpha) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::predictor(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
*u_val += (1. - alpha) * delta_t * *u_dot_val;
}
u_val++;
u_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _temperature:
this->allCorrector<_temperature>(delta_t, u, u_dot, blocked_dofs, delta);
break;
case _temperature_rate:
this->allCorrector<_temperature_rate>(delta_t, u, u_dot, blocked_dofs,
delta);
break;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1.;
case _temperature_rate:
return alpha * delta_t;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureRateCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1. / (alpha * delta_t);
case _temperature_rate:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void GeneralizedTrapezoidal::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real e = getTemperatureCoefficient(type, delta_t);
Real d = getTemperatureRateCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
}
u_val++;
u_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::assembleJacobian(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
does_j_need_update |= this->dof_manager.hasBlockedDOFsChanged();
if (not does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.copyProfile(K);
// J.zero();
Real c = this->getTemperatureRateCoefficient(type, delta_t);
Real e = this->getTemperatureCoefficient(type, delta_t);
J.add(M, e);
J.add(K, c);
m_release = M.getRelease();
k_release = K.getRelease();
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/common/integration_scheme/generalized_trapezoidal.hh b/src/model/common/integration_scheme/generalized_trapezoidal.hh
index 556dbbcc2..91c0bb9a8 100644
--- a/src/model/common/integration_scheme/generalized_trapezoidal.hh
+++ b/src/model/common/integration_scheme/generalized_trapezoidal.hh
@@ -1,161 +1,163 @@
/**
* @file generalized_trapezoidal.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 04 2011
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 13 2019
*
* @brief Generalized Trapezoidal Method. This implementation is taken from
* Méthodes numériques en mécanique des solides by Alain Curnier \note{ISBN:
* 2-88074-247-1}
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GENERALIZED_TRAPEZOIDAL_HH_
#define AKANTU_GENERALIZED_TRAPEZOIDAL_HH_
#include "integration_scheme_1st_order.hh"
namespace akantu {
/**
* The two differentiate equation (thermal and kinematic) are :
* \f{eqnarray*}{
* C\dot{u}_{n+1} + Ku_{n+1} = q_{n+1}\\
* u_{n+1} = u_{n} + (1-\alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1}
* \f}
*
* To solve it :
* Predictor :
* \f{eqnarray*}{
* u^0_{n+1} &=& u_{n} + (1-\alpha) \Delta t v_{n} \\
* \dot{u}^0_{n+1} &=& \dot{u}_{n}
* \f}
*
* Solve :
* \f[ (a C + b K^i_{n+1}) w = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1} \f]
*
* Corrector :
* \f{eqnarray*}{
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + a w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + b w
* \f}
*
* a and b depends on the resolution method : temperature (u) or temperature
*rate (\f$\dot{u}\f$)
*
* For temperature : \f$ w = \delta u, a = 1 / (\alpha \Delta t) , b = 1 \f$ @n
* For temperature rate : \f$ w = \delta \dot{u}, a = 1, b = \alpha \Delta t \f$
*/
class GeneralizedTrapezoidal : public IntegrationScheme1stOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GeneralizedTrapezoidal(DOFManager & dof_manager, const ID & dof_id,
Real alpha = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
/// the coeffichent \f$ b \f$ in the description
Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const override;
/// the coeffichent \f$ a \f$ in the description
Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the \f$\alpha\f$ parameter
Real alpha;
/// last release of K matrix
UInt k_release;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Forward Euler (explicit) -> condition on delta_t
*/
class ForwardEuler : public GeneralizedTrapezoidal {
public:
ForwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 0.){};
std::vector<std::string> getNeededMatrixList() override { return {"M"}; }
};
/**
* Trapezoidal rule (implicit), midpoint rule or Crank-Nicolson
*/
class TrapezoidalRule1 : public GeneralizedTrapezoidal {
public:
TrapezoidalRule1(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, .5){};
};
/**
* Backward Euler (implicit)
*/
class BackwardEuler : public GeneralizedTrapezoidal {
public:
BackwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 1.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_GENERALIZED_TRAPEZOIDAL_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme.cc b/src/model/common/integration_scheme/integration_scheme.cc
index 9fea35044..efe03552f 100644
--- a/src/model/common/integration_scheme/integration_scheme.cc
+++ b/src/model/common/integration_scheme/integration_scheme.cc
@@ -1,92 +1,94 @@
/**
* @file integration_scheme.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief Common interface to all interface schemes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
IntegrationScheme::IntegrationScheme(DOFManager & dof_manager,
const ID & dof_id, UInt order)
: Parsable(ParserType::_integration_scheme, dof_id),
dof_manager(dof_manager), dof_id(dof_id), order(order), u_store(order + 1) {}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for SolutionType
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type) {
std::string str;
stream >> str;
if (str == "displacement") {
type = IntegrationScheme::_displacement;
} else if (str == "temperature") {
type = IntegrationScheme::_temperature;
} else if (str == "velocity") {
type = IntegrationScheme::_velocity;
} else if (str == "temperature_rate") {
type = IntegrationScheme::_temperature_rate;
} else if (str == "acceleration") {
type = IntegrationScheme::_acceleration;
} else if (str == "damage") {
type = IntegrationScheme::_damage;
} else {
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme::store() {
for (auto data : enumerate(u_store)) {
auto o = std::get<0>(data);
auto & u_store = std::get<1>(data);
auto & u_o = dof_manager.getDOFsDerivatives(dof_id, o);
if (not u_store) {
u_store = std::make_unique<Array<Real>>(
u_o, "integration_scheme_store:" + dof_id + ":" + std::to_string(o));
} else {
u_store->copy(u_o);
}
}
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme::restore() {
for (auto o : arange(order)) {
auto & u_o = dof_manager.getDOFsDerivatives(dof_id, o);
u_o.copy(*u_store[o]);
}
}
} // namespace akantu
diff --git a/src/model/common/integration_scheme/integration_scheme.hh b/src/model/common/integration_scheme/integration_scheme.hh
index c6706df0a..112f30c07 100644
--- a/src/model/common/integration_scheme/integration_scheme.hh
+++ b/src/model/common/integration_scheme/integration_scheme.hh
@@ -1,123 +1,125 @@
/**
* @file integration_scheme.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief This class is just a base class for the integration schemes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTEGRATION_SCHEME_HH_
#define AKANTU_INTEGRATION_SCHEME_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class IntegrationScheme : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
enum SolutionType {
_not_defined = -1,
_displacement = 0,
_temperature = 0,
_damage = 0,
_velocity = 1,
_temperature_rate = 1,
_acceleration = 2,
};
IntegrationScheme(DOFManager & dof_manager, const ID & dof_id, UInt order);
~IntegrationScheme() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t) = 0;
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t) = 0;
/// assemble the jacobian matrix
virtual void assembleJacobian(const SolutionType & type, Real delta_t) = 0;
/// assemble the residual
virtual void assembleResidual(bool is_lumped) = 0;
/// returns a list of needed matrices
virtual std::vector<std::string> getNeededMatrixList() = 0;
/// store dofs info (beginning of steps)
virtual void store();
/// restore dofs (solve failed)
virtual void restore();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the order of the integration scheme
UInt getOrder() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// The underlying DOFManager
DOFManager & dof_manager;
/// The id of the dof treated by this integration scheme.
ID dof_id;
/// The order of the integrator
UInt order;
/// last release of M matrix
UInt m_release{UInt(-1)};
/// stores the values at begining of solve
std::vector<std::unique_ptr<Array<Real>>> u_store;
};
/* -------------------------------------------------------------------------- */
// std::ostream & operator<<(std::ostream & stream,
// const IntegrationScheme::SolutionType & type);
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type);
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_INTEGRATION_SCHEME_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme_1st_order.cc b/src/model/common/integration_scheme/integration_scheme_1st_order.cc
index f8902c75e..c61b52d40 100644
--- a/src/model/common/integration_scheme/integration_scheme_1st_order.cc
+++ b/src/model/common/integration_scheme/integration_scheme_1st_order.cc
@@ -1,97 +1,99 @@
/**
* @file integration_scheme_1st_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the common functions for 1st order time
* integrations
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_1st_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
std::vector<std::string> IntegrationScheme1stOrder::getNeededMatrixList() {
return {"K", "M"};
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
const Array<Real> & first_derivative =
dof_manager.getDOFsDerivatives(this->dof_id, 1);
if (not is_lumped) {
if (this->dof_manager.hasMatrix("M")) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
first_derivative, -1);
}
} else {
if (this->dof_manager.hasLumpedMatrix("M")) {
this->dof_manager.assembleLumpedMatMulVectToResidual(
this->dof_id, "M", first_derivative, -1);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/integration_scheme_1st_order.hh b/src/model/common/integration_scheme/integration_scheme_1st_order.hh
index fbdbfce63..a60424531 100644
--- a/src/model/common/integration_scheme/integration_scheme_1st_order.hh
+++ b/src/model/common/integration_scheme/integration_scheme_1st_order.hh
@@ -1,94 +1,96 @@
/**
* @file integration_scheme_1st_order.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Nov 27 2019
*
* @brief Interface of the time integrator of first order
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_
#define AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_
namespace akantu {
class IntegrationScheme1stOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme1stOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 1){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 1st order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary) const = 0;
/// generic interface of a corrector of 1st order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::unique_ptr<Real> u_dot_store;
};
} // namespace akantu
#include "generalized_trapezoidal.hh"
#endif /* AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH_ */
diff --git a/src/model/common/integration_scheme/integration_scheme_2nd_order.cc b/src/model/common/integration_scheme/integration_scheme_2nd_order.cc
index c7025a3fa..22049e95f 100644
--- a/src/model/common/integration_scheme/integration_scheme_2nd_order.cc
+++ b/src/model/common/integration_scheme/integration_scheme_2nd_order.cc
@@ -1,105 +1,107 @@
/**
* @file integration_scheme_2nd_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 23 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Apr 05 2019
*
* @brief Implementation of the common part of 2nd order integration schemes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
std::vector<std::string> IntegrationScheme2ndOrder::getNeededMatrixList() {
return {"K", "M", "C"};
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, u_dot_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, u_dot_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
if (this->dof_manager.hasMatrix("C")) {
const Array<Real> & first_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "C",
first_derivative, -1);
}
const Array<Real> & second_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
if (not is_lumped) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
} else {
this->dof_manager.assembleLumpedMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/integration_scheme_2nd_order.hh b/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
index 1ee1b7c3e..a8d62a889 100644
--- a/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
+++ b/src/model/common/integration_scheme/integration_scheme_2nd_order.hh
@@ -1,106 +1,108 @@
/**
* @file integration_scheme_2nd_order.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Interface of the integrator of second order
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_
#define AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_
namespace akantu {
class SparseMatrix;
}
namespace akantu {
class IntegrationScheme2ndOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme2ndOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 2){};
~IntegrationScheme2ndOrder() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 2nd order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const = 0;
/// generic interface of a corrector of 2nd order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "newmark-beta.hh"
#endif /* AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH_ */
diff --git a/src/model/common/integration_scheme/newmark-beta.cc b/src/model/common/integration_scheme/newmark-beta.cc
index 9340dc3fc..8a2f0b91a 100644
--- a/src/model/common/integration_scheme/newmark-beta.cc
+++ b/src/model/common/integration_scheme/newmark-beta.cc
@@ -1,262 +1,264 @@
/**
* @file newmark-beta.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 23 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 27 2019
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "newmark-beta.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NewmarkBeta::NewmarkBeta(DOFManager & dof_manager, const ID & dof_id,
Real alpha, Real beta)
: IntegrationScheme2ndOrder(dof_manager, dof_id), beta(beta), alpha(alpha),
k(0.), h(0.), m_release(0), k_release(0), c_release(0) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
this->registerParam("beta", this->beta, beta, _pat_parsmod,
"The beta parameter");
}
/* -------------------------------------------------------------------------- */
/*
* @f$ \tilde{u_{n+1}} = u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
* \ddot{u}_n @f$
* @f$ \tilde{\dot{u}_{n+1}} = \dot{u}_{n} + \Delta t \ddot{u}_{n} @f$
* @f$ \tilde{\ddot{u}_{n}} = \ddot{u}_{n} @f$
*/
void NewmarkBeta::predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
Real dt_a_n = delta_t * *u_dot_dot_val;
*u_val += (1 - k * alpha) * delta_t * *u_dot_val +
(.5 - h * alpha * beta) * delta_t * dt_a_n;
*u_dot_val = (1 - k) * *u_dot_val + (1 - h * beta) * dt_a_n;
*u_dot_dot_val = (1 - h) * *u_dot_dot_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _acceleration: {
this->allCorrector<_acceleration>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
case _velocity: {
this->allCorrector<_velocity>(delta_t, u, u_dot, u_dot_dot, blocked_dofs,
delta);
break;
}
case _displacement: {
this->allCorrector<_displacement>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return 1.;
case _velocity:
return 1. / (beta * delta_t);
case _displacement:
return 1. / (alpha * beta * delta_t * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getVelocityCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return beta * delta_t;
case _velocity:
return 1.;
case _displacement:
return 1. / (alpha * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return alpha * beta * delta_t * delta_t;
case _velocity:
return alpha * delta_t;
case _displacement:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void NewmarkBeta::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.size();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real c = getAccelerationCoefficient(type, delta_t);
Real d = getVelocityCoefficient(type, delta_t);
Real e = getDisplacementCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
*u_dot_dot_val += c * *delta_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::assembleJacobian(const SolutionType & type, Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (this->dof_manager.hasMatrix("C")) {
const SparseMatrix & C = this->dof_manager.getMatrix("C");
does_j_need_update |= C.getRelease() != c_release;
}
does_j_need_update |= this->dof_manager.hasBlockedDOFsChanged();
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.copyProfile(K);
// J.zero();
Real c = this->getAccelerationCoefficient(type, delta_t);
Real e = this->getDisplacementCoefficient(type, delta_t);
if (!(e == 0.)) { // in explicit this coefficient is exactly 0.
J.add(K, e);
}
J.add(M, c);
m_release = M.getRelease();
k_release = K.getRelease();
if (this->dof_manager.hasMatrix("C")) {
Real d = this->getVelocityCoefficient(type, delta_t);
const SparseMatrix & C = this->dof_manager.getMatrix("C");
J.add(C, d);
c_release = C.getRelease();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/newmark-beta.hh b/src/model/common/integration_scheme/newmark-beta.hh
index 57213973c..d7a4ee298 100644
--- a/src/model/common/integration_scheme/newmark-beta.hh
+++ b/src/model/common/integration_scheme/newmark-beta.hh
@@ -1,194 +1,197 @@
/**
* @file newmark-beta.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Sat Sep 12 2020
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NEWMARK_BETA_HH_
#define AKANTU_NEWMARK_BETA_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* The three differentiate equations (dynamic and cinematic) are :
* \f{eqnarray*}{
* M \ddot{u}_{n+1} + C \dot{u}_{n+1} + K u_{n+1} &=& q_{n+1} \\
* u_{n+1} &=& u_{n} + (1 - \alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1} + (1/2 - \alpha) \Delta t^2 \ddot{u}_n \\
* \dot{u}_{n+1} &=& \dot{u}_{n} + (1 - \beta) \Delta t \ddot{u}_{n} + \beta
*\Delta t \ddot{u}_{n+1}
* \f}
*
* Predictor:
* \f{eqnarray*}{
* u^{0}_{n+1} &=& u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
*\ddot{u}_n \\
* \dot{u}^{0}_{n+1} &=& \dot{u}_{n} + \Delta t \ddot{u}_{n} \\
* \ddot{u}^{0}_{n+1} &=& \ddot{u}_{n}
* \f}
*
* Solve :
* \f[ (c M + d C + e K^i_{n+1}) w = = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1}
*- M \ddot{u}^i_{n+1} \f]
*
* Corrector :
* \f{eqnarray*}{
* \ddot{u}^{i+1}_{n+1} &=& \ddot{u}^{i}_{n+1} + c w \\
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + d w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + e w
* \f}
*
* c, d and e are parameters depending on the method used to solve the equations
*\n
* For acceleration : \f$ w = \delta \ddot{u}, e = \alpha \beta \Delta t^2, d =
*\beta \Delta t, c = 1 \f$ \n
* For velocity : \f$ w = \delta \dot{u}, e = 1/\beta \Delta t, d =
*1, c = \alpha \Delta t \f$ \n
* For displacement : \f$ w = \delta u, e = 1, d =
*1/\alpha \Delta t, c = 1/\alpha \beta \Delta t^2 \f$
*/
class NewmarkBeta : public IntegrationScheme2ndOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NewmarkBeta(DOFManager & dof_manager, const ID & dof_id, Real alpha = 0.,
Real beta = 0.);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Beta, beta, Real);
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the \f$\beta\f$ parameter
Real beta;
/// the \f$\alpha\f$ parameter
Real alpha;
Real k;
Real h;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
/// last release of C matrix
UInt c_release;
};
/**
* central difference method (explicit)
* undamped stability condition :
* \f$ \Delta t = \alpha \Delta t_{crit} = \frac{2}{\omega_{max}} \leq \min_{e}
*\frac{l_e}{c_e}\f$
*
*/
class CentralDifference : public NewmarkBeta {
public:
CentralDifference(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 0., 1./2.){};
std::vector<std::string> getNeededMatrixList() override { return {"M", "C"}; }
};
//#include "integration_scheme/central_difference.hh"
/// undamped trapezoidal rule (implicit)
class TrapezoidalRule2 : public NewmarkBeta {
public:
TrapezoidalRule2(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 2., 1. / 2.){};
};
/// Fox-Goodwin rule (implicit)
class FoxGoodwin : public NewmarkBeta {
public:
FoxGoodwin(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 6., 1. / 2.){};
};
/// Linear acceleration (implicit)
class LinearAceleration : public NewmarkBeta {
public:
LinearAceleration(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 3., 1. / 2.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_NEWMARK_BETA_HH_ */
diff --git a/src/model/common/integration_scheme/pseudo_time.cc b/src/model/common/integration_scheme/pseudo_time.cc
index 4f5f78950..aaeacd5a7 100644
--- a/src/model/common/integration_scheme/pseudo_time.cc
+++ b/src/model/common/integration_scheme/pseudo_time.cc
@@ -1,89 +1,91 @@
/**
* @file pseudo_time.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 19 2016
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 27 2019
*
* @brief Implementation of a really simple integration scheme
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "pseudo_time.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PseudoTime::PseudoTime(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 0), k_release(0) {}
/* -------------------------------------------------------------------------- */
std::vector<std::string> PseudoTime::getNeededMatrixList() { return {"K"}; }
/* -------------------------------------------------------------------------- */
void PseudoTime::predictor(Real /*delta_t*/) {}
/* -------------------------------------------------------------------------- */
void PseudoTime::corrector(const SolutionType & /*type*/, Real /*delta_t*/) {
auto & us = this->dof_manager.getDOFs(this->dof_id);
const auto & deltas = this->dof_manager.getSolution(this->dof_id);
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs(this->dof_id);
for (auto && tuple : zip(make_view(us), deltas, make_view(blocked_dofs))) {
auto & u = std::get<0>(tuple);
const auto & delta = std::get<1>(tuple);
const auto & bld = std::get<2>(tuple);
if (not bld) {
u += delta;
}
}
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleJacobian(const SolutionType & /*type*/,
Real /*delta_t*/) {
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= K.getRelease() != k_release;
does_j_need_update |= this->dof_manager.hasBlockedDOFsChanged();
if (not does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.copyProfile(K);
// J.zero();
J.add(K);
k_release = K.getRelease();
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleResidual(bool /*is_lumped*/) {}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/integration_scheme/pseudo_time.hh b/src/model/common/integration_scheme/pseudo_time.hh
index 201302eaf..363b3bdc2 100644
--- a/src/model/common/integration_scheme/pseudo_time.hh
+++ b/src/model/common/integration_scheme/pseudo_time.hh
@@ -1,72 +1,74 @@
/**
* @file pseudo_time.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Pseudo time integration scheme
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PSEUDO_TIME_HH_
#define AKANTU_PSEUDO_TIME_HH_
namespace akantu {
class PseudoTime : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PseudoTime(DOFManager & dof_manager, const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
/// assemble the jacobian matrix
void assembleJacobian(const SolutionType & type, Real delta_t) override;
/// assemble the residual
void assembleResidual(bool is_lumped) override;
protected:
/// last release of K matrix
UInt k_release;
};
} // namespace akantu
#endif /* AKANTU_PSEUDO_TIME_HH_ */
diff --git a/src/model/common/model_solver.cc b/src/model/common/model_solver.cc
index 3b680522e..d839deade 100644
--- a/src/model/common/model_solver.cc
+++ b/src/model/common/model_solver.cc
@@ -1,403 +1,406 @@
/**
* @file model_solver.cc
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Mar 30 2021
*
* @brief Implementation of ModelSolver
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model_solver.hh"
#include "dof_manager.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "time_step_solver.hh"
#if defined(AKANTU_USE_PETSC)
#include "dof_manager_petsc.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> static T getOptionToType(const std::string & opt_str) {
std::stringstream sstr(opt_str);
T opt;
sstr >> opt;
return opt;
}
/* -------------------------------------------------------------------------- */
ModelSolver::ModelSolver(Mesh & mesh, const ModelType & type, const ID & id)
: Parsable(ParserType::_model, id), model_type(type),
parent_id(id), mesh(mesh) {
}
/* -------------------------------------------------------------------------- */
ModelSolver::ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
std::shared_ptr<DOFManager> dof_manager)
: ModelSolver(mesh, type, id) {
if (not dof_manager) {
this->initDOFManager();
} else {
this->dof_manager = dof_manager;
this->setDOFManager(*this->dof_manager);
}
}
/* -------------------------------------------------------------------------- */
ModelSolver::~ModelSolver() = default;
/* -------------------------------------------------------------------------- */
std::tuple<ParserSection, bool> ModelSolver::getParserSection() {
auto sub_sections = getStaticParser().getSubSections(ParserType::_model);
auto it = std::find_if(
sub_sections.begin(), sub_sections.end(), [&](auto && section) {
auto type = getOptionToType<ModelType>(section.getName());
// default id should be the model type if not defined
std::string name = section.getParameter("name", this->parent_id);
return type == model_type and name == this->parent_id;
});
if (it == sub_sections.end()) {
return std::make_tuple(ParserSection(), true);
}
return std::make_tuple(*it, false);
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<DOFManager> ModelSolver::initDOFManager() {
// default without external solver activated at compilation same as mumps that
// is the historical solver but with only the lumped solver
ID solver_type = "default";
#if defined(AKANTU_USE_MUMPS)
solver_type = "default";
#elif defined(AKANTU_USE_PETSC)
solver_type = "petsc";
#endif
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
solver_type = section.getOption(solver_type);
return this->initDOFManager(section, solver_type);
} else {
return this->initDOFManager(solver_type);
}
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<DOFManager>
ModelSolver::initDOFManager(const ID & solver_type) {
if (dof_manager) {
AKANTU_EXCEPTION("The DOF manager for this model is already initialized !");
}
try {
this->dof_manager = DOFManagerFactory::getInstance().allocate(
solver_type, mesh, this->parent_id + ":dof_manager_" + solver_type);
} catch (...) {
AKANTU_EXCEPTION(
"To use the solver "
<< solver_type
<< " you will have to code it. This is an unknown solver type.");
}
this->setDOFManager(*this->dof_manager);
return this->dof_manager;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<DOFManager>
ModelSolver::initDOFManager(const ParserSection & section,
const ID & solver_type) {
this->initDOFManager(solver_type);
auto sub_sections = section.getSubSections(ParserType::_time_step_solver);
// parsing the time step solvers
for (auto && section : sub_sections) {
ID type = section.getName();
ID solver_id = section.getParameter("name", type);
auto tss_type = getOptionToType<TimeStepSolverType>(type);
auto tss_options = this->getDefaultSolverOptions(tss_type);
auto sub_solvers_sect =
section.getSubSections(ParserType::_non_linear_solver);
auto nb_non_linear_solver_section =
section.getNbSubSections(ParserType::_non_linear_solver);
auto nls_type = tss_options.non_linear_solver_type;
if (nb_non_linear_solver_section == 1) {
auto && nls_section = *(sub_solvers_sect.first);
nls_type = getOptionToType<NonLinearSolverType>(nls_section.getName());
} else if (nb_non_linear_solver_section > 0) {
AKANTU_EXCEPTION("More than one non linear solver are provided for the "
"time step solver "
<< solver_id);
}
this->getNewSolver(solver_id, tss_type, nls_type);
if (nb_non_linear_solver_section == 1) {
const auto & nls_section = *(sub_solvers_sect.first);
this->dof_manager->getNonLinearSolver(solver_id).parseSection(
nls_section);
}
auto sub_integrator_sections =
section.getSubSections(ParserType::_integration_scheme);
for (auto && is_section : sub_integrator_sections) {
const auto & dof_type_str = is_section.getName();
ID dof_id;
try {
ID tmp = is_section.getParameter("name");
dof_id = tmp;
} catch (...) {
AKANTU_EXCEPTION("No degree of freedom name specified for the "
"integration scheme of type "
<< dof_type_str);
}
auto it_type = getOptionToType<IntegrationSchemeType>(dof_type_str);
IntegrationScheme::SolutionType s_type = is_section.getParameter(
"solution_type", tss_options.solution_type[dof_id]);
this->setIntegrationScheme(solver_id, dof_id, it_type, s_type);
}
for (auto & is_type : tss_options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_id, is_type.first)) {
this->setIntegrationScheme(solver_id, is_type.first, is_type.second,
tss_options.solution_type[is_type.first]);
}
}
}
if (section.hasParameter("default_solver")) {
ID default_solver = section.getParameter("default_solver");
if (this->hasSolver(default_solver)) {
this->setDefaultSolver(default_solver);
} else {
AKANTU_EXCEPTION(
"The solver \""
<< default_solver
<< "\" was not created, it cannot be set as default solver");
}
}
return this->dof_manager;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) {
ID tmp_solver_id = solver_id;
if (tmp_solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
}
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
}
const TimeStepSolver & tss =
this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getTimeStepSolver(const ID & solver_id) {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver &
ModelSolver::getTimeStepSolver(const ID & solver_id) const {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & ModelSolver::getNonLinearSolver(const ID & solver_id) {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
const NonLinearSolver &
ModelSolver::getNonLinearSolver(const ID & solver_id) const {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id.empty()) {
tmp_solver_id = this->default_solver_id;
}
if (not this->dof_manager) {
AKANTU_EXCEPTION("No DOF manager was initialized");
}
return this->dof_manager->hasTimeStepSolver(tmp_solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setDefaultSolver(const ID & solver_id) {
AKANTU_DEBUG_ASSERT(
this->hasSolver(solver_id),
"Cannot set the default solver to a solver that does not exists");
this->default_solver_id = solver_id;
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(SolverCallback & callback, const ID & solver_id) {
AKANTU_DEBUG_IN();
TimeStepSolver & tss = this->getSolver(solver_id);
// make one non linear solve
tss.solveStep(callback);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(const ID & solver_id) {
solveStep(*this, solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
if (this->default_solver_id.empty()) {
this->default_solver_id = solver_id;
}
if (non_linear_solver_type == NonLinearSolverType::_auto) {
switch (time_step_solver_type) {
case TimeStepSolverType::_dynamic:
case TimeStepSolverType::_static:
non_linear_solver_type = NonLinearSolverType::_newton_raphson;
break;
case TimeStepSolverType::_dynamic_lumped:
non_linear_solver_type = NonLinearSolverType::_lumped;
break;
case TimeStepSolverType::_not_defined:
AKANTU_EXCEPTION(time_step_solver_type
<< " is not a valid time step solver type");
break;
}
}
this->initSolver(time_step_solver_type, non_linear_solver_type);
NonLinearSolver & nls = this->dof_manager->getNewNonLinearSolver(
solver_id, non_linear_solver_type);
this->dof_manager->getNewTimeStepSolver(solver_id, time_step_solver_type, nls,
*this);
}
/* -------------------------------------------------------------------------- */
Real ModelSolver::getTimeStep(const ID & solver_id) const {
const TimeStepSolver & tss = this->getSolver(solver_id);
return tss.getTimeStep();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setTimeStep(Real time_step, const ID & solver_id) {
TimeStepSolver & tss = this->getSolver(solver_id);
return tss.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setIntegrationScheme(
const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type) {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
tss.setIntegrationScheme(dof_id, integration_scheme_type, solution_type);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setIntegrationScheme(
const ID & solver_id, const ID & dof_id,
std::unique_ptr<IntegrationScheme> & integration_scheme,
IntegrationScheme::SolutionType solution_type) {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
tss.setIntegrationScheme(dof_id, integration_scheme, solution_type);
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasDefaultSolver() const {
return (not this->default_solver_id.empty());
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasIntegrationScheme(const ID & solver_id,
const ID & dof_id) const {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
return tss.hasIntegrationScheme(dof_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::predictor() {}
/* -------------------------------------------------------------------------- */
void ModelSolver::corrector() {}
/* -------------------------------------------------------------------------- */
TimeStepSolverType ModelSolver::getDefaultSolverType() const {
return TimeStepSolverType::_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions
ModelSolver::getDefaultSolverOptions(__attribute__((unused))
const TimeStepSolverType & type) const {
ModelSolverOptions options;
options.non_linear_solver_type = NonLinearSolverType::_auto;
return options;
}
} // namespace akantu
diff --git a/src/model/common/model_solver.hh b/src/model/common/model_solver.hh
index abe3b7c44..71aca285b 100644
--- a/src/model/common/model_solver.hh
+++ b/src/model/common/model_solver.hh
@@ -1,202 +1,205 @@
/**
* @file model_solver.hh
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri May 14 2021
*
* @brief Class regrouping the common solve interface to the different models
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "integration_scheme.hh"
#include "parsable.hh"
#include "solver_callback.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MODEL_SOLVER_HH_
#define AKANTU_MODEL_SOLVER_HH_
namespace akantu {
class Mesh;
class DOFManager;
class TimeStepSolver;
class NonLinearSolver;
struct ModelSolverOptions;
} // namespace akantu
namespace akantu {
class ModelSolver : public Parsable,
public SolverCallback,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelSolver(Mesh & mesh, const ModelType & type, const ID & id);
ModelSolver(Mesh & mesh, const ModelType & type, const ID & id,
std::shared_ptr<DOFManager> dof_manager);
~ModelSolver() override;
/// initialize the dof manager based on solver type passed in the input file
std::shared_ptr<DOFManager> initDOFManager();
/// initialize the dof manager based on the used chosen solver type
std::shared_ptr<DOFManager> initDOFManager(const ID & solver_type);
protected:
/// initialize the dof manager based on the used chosen solver type
std::shared_ptr<DOFManager> initDOFManager(const ParserSection & section,
const ID & solver_type);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Callback for the model to instantiate the matricees when needed
virtual void initSolver(TimeStepSolverType /*time_step_solver_type*/,
NonLinearSolverType /*non_linear_solver_type*/) {}
/// get the section in the input file (if it exsits) corresponding to this
/// model
std::tuple<ParserSection, bool> getParserSection();
/// solve a step using a given pre instantiated time step solver and
/// non linear solver
virtual void solveStep(const ID & solver_id = "");
/// solve a step using a given pre instantiated time step solver and
/// non linear solver with a user defined callback instead of the
/// model itself /!\ This can mess up everything
virtual void solveStep(SolverCallback & callback, const ID & solver_id = "");
/// Initialize a time solver that can be used afterwards with its id
void getNewSolver(
const ID & solver_id, TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type = NonLinearSolverType::_auto);
/// set an integration scheme for a given dof and a given solver
void
setIntegrationScheme(const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/// set an externally instantiated integration scheme
void
setIntegrationScheme(const ID & solver_id, const ID & dof_id,
std::unique_ptr<IntegrationScheme> & integration_scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/* ------------------------------------------------------------------------ */
/* SolverCallback interface */
/* ------------------------------------------------------------------------ */
public:
/// Predictor interface for the callback
void predictor() override;
/// Corrector interface for the callback
void corrector() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Default time step solver to instantiate for this model
virtual TimeStepSolverType getDefaultSolverType() const;
/// Default configurations for a given time step solver
virtual ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const;
/// get access to the internal dof manager
DOFManager & getDOFManager() { return *this->dof_manager; }
/// get the time step of a given solver
Real getTimeStep(const ID & solver_id = "") const;
/// set the time step of a given solver
virtual void setTimeStep(Real time_step, const ID & solver_id = "");
/// set the parameter 'param' of the solver 'solver_id'
// template <typename T>
// void set(const ID & param, const T & value, const ID & solver_id = "");
/// get the parameter 'param' of the solver 'solver_id'
// const Parameter & get(const ID & param, const ID & solver_id = "") const;
/// answer to the question "does the solver exists ?"
bool hasSolver(const ID & solver_id) const;
/// changes the current default solver
void setDefaultSolver(const ID & solver_id);
/// is a default solver defined
bool hasDefaultSolver() const;
/// is an integration scheme set for a given solver and a given dof
bool hasIntegrationScheme(const ID & solver_id, const ID & dof_id) const;
TimeStepSolver & getTimeStepSolver(const ID & solver_id = "");
NonLinearSolver & getNonLinearSolver(const ID & solver_id = "");
const TimeStepSolver & getTimeStepSolver(const ID & solver_id = "") const;
const NonLinearSolver & getNonLinearSolver(const ID & solver_id = "") const;
private:
TimeStepSolver & getSolver(const ID & solver_id);
const TimeStepSolver & getSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ModelType model_type;
/// Underlying dof_manager (the brain...)
std::shared_ptr<DOFManager> dof_manager;
private:
ID parent_id;
/// Underlying mesh
Mesh & mesh;
/// Default time step solver to use
ID default_solver_id;
};
struct ModelSolverOptions {
NonLinearSolverType non_linear_solver_type;
std::map<ID, IntegrationSchemeType> integration_scheme_type;
std::map<ID, IntegrationScheme::SolutionType> solution_type;
};
} // namespace akantu
#endif /* AKANTU_MODEL_SOLVER_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver.cc b/src/model/common/non_linear_solver/non_linear_solver.cc
index ed9814301..bf784c111 100644
--- a/src/model/common/non_linear_solver/non_linear_solver.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver.cc
@@ -1,77 +1,80 @@
/**
* @file non_linear_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Jan 01 2019
*
* @brief Implementation of the base class NonLinearSolver
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "dof_manager.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolver::NonLinearSolver(
DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id)
: Parsable(ParserType::_non_linear_solver, id), id(id),
_dof_manager(dof_manager),
non_linear_solver_type(non_linear_solver_type) {
this->registerParam("type", this->non_linear_solver_type, _pat_parsable,
"Non linear solver type");
}
/* -------------------------------------------------------------------------- */
NonLinearSolver::~NonLinearSolver() = default;
/* -------------------------------------------------------------------------- */
void NonLinearSolver::checkIfTypeIsSupported() {
if (this->supported_type.find(this->non_linear_solver_type) ==
this->supported_type.end() and
this->non_linear_solver_type != NonLinearSolverType::_auto) {
AKANTU_EXCEPTION("The resolution method "
<< this->non_linear_solver_type
<< " is not implemented in the non linear solver "
<< this->id << "!");
}
}
/* -------------------------------------------------------------------------- */
void NonLinearSolver::assembleResidual(SolverCallback & solver_callback) {
if (solver_callback.canSplitResidual() and
non_linear_solver_type == NonLinearSolverType::_linear) {
this->_dof_manager.zeroResidual();
solver_callback.assembleResidual("external");
this->_dof_manager.assembleMatMulDOFsToResidual("K", -1.);
solver_callback.assembleResidual("inertial");
} else {
solver_callback.assembleResidual();
}
}
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver.hh b/src/model/common/non_linear_solver/non_linear_solver.hh
index 626e59068..6e0561ba7 100644
--- a/src/model/common/non_linear_solver/non_linear_solver.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver.hh
@@ -1,113 +1,115 @@
/**
* @file non_linear_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Wed Mar 27 2019
*
* @brief Non linear solver interface
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_HH_
#define AKANTU_NON_LINEAR_SOLVER_HH_
namespace akantu {
class DOFManager;
class SolverCallback;
} // namespace akantu
namespace akantu {
class NonLinearSolver : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolver(DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver");
~NonLinearSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
virtual void solve(SolverCallback & callback) = 0;
/// intercept the call to set for options
template <typename T> void set(const ID & param, T && t) {
if (has_internal_set_param) {
set_param(param, std::to_string(t));
} else {
ParameterRegistry::set(param, t);
}
}
protected:
void checkIfTypeIsSupported();
void assembleResidual(SolverCallback & callback);
/// internal set param for solvers that should intercept the parameters
virtual void set_param(const ID & /*param*/, const std::string & /*value*/) {}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
DOFManager & _dof_manager;
/// type of non linear solver
NonLinearSolverType non_linear_solver_type;
/// list of supported non linear solver types
std::set<NonLinearSolverType> supported_type;
/// specifies if the set param should be redirected
bool has_internal_set_param{false};
};
namespace debug {
class NLSNotConvergedException : public Exception {
public:
NLSNotConvergedException(Real threshold, UInt niter, Real error)
: Exception("The non linear solver did not converge."),
threshold(threshold), niter(niter), error(error) {}
Real threshold;
UInt niter;
Real error;
};
} // namespace debug
} // namespace akantu
#endif /* AKANTU_NON_LINEAR_SOLVER_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_default.hh b/src/model/common/non_linear_solver/non_linear_solver_default.hh
index dff69cdfd..56712fc87 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_default.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_default.hh
@@ -1,44 +1,46 @@
/**
* @file non_linear_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Dec 18 2019
*
* @brief Include for the default non linear solvers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_
#define AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_
#if defined(AKANTU_USE_MUMPS)
#include "non_linear_solver_linear.hh"
#include "non_linear_solver_newton_raphson.hh"
#endif
#include "non_linear_solver_lumped.hh"
#endif /* AKANTU_NON_LINEAR_SOLVER_DEFAULT_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_linear.cc b/src/model/common/non_linear_solver/non_linear_solver_linear.cc
index 2b1c16fa7..18a920440 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_linear.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_linear.cc
@@ -1,79 +1,83 @@
/**
* @file non_linear_solver_linear.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Feb 05 2021
*
* @brief Implementation of the default NonLinearSolver
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_linear.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::NonLinearSolverLinear(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id),
dof_manager(dof_manager),
solver(dof_manager, "J", id + ":sparse_solver") {
this->supported_type.insert(NonLinearSolverType::_linear);
this->checkIfTypeIsSupported();
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::~NonLinearSolverLinear() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverLinear::solve(SolverCallback & solver_callback) {
solver_callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleMatrix("J");
// Residual computed after J to allow the model to use K to compute the
// residual
this->assembleResidual(solver_callback);
this->solver.solve();
solver_callback.corrector();
if (solver_callback.canSplitResidual()) {
solver_callback.assembleResidual("internal");
+ } else {
+ this->assembleResidual(solver_callback);
}
solver_callback.afterSolveStep(true);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_linear.hh b/src/model/common/non_linear_solver/non_linear_solver_linear.hh
index a7c2a58fe..07382f525 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_linear.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_linear.hh
@@ -1,78 +1,80 @@
/**
* @file non_linear_solver_linear.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_
#define AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLinear : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLinear(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_linear");
~NonLinearSolverLinear() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, solver, const SparseSolverMumps &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
SparseSolverMumps solver;
};
} // namespace akantu
#endif /* AKANTU_NON_LINEAR_SOLVER_LINEAR_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_lumped.cc b/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
index c6ef42b74..316c884de 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_lumped.cc
@@ -1,101 +1,103 @@
/**
* @file non_linear_solver_lumped.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 16 2016
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Sat May 23 2020
*
* @brief Implementation of the default NonLinearSolver
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_lumped.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::NonLinearSolverLumped(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id),
dof_manager(dof_manager) {
this->supported_type.insert(NonLinearSolverType::_lumped);
this->checkIfTypeIsSupported();
this->registerParam("b_a2x", this->alpha, 1., _pat_parsmod,
"Conversion coefficient between x and A^{-1} b");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::~NonLinearSolverLumped() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverLumped::solve(SolverCallback & solver_callback) {
solver_callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleResidual();
auto & x = aka::as_type<SolverVectorDefault>(this->dof_manager.getSolution());
const auto & b = this->dof_manager.getResidual();
x.resize();
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs();
const auto & A = this->dof_manager.getLumpedMatrix("M");
// alpha is the conversion factor from from force/mass to acceleration needed
// in model coupled with atomistic \todo find a way to define alpha per dof
// type
NonLinearSolverLumped::solveLumped(A, x, b, alpha, blocked_dofs);
this->dof_manager.splitSolutionPerDOFs();
solver_callback.corrector();
solver_callback.afterSolveStep(true);
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverLumped::solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b, Real alpha,
const Array<bool> & blocked_dofs) {
for (auto && data :
zip(make_view(A), make_view(x), make_view(b), make_view(blocked_dofs))) {
const auto & A = std::get<0>(data);
auto & x = std::get<1>(data);
const auto & b = std::get<2>(data);
const auto & blocked = std::get<3>(data);
if (not blocked) {
x = alpha * (b / A);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_lumped.hh b/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
index 9c9127549..5d8ca75cc 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_lumped.hh
@@ -1,79 +1,81 @@
/**
* @file non_linear_solver_lumped.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Mar 13 2019
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_
#define AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLumped : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLumped(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_lumped");
~NonLinearSolverLumped() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
static void solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b, Real alpha,
const Array<bool> & blocked_dofs);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Coefficient to apply between x and A^{-1} b
Real alpha;
};
} // namespace akantu
#endif /* AKANTU_NON_LINEAR_SOLVER_LUMPED_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
index e5f8e3aa9..3def8f178 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.cc
@@ -1,209 +1,211 @@
/**
* @file non_linear_solver_newton_raphson.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 15 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Mar 30 2021
*
* @brief Implementation of the default NonLinearSolver
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_newton_raphson.hh"
#include "communicator.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "solver_vector.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id),
dof_manager(dof_manager),
solver(std::make_unique<SparseSolverMumps>(
dof_manager, "J", id + ":sparse_solver")) {
this->supported_type.insert(NonLinearSolverType::_newton_raphson_modified);
this->supported_type.insert(NonLinearSolverType::_newton_raphson_contact);
this->supported_type.insert(NonLinearSolverType::_newton_raphson);
this->supported_type.insert(NonLinearSolverType::_linear);
this->checkIfTypeIsSupported();
this->registerParam("threshold", convergence_criteria, 1e-10, _pat_parsmod,
"Threshold to consider results as converged");
this->registerParam("convergence_type", convergence_criteria_type,
SolveConvergenceCriteria::_solution, _pat_parsmod,
"Type of convergence criteria");
this->registerParam("max_iterations", max_iterations, 10, _pat_parsmod,
"Max number of iterations");
this->registerParam("error", error, _pat_readable, "Last reached error");
this->registerParam("nb_iterations", n_iter, _pat_readable,
"Last reached number of iterations");
this->registerParam("converged", converged, _pat_readable,
"Did last solve converged");
this->registerParam("force_linear_recompute", force_linear_recompute, true,
_pat_modifiable,
"Force reassembly of the jacobian matrix");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::~NonLinearSolverNewtonRaphson() = default;
/* ------------------------------------------------------------------------ */
void NonLinearSolverNewtonRaphson::solve(SolverCallback & solver_callback) {
solver_callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
if (non_linear_solver_type == NonLinearSolverType::_linear and
solver_callback.canSplitResidual()) {
solver_callback.assembleMatrix("K");
}
this->assembleResidual(solver_callback);
if (this->non_linear_solver_type ==
NonLinearSolverType::_newton_raphson_modified ||
(this->non_linear_solver_type == NonLinearSolverType::_linear &&
this->force_linear_recompute)) {
solver_callback.assembleMatrix("J");
this->force_linear_recompute = false;
}
this->n_iter = 0;
this->converged = false;
this->convergence_criteria_normalized = this->convergence_criteria;
if (this->convergence_criteria_type == SolveConvergenceCriteria::_residual) {
this->converged = this->testConvergence(this->dof_manager.getResidual());
if (this->converged) {
return;
}
this->convergence_criteria_normalized =
this->error * this->convergence_criteria;
}
do {
if (this->non_linear_solver_type == NonLinearSolverType::_newton_raphson or
this->non_linear_solver_type ==
NonLinearSolverType::_newton_raphson_contact) {
solver_callback.assembleMatrix("J");
}
this->solver->solve();
solver_callback.corrector();
// EventManager::sendEvent(NonLinearSolver::AfterSparseSolve(method));
if (this->convergence_criteria_type ==
SolveConvergenceCriteria::_residual) {
this->assembleResidual(solver_callback);
this->converged = this->testConvergence(this->dof_manager.getResidual());
} else {
this->converged = this->testConvergence(this->dof_manager.getSolution());
}
if (this->convergence_criteria_type ==
SolveConvergenceCriteria::_solution and
not this->converged) {
this->assembleResidual(solver_callback);
}
this->n_iter++;
AKANTU_DEBUG_INFO(
"[" << this->convergence_criteria_type << "] Convergence iteration "
<< std::setw(std::log10(this->max_iterations)) << this->n_iter
<< ": error " << this->error << (this->converged ? " < " : " > ")
<< this->convergence_criteria);
} while (not this->converged and this->n_iter <= this->max_iterations);
// this makes sure that you have correct strains and stresses after the
// solveStep function (e.g., for dumping)
if (this->convergence_criteria_type == SolveConvergenceCriteria::_solution) {
this->assembleResidual(solver_callback);
}
this->converged =
this->converged and not(this->n_iter > this->max_iterations);
solver_callback.afterSolveStep(this->converged);
if (not this->converged) {
AKANTU_CUSTOM_EXCEPTION(debug::NLSNotConvergedException(
this->convergence_criteria, this->n_iter, this->error));
AKANTU_DEBUG_WARNING("[" << this->convergence_criteria_type
<< "] Convergence not reached after "
<< std::setw(std::log10(this->max_iterations))
<< this->n_iter << " iteration"
<< (this->n_iter == 1 ? "" : "s") << "!");
}
}
/* -------------------------------------------------------------------------- */
bool NonLinearSolverNewtonRaphson::testConvergence(
const SolverVector & solver_vector) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getBlockedDOFs();
const Array<Real> & array(solver_vector);
UInt nb_degree_of_freedoms = array.size();
auto arr_it = array.begin();
auto bld_it = blocked_dofs.begin();
Real norm = 0.;
for (UInt n = 0; n < nb_degree_of_freedoms; ++n, ++arr_it, ++bld_it) {
bool is_local_node = this->dof_manager.isLocalOrMasterDOF(n);
if ((!*bld_it) && is_local_node) {
norm += *arr_it * *arr_it;
}
}
dof_manager.getCommunicator().allReduce(norm, SynchronizerOperation::_sum);
norm = std::sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something went wrong in the solve phase");
this->error = norm;
return (error < this->convergence_criteria_normalized);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
index 37fa51ac5..6f53eeda0 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_newton_raphson.hh
@@ -1,109 +1,111 @@
/**
* @file non_linear_solver_newton_raphson.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Nov 27 2019
*
* @brief Default implementation of NonLinearSolver, in case no external
* library
* is there to do the job
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_
#define AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_
namespace akantu {
class DOFManagerDefault;
class SparseSolverMumps;
class SolverVector;
} // namespace akantu
namespace akantu {
class NonLinearSolverNewtonRaphson : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_newton_raphson");
~NonLinearSolverNewtonRaphson() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, *solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, *solver, const SparseSolverMumps &);
protected:
/// test the convergence compare norm of array to convergence_criteria
bool testConvergence(const SolverVector & solver_vector);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
std::unique_ptr<SparseSolverMumps> solver;
/// Type of convergence criteria
SolveConvergenceCriteria convergence_criteria_type;
/// convergence threshold
Real convergence_criteria;
/// convergence threshold
Real convergence_criteria_normalized;
/// Max number of iterations
int max_iterations;
/// Number of iterations at last solve call
int n_iter{0};
/// Convergence error at last solve call
Real error{0.};
/// Did the last call to solve reached convergence
bool converged{false};
/// Force a re-computation of the jacobian matrix
bool force_linear_recompute{true};
};
} // namespace akantu
#endif /* AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH_ */
diff --git a/src/model/common/non_linear_solver/non_linear_solver_petsc.cc b/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
index e936282f4..246922de5 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
+++ b/src/model/common/non_linear_solver/non_linear_solver_petsc.cc
@@ -1,223 +1,227 @@
/**
* @file non_linear_solver_petsc.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Mon Dec 31 2018
+ * @date creation: Sat Feb 03 2018
+ * @date last modification: Sat May 23 2020
*
- * @brief A Documented file.
+ * @brief Interface to non linear solver of PETSc
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "non_linear_solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_callback.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
/* -------------------------------------------------------------------------- */
#include <petscoptions.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
NonLinearSolverPETSc::NonLinearSolverPETSc(
DOFManagerPETSc & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id),
dof_manager(dof_manager) {
std::unordered_map<NonLinearSolverType, SNESType>
petsc_non_linear_solver_types{
{NonLinearSolverType::_newton_raphson, SNESNEWTONLS},
{NonLinearSolverType::_linear, SNESKSPONLY},
{NonLinearSolverType::_gmres, SNESNGMRES},
{NonLinearSolverType::_bfgs, SNESQN},
{NonLinearSolverType::_cg, SNESNCG}};
this->has_internal_set_param = true;
for (const auto & pair : petsc_non_linear_solver_types) {
supported_type.insert(pair.first);
}
this->checkIfTypeIsSupported();
auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(SNESCreate, mpi_comm, &snes);
auto it = petsc_non_linear_solver_types.find(non_linear_solver_type);
if (it != petsc_non_linear_solver_types.end()) {
PETSc_call(SNESSetType, snes, it->second);
}
SNESSetFromOptions(snes);
}
/* -------------------------------------------------------------------------- */
NonLinearSolverPETSc::~NonLinearSolverPETSc() {
PETSc_call(SNESDestroy, &snes);
}
/* -------------------------------------------------------------------------- */
class NonLinearSolverPETScCallback {
public:
NonLinearSolverPETScCallback(DOFManagerPETSc & dof_manager,
SolverVectorPETSc & x)
: dof_manager(dof_manager), x(x), x_prev(x, "previous_solution") {}
void corrector() {
auto & dx = dof_manager.getSolution();
PETSc_call(VecWAXPY, dx, -1., x_prev, x);
dof_manager.splitSolutionPerDOFs();
callback->corrector();
PETSc_call(VecCopy, x, x_prev);
}
void assembleResidual() {
corrector();
callback->assembleResidual();
}
void assembleJacobian() {
// corrector();
callback->assembleMatrix("J");
}
void setInitialSolution(SolverVectorPETSc & x) {
PETSc_call(VecCopy, x, x_prev);
}
void setCallback(SolverCallback & callback) { this->callback = &callback; }
private:
// SNES & snes;
SolverCallback * callback;
DOFManagerPETSc & dof_manager;
SolverVectorPETSc & x;
SolverVectorPETSc x_prev;
}; // namespace akantu
/* -------------------------------------------------------------------------- */
PetscErrorCode NonLinearSolverPETSc::FormFunction(SNES /*snes*/, Vec /*dx*/,
Vec /*f*/, void * ctx) {
auto * _this = reinterpret_cast<NonLinearSolverPETScCallback *>(ctx);
_this->assembleResidual();
return 0;
}
/* -------------------------------------------------------------------------- */
PetscErrorCode NonLinearSolverPETSc::FormJacobian(SNES /*snes*/, Vec /*dx*/,
Mat /*J*/, Mat /*P*/,
void * ctx) {
auto * _this = reinterpret_cast<NonLinearSolverPETScCallback *>(ctx);
_this->assembleJacobian();
return 0;
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::solve(SolverCallback & callback) {
callback.beforeSolveStep();
this->dof_manager.updateGlobalBlockedDofs();
callback.assembleMatrix("J");
auto & global_x = dof_manager.getSolution();
global_x.zero();
if (not x) {
x = std::make_unique<SolverVectorPETSc>(global_x, "temporary_solution");
}
*x = global_x;
if (not ctx) {
ctx = std::make_unique<NonLinearSolverPETScCallback>(dof_manager, *x);
}
ctx->setCallback(callback);
ctx->setInitialSolution(global_x);
auto & rhs = dof_manager.getResidual();
auto & J = dof_manager.getMatrix("J");
PETSc_call(SNESSetFunction, snes, rhs, NonLinearSolverPETSc::FormFunction,
ctx.get());
PETSc_call(SNESSetJacobian, snes, J, J, NonLinearSolverPETSc::FormJacobian,
ctx.get());
rhs.zero();
callback.predictor();
callback.assembleResidual();
PETSc_call(SNESSolve, snes, nullptr, *x);
PETSc_call(SNESGetConvergedReason, snes, &reason);
PETSc_call(SNESGetIterationNumber, snes, &n_iter);
PETSc_call(VecAXPY, global_x, -1.0, *x);
dof_manager.splitSolutionPerDOFs();
callback.corrector();
bool converged = reason >= 0;
callback.afterSolveStep(converged);
if (not converged) {
PetscReal atol;
PetscReal rtol;
PetscReal stol;
PetscInt maxit;
PetscInt maxf;
PETSc_call(SNESGetTolerances, snes, &atol, &rtol, &stol, &maxit, &maxf);
AKANTU_CUSTOM_EXCEPTION(debug::SNESNotConvergedException(
this->reason, this->n_iter, stol, atol, rtol, maxit));
}
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::set_param(const ID & param,
const std::string & value) {
std::map<ID, ID> akantu_to_petsc_option = {{"max_iterations", "snes_max_it"},
{"threshold", "snes_stol"}};
auto it = akantu_to_petsc_option.find(param);
auto p = it == akantu_to_petsc_option.end() ? param : it->second;
PetscOptionsSetValue(nullptr, p.c_str(), value.c_str());
SNESSetFromOptions(snes);
PetscOptionsClear(nullptr);
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverPETSc::parseSection(const ParserSection & section) {
auto parameters = section.getParameters();
for (auto && param : range(parameters.first, parameters.second)) {
PetscOptionsSetValue(nullptr, param.getName().c_str(),
param.getValue().c_str());
}
SNESSetFromOptions(snes);
PetscOptionsClear(nullptr);
}
} // namespace akantu
diff --git a/src/model/common/non_linear_solver/non_linear_solver_petsc.hh b/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
index 5e90c3b7e..21951a09c 100644
--- a/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
+++ b/src/model/common/non_linear_solver/non_linear_solver_petsc.hh
@@ -1,107 +1,111 @@
/**
* @file non_linear_solver_petsc.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Sat Feb 03 2018
+ * @date last modification: Sat May 23 2020
*
- * @brief A Documented file.
+ * @brief Interface to non linear solver of PETSc
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscsnes.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LINEAR_SOLVER_PETSC_HH_
#define AKANTU_NON_LINEAR_SOLVER_PETSC_HH_
namespace akantu {
class DOFManagerPETSc;
class NonLinearSolverPETScCallback;
class SolverVectorPETSc;
} // namespace akantu
namespace akantu {
class NonLinearSolverPETSc : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverPETSc(DOFManagerPETSc & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_petsc");
~NonLinearSolverPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
void solve(SolverCallback & callback) override;
/// parse the arguments from the input file
void parseSection(const ParserSection & section) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
static PetscErrorCode FormFunction(SNES snes, Vec dx, Vec f, void * ctx);
static PetscErrorCode FormJacobian(SNES snes, Vec dx, Mat J, Mat P,
void * ctx);
void set_param(const ID & param, const std::string & value) override;
DOFManagerPETSc & dof_manager;
/// PETSc non linear solver
SNES snes;
SNESConvergedReason reason;
SolverCallback * callback{nullptr};
std::unique_ptr<SolverVectorPETSc> x;
std::unique_ptr<NonLinearSolverPETScCallback> ctx;
Int n_iter{0};
};
namespace debug {
class SNESNotConvergedException : public NLSNotConvergedException {
public:
SNESNotConvergedException(SNESConvergedReason reason, UInt niter,
Real error, Real absolute_tolerance,
Real relative_tolerance, UInt max_iterations)
: NLSNotConvergedException(relative_tolerance, niter, error),
reason(reason), absolute_tolerance(absolute_tolerance),
max_iterations(max_iterations) {}
SNESConvergedReason reason;
Real absolute_tolerance;
UInt max_iterations;
};
} // namespace debug
} // namespace akantu
#endif /* AKANTU_NON_LINEAR_SOLVER_PETSC_HH_ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function.hh b/src/model/common/non_local_toolbox/base_weight_function.hh
index 95a80e25c..99d294003 100644
--- a/src/model/common/non_local_toolbox/base_weight_function.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function.hh
@@ -1,171 +1,173 @@
/**
* @file base_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Base weight function for non local materials
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BASE_WEIGHT_FUNCTION_HH_
#define AKANTU_BASE_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
class BaseWeightFunction : public Parsable, public DataAccessor<Element> {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
BaseWeightFunction(NonLocalManager & manager,
const std::string & type = "base")
: Parsable(ParserType::_weight_function, "weight_function:" + type),
manager(manager), type(type),
spatial_dimension(manager.getModel().getMesh().getSpatialDimension()) {
this->registerParam("update_rate", update_rate, UInt(1), _pat_parsmod,
"Update frequency");
}
~BaseWeightFunction() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// initialize the weight function
virtual inline void init();
/// update the internal parameters
virtual void updateInternals(){};
/* ------------------------------------------------------------------------ */
/// set the non-local radius
inline void setRadius(Real radius);
/* ------------------------------------------------------------------------ */
/// compute the weight for a given distance between two quadrature points
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2) const;
/// print function
void printself(std::ostream & stream, int indent = 0) const override {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT) {
;
}
stream << space << "WeightFunction " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/// get the radius
Real getRadius() const { return R; }
/// get the update rate
UInt getUpdateRate() const { return update_rate; }
public:
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override {
return 0;
}
inline void packData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) const override {}
inline void unpackData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Type, type, const ID &);
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// reference to the non-local manager
NonLocalManager & manager;
/// the non-local radius
Real R;
/// the non-local radius squared
Real R2;
/// the update rate
UInt update_rate;
/// name of the type of weight function
const std::string type;
/// the spatial dimension
UInt spatial_dimension;
};
inline std::ostream & operator<<(std::ostream & stream,
const BaseWeightFunction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "base_weight_function_inline_impl.hh"
/* -------------------------------------------------------------------------- */
/* Include all other weight function types */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DAMAGE_NON_LOCAL)
#include "damaged_weight_function.hh"
#include "remove_damaged_weight_function.hh"
#include "remove_damaged_with_damage_rate_weight_function.hh"
#include "stress_based_weight_function.hh"
#endif
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_BASE_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
index 36533b13e..b116171d5 100644
--- a/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function_inline_impl.hh
@@ -1,71 +1,73 @@
/**
* @file base_weight_function_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Wed Sep 27 2017
*
* @brief Implementation of inline function of base weight function
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_
#define AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::init() {
/// compute R^2 for a given non-local radius
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
inline void BaseWeightFunction::setRadius(Real radius) {
/// set the non-local radius and update R^2 accordingly
this->R = radius;
this->R2 = this->R * this->R;
}
/* -------------------------------------------------------------------------- */
inline Real
BaseWeightFunction::operator()(Real r, const IntegrationPoint & /* q1 */,
const IntegrationPoint & /* q2 */) const {
/// initialize the weight
Real w = 0;
/// compute weight for given r
if (r <= this->R) {
Real alpha = (1. - r * r / this->R2);
w = alpha * alpha;
// *weight = 1 - sqrt(r / radius);
}
return w;
}
} // namespace akantu
#endif /* AKANTU_BASE_WEIGHT_FUNCTION_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhood_base.cc b/src/model/common/non_local_toolbox/neighborhood_base.cc
index 990dd6e96..5f2b1f17a 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/neighborhood_base.cc
@@ -1,303 +1,305 @@
/**
* @file neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of generic neighborhood base
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "mesh_accessor.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodBase::NeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id)
: id(id), model(model), quad_coordinates(quad_coordinates),
spatial_dimension(this->model.getMesh().getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodBase::~NeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
// void NeighborhoodBase::createSynchronizerRegistry(
// DataAccessor<Element> * data_accessor) {
// this->synch_registry = new SynchronizerRegistry(*data_accessor);
// }
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::initNeighborhood() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void NeighborhoodBase::createGrid() {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model.getMesh();
const auto & lower_bounds = mesh.getLocalLowerBounds();
const auto & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension,
this->neighborhood_radius * safety_factor);
spatial_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
spatial_dimension, spacing, center);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::updatePairList() {
AKANTU_DEBUG_IN();
//// loop over all quads -> all cells
for (auto && cell_id : *spatial_grid) {
AKANTU_DEBUG_INFO("Looping on next cell");
for (auto && q1 : spatial_grid->getCell(cell_id)) {
if (q1.ghost_type == _ghost) {
break;
}
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
auto cell_id = spatial_grid->getCellID(q1_coords);
/// loop over all the neighboring cells of the current quad
for (auto && neighbor_cell : cell_id.neighbors()) {
// loop over the quadrature point in the current neighboring cell
for (auto && q2 : spatial_grid->getCell(neighbor_cell)) {
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
Real distance = q1_coords.distance(q2_coords);
if (distance <= this->neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <= q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::savePairs(const std::string & filename) const {
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
const auto & q1 = pair.first;
const auto & q2 = pair.second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
pout.close();
if (comm.getNbProc() != 1) {
return;
}
Mesh mesh_out(spatial_dimension);
MeshAccessor mesh_accessor(mesh_out);
auto & connectivity = mesh_accessor.getConnectivity(_segment_2);
auto & tag = mesh_accessor.getData<UInt>("tag_1", _segment_2);
auto & nodes = mesh_accessor.getNodes();
std::map<IntegrationPoint, UInt> quad_to_nodes;
UInt node = 0;
IntegrationPoint q1;
IntegrationPoint q2;
bool inserted;
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
auto add_node = [&](auto && q) {
std::tie(std::ignore, inserted) =
quad_to_nodes.insert(std::make_pair(q, node));
if (not inserted) {
return;
}
auto coords_it = this->quad_coordinates(q.type, q.ghost_type)
.begin(spatial_dimension);
auto && coords = Vector<Real>(coords_it[q.global_num]);
nodes.push_back(coords);
++node;
};
add_node(q1);
add_node(q2);
}
}
for (auto && ghost_type : ghost_types) {
for (const auto & pair : pair_list[ghost_type]) {
std::tie(q1, q2) = pair;
UInt node1 = quad_to_nodes[q1];
UInt node2 = quad_to_nodes[q2];
connectivity.push_back(Vector<UInt>{node1, node2});
tag.push_back(node1 + 1);
if (node1 != node2) {
connectivity.push_back(Vector<UInt>{node2, node1});
tag.push_back(node2 + 1);
}
}
}
mesh_out.write(filename + ".msh");
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
// this function is not optimized and only used for tests on small meshes
// @todo maybe optimize this function for better performance?
IntegrationPoint q2;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
std::ofstream pout;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
for (auto && cell_id : *spatial_grid) {
for (auto && q1 : spatial_grid->getCell(cell_id)) {
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
auto && q1_coords = Vector<Real>(coords_type_1_it[q1.global_num]);
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (auto && ghost_type2 : ghost_types) {
for (auto && pair : pair_list[ghost_type2]) {
if (q1 == pair.first && pair.second != q1) {
q2 = pair.second;
} else if (q1 == pair.second && pair.first != q1) {
q2 = pair.first;
} else {
continue;
}
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
auto && q2_coords = Vector<Real>(coords_type_2_it[q2.global_num]);
pout << q2_coords << std::endl;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = 0;
auto cleanPoint = [&](auto && q) {
if (new_numbering.exists(q.type, q.ghost_type)) {
UInt q_new_el = new_numbering(q.type, q.ghost_type)(q.element);
AKANTU_DEBUG_ASSERT(q_new_el != UInt(-1),
"A local quadrature_point "
<< q
<< " as been removed instead of "
"just being renumbered: "
<< id);
q.element = q_new_el;
nb_quad = fem.getNbIntegrationPoints(q.type, q.ghost_type);
q.global_num = nb_quad * q.element + q.num_point;
}
};
// Change the pairs in new global numbering
for (auto ghost_type : ghost_types) {
auto & pair_list = this->pair_list.at(ghost_type);
for (auto && pair : pair_list) {
if (pair.first.ghost_type == _ghost) {
cleanPoint(pair.first);
}
if (pair.second.ghost_type == _ghost) {
cleanPoint(pair.second);
}
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/neighborhood_base.hh b/src/model/common/non_local_toolbox/neighborhood_base.hh
index 8b6966e22..5f39e7a45 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/neighborhood_base.hh
@@ -1,151 +1,153 @@
/**
* @file neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Generic neighborhood of quadrature points
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NEIGHBORHOOD_BASE_HH_
#define AKANTU_NEIGHBORHOOD_BASE_HH_
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
template <class T> class SpatialGrid;
class GridSynchronizer;
class RemovedElementsEvent;
} // namespace akantu
namespace akantu {
class NeighborhoodBase : public DataAccessor<Element>,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodBase(Model & model,
const ElementTypeMapArray<Real> & quad_coordinates,
const ID & id = "neighborhood");
~NeighborhoodBase() override;
using PairList = std::vector<std::pair<IntegrationPoint, IntegrationPoint>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// intialize the neighborhood
virtual void initNeighborhood();
// /// create a synchronizer registry
// void createSynchronizerRegistry(DataAccessor * data_accessor);
/// initialize the material computed parameter
inline void insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords);
/// create the pairs of quadrature points
void updatePairList();
/// save the pairs of quadrature points in a file
void savePairs(const std::string & filename) const;
/// save the coordinates of all neighbors of a quad
void saveNeighborCoords(const std::string & filename) const;
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer() = 0;
virtual void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) = 0;
/// inherited function from MeshEventHandler
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
protected:
/// create the grid
void createGrid();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
/// return the object handling synchronizers
const PairList & getPairLists(GhostType type) {
return pair_list[type == _not_ghost ? 0 : 1];
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// the model to which the neighborhood belongs
Model & model;
/// Radius of impact: to determine if two quadrature points influence each
/// other
Real neighborhood_radius{0.};
/**
* the pairs of quadrature points
* 0: not ghost to not ghost
* 1: not ghost to ghost
*/
std::array<PairList, 2> pair_list;
/// the regular grid to construct/update the pair lists
std::unique_ptr<SpatialGrid<IntegrationPoint>> spatial_grid;
bool is_creating_grid{false};
/// the grid synchronizer for parallel computations
std::unique_ptr<GridSynchronizer> grid_synchronizer;
/// the quadrature point positions
const ElementTypeMapArray<Real> & quad_coordinates;
/// the spatial dimension of the problem
const UInt spatial_dimension;
};
} // namespace akantu
#include "neighborhood_base_inline_impl.hh"
#endif /* AKANTU_NEIGHBORHOOD_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh b/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
index 06fab302c..a5e79c170 100644
--- a/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/neighborhood_base_inline_impl.hh
@@ -1,49 +1,51 @@
/**
* @file neighborhood_base_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Inline implementation of neighborhood base functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_grid_dynamic.hh"
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_
#define AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_
namespace akantu {
inline void
NeighborhoodBase::insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords) {
this->spatial_grid->insert(quad, coords);
}
} // namespace akantu
#endif /* AKANTU_NEIGHBORHOOD_BASE_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
index 80b7dc24e..47e35297c 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
@@ -1,290 +1,292 @@
/**
* @file neighborhood_max_criterion.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Thu Oct 15 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of class NeighborhoodMaxCriterion
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_max_criterion.hh"
#include "grid_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::NeighborhoodMaxCriterion(
Model & model, const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id, const ID & id)
: NeighborhoodBase(model, quad_coordinates, id),
Parsable(ParserType::_non_local, id),
is_highest("is_highest", id),
criterion(criterion_id, id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
Mesh & mesh = this->model.getMesh();
/// allocate the element type map arrays for _not_ghosts: One entry per quad
GhostType ghost_type = _not_ghost;
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt new_size = this->quad_coordinates(type, ghost_type).size();
this->is_highest.alloc(new_size, 1, type, ghost_type, true);
this->criterion.alloc(new_size, 1, type, ghost_type, 1.);
}
/// criterion needs allocation also for ghost
ghost_type = _ghost;
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt new_size = this->quad_coordinates(type, ghost_type).size();
this->criterion.alloc(new_size, 1, type, ghost_type, 1.);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::~NeighborhoodMaxCriterion() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::initNeighborhood() {
AKANTU_DEBUG_IN();
/// parse the input parameter
const Parser & parser = getStaticParser();
const ParserSection & section_neighborhood =
*(parser.getSubSections(ParserType::_neighborhood).first);
this->parseSection(section_neighborhood);
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
/// insert the non-ghost quads into the grid
this->insertAllQuads(_not_ghost);
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, _ghost)) {
nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _ghost);
}
/// create the grid synchronizer
this->createGridSynchronizer();
/// insert the ghost quads into the grid
this->insertAllQuads(_ghost);
/// create the pair lists
this->updatePairList();
/// remove the unneccessary ghosts
this->cleanupExtraGhostElements(nb_ghost_protected);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::createGridSynchronizer() {
this->is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(SynchronizationTag::_nh_criterion);
std::stringstream sstr;
sstr << id << ":grid_synchronizer";
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this, tags, sstr.str(), false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::insertAllQuads(GhostType ghost_type) {
IntegrationPoint q;
q.ghost_type = ghost_type;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type)) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_quad =
this->model.getFEEngine().getNbIntegrationPoints(type, ghost_type);
const Array<Real> & quads = this->quad_coordinates(type, ghost_type);
q.type = type;
auto quad = quads.begin(spatial_dimension);
for (UInt e = 0; e < nb_element; ++e) {
q.element = e;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
spatial_grid->insert(q, *quad);
++quad;
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::findMaxQuads(
std::vector<IntegrationPoint> & max_quads) {
AKANTU_DEBUG_IN();
/// clear the element type maps
this->is_highest.zero();
this->criterion.zero();
/// update the values of the criterion
this->model.updateDataForNonLocalCriterion(criterion);
/// start the exchange the value of the criterion on the ghost elements
this->model.asynchronousSynchronize(SynchronizationTag::_nh_criterion);
/// compare to not-ghost neighbors
checkNeighbors(_not_ghost);
/// finish the exchange
this->model.waitEndSynchronize(SynchronizationTag::_nh_criterion);
/// compare to ghost neighbors
checkNeighbors(_ghost);
/// extract the quads with highest criterion in their neighborhood
IntegrationPoint quad;
quad.ghost_type = _not_ghost;
Mesh & mesh = this->model.getMesh();
for (auto type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
quad.type = type;
UInt nb_quadrature_points =
this->model.getFEEngine().getNbIntegrationPoints(type, _not_ghost);
/// loop over is_highest for the current element type
for (auto data : enumerate(is_highest(type, _not_ghost))) {
const auto & is_highest = std::get<1>(data);
if (is_highest) {
auto q = std::get<0>(data);
/// gauss point has the highest stress in his neighbourhood
quad.element = q / nb_quadrature_points;
quad.global_num = q;
quad.num_point = q % nb_quadrature_points;
max_quads.push_back(quad);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::checkNeighbors(GhostType ghost_type2) {
AKANTU_DEBUG_IN();
// Compute the weights
for (auto & pair : pair_list[ghost_type2]) {
const auto & lq1 = pair.first;
const auto & lq2 = pair.second;
Array<bool> & has_highest_eq_stress_1 =
is_highest(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_1 = this->criterion(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_2 = this->criterion(lq2.type, lq2.ghost_type);
if (criterion_1(lq1.global_num) < criterion_2(lq2.global_num)) {
has_highest_eq_stress_1(lq1.global_num) = false;
} else if (ghost_type2 != _ghost) {
Array<bool> & has_highest_eq_stress_2 =
is_highest(lq2.type, lq2.ghost_type);
has_highest_eq_stress_2(lq2.global_num) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::cleanupExtraGhostElements(
const ElementTypeMap<UInt> & nb_ghost_protected) {
Mesh & mesh = this->model.getMesh();
/// create remove elements event
RemovedElementsEvent remove_elem(mesh);
/// create set of ghosts to keep
std::set<Element> relevant_ghost_elements;
for (auto & pair : pair_list[_ghost]) {
const auto & q2 = pair.second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
Element element;
element.ghost_type = _ghost;
auto end = relevant_ghost_elements.end();
for (const auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
element.type = type;
UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
} catch (...) {
}
if (!remove_elem.getNewNumbering().exists(type, _ghost)) {
remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, type, _ghost);
} else {
remove_elem.getNewNumbering(type, _ghost).resize(nb_ghost_elem);
}
Array<UInt> & new_numbering = remove_elem.getNewNumbering(type, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
mesh.sendEvent(remove_elem);
this->onElementsRemoved(ghosts_to_erase, remove_elem.getNewNumbering(),
remove_elem);
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
index 4e2f23860..c58328575 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
@@ -1,113 +1,115 @@
/**
* @file neighborhood_max_criterion.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Neighborhood to find a maximum value in a neighborhood
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_
#define AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NeighborhoodMaxCriterion : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodMaxCriterion(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id,
const ID & id = "neighborhood_max_criterion");
~NeighborhoodMaxCriterion() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the neighborhood
void initNeighborhood() override;
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
/// find the quads which have the maximum criterion in their neighborhood
void findMaxQuads(std::vector<IntegrationPoint> & max_quads);
protected:
/// remove unneccessary ghost elements
void
cleanupExtraGhostElements(const ElementTypeMap<UInt> & nb_ghost_protected);
/// insert the quadrature points in the grid
void insertAllQuads(GhostType ghost_type);
/// compare criterion with neighbors
void checkNeighbors(GhostType ghost_type);
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* -------------------------------------------------------------------------*/
/* Accessors */
/* -------------------------------------------------------------------------*/
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// a boolean to store the information if a quad has the max
/// criterion in the neighborhood
ElementTypeMapArray<bool> is_highest;
/// an element type map to store the flattened internal of the criterion
ElementTypeMapReal criterion;
};
} // namespace akantu
#include "neighborhood_max_criterion_inline_impl.hh"
#endif /* AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
index 15feef9d8..c48f43d6b 100644
--- a/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/neighborhoods_criterion_evaluation/neighborhood_max_criterion_inline_impl.hh
@@ -1,81 +1,83 @@
/**
* @file neighborhood_max_criterion_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of inline functions for class NeighborhoodMaxCriterion
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "neighborhood_max_criterion.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_
#define AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt
NeighborhoodMaxCriterion::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
UInt size = 0;
if (tag == SynchronizationTag::_nh_criterion) {
size += sizeof(Real) * nb_quadrature_points;
}
return size;
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if (tag == SynchronizationTag::_nh_criterion) {
NeighborhoodMaxCriterion::packElementalDataHelper(
criterion, buffer, elements, true, this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
NeighborhoodMaxCriterion::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if (tag == SynchronizationTag::_nh_criterion) {
NeighborhoodMaxCriterion::unpackElementalDataHelper(
criterion, buffer, elements, true, this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_NEIGHBORHOOD_MAX_CRITERION_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager.cc b/src/model/common/non_local_toolbox/non_local_manager.cc
index fa2f9a088..84bf32562 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager.cc
@@ -1,652 +1,654 @@
/**
* @file non_local_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Tue Jan 16 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of non-local manager
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_manager.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalManager::NonLocalManager(Model & model,
NonLocalManagerCallback & callback,
const ID & id)
: Parsable(ParserType::_neighborhoods, id),
spatial_dimension(model.getMesh().getSpatialDimension()), id(id), model(model),
integration_points_positions("integration_points_positions", id),
volumes("volumes", id), compute_stress_calls(0),
dummy_registry(nullptr), dummy_grid(nullptr) {
/// parse the neighborhood information from the input file
const Parser & parser = getStaticParser();
/// iterate over all the non-local sections and store them in a map
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
weight_sect = parser.getSubSections(ParserType::_non_local);
Parser::const_section_iterator it = weight_sect.first;
for (; it != weight_sect.second; ++it) {
const ParserSection & section = *it;
ID name = section.getName();
this->weight_function_types[name] = section;
}
this->callback = &callback;
}
/* -------------------------------------------------------------------------- */
NonLocalManager::~NonLocalManager() = default;
/* -------------------------------------------------------------------------- */
void NonLocalManager::initialize() {
volumes.initialize(this->model.getFEEngine(),
_spatial_dimension = spatial_dimension);
AKANTU_DEBUG_ASSERT(this->callback,
"A callback should be registered prior to this call");
this->callback->insertIntegrationPointsInNeighborhoods(_not_ghost);
auto & mesh = this->model.getMesh();
mesh.registerEventHandler(*this, _ehp_non_local_manager);
/// store the number of current ghost elements for each type in the mesh
// ElementTypeMap<UInt> nb_ghost_protected;
// for (auto type : mesh.elementTypes(spatial_dimension, _ghost))
// nb_ghost_protected(mesh.getNbElement(type, _ghost), type, _ghost);
/// exchange the missing ghosts for the non-local neighborhoods
this->createNeighborhoodSynchronizers();
/// insert the ghost quadrature points of the non-local materials into the
/// non-local neighborhoods
this->callback->insertIntegrationPointsInNeighborhoods(_ghost);
FEEngine & fee = this->model.getFEEngine();
this->updatePairLists();
/// cleanup the unneccessary ghost elements
this->cleanupExtraGhostElements(); // nb_ghost_protected);
this->callback->initializeNonLocal();
this->setJacobians(fee, _ek_regular);
this->initNonLocalVariables();
this->computeWeights();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::setJacobians(const FEEngine & fe_engine,
ElementKind kind) {
Mesh & mesh = this->model.getMesh();
for (auto ghost_type : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type, kind)) {
jacobians(type, ghost_type) =
&fe_engine.getIntegratorInterface().getJacobians(type, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhood(const ID & weight_func,
const ID & neighborhood_id) {
AKANTU_DEBUG_IN();
auto weight_func_it = this->weight_function_types.find(weight_func);
AKANTU_DEBUG_ASSERT(weight_func_it != weight_function_types.end(),
"No info found in the input file for the weight_function "
<< weight_func << " in the neighborhood "
<< neighborhood_id);
const ParserSection & section = weight_func_it->second;
const ID weight_func_type = section.getOption();
/// create new neighborhood for given ID
std::stringstream sstr;
sstr << id << ":neighborhood:" << neighborhood_id;
if (weight_func_type == "base_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<BaseWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#if defined(AKANTU_DAMAGE_NON_LOCAL)
} else if (weight_func_type == "remove_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<RemoveDamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
} else if (weight_func_type == "stress_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<StressBasedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
} else if (weight_func_type == "damage_wf") {
neighborhoods[neighborhood_id] =
std::make_unique<NonLocalNeighborhood<DamagedWeightFunction>>(
*this, this->integration_points_positions, sstr.str());
#endif
} else {
AKANTU_EXCEPTION("error in weight function type provided in material file");
}
neighborhoods[neighborhood_id]->parseSection(section);
neighborhoods[neighborhood_id]->initNeighborhood();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhoodSynchronizers() {
/// exchange all the neighborhood IDs, so that every proc knows how many
/// neighborhoods exist globally
/// First: Compute locally the maximum ID size
UInt max_id_size = 0;
UInt current_size = 0;
NeighborhoodMap::const_iterator it;
for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
current_size = it->first.size();
if (current_size > max_id_size) {
max_id_size = current_size;
}
}
/// get the global maximum ID size on each proc
const Communicator & static_communicator = model.getMesh().getCommunicator();
static_communicator.allReduce(max_id_size, SynchronizerOperation::_max);
/// get the rank for this proc and the total nb proc
UInt prank = static_communicator.whoAmI();
UInt psize = static_communicator.getNbProc();
/// exchange the number of neighborhoods on each proc
Array<Int> nb_neighborhoods_per_proc(psize);
nb_neighborhoods_per_proc(prank) = neighborhoods.size();
static_communicator.allGather(nb_neighborhoods_per_proc);
/// compute the total number of neighborhoods
UInt nb_neighborhoods_global = std::accumulate(
nb_neighborhoods_per_proc.begin(), nb_neighborhoods_per_proc.end(), 0);
/// allocate an array of chars to store the names of all neighborhoods
Array<char> buffer(nb_neighborhoods_global, max_id_size);
/// starting index on this proc
UInt starting_index =
std::accumulate(nb_neighborhoods_per_proc.begin(),
nb_neighborhoods_per_proc.begin() + prank, 0);
it = neighborhoods.begin();
/// store the names of local neighborhoods in the buffer
for (UInt i = 0; i < neighborhoods.size(); ++i, ++it) {
UInt c = 0;
for (; c < it->first.size(); ++c) {
buffer(i + starting_index, c) = it->first[c];
}
for (; c < max_id_size; ++c) {
buffer(i + starting_index, c) = char(0);
}
}
/// store the nb of data to send in the all gather
Array<Int> buffer_size(nb_neighborhoods_per_proc);
buffer_size *= max_id_size;
/// exchange the names of all the neighborhoods with all procs
static_communicator.allGatherV(buffer, buffer_size);
for (UInt i = 0; i < nb_neighborhoods_global; ++i) {
std::stringstream neighborhood_id;
for (UInt c = 0; c < max_id_size; ++c) {
if (buffer(i, c) == char(0)) {
break;
}
neighborhood_id << buffer(i, c);
}
global_neighborhoods.insert(neighborhood_id.str());
}
/// this proc does not know all the neighborhoods -> create dummy
/// grid so that this proc can participate in the all gather for
/// detecting the overlap of neighborhoods this proc doesn't know
Vector<Real> grid_center(this->spatial_dimension,
std::numeric_limits<Real>::max());
Vector<Real> spacing(this->spatial_dimension, 0.);
dummy_grid = std::make_unique<SpatialGrid<IntegrationPoint>>(
this->spatial_dimension, spacing, grid_center);
for (const auto & neighborhood_id : global_neighborhoods) {
it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->createGridSynchronizer();
} else {
dummy_synchronizers[neighborhood_id] = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *dummy_grid,
std::string(this->id + ":" + neighborhood_id + ":grid_synchronizer"),
false);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) {
for (const auto & neighborhood_id : global_neighborhoods) {
auto it = neighborhoods.find(neighborhood_id);
if (it != neighborhoods.end()) {
it->second->synchronize(data_accessor, tag);
} else {
auto synchronizer_it = dummy_synchronizers.find(neighborhood_id);
if (synchronizer_it == dummy_synchronizers.end()) {
continue;
}
synchronizer_it->second->synchronizeOnce(data_accessor, tag);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::averageInternals(GhostType ghost_type) {
/// update the weights of the weight function
if (ghost_type == _not_ghost) {
this->computeWeights();
}
/// loop over all neighborhoods and compute the non-local variables
for (auto & neighborhood : neighborhoods) {
/// loop over all the non-local variables of the given neighborhood
for (auto & non_local_variable : non_local_variables) {
NonLocalVariable & non_local_var = *non_local_variable.second;
neighborhood.second->weightedAverageOnNeighbours(
non_local_var.local, non_local_var.non_local,
non_local_var.nb_component, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeWeights() {
AKANTU_DEBUG_IN();
this->updateWeightFunctionInternals();
this->volumes.zero();
for (const auto & global_neighborhood : global_neighborhoods) {
auto it = neighborhoods.find(global_neighborhood);
if (it != neighborhoods.end()) {
it->second->updateWeights();
} else {
dummy_synchronizers[global_neighborhood]->synchronize(
dummy_accessor, SynchronizationTag::_mnl_weight);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updatePairLists() {
AKANTU_DEBUG_IN();
integration_points_positions.initialize(
this->model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension);
/// compute the position of the quadrature points
this->model.getFEEngine().computeIntegrationPointsCoordinates(
integration_points_positions);
for (auto & pair : neighborhoods) {
pair.second->updatePairList();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name,
UInt nb_component) {
AKANTU_DEBUG_IN();
auto non_local_variable_it = non_local_variables.find(variable_name);
if (non_local_variable_it == non_local_variables.end()) {
non_local_variables[nl_variable_name] = std::make_unique<NonLocalVariable>(
variable_name, nl_variable_name, this->id, nb_component);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapReal &
NonLocalManager::registerWeightFunctionInternal(const ID & field_name) {
AKANTU_DEBUG_IN();
auto it = this->weight_function_internals.find(field_name);
if (it == weight_function_internals.end()) {
weight_function_internals[field_name] =
std::make_unique<ElementTypeMapReal>(field_name, this->id);
}
AKANTU_DEBUG_OUT();
return *(weight_function_internals[field_name]);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::updateWeightFunctionInternals() {
for (auto & pair : this->weight_function_internals) {
auto & internals = *pair.second;
internals.zero();
for (auto ghost_type : ghost_types) {
this->callback->updateLocalInternal(internals, ghost_type, _ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::initNonLocalVariables() {
/// loop over all the non-local variables
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
variable.non_local.initialize(this->model.getFEEngine(),
_nb_component = variable.nb_component,
_spatial_dimension = spatial_dimension);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeAllNonLocalStresses() {
/// update the flattened version of the internals
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
variable.local.zero();
variable.non_local.zero();
for (auto ghost_type : ghost_types) {
this->callback->updateLocalInternal(variable.local, ghost_type,
_ek_regular);
}
}
this->volumes.zero();
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.asynchronousSynchronize(SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_not_ghost);
AKANTU_DEBUG_INFO("Wait distant non local stresses");
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.waitEndSynchronize(SynchronizationTag::_mnl_for_average);
}
this->averageInternals(_ghost);
/// copy the results in the materials
for (auto & pair : non_local_variables) {
auto & variable = *pair.second;
for (auto ghost_type : ghost_types) {
this->callback->updateNonLocalInternal(variable.non_local, ghost_type,
_ek_regular);
}
}
this->callback->computeNonLocalStresses(_not_ghost);
++this->compute_stress_calls;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::cleanupExtraGhostElements() {
// ElementTypeMap<UInt> & nb_ghost_protected) {
using ElementSet = std::set<Element>;
ElementSet relevant_ghost_elements;
/// loop over all the neighborhoods and get their protected ghosts
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
ElementSet to_keep_per_neighborhood;
neighborhood.getRelevantGhostElements(to_keep_per_neighborhood);
relevant_ghost_elements.insert(to_keep_per_neighborhood.begin(),
to_keep_per_neighborhood.end());
}
for (auto & pair : neighborhoods) {
auto & neighborhood = *pair.second;
neighborhood.cleanupExtraGhostElements(relevant_ghost_elements);
}
// /// remove all unneccessary ghosts from the mesh
// /// Create list of element to remove and new numbering for element to keep
// Mesh & mesh = this->model.getMesh();
// ElementSet ghost_to_erase;
// RemovedElementsEvent remove_elem(mesh);
// auto & new_numberings = remove_elem.getNewNumbering();
// Element element;
// element.ghost_type = _ghost;
// for (auto & type : mesh.elementTypes(spatial_dimension, _ghost)) {
// element.type = type;
// UInt nb_ghost_elem = mesh.getNbElement(type, _ghost);
// // UInt nb_ghost_elem_protected = 0;
// // try {
// // nb_ghost_elem_protected = nb_ghost_protected(type, _ghost);
// // } catch (...) {
// // }
// if (!new_numberings.exists(type, _ghost))
// new_numberings.alloc(nb_ghost_elem, 1, type, _ghost);
// else
// new_numberings(type, _ghost).resize(nb_ghost_elem);
// Array<UInt> & new_numbering = new_numberings(type, _ghost);
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// element.element = g;
// if (element.element >= nb_ghost_elem_protected &&
// relevant_ghost_elements.find(element) ==
// relevant_ghost_elements.end()) {
// remove_elem.getList().push_back(element);
// new_numbering(element.element) = UInt(-1);
// }
// }
// /// renumber remaining ghosts
// UInt ng = 0;
// for (UInt g = 0; g < nb_ghost_elem; ++g) {
// if (new_numbering(g) != UInt(-1)) {
// new_numbering(g) = ng;
// ++ng;
// }
// }
// }
// for (auto & type : mesh.elementTypes(spatial_dimension, _not_ghost)) {
// UInt nb_elem = mesh.getNbElement(type, _not_ghost);
// if (!new_numberings.exists(type, _not_ghost))
// new_numberings.alloc(nb_elem, 1, type, _not_ghost);
// Array<UInt> & new_numbering = new_numberings(type, _not_ghost);
// for (UInt e = 0; e < nb_elem; ++e) {
// new_numbering(e) = e;
// }
// }
// mesh.sendEvent(remove_elem);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine();
NonLocalManager::removeIntegrationPointsFromMap(
event.getNewNumbering(), spatial_dimension, integration_points_positions,
fee, _ek_regular);
NonLocalManager::removeIntegrationPointsFromMap(event.getNewNumbering(), 1,
volumes, fee, _ek_regular);
/// loop over all the neighborhoods and call onElementsRemoved
auto global_neighborhood_it = global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end()) {
it->second->onElementsRemoved(element_list, new_numbering, event);
} else {
dummy_synchronizers[*global_neighborhood_it]->onElementsRemoved(
element_list, new_numbering, event);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsAdded(const Array<Element> & /*unused*/,
const NewElementsEvent & /*unused*/) {
this->resizeElementTypeMap(1, volumes, model.getFEEngine());
this->resizeElementTypeMap(spatial_dimension, integration_points_positions,
model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::resizeElementTypeMap(UInt nb_component,
ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind) {
Mesh & mesh = this->model.getMesh();
for (auto gt : ghost_types) {
for (auto type : mesh.elementTypes(spatial_dimension, gt, el_kind)) {
UInt nb_element = mesh.getNbElement(type, gt);
UInt nb_quads = fee.getNbIntegrationPoints(type, gt);
if (!element_map.exists(type, gt)) {
element_map.alloc(nb_element * nb_quads, nb_component, type, gt);
} else {
element_map(type, gt).resize(nb_element * nb_quads);
}
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind) {
for (auto gt : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, gt, el_kind)) {
if (element_map.exists(type, gt)) {
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<Real> & vect = element_map(type, gt);
UInt nb_quad_per_elem = fee.getNbIntegrationPoints(type, gt);
Array<Real> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(Real));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt NonLocalManager::getNbData(const Array<Element> & elements,
const ID & id) const {
UInt size = 0;
UInt nb_quadrature_points = this->model.getNbIntegrationPoints(elements);
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
size += it->second->nb_component * sizeof(Real) * nb_quadrature_points;
return size;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::packElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & id) const {
auto it = non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor<Element>::unpackElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_manager.hh b/src/model/common/non_local_toolbox/non_local_manager.hh
index ff214c325..700b39c69 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager.hh
@@ -1,284 +1,286 @@
/**
* @file non_local_manager.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Classes that manages all the non-local neighborhoods
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "mesh_events.hh"
#include "non_local_manager_callback.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_MANAGER_HH_
#define AKANTU_NON_LOCAL_MANAGER_HH_
namespace akantu {
class Model;
class NonLocalNeighborhoodBase;
class GridSynchronizer;
class SynchronizerRegistry;
class IntegrationPoint;
template <typename T> class SpatialGrid;
class FEEngine;
} // namespace akantu
namespace akantu {
class NonLocalManager : public MeshEventHandler, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManager(Model & model, NonLocalManagerCallback & callback,
const ID & id = "non_local_manager");
~NonLocalManager() override;
using NeighborhoodMap =
std::map<ID, std::unique_ptr<NonLocalNeighborhoodBase>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ----------------------------------------------------------------------- */
public:
/// register a new internal needed for the weight computations
ElementTypeMapReal & registerWeightFunctionInternal(const ID & field_name);
/// register a non-local variable
void registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name, UInt nb_component);
/// register non-local neighborhood
inline void registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id);
// void registerNonLocalManagerCallback(NonLocalManagerCallback & callback);
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void initialize();
/// synchronize once on a given tag using the neighborhoods synchronizer
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & /*tag*/);
protected:
/// create the grid synchronizers for each neighborhood
void createNeighborhoodSynchronizers();
/// compute the weights in each neighborhood for non-local averaging
void computeWeights();
/// compute the weights in each neighborhood for non-local averaging
void updatePairLists();
/// average the non-local variables
void averageInternals(GhostType ghost_type = _not_ghost);
/// update the flattened version of the weight function internals
void updateWeightFunctionInternals();
protected:
/// create a new neighborhood for a given domain ID
void createNeighborhood(const ID & weight_func, const ID & neighborhood);
/// set the values of the jacobians
void setJacobians(const FEEngine & fe_engine, ElementKind kind);
/// allocation of eelment type maps
// void initElementTypeMap(UInt nb_component,
// ElementTypeMapReal & element_map,
// const FEEngine & fe_engine,
// const ElementKind el_kind = _ek_regular);
/// resizing of element type maps
void resizeElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
const FEEngine & fee,
ElementKind el_kind = _ek_regular);
/// remove integration points from element type maps
static void removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
ElementKind el_kind = _ek_regular);
/// allocate the non-local variables
void initNonLocalVariables();
/// cleanup unneccessary ghosts
void
cleanupExtraGhostElements(); // ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* DataAccessor kind of interface */
/* ------------------------------------------------------------------------ */
public:
/// get Nb data for synchronization in parallel
UInt getNbData(const Array<Element> & elements, const ID & id) const;
/// pack data for synchronization in parallel
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/// unpack data for synchronization in parallel
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
AKANTU_GET_MACRO_NOT_CONST(Model, model, Model &);
AKANTU_GET_MACRO_NOT_CONST(Volumes, volumes, ElementTypeMapReal &)
AKANTU_GET_MACRO(NbStressCalls, compute_stress_calls, UInt);
/// return the fem object associated with a provided name
inline NonLocalNeighborhoodBase & getNeighborhood(const ID & name) const;
inline const Array<Real> & getJacobians(ElementType type,
GhostType ghost_type) {
return *jacobians(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the spatial dimension
const UInt spatial_dimension;
ID id;
protected:
/// the non-local neighborhoods present
NeighborhoodMap neighborhoods;
/// list of all the non-local materials in the model
// std::vector<ID> non_local_materials;
struct NonLocalVariable {
NonLocalVariable(const ID & variable_name, const ID & nl_variable_name,
const ID & id, UInt nb_component)
: local(variable_name, id), non_local(nl_variable_name, id),
nb_component(nb_component) {}
ElementTypeMapReal local;
ElementTypeMapReal non_local;
UInt nb_component;
};
/// the non-local variables associated to a certain neighborhood
std::map<ID, std::unique_ptr<NonLocalVariable>> non_local_variables;
/// reference to the model
Model & model;
/// jacobians for all the elements in the mesh
ElementTypeMap<const Array<Real> *> jacobians;
/// store the position of the quadrature points
ElementTypeMapReal integration_points_positions;
/// store the volume of each quadrature point for the non-local weight
/// normalization
ElementTypeMapReal volumes;
/// counter for computeStress calls
UInt compute_stress_calls;
/// map to store weight function types from input file
std::map<ID, ParserSection> weight_function_types;
/// map to store the internals needed by the weight functions
std::map<ID, std::unique_ptr<ElementTypeMapReal>> weight_function_internals;
/* --------------------------------------------------------------------------
*/
/// the following are members needed to make this processor participate in the
/// grid creation of neighborhoods he doesn't own as a member. For details see
/// createGridSynchronizers function
/// synchronizer registry for dummy grid synchronizers
std::unique_ptr<SynchronizerRegistry> dummy_registry;
/// map of dummy synchronizers
std::map<ID, std::unique_ptr<GridSynchronizer>> dummy_synchronizers;
/// dummy spatial grid
std::unique_ptr<SpatialGrid<IntegrationPoint>> dummy_grid;
/// create a set of all neighborhoods present in the simulation
std::set<ID> global_neighborhoods;
class DummyDataAccessor : public DataAccessor<Element> {
public:
inline UInt getNbData(const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override {
return 0;
};
inline void packData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) const override{};
inline void unpackData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) override{};
};
DummyDataAccessor dummy_accessor;
/* ------------------------------------------------------------------------ */
NonLocalManagerCallback * callback;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_manager_inline_impl.hh"
#endif /* AKANTU_NON_LOCAL_MANAGER_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_callback.hh b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
index ac23221b1..b4be45854 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_callback.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager_callback.hh
@@ -1,67 +1,69 @@
/**
* @file non_local_manager_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 21 2017
* @date last modification: Tue Sep 19 2017
*
* @brief Callback functions for the non local manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_
#define AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_
namespace akantu {
class NonLocalManager;
} // namespace akantu
namespace akantu {
class NonLocalManagerCallback {
public:
virtual void initializeNonLocal() {}
/* ------------------------------------------------------------------------ */
virtual void
insertIntegrationPointsInNeighborhoods(GhostType ghost_type) = 0;
virtual void computeNonLocalStresses(GhostType ghost_type) = 0;
/// update the values of the non local internal
virtual void updateLocalInternal(ElementTypeMapReal & internal_flat,
GhostType ghost_type,
ElementKind kind) = 0;
/// copy the results of the averaging in the materials
virtual void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
GhostType ghost_type,
ElementKind kind) = 0;
};
} // namespace akantu
#endif /* AKANTU_NON_LOCAL_MANAGER_CALLBACK_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
index df6981b35..7b546740e 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.hh
@@ -1,67 +1,69 @@
/**
* @file non_local_manager_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Sep 11 2017
*
* @brief inline implementation of non-local manager functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_
#define AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id) {
/// check if neighborhood has already been created
auto it = neighborhoods.find(neighborhood);
if (it == neighborhoods.end()) {
this->createNeighborhood(weight_func_id, neighborhood);
}
}
/* -------------------------------------------------------------------------- */
inline NonLocalNeighborhoodBase &
NonLocalManager::getNeighborhood(const ID & name) const {
AKANTU_DEBUG_IN();
auto it = neighborhoods.find(name);
AKANTU_DEBUG_ASSERT(it != neighborhoods.end(),
"The neighborhood " << name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
} // namespace akantu
#endif /* AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood.hh b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
index c265f5db5..6e9e94535 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
@@ -1,133 +1,135 @@
/**
* @file non_local_neighborhood.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Non-local neighborhood for non-local averaging based on
* weight function
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_
#define AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
#include "non_local_neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalManager;
class BaseWeightFunction;
} // namespace akantu
namespace akantu {
template <class WeightFunction = BaseWeightFunction>
class NonLocalNeighborhood : public NonLocalNeighborhoodBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhood(NonLocalManager & manager,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "neighborhood");
~NonLocalNeighborhood() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute the weights for non-local averaging
void computeWeights() override;
/// save the pair of weights in a file
void saveWeights(const std::string & filename) const override;
/// compute the non-local counter part for a given element type map
// compute the non-local counter part for a given element type map
void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
GhostType ghost_type2) const override;
/// update the weights based on the weight function
void updateWeights() override;
/// register a new non-local variable in the neighborhood
// void registerNonLocalVariable(const ID & id);
protected:
template <class Func>
inline void foreach_weight(GhostType ghost_type, Func && func);
template <class Func>
inline void foreach_weight(GhostType ghost_type, Func && func) const;
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(NonLocalManager, non_local_manager, const NonLocalManager &);
AKANTU_GET_MACRO_NOT_CONST(NonLocalManager, non_local_manager,
NonLocalManager &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Pointer to non-local manager class
NonLocalManager & non_local_manager;
/// the weights associated to the pairs
std::array<std::unique_ptr<Array<Real>>, 2> pair_weight;
/// weight function
std::unique_ptr<WeightFunction> weight_function;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Implementation of template functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_inline_impl.hh"
#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
index 317625b30..75755ba81 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
@@ -1,124 +1,126 @@
/**
* @file non_local_neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Fri Jul 10 2020
*
* @brief Implementation of non-local neighborhood base
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_base.hh"
#include "grid_synchronizer.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::NonLocalNeighborhoodBase(
Model & model, const ElementTypeMapReal & quad_coordinates, const ID & id)
: NeighborhoodBase(model, quad_coordinates, id),
Parsable(ParserType::_non_local, id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::~NonLocalNeighborhoodBase() = default;
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::createGridSynchronizer() {
this->is_creating_grid = true;
this->grid_synchronizer = std::make_unique<GridSynchronizer>(
this->model.getMesh(), *spatial_grid, *this,
std::set<SynchronizationTag>{SynchronizationTag::_mnl_weight,
SynchronizationTag::_mnl_for_average},
std::string(id + ":grid_synchronizer"), false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::synchronize(
DataAccessor<Element> & data_accessor, const SynchronizationTag & tag) {
if (not grid_synchronizer) {
return;
}
grid_synchronizer->synchronizeOnce(data_accessor, tag);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::getRelevantGhostElements(
std::set<Element> & relevant_ghost_elements) {
for (auto && ghost_type : ghost_type_t{}) {
auto & pair_list = this->pair_list.at(ghost_type);
for (auto && pair : pair_list) {
if (pair.first.ghost_type == _ghost) {
relevant_ghost_elements.insert(pair.first);
}
if (pair.second.ghost_type == _ghost) {
relevant_ghost_elements.insert(pair.second);
}
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::cleanupExtraGhostElements(
std::set<Element> & relevant_ghost_elements) {
Array<Element> ghosts_to_erase;
auto & mesh = this->model.getMesh();
auto end = relevant_ghost_elements.end();
for (const auto & type : mesh.elementTypes(
_spatial_dimension = spatial_dimension, _ghost_type = _ghost)) {
auto nb_ghost_elem = mesh.getNbElement(type, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
Element element{type, g, _ghost};
if (relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
}
}
}
/// remove the unneccessary ghosts from the synchronizer
mesh.eraseElements(ghosts_to_erase);
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::registerNonLocalVariable(const ID & id) {
this->non_local_variables.insert(id);
}
} // namespace akantu
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
index 28214e2fe..ee68d9328 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
@@ -1,134 +1,136 @@
/**
* @file non_local_neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Non-local neighborhood base class
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_
#define AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_
namespace akantu {
class Model;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalNeighborhoodBase : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "non_local_neighborhood");
~NonLocalNeighborhoodBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) override;
/// compute weights, for instance needed for non-local damage computation
virtual void computeWeights(){};
// compute the non-local counter part for a given element type map
virtual void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
GhostType ghost_type2) const = 0;
/// update the weights for the non-local averaging
virtual void updateWeights() = 0;
/// update the weights for the non-local averaging
virtual void saveWeights(const std::string & /*unused*/) const {
AKANTU_TO_IMPLEMENT();
}
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(const ID & id);
/// clean up the unneccessary ghosts
void cleanupExtraGhostElements(std::set<Element> & relevant_ghost_elements);
/// list releveant ghosts
void getRelevantGhostElements(std::set<Element> & relevant_ghost_elements);
protected:
/// create the grid
void createGrid();
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
inline UInt getNbData(const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override {
return 0;
}
inline void packData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) const override {}
inline void unpackData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*element*/,
const SynchronizationTag & /*tag*/) override {}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
AKANTU_GET_MACRO(NonLocalVariables, non_local_variables,
const std::set<ID> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of non-local variables associated to the neighborhood
std::set<ID> non_local_variables;
};
} // namespace akantu
#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
index 08e0b5474..aab11099e 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.hh
@@ -1,86 +1,88 @@
/**
* @file non_local_neighborhood_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 06 2015
- * @date last modification: Thu Jul 06 2017
+ * @date last modification: Sun Dec 30 2018
*
* @brief Implementation of inline functions of non-local neighborhood class
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_
#define AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline UInt NonLocalNeighborhood<WeightFunction>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
UInt size = 0;
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
size += this->non_local_manager.getNbData(elements, variable_id);
}
}
size += this->weight_function->getNbData(elements, tag);
return size;
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.packData(buffer, elements, variable_id);
}
}
this->weight_function->packData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::unpackData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_mnl_for_average) {
for (auto & variable_id : non_local_variables) {
this->non_local_manager.unpackData(buffer, elements, variable_id);
}
}
this->weight_function->unpackData(buffer, elements, tag);
}
} // namespace akantu
#endif /* AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_HH_ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
index e4282845b..60dfd780a 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
@@ -1,277 +1,279 @@
/**
* @file non_local_neighborhood_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 28 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of class non-local neighborhood
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH_
#define AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
GhostType ghost_type, Func && func) {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
GhostType ghost_type, Func && func) const {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::NonLocalNeighborhood(
NonLocalManager & manager, const ElementTypeMapReal & quad_coordinates,
const ID & id)
: NonLocalNeighborhoodBase(manager.getModel(), quad_coordinates, id),
non_local_manager(manager) {
AKANTU_DEBUG_IN();
this->weight_function = std::make_unique<WeightFunction>(manager);
this->registerSubSection(ParserType::_weight_function, "weight_parameter",
*weight_function);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::~NonLocalNeighborhood() = default;
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::computeWeights() {
AKANTU_DEBUG_IN();
this->weight_function->setRadius(this->neighborhood_radius);
Vector<Real> q1_coord(this->spatial_dimension);
Vector<Real> q2_coord(this->spatial_dimension);
UInt nb_weights_per_pair = 2; /// w1: q1->q2, w2: q2->q1
/// get the elementtypemap for the neighborhood volume for each quadrature
/// point
ElementTypeMapReal & quadrature_points_volumes =
this->non_local_manager.getVolumes();
/// update the internals of the weight function if applicable (not
/// all the weight functions have internals and do noting in that
/// case)
weight_function->updateInternals();
for (auto ghost_type : ghost_types) {
/// allocate the array to store the weight, if it doesn't exist already
if (!(pair_weight[ghost_type])) {
pair_weight[ghost_type] =
std::make_unique<Array<Real>>(0, nb_weights_per_pair);
}
/// resize the array to the correct size
pair_weight[ghost_type]->resize(pair_list[ghost_type].size());
/// set entries to zero
pair_weight[ghost_type]->zero();
/// loop over all pairs in the current pair list array and their
/// corresponding weights
auto first_pair = pair_list[ghost_type].begin();
auto last_pair = pair_list[ghost_type].end();
auto weight_it = pair_weight[ghost_type]->begin(nb_weights_per_pair);
// Compute the weights
for (; first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
/// get the coordinates for the given pair of quads
auto coords_type_1_it = this->quad_coordinates(q1.type, q1.ghost_type)
.begin(this->spatial_dimension);
q1_coord = coords_type_1_it[q1.global_num];
auto coords_type_2_it = this->quad_coordinates(q2.type, q2.ghost_type)
.begin(this->spatial_dimension);
q2_coord = coords_type_2_it[q2.global_num];
Array<Real> & quad_volumes_1 =
quadrature_points_volumes(q1.type, q1.ghost_type);
const Array<Real> & jacobians_2 =
this->non_local_manager.getJacobians(q2.type, q2.ghost_type);
const Real & q2_wJ = jacobians_2(q2.global_num);
/// compute distance between the two quadrature points
Real r = q1_coord.distance(q2_coord);
/// compute the weight for averaging on q1 based on the distance
Real w1 = this->weight_function->operator()(r, q1, q2);
weight(0) = q2_wJ * w1;
quad_volumes_1(q1.global_num) += weight(0);
if (q2.ghost_type != _ghost && q1.global_num != q2.global_num) {
const Array<Real> & jacobians_1 =
this->non_local_manager.getJacobians(q1.type, q1.ghost_type);
Array<Real> & quad_volumes_2 =
quadrature_points_volumes(q2.type, q2.ghost_type);
/// compute the weight for averaging on q2
const Real & q1_wJ = jacobians_1(q1.global_num);
Real w2 = this->weight_function->operator()(r, q2, q1);
weight(1) = q1_wJ * w2;
quad_volumes_2(q2.global_num) += weight(1);
} else {
weight(1) = 0.;
}
}
}
/// normalize the weights
for (auto ghost_type : ghost_types) {
foreach_weight(ghost_type, [&](const auto & q1, const auto & q2,
auto & weight) {
auto & quad_volumes_1 = quadrature_points_volumes(q1.type, q1.ghost_type);
auto & quad_volumes_2 = quadrature_points_volumes(q2.type, q2.ghost_type);
Real q1_volume = quad_volumes_1(q1.global_num);
auto ghost_type2 = q2.ghost_type;
weight(0) *= 1. / q1_volume;
if (ghost_type2 != _ghost) {
Real q2_volume = quad_volumes_2(q2.global_num);
weight(1) *= 1. / q2_volume;
}
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::saveWeights(
const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
auto ghost_type = (GhostType)gt;
AKANTU_DEBUG_ASSERT((pair_weight[ghost_type]),
"the weights have not been computed yet");
Array<Real> & weights = *(pair_weight[ghost_type]);
auto weights_it = weights.begin(2);
for (UInt i = 0; i < weights.size(); ++i, ++weights_it) {
pout << "w1: " << (*weights_it)(0) << " w2: " << (*weights_it)(1)
<< std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::weightedAverageOnNeighbours(
const ElementTypeMapReal & to_accumulate, ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom, GhostType ghost_type2) const {
auto it = non_local_variables.find(accumulated.getName());
// do averaging only for variables registered in the neighborhood
if (it == non_local_variables.end()) {
return;
}
foreach_weight(
ghost_type2,
[ghost_type2, nb_degree_of_freedom, &to_accumulate,
&accumulated](const auto & q1, const auto & q2, auto & weight) {
const Vector<Real> to_acc_1 =
to_accumulate(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
const Vector<Real> to_acc_2 =
to_accumulate(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
Vector<Real> acc_1 = accumulated(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
Vector<Real> acc_2 = accumulated(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
acc_1 += weight(0) * to_acc_2;
if (ghost_type2 != _ghost) {
acc_2 += weight(1) * to_acc_1;
}
});
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::updateWeights() {
// Update the weights for the non local variable averaging
if (this->weight_function->getUpdateRate() &&
(this->non_local_manager.getNbStressCalls() %
this->weight_function->getUpdateRate() ==
0)) {
SynchronizerRegistry::synchronize(SynchronizationTag::_mnl_weight);
this->computeWeights();
}
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL__ */
diff --git a/src/model/common/solver_callback.cc b/src/model/common/solver_callback.cc
index c28e31784..756203ab9 100644
--- a/src/model/common/solver_callback.cc
+++ b/src/model/common/solver_callback.cc
@@ -1,53 +1,55 @@
/**
* @file solver_callback.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue Jul 20 2010
+ * @date creation: Thu Feb 21 2013
* @date last modification: Wed Jan 31 2018
*
* @brief Default behavior of solver_callbacks
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_callback.hh"
#include "dof_manager.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback(DOFManager & dof_manager)
: sc_dof_manager(&dof_manager) {}
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback() = default;
/* -------------------------------------------------------------------------- */
SolverCallback::~SolverCallback() = default;
/* -------------------------------------------------------------------------- */
void SolverCallback::setDOFManager(DOFManager & dof_manager) {
this->sc_dof_manager = &dof_manager;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/solver_callback.hh b/src/model/common/solver_callback.hh
index 7d72cdcd7..679eeeb08 100644
--- a/src/model/common/solver_callback.hh
+++ b/src/model/common/solver_callback.hh
@@ -1,108 +1,110 @@
/**
* @file solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Wed Nov 27 2019
*
* @brief Class defining the interface for non_linear_solver callbacks
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_CALLBACK_HH_
#define AKANTU_SOLVER_CALLBACK_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit SolverCallback(DOFManager & dof_manager);
explicit SolverCallback();
/* ------------------------------------------------------------------------ */
virtual ~SolverCallback();
protected:
void setDOFManager(DOFManager & dof_manager);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the type of matrix needed
virtual MatrixType getMatrixType(const ID &) = 0;
/// callback to assemble a Matrix
virtual void assembleMatrix(const ID &) = 0;
/// callback to assemble a lumped Matrix
virtual void assembleLumpedMatrix(const ID &) = 0;
/// callback to assemble the residual (rhs)
virtual void assembleResidual() = 0;
/// callback to assemble the rhs parts, (e.g. internal_forces +
/// external_forces)
virtual void assembleResidual(const ID & /*residual_part*/) {}
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() {}
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() {}
/// tells if the residual can be computed in separated parts
virtual bool canSplitResidual() { return false; }
/* ------------------------------------------------------------------------ */
/* management callbacks */
/* ------------------------------------------------------------------------ */
virtual void beforeSolveStep(){};
virtual void afterSolveStep(bool /*converged*/ = true){};
protected:
/// DOFManager prefixed to avoid collision in multiple inheritance cases
DOFManager * sc_dof_manager{nullptr};
};
namespace debug {
class SolverCallbackResidualPartUnknown : public Exception {
public:
SolverCallbackResidualPartUnknown(const ID & residual_part)
: Exception(residual_part + " is not known here.") {}
};
} // namespace debug
} // namespace akantu
#endif /* AKANTU_SOLVER_CALLBACK_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver.cc b/src/model/common/time_step_solvers/time_step_solver.cc
index bce3372e4..8f5c1fb92 100644
--- a/src/model/common/time_step_solvers/time_step_solver.cc
+++ b/src/model/common/time_step_solvers/time_step_solver.cc
@@ -1,205 +1,208 @@
/**
* @file time_step_solver.cc
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Sep 08 2020
*
* @brief Implementation of common part of TimeStepSolvers
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver.hh"
#include "dof_manager.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolver::TimeStepSolver(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id)
: SolverCallback(dof_manager), id(id),
_dof_manager(dof_manager), type(type), time_step(0.),
solver_callback(&solver_callback), non_linear_solver(non_linear_solver) {
this->registerSubRegistry("non_linear_solver", non_linear_solver);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver::~TimeStepSolver() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolver::setIntegrationScheme(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type) {
auto scheme = this->getIntegrationSchemeInternal(dof_id, type, solution_type);
this->setIntegrationScheme(dof_id, scheme, solution_type);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::setIntegrationScheme(
const ID & dof_id, std::unique_ptr<IntegrationScheme> & scheme,
IntegrationScheme::SolutionType solution_type) {
this->setIntegrationSchemeInternal(dof_id, scheme, solution_type);
for (auto & pair : needed_matrices) {
auto & mat_type = pair.second;
const auto & name = pair.first;
if (mat_type == _mt_not_defined) {
mat_type = this->solver_callback->getMatrixType(name);
}
if (mat_type == _mt_not_defined) {
continue;
}
if (not _dof_manager.hasMatrix(name)) {
_dof_manager.getNewMatrix(name, mat_type);
}
}
}
/* -------------------------------------------------------------------------- */
MatrixType TimeStepSolver::getCommonMatrixType() {
MatrixType common_type = _mt_not_defined;
for (auto & pair : needed_matrices) {
auto & type = pair.second;
common_type = std::min(common_type, type);
}
AKANTU_DEBUG_ASSERT(common_type != _mt_not_defined,
"No type defined for the matrices");
return common_type;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::predictor() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->predictor();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::corrector() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->corrector();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::beforeSolveStep() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::afterSolveStep(bool converged) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleLumpedMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
if (not _dof_manager.hasLumpedMatrix(matrix_id)) {
_dof_manager.getNewLumpedMatrix(matrix_id);
}
this->solver_callback->assembleLumpedMatrix(matrix_id);
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
auto common_type = this->getCommonMatrixType();
if (matrix_id != "J") {
auto type = needed_matrices[matrix_id];
if (type == _mt_not_defined) {
return;
}
if (not _dof_manager.hasMatrix(matrix_id)) {
_dof_manager.getNewMatrix(matrix_id, type);
}
this->solver_callback->assembleMatrix(matrix_id);
return;
}
if (not _dof_manager.hasMatrix("J")) {
_dof_manager.getNewMatrix("J", common_type);
}
MatrixType type;
ID name;
for (auto & pair : needed_matrices) {
std::tie(name, type) = pair;
if (type == _mt_not_defined) {
continue;
}
this->solver_callback->assembleMatrix(name);
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->_dof_manager.zeroResidual();
this->solver_callback->assembleResidual();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_ASSERT(
this->solver_callback != nullptr,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->assembleResidual(residual_part);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/time_step_solvers/time_step_solver.hh b/src/model/common/time_step_solvers/time_step_solver.hh
index 2fb4378fe..60c697896 100644
--- a/src/model/common/time_step_solvers/time_step_solver.hh
+++ b/src/model/common/time_step_solvers/time_step_solver.hh
@@ -1,163 +1,167 @@
/**
* @file time_step_solver.hh
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Sep 08 2020
*
* @brief This corresponding to the time step evolution solver
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "integration_scheme.hh"
#include "parameter_registry.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TIME_STEP_SOLVER_HH_
#define AKANTU_TIME_STEP_SOLVER_HH_
namespace akantu {
class DOFManager;
class NonLinearSolver;
} // namespace akantu
namespace akantu {
class TimeStepSolver : public ParameterRegistry, public SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolver(DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id);
~TimeStepSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solves on step
virtual void solveStep(SolverCallback & solver_callback) = 0;
/// register an integration scheme for a given dof
void setIntegrationScheme(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/// register an integration scheme for a given dof
void setIntegrationScheme(const ID & dof_id,
std::unique_ptr<IntegrationScheme> & scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
protected:
/// register an integration scheme for a given dof
virtual std::unique_ptr<IntegrationScheme>
getIntegrationSchemeInternal(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) = 0;
virtual void
setIntegrationSchemeInternal(const ID & dof_id,
std::unique_ptr<IntegrationScheme> & scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) = 0;
public:
/// replies if a integration scheme has been set
virtual bool hasIntegrationScheme(const ID & dof_id) const = 0;
/* ------------------------------------------------------------------------ */
/* Solver Callback interface */
/* ------------------------------------------------------------------------ */
public:
/// implementation of the SolverCallback::getMatrixType()
MatrixType getMatrixType(const ID & /*unused*/) final {
return _mt_not_defined;
}
/// implementation of the SolverCallback::predictor()
void predictor() override;
/// implementation of the SolverCallback::corrector()
void corrector() override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleLumpedMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual() override;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual(const ID & residual_part) override;
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
bool canSplitResidual() override {
return solver_callback->canSplitResidual();
}
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(TimeStep, time_step, Real);
AKANTU_SET_MACRO(TimeStep, time_step, Real);
AKANTU_GET_MACRO(NonLinearSolver, non_linear_solver, const NonLinearSolver &);
AKANTU_GET_MACRO_NOT_CONST(NonLinearSolver, non_linear_solver,
NonLinearSolver &);
protected:
MatrixType getCommonMatrixType();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// Underlying dof manager containing the dof to treat
DOFManager & _dof_manager;
/// Type of solver
TimeStepSolverType type;
/// The time step for this solver
Real time_step;
/// Temporary storage for solver callback
SolverCallback * solver_callback;
/// NonLinearSolver used by this tome step solver
NonLinearSolver & non_linear_solver;
/// List of required matrices
std::map<std::string, MatrixType> needed_matrices;
/// specifies if the solvers gives to full solution or just the increment of
/// solution
bool is_solution_increment{true};
};
} // namespace akantu
#endif /* AKANTU_TIME_STEP_SOLVER_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver_default.cc b/src/model/common/time_step_solvers/time_step_solver_default.cc
index 55c37f267..6ef8bf6f6 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default.cc
+++ b/src/model/common/time_step_solvers/time_step_solver_default.cc
@@ -1,340 +1,343 @@
/**
* @file time_step_solver_default.cc
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 15 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Sep 08 2020
*
* @brief Default implementation of the time step solver
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "time_step_solver_default.hh"
#include "dof_manager_default.hh"
#include "integration_scheme_1st_order.hh"
#include "integration_scheme_2nd_order.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "pseudo_time.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::TimeStepSolverDefault(
DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, SolverCallback & solver_callback,
const ID & id)
: TimeStepSolver(dof_manager, type, non_linear_solver, solver_callback, id) {
switch (type) {
case TimeStepSolverType::_dynamic:
break;
case TimeStepSolverType::_dynamic_lumped:
this->is_mass_lumped = true;
break;
case TimeStepSolverType::_static:
/// initialize a static time solver for callback dofs
break;
default:
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
std::unique_ptr<IntegrationScheme>
TimeStepSolverDefault::getIntegrationSchemeInternal(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType /*solution_type*/) {
std::unique_ptr<IntegrationScheme> integration_scheme;
if (this->is_mass_lumped) {
switch (type) {
case IntegrationSchemeType::_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(_dof_manager, dof_id);
break;
}
default:
AKANTU_EXCEPTION(
"This integration scheme cannot be used in lumped dynamic");
}
} else {
switch (type) {
case IntegrationSchemeType::_pseudo_time: {
integration_scheme = std::make_unique<PseudoTime>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_trapezoidal_rule_1: {
integration_scheme =
std::make_unique<TrapezoidalRule1>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_backward_euler: {
integration_scheme =
std::make_unique<BackwardEuler>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_fox_goodwin: {
integration_scheme = std::make_unique<FoxGoodwin>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_trapezoidal_rule_2: {
integration_scheme =
std::make_unique<TrapezoidalRule2>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_linear_acceleration: {
integration_scheme =
std::make_unique<LinearAceleration>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_generalized_trapezoidal: {
integration_scheme =
std::make_unique<GeneralizedTrapezoidal>(_dof_manager, dof_id);
break;
}
case IntegrationSchemeType::_newmark_beta:
integration_scheme = std::make_unique<NewmarkBeta>(_dof_manager, dof_id);
break;
}
}
AKANTU_DEBUG_ASSERT(integration_scheme,
"No integration scheme was found for the provided types");
return integration_scheme;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::setIntegrationSchemeInternal(
const ID & dof_id, std::unique_ptr<IntegrationScheme> & integration_scheme,
IntegrationScheme::SolutionType solution_type) {
if (this->integration_schemes.find(dof_id) !=
this->integration_schemes.end()) {
AKANTU_EXCEPTION("Their DOFs "
<< dof_id
<< " have already an integration scheme associated");
}
auto && matrices_names = integration_scheme->getNeededMatrixList();
for (auto && name : matrices_names) {
needed_matrices.insert({name, _mt_not_defined});
}
this->integration_schemes[dof_id] = std::move(integration_scheme);
this->solution_types[dof_id] = solution_type;
this->integration_schemes_owner.insert(dof_id);
}
/* -------------------------------------------------------------------------- */
bool TimeStepSolverDefault::hasIntegrationScheme(const ID & dof_id) const {
return this->integration_schemes.find(dof_id) !=
this->integration_schemes.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::~TimeStepSolverDefault() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::solveStep(SolverCallback & solver_callback) {
this->solver_callback = &solver_callback;
this->non_linear_solver.solve(*this);
this->solver_callback = nullptr;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::predictor() {
TimeStepSolver::predictor();
for (auto && pair : this->integration_schemes) {
const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
if (this->_dof_manager.hasPreviousDOFs(dof_id)) {
this->_dof_manager.savePreviousDOFs(dof_id);
}
/// integrator predictor
integration_scheme->predictor(this->time_step);
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::corrector() {
AKANTU_DEBUG_IN();
for (auto & pair : this->integration_schemes) {
const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->corrector(solution_type, this->time_step);
/// computing the increment of dof if needed
if (this->_dof_manager.hasDOFsIncrement(dof_id)) {
if (not this->_dof_manager.hasPreviousDOFs(dof_id)) {
AKANTU_DEBUG_WARNING("In order to compute the increment of "
<< dof_id << " a 'previous' has to be registered");
continue;
}
auto & increment = this->_dof_manager.getDOFsIncrement(dof_id);
auto & previous = this->_dof_manager.getPreviousDOFs(dof_id);
auto dof_array_comp = this->_dof_manager.getDOFs(dof_id).getNbComponent();
increment.copy(this->_dof_manager.getDOFs(dof_id));
for (auto && data : zip(make_view(increment, dof_array_comp),
make_view(previous, dof_array_comp))) {
std::get<0>(data) -= std::get<1>(data);
}
}
}
TimeStepSolver::corrector();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_IN();
TimeStepSolver::assembleMatrix(matrix_id);
if (matrix_id != "J") {
return;
}
for_each_integrator([&](auto && dof_id, auto && integration_scheme) {
const auto & solution_type = this->solution_types[dof_id];
integration_scheme.assembleJacobian(solution_type, this->time_step);
});
this->_dof_manager.applyBoundary("J");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void TimeStepSolverDefault::assembleLumpedMatrix(const ID & matrix_id) {
// AKANTU_DEBUG_IN();
// TimeStepSolver::assembleLumpedMatrix(matrix_id);
// if (matrix_id != "J")
// return;
// for (auto & pair : this->integration_schemes) {
// auto & dof_id = pair.first;
// auto & integration_scheme = pair.second;
// const auto & solution_type = this->solution_types[dof_id];
// integration_scheme->assembleJacobianLumped(solution_type,
// this->time_step);
// }
// this->_dof_manager.applyBoundaryLumped("J");
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual() {
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
TimeStepSolver::assembleResidual();
for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.assembleResidual(this->is_mass_lumped);
});
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
if (residual_part != "inertial") {
TimeStepSolver::assembleResidual(residual_part);
}
if (residual_part == "inertial") {
for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.assembleResidual(this->is_mass_lumped);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::beforeSolveStep() {
TimeStepSolver::beforeSolveStep();
for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.store();
});
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::afterSolveStep(bool converged) {
if (not converged) {
for_each_integrator([&](auto && /*unused*/, auto && integration_scheme) {
integration_scheme.restore();
});
}
TimeStepSolver::afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/common/time_step_solvers/time_step_solver_default.hh b/src/model/common/time_step_solvers/time_step_solver_default.hh
index 08faf6c14..dab770873 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default.hh
+++ b/src/model/common/time_step_solvers/time_step_solver_default.hh
@@ -1,132 +1,135 @@
/**
* @file time_step_solver_default.hh
*
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Sep 08 2020
*
* @brief Default implementation for the time stepper
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integration_scheme.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_
#define AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class TimeStepSolverDefault : public TimeStepSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefault(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
SolverCallback & solver_callback, const ID & id);
~TimeStepSolverDefault() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// registers an integration scheme for a given dof
std::unique_ptr<IntegrationScheme>
getIntegrationSchemeInternal(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) override;
void setIntegrationSchemeInternal(
const ID & dof_id, std::unique_ptr<IntegrationScheme> & integration_scheme,
IntegrationScheme::SolutionType solution_type) override;
public:
bool hasIntegrationScheme(const ID & dof_id) const override;
/// implementation of the TimeStepSolver::predictor()
void predictor() override;
/// implementation of the TimeStepSolver::corrector()
void corrector() override;
/// implementation of the TimeStepSolver::assembleMatrix()
void assembleMatrix(const ID & matrix_id) override;
// void assembleLumpedMatrix(const ID & matrix_id) override;
/// implementation of the TimeStepSolver::assembleResidual()
void assembleResidual() override;
void assembleResidual(const ID & residual_part) override;
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
/// implementation of the generic TimeStepSolver::solveStep()
void solveStep(SolverCallback & solver_callback) override;
private:
template<class Func>
void for_each_integrator(Func && function) {
for (auto & pair : this->integration_schemes) {
const auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
function(dof_id, *integration_scheme);
}
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using DOFsIntegrationSchemes =
std::map<ID, std::unique_ptr<IntegrationScheme>>;
using DOFsIntegrationSchemesSolutionTypes =
std::map<ID, IntegrationScheme::SolutionType>;
using DOFsIntegrationSchemesOwner = std::set<ID>;
/// Underlying integration scheme per dof, \todo check what happens in dynamic
/// in case of coupled equations
DOFsIntegrationSchemes integration_schemes;
/// defines if the solver is owner of the memory or not
DOFsIntegrationSchemesOwner integration_schemes_owner;
/// Type of corrector to use
DOFsIntegrationSchemesSolutionTypes solution_types;
/// define if the mass matrix is lumped or not
bool is_mass_lumped{false};
};
} // namespace akantu
#endif /* AKANTU_TIME_STEP_SOLVER_DEFAULT_HH_ */
diff --git a/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh b/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
index c339454ce..6108e2023 100644
--- a/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
+++ b/src/model/common/time_step_solvers/time_step_solver_default_explicit.hh
@@ -1,77 +1,79 @@
/**
* @file time_step_solver_default_explicit.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Default solver for explicit resolution
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_
#define AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_
namespace akantu {
class TimeStepSolverDefaultExplicit : public TimeStepSolverDefault {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefaultExplicit();
virtual ~TimeStepSolverDefaultExplicit();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverDefaultExplicit & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
//#include "time_step_solver_default_explicit_inline_impl.hh"
#endif /* AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH_ */
diff --git a/src/model/contact_mechanics/contact_detector.cc b/src/model/contact_mechanics/contact_detector.cc
index 20ea3c8de..d9dbfcc1c 100644
--- a/src/model/contact_mechanics/contact_detector.cc
+++ b/src/model/contact_mechanics/contact_detector.cc
@@ -1,293 +1,294 @@
/**
- * @file contact_detector.cc
+ * @file contact_detector.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 12 2018
- * @date last modification: Fri Sep 21 2018
+ * @date creation: Wed Dec 05 2018
+ * @date last modification: Thu Jun 24 2021
*
* @brief Mother class for all detection algorithms
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "contact_detector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ContactDetector::ContactDetector(Mesh & mesh, const ID & id)
: ContactDetector(mesh, mesh.getNodes(), id) {}
/* -------------------------------------------------------------------------- */
ContactDetector::ContactDetector(Mesh & mesh, Array<Real> positions,
const ID & id)
: Parsable(ParserType::_contact_detector, id), mesh(mesh),
positions(0, mesh.getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->spatial_dimension = mesh.getSpatialDimension();
this->positions.copy(positions);
const Parser & parser = getStaticParser();
const ParserSection & section =
*(parser.getSubSections(ParserType::_contact_detector).first);
this->parseSection(section);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactDetector::parseSection(const ParserSection & section) {
auto type = section.getParameterValue<std::string>("type");
if (type == "implicit") {
this->detection_type = _implicit;
} else if (type == "explicit") {
this->detection_type = _explicit;
} else {
AKANTU_ERROR("Unknown detection type : " << type);
}
this->projection_tolerance =
section.getParameterValue<Real>("projection_tolerance");
this->max_iterations = section.getParameterValue<Real>("max_iterations");
this->extension_tolerance =
section.getParameterValue<Real>("extension_tolerance");
}
/* -------------------------------------------------------------------------- */
void ContactDetector::search(Array<ContactElement> & elements,
Array<Real> & gaps, Array<Real> & normals,
Array<Real> & tangents,
Array<Real> & projections) {
auto surface_dimension = spatial_dimension - 1;
this->mesh.fillNodesToElements(surface_dimension);
this->computeMaximalDetectionDistance();
contact_pairs.clear();
SpatialGrid<UInt> master_grid(spatial_dimension);
SpatialGrid<UInt> slave_grid(spatial_dimension);
this->globalSearch(slave_grid, master_grid);
this->localSearch(slave_grid, master_grid);
this->createContactElements(elements, gaps, normals, tangents, projections);
}
/* -------------------------------------------------------------------------- */
void ContactDetector::globalSearch(SpatialGrid<UInt> & slave_grid,
SpatialGrid<UInt> & master_grid) {
auto & master_list = surface_selector->getMasterList();
auto & slave_list = surface_selector->getSlaveList();
BBox bbox_master(spatial_dimension);
this->constructBoundingBox(bbox_master, master_list);
BBox bbox_slave(spatial_dimension);
this->constructBoundingBox(bbox_slave, slave_list);
auto && bbox_intersection = bbox_master.intersection(bbox_slave);
AKANTU_DEBUG_INFO("Intersection BBox " << bbox_intersection);
Vector<Real> center(spatial_dimension);
bbox_intersection.getCenter(center);
Vector<Real> spacing(spatial_dimension);
this->computeCellSpacing(spacing);
master_grid.setCenter(center);
master_grid.setSpacing(spacing);
this->constructGrid(master_grid, bbox_intersection, master_list);
slave_grid.setCenter(center);
slave_grid.setSpacing(spacing);
this->constructGrid(slave_grid, bbox_intersection, slave_list);
// search slave grid nodes in contactelement array and if they exits
// and still have orthogonal projection on its associated master
// facetremove it from the spatial grid or do not consider it for
// local search, maybe better option will be to have spatial grid of
// type node info and one of the variable of node info should be
// facet already exits
// so contact elements will be updated based on the above
// consideration , this means only those contact elements will be
// keep whose slave node is still in intersection bbox and still has
// projection in its master facet
// also if slave node is already exists in contact element and
// orthogonal projection does not exits then search the associated
// master facets with the current master facets within a given
// radius , this is subjected to computational cost as searching
// neighbbor cells can be more effective.
}
/* -------------------------------------------------------------------------- */
void ContactDetector::localSearch(SpatialGrid<UInt> & slave_grid,
SpatialGrid<UInt> & master_grid) {
// local search
// out of these array check each cell for closet node in that cell
// and neighbouring cells find the actual orthogonally closet
// check the projection of slave node on master facets connected to
// the closet master node, if yes update the contact element with
// slave node and master node and master surfaces connected to the
// master node
// these master surfaces will be needed later to update contact
// elements
/// find the closet master node for each slave node
for (auto && cell_id : slave_grid) {
/// loop over all the slave nodes of the current cell
for (auto && slave_node : slave_grid.getCell(cell_id)) {
bool pair_exists = false;
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = this->positions(slave_node, s);
}
Real closet_distance = std::numeric_limits<Real>::max();
UInt closet_master_node;
/// loop over all the neighboring cells of the current cell
for (auto && neighbor_cell : cell_id.neighbors()) {
/// loop over the data of neighboring cells from master grid
for (auto && master_node : master_grid.getCell(neighbor_cell)) {
/// check for self contact
if (slave_node == master_node) {
continue;
}
bool is_valid = true;
Array<Element> elements;
this->mesh.getAssociatedElements(slave_node, elements);
for (auto & elem : elements) {
if (elem.kind() != _ek_regular) {
continue;
}
Vector<UInt> connectivity =
const_cast<const Mesh &>(this->mesh).getConnectivity(elem);
auto node_iter = std::find(connectivity.begin(), connectivity.end(),
master_node);
if (node_iter != connectivity.end()) {
is_valid = false;
break;
}
}
Vector<Real> pos2(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos2(s) = this->positions(master_node, s);
}
Real distance = pos.distance(pos2);
if (distance <= closet_distance and is_valid) {
closet_master_node = master_node;
closet_distance = distance;
pair_exists = true;
}
}
}
if (pair_exists) {
contact_pairs.emplace_back(std::make_pair(slave_node, closet_master_node));
}
}
}
}
/* -------------------------------------------------------------------------- */
void ContactDetector::createContactElements(
Array<ContactElement> & contact_elements, Array<Real> & gaps,
Array<Real> & normals, Array<Real> & tangents, Array<Real> & projections) {
auto surface_dimension = spatial_dimension - 1;
Real alpha;
switch (detection_type) {
case _explicit: {
alpha = 1.0;
break;
}
case _implicit: {
alpha = -1.0;
break;
}
default:
AKANTU_EXCEPTION(detection_type
<< " is not a valid contact detection type");
break;
}
for (auto & pairs : contact_pairs) {
const auto & slave_node = pairs.first;
Vector<Real> slave(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
slave(s) = this->positions(slave_node, s);
}
const auto & master_node = pairs.second;
Array<Element> elements;
this->mesh.getAssociatedElements(master_node, elements);
auto & gap = gaps.begin()[slave_node];
Vector<Real> normal(normals.begin(spatial_dimension)[slave_node]);
Vector<Real> projection(projections.begin(surface_dimension)[slave_node]);
Matrix<Real> tangent(
tangents.begin(surface_dimension, spatial_dimension)[slave_node]);
auto index = GeometryUtils::orthogonalProjection(
mesh, positions, slave, elements, gap, projection, normal, tangent,
alpha, this->max_iterations, this->projection_tolerance,
this->extension_tolerance);
// if a valid projection is not found on the patch of elements
// index is -1 or if not a valid self contact, the contact element
// is not created
if (index == UInt(-1) or !isValidSelfContact(slave_node, gap, normal)) {
gap *= 0;
normal *= 0;
projection *= 0;
tangent *= 0;
continue;
}
// create contact element
contact_elements.push_back(ContactElement(slave_node, elements[index]));
}
contact_pairs.clear();
}
} // namespace akantu
diff --git a/src/model/contact_mechanics/contact_detector.hh b/src/model/contact_mechanics/contact_detector.hh
index 58fbd318d..edadba8af 100644
--- a/src/model/contact_mechanics/contact_detector.hh
+++ b/src/model/contact_mechanics/contact_detector.hh
@@ -1,215 +1,216 @@
/**
- * @file contact_detection.hh
+ * @file contact_detector.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 12 2018
- * @date last modification: Tue Oct 23 2018
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Thu Jun 24 2021
*
* @brief Mother class for all detection algorithms
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_bbox.hh"
#include "aka_common.hh"
#include "aka_grid_dynamic.hh"
#include "contact_element.hh"
#include "element_class.hh"
#include "element_group.hh"
#include "fe_engine.hh"
#include "geometry_utils.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "parsable.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_CONTACT_DETECTOR_HH__
#define __AKANTU_CONTACT_DETECTOR_HH__
namespace akantu {
enum class Surface { master, slave };
/* -------------------------------------------------------------------------- */
class ContactDetector : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructor/Destructors */
/* ------------------------------------------------------------------------ */
public:
ContactDetector(Mesh &, const ID & id = "contact_detector");
ContactDetector(Mesh &, Array<Real> positions,
const ID & id = "contact_detector");
~ContactDetector() override = default;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
public:
/// performs all search steps
void search(Array<ContactElement> & elements, Array<Real> & gaps,
Array<Real> & normals, Array<Real> & tangents,
Array<Real> & projections);
/// performs global spatial search to construct spatial grids
void globalSearch(SpatialGrid<UInt> &, SpatialGrid<UInt> &);
/// performs local search to find closet master node to a slave node
void localSearch(SpatialGrid<UInt> &, SpatialGrid<UInt> &);
/// create contact elements
void createContactElements(Array<ContactElement> & elements,
Array<Real> & gaps, Array<Real> & normals,
Array<Real> & tangents, Array<Real> & projections);
private:
/// reads the input file to get contact detection options
void parseSection(const ParserSection & section) override;
/* ------------------------------------------------------------------------ */
/* Inline Methods */
/* ------------------------------------------------------------------------ */
public:
/// checks whether the natural projection is valid or not
inline bool checkValidityOfProjection(Vector<Real> & projection) const;
/// extracts the coordinates of an element
inline void coordinatesOfElement(const Element & el,
Matrix<Real> & coords) const;
/// computes the optimal cell size for grid
inline void computeCellSpacing(Vector<Real> & spacing) const;
/// constructs a grid containing nodes lying within bounding box
inline void constructGrid(SpatialGrid<UInt> & grid, BBox & bbox,
const Array<UInt> & nodes_list) const;
/// constructs the bounding box based on nodes list
inline void constructBoundingBox(BBox & bbox,
const Array<UInt> & nodes_list) const;
/// computes the maximum in radius for a given mesh
inline void computeMaximalDetectionDistance();
/// constructs the connectivity for a contact element
inline Vector<UInt> constructConnectivity(UInt & slave,
const Element & master) const;
/// computes normal on an element
inline void computeNormalOnElement(const Element & element,
Vector<Real> & normal) const;
/// extracts vectors which forms the plane of element
inline void vectorsAlongElement(const Element & el,
Matrix<Real> & vectors) const;
/// computes the gap between slave and its projection on master
/// surface
inline Real computeGap(const Vector<Real> & slave,
const Vector<Real> & master) const;
/// filter boundary elements
inline void filterBoundaryElements(const Array<Element> & elements,
Array<Element> & boundary_elements) const;
/// checks whether self contact condition leads to a master element
/// which is closet but not orthogonally opposite to slave surface
inline bool isValidSelfContact(const UInt & slave_node, const Real & gap,
const Vector<Real> & normal) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the mesh
AKANTU_GET_MACRO(Mesh, mesh, Mesh &)
/// returns the maximum detection distance
AKANTU_GET_MACRO(MaximumDetectionDistance, max_dd, Real);
AKANTU_SET_MACRO(MaximumDetectionDistance, max_dd, Real);
/// returns the bounding box extension
AKANTU_GET_MACRO(MaximumBoundingBox, max_bb, Real);
AKANTU_SET_MACRO(MaximumBoundingBox, max_bb, Real);
/// returns the minimum detection distance
AKANTU_GET_MACRO(MinimumDetectionDistance, min_dd, Real);
AKANTU_SET_MACRO(MinimumDetectionDistance, min_dd, Real);
AKANTU_GET_MACRO_NOT_CONST(Positions, positions, Array<Real> &);
AKANTU_SET_MACRO(Positions, positions, Array<Real>);
AKANTU_GET_MACRO_NOT_CONST(SurfaceSelector, *surface_selector,
SurfaceSelector &);
AKANTU_SET_MACRO(SurfaceSelector, surface_selector,
std::shared_ptr<SurfaceSelector>);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// maximal detection distance for grid spacing
Real max_dd;
/// minimal detection distance for grid spacing
Real min_dd;
/// maximal bounding box extension
Real max_bb;
/// tolerance for finding natural projection
Real projection_tolerance;
/// iterations for finding natural projection
UInt max_iterations;
/// tolerance for extending a master elements on all sides
Real extension_tolerance;
/// Mesh
Mesh & mesh;
/// dimension of the model
UInt spatial_dimension{0};
/// node selector for selecting master and slave nodes
std::shared_ptr<SurfaceSelector> surface_selector;
/// contact pair slave node to closet master node
std::vector<std::pair<UInt, UInt>> contact_pairs;
/// contains the updated positions of the nodes
Array<Real> positions;
/// type of detection explicit/implicit
DetectionType detection_type;
};
} // namespace akantu
#include "contact_detector_inline_impl.cc"
#endif /* __AKANTU_CONTACT_DETECTOR_HH__ */
diff --git a/src/model/contact_mechanics/contact_detector_inline_impl.cc b/src/model/contact_mechanics/contact_detector_inline_impl.cc
index e1a21502f..29416fb7e 100644
--- a/src/model/contact_mechanics/contact_detector_inline_impl.cc
+++ b/src/model/contact_mechanics/contact_detector_inline_impl.cc
@@ -1,316 +1,317 @@
/**
- * @file contact_detection.hh
+ * @file contact_detector_inline_impl.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Apr 29 2019
- * @date last modification: Mon Apr 29 2019
+ * @date creation: Wed May 08 2019
+ * @date last modification: Thu Jun 24 2021
*
* @brief inine implementation of the contact detector class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "contact_detector.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_CONTACT_DETECTOR_INLINE_IMPL_CC__
#define __AKANTU_CONTACT_DETECTOR_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool
ContactDetector::checkValidityOfProjection(Vector<Real> & projection) const {
Real tolerance = 1e-3;
return std::all_of(projection.begin(), projection.end(),
[&tolerance](auto && xi) {
return (xi > -1.0 - tolerance) or (xi < 1.0 + tolerance);
});
}
/* -------------------------------------------------------------------------- */
inline void ContactDetector::coordinatesOfElement(const Element & el,
Matrix<Real> & coords) const {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
const Vector<UInt> connect = mesh.getConnectivity(el.type, _not_ghost)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
for (UInt s : arange(spatial_dimension)) {
coords(s, n) = this->positions(node, s);
}
}
}
/* -------------------------------------------------------------------------- */
inline void ContactDetector::computeCellSpacing(Vector<Real> & spacing) const {
for (UInt s : arange(spatial_dimension)) {
spacing(s) = std::sqrt(2.0) * max_dd;
}
}
/* -------------------------------------------------------------------------- */
inline void
ContactDetector::constructGrid(SpatialGrid<UInt> & grid, BBox & bbox,
const Array<UInt> & nodes_list) const {
auto to_grid = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = this->positions(node, s);
}
if (bbox.contains(pos)) {
grid.insert(node, pos);
}
};
std::for_each(nodes_list.begin(), nodes_list.end(), to_grid);
}
/* -------------------------------------------------------------------------- */
inline void
ContactDetector::constructBoundingBox(BBox & bbox,
const Array<UInt> & nodes_list) const {
auto to_bbox = [&](UInt node) {
Vector<Real> pos(spatial_dimension);
for (UInt s : arange(spatial_dimension)) {
pos(s) = this->positions(node, s);
}
bbox += pos;
};
std::for_each(nodes_list.begin(), nodes_list.end(), to_bbox);
auto & lower_bound = bbox.getLowerBounds();
auto & upper_bound = bbox.getUpperBounds();
lower_bound -= this->max_bb;
upper_bound += this->max_bb;
AKANTU_DEBUG_INFO("BBox" << bbox);
}
/* -------------------------------------------------------------------------- */
inline void ContactDetector::computeMaximalDetectionDistance() {
Real elem_size;
Real max_elem_size = std::numeric_limits<Real>::min();
Real min_elem_size = std::numeric_limits<Real>::max();
auto & master_nodes = this->surface_selector->getMasterList();
for (auto & master : master_nodes) {
Array<Element> elements;
this->mesh.getAssociatedElements(master, elements);
for (auto element : elements) {
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element.type);
Matrix<Real> elem_coords(spatial_dimension, nb_nodes_per_element);
this->coordinatesOfElement(element, elem_coords);
elem_size = FEEngine::getElementInradius(elem_coords, element.type);
max_elem_size = std::max(max_elem_size, elem_size);
min_elem_size = std::min(min_elem_size, elem_size);
}
}
AKANTU_DEBUG_INFO("The maximum element size : " << max_elem_size);
this->min_dd = min_elem_size;
this->max_dd = max_elem_size;
this->max_bb = max_elem_size;
}
/* -------------------------------------------------------------------------- */
inline Vector<UInt>
ContactDetector::constructConnectivity(UInt & slave,
const Element & master) const {
const Vector<UInt> master_conn = this->mesh.getConnectivity(master);
Vector<UInt> elem_conn(master_conn.size() + 1);
elem_conn[0] = slave;
for (UInt i = 1; i < elem_conn.size(); ++i) {
elem_conn[i] = master_conn[i - 1];
}
return elem_conn;
}
/* -------------------------------------------------------------------------- */
inline void
ContactDetector::computeNormalOnElement(const Element & element,
Vector<Real> & normal) const {
Matrix<Real> vectors(spatial_dimension, spatial_dimension - 1);
this->vectorsAlongElement(element, vectors);
switch (this->spatial_dimension) {
case 2: {
Math::normal2(vectors.storage(), normal.storage());
break;
}
case 3: {
Math::normal3(vectors(0).storage(), vectors(1).storage(), normal.storage());
break;
}
default: {
AKANTU_ERROR("Unknown dimension : " << spatial_dimension);
}
}
// to ensure that normal is always outwards from master surface
const auto & element_to_subelement =
mesh.getElementToSubelement(element.type)(element.element);
Vector<Real> outside(spatial_dimension);
mesh.getBarycenter(element, outside);
// check if mesh facets exists for cohesive elements contact
Vector<Real> inside(spatial_dimension);
if (mesh.isMeshFacets()) {
mesh.getMeshParent().getBarycenter(element_to_subelement[0], inside);
} else {
mesh.getBarycenter(element_to_subelement[0], inside);
}
Vector<Real> inside_to_outside = outside - inside;
auto projection = inside_to_outside.dot(normal);
if (projection < 0) {
normal *= -1.0;
}
}
/* -------------------------------------------------------------------------- */
inline void ContactDetector::vectorsAlongElement(const Element & el,
Matrix<Real> & vectors) const {
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Matrix<Real> coords(spatial_dimension, nb_nodes_per_element);
this->coordinatesOfElement(el, coords);
for (auto i : arange(spatial_dimension - 1)) {
vectors(i) = Vector<Real>(coords(i + 1)) - Vector<Real>(coords(0));
}
}
/* -------------------------------------------------------------------------- */
inline Real ContactDetector::computeGap(const Vector<Real> & slave,
const Vector<Real> & master) const {
auto gap = (master - slave).norm();
return gap;
}
/* -------------------------------------------------------------------------- */
inline void ContactDetector::filterBoundaryElements(
const Array<Element> & elements, Array<Element> & boundary_elements) const {
for (auto elem : elements) {
const auto & element_to_subelement =
mesh.getElementToSubelement(elem.type)(elem.element);
// for regular boundary elements
if (element_to_subelement.size() == 1 and
element_to_subelement[0].kind() == _ek_regular) {
boundary_elements.push_back(elem);
continue;
}
// for cohesive boundary elements
UInt nb_subelements_regular = 0;
for (auto subelem : element_to_subelement) {
if (subelem == ElementNull) {
continue;
}
if (subelem.kind() == _ek_regular) {
++nb_subelements_regular;
}
}
auto nb_subelements = element_to_subelement.size();
if (nb_subelements_regular < nb_subelements) {
boundary_elements.push_back(elem);
}
}
}
/* -------------------------------------------------------------------------- */
inline bool
ContactDetector::isValidSelfContact(const UInt & slave_node, const Real & gap,
const Vector<Real> & normal) const {
UInt master_node;
// finding the master node corresponding to slave node
for (auto && pair : contact_pairs) {
if (pair.first == slave_node) {
master_node = pair.second;
break;
}
}
Array<Element> slave_elements;
this->mesh.getAssociatedElements(slave_node, slave_elements);
// Check 1 : master node is not connected to elements connected to
// slave node
Vector<Real> slave_normal(spatial_dimension);
for (auto & element : slave_elements) {
if (element.kind() != _ek_regular) {
continue;
}
const Vector<UInt> connectivity =
this->mesh.getConnectivity(element);
// finding the normal at slave node by averaging of normals
Vector<Real> normal(spatial_dimension);
GeometryUtils::normal(mesh, positions, element, normal);
slave_normal = slave_normal + normal;
auto node_iter =
std::find(connectivity.begin(), connectivity.end(), master_node);
if (node_iter != connectivity.end()) {
return false;
}
}
// Check 2 : if gap is twice the size of smallest element
if (std::abs(gap) > 2.0 * min_dd) {
return false;
}
// Check 3 : check the directions of normal at slave node and at
// master element, should be in opposite directions
auto norm = slave_normal.norm();
if (norm != 0) {
slave_normal /= norm;
}
auto product = slave_normal.dot(normal);
return not (product >= 0);
}
} // namespace akantu
#endif /* __AKANTU_CONTACT_DETECTOR_INLINE_IMPL_CC__ */
diff --git a/src/model/contact_mechanics/contact_element.hh b/src/model/contact_mechanics/contact_element.hh
index aaeffa1d3..cbe8db606 100644
--- a/src/model/contact_mechanics/contact_element.hh
+++ b/src/model/contact_mechanics/contact_element.hh
@@ -1,82 +1,86 @@
/**
- * @file contact_element.hh
+ * @file contact_element.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 12 2018
- * @date last modification: Tue Oct 23 2018
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Tue Jun 08 2021
*
* @brief Mother class for all detection algorithms
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_CONTACT_ELEMENT_HH__
#define __AKANTU_CONTACT_ELEMENT_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
using SlaveType = UInt;
using MasterType = Element;
-
+
class ContactElement {
/* ------------------------------------------------------------------------ */
/* Constructor/ Destructors */
/* ------------------------------------------------------------------------ */
public:
-
ContactElement() = default;
ContactElement(const SlaveType & slave, const MasterType & master)
- : slave(slave), master(master) {}
-
+ : slave(slave), master(master) {}
+
~ContactElement() = default;
+ bool operator==(const ContactElement & other) const {
+ return slave == other.slave and master == other.master;
+ }
+
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbNodes() const {
auto nb_master_nodes = Mesh::getNbNodesPerElement(master.type);
return nb_master_nodes + 1;
}
-
+
/* ------------------------------------------------------------------------ */
/* Class Members */
- /* ------------------------------------------------------------------------ */
+ /* ------------------------------------------------------------------------ */
public:
/// slave node
SlaveType slave;
-
+
/// master element/node
MasterType master;
};
-} // akantu
+} // namespace akantu
#endif /* __AKANTU_CONTACT_ELEMENT_HH__ */
diff --git a/src/model/contact_mechanics/contact_mechanics_model.cc b/src/model/contact_mechanics/contact_mechanics_model.cc
index 2fcba0557..3e7d69c31 100644
--- a/src/model/contact_mechanics/contact_mechanics_model.cc
+++ b/src/model/contact_mechanics/contact_mechanics_model.cc
@@ -1,707 +1,708 @@
/**
- * @file coontact_mechanics_model.cc
+ * @file contact_mechanics_model.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Wed Feb 21 2018
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Jul 28 2021
*
* @brief Contact mechanics model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
#include "boundary_condition_functor.hh"
#include "dumpable_inline_impl.hh"
#include "group_manager_inline_impl.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ContactMechanicsModel::ContactMechanicsModel(
Mesh & mesh, UInt dim, const ID & id,
std::shared_ptr<DOFManager> dof_manager, const ModelType model_type)
: Model(mesh, model_type, dof_manager, dim, id) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("ContactMechanicsModel", mesh,
Model::spatial_dimension);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("contact_mechanics", id, true);
this->mesh.addDumpMeshToDumper("contact_mechanics", mesh,
Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
this->registerDataAccessor(*this);
this->detector =
std::make_unique<ContactDetector>(this->mesh, id + ":contact_detector");
registerFEEngineObject<MyFEEngineType>("ContactFacetsFEEngine", mesh,
Model::spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ContactMechanicsModel::~ContactMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
// initalize the resolutions
if (not this->parser.getLastParsedFile().empty()) {
this->instantiateResolutions();
this->initResolutions();
}
this->initBC(*this, *displacement, *displacement_increment, *external_force);
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::instantiateResolutions() {
ParserSection model_section;
bool is_empty;
std::tie(model_section, is_empty) = this->getParserSection();
if (not is_empty) {
auto model_resolutions =
model_section.getSubSections(ParserType::_contact_resolution);
for (const auto & section : model_resolutions) {
this->registerNewResolution(section);
}
}
auto sub_sections =
this->parser.getSubSections(ParserType::_contact_resolution);
for (const auto & section : sub_sections) {
this->registerNewResolution(section);
}
if (resolutions.empty())
AKANTU_EXCEPTION("No contact resolutions where instantiated for the model"
<< getID());
are_resolutions_instantiated = true;
}
/* -------------------------------------------------------------------------- */
Resolution &
ContactMechanicsModel::registerNewResolution(const ParserSection & section) {
std::string res_name;
std::string res_type = section.getName();
std::string opt_param = section.getOption();
try {
std::string tmp = section.getParameter("name");
res_name = tmp; /** this can seem weird, but there is an ambiguous operator
* overload that i couldn't solve. @todo remove the
* weirdness of this code
*/
} catch (debug::Exception &) {
AKANTU_ERROR("A contact resolution of type \'"
<< res_type
<< "\' in the input file has been defined without a name!");
}
Resolution & res = this->registerNewResolution(res_name, res_type, opt_param);
res.parseSection(section);
return res;
}
/* -------------------------------------------------------------------------- */
Resolution & ContactMechanicsModel::registerNewResolution(
const ID & res_name, const ID & res_type, const ID & opt_param) {
AKANTU_DEBUG_ASSERT(resolutions_names_to_id.find(res_name) ==
resolutions_names_to_id.end(),
"A resolution with this name '"
<< res_name << "' has already been registered. "
<< "Please use unique names for resolutions");
UInt res_count = resolutions.size();
resolutions_names_to_id[res_name] = res_count;
std::stringstream sstr_res;
sstr_res << this->id << ":" << res_count << ":" << res_type;
ID res_id = sstr_res.str();
std::unique_ptr<Resolution> resolution =
ResolutionFactory::getInstance().allocate(res_type, spatial_dimension,
opt_param, *this, res_id);
resolutions.push_back(std::move(resolution));
return *(resolutions.back());
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::initResolutions() {
AKANTU_DEBUG_ASSERT(resolutions.size() != 0,
"No resolutions to initialize !");
if (!are_resolutions_instantiated) {
instantiateResolutions();
}
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::initModel() {
AKANTU_DEBUG_IN();
getFEEngine("ContactMechanicsModel").initShapeFunctions(_not_ghost);
getFEEngine("ContactMechanicsModel").initShapeFunctions(_ghost);
getFEEngine("ContactFacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("ContactFacetsFEEngine").initShapeFunctions(_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
FEEngine & ContactMechanicsModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(
getFEEngineClassBoundary<MyFEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::initSolver(
TimeStepSolverType /*time_step_solver_type*/, NonLinearSolverType) {
// for alloc type of solvers
this->allocNodalField(this->displacement, spatial_dimension, "displacement");
this->allocNodalField(this->displacement_increment, spatial_dimension,
"displacement_increment");
this->allocNodalField(this->internal_force, spatial_dimension,
"internal_force");
this->allocNodalField(this->external_force, spatial_dimension,
"external_force");
this->allocNodalField(this->normal_force, spatial_dimension, "normal_force");
this->allocNodalField(this->tangential_force, spatial_dimension,
"tangential_force");
this->allocNodalField(this->gaps, 1, "gaps");
this->allocNodalField(this->nodal_area, 1, "areas");
this->allocNodalField(this->blocked_dofs, 1, "blocked_dofs");
this->allocNodalField(this->contact_state, 1, "contact_state");
this->allocNodalField(this->previous_master_elements, 1,
"previous_master_elements");
this->allocNodalField(this->normals, spatial_dimension, "normals");
auto surface_dimension = spatial_dimension - 1;
this->allocNodalField(this->tangents, surface_dimension * spatial_dimension,
"tangents");
this->allocNodalField(this->projections, surface_dimension, "projections");
this->allocNodalField(this->previous_projections, surface_dimension,
"previous_projections");
this->allocNodalField(this->previous_tangents,
surface_dimension * spatial_dimension,
"previous_tangents");
this->allocNodalField(this->tangential_tractions, surface_dimension,
"tangential_tractions");
this->allocNodalField(this->previous_tangential_tractions, surface_dimension,
"previous_tangential_tractions");
// todo register multipliers as dofs for lagrange multipliers
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
ContactMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", TimeStepSolverType::_dynamic);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions ContactMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type =
NonLinearSolverType::_newton_raphson_contact;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
break;
}
return options;
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
// computes the internal forces
this->assembleInternalForces();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the contact forces");
UInt nb_nodes = mesh.getNbNodes();
this->internal_force->clear();
this->normal_force->clear();
this->tangential_force->clear();
internal_force->resize(nb_nodes, 0.);
normal_force->resize(nb_nodes, 0.);
tangential_force->resize(nb_nodes, 0.);
// assemble the forces due to contact
auto assemble = [&](auto && ghost_type) {
for (auto & resolution : resolutions) {
resolution->assembleInternalForces(ghost_type);
}
};
AKANTU_DEBUG_INFO("Assemble residual for local elements");
assemble(_not_ghost);
// assemble the stresses due to ghost elements
// AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
// assemble(_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::search() {
// save the previous state
this->savePreviousState();
contact_elements.clear();
// this needs to be resized if cohesive elements are added
UInt nb_nodes = mesh.getNbNodes();
auto resize_arrays = [&](auto & internal_array) {
internal_array->resize(nb_nodes);
internal_array->zero();
};
resize_arrays(gaps);
resize_arrays(normals);
resize_arrays(tangents);
resize_arrays(projections);
resize_arrays(tangential_tractions);
resize_arrays(contact_state);
resize_arrays(nodal_area);
resize_arrays(external_force);
this->detector->search(contact_elements, *gaps, *normals, *tangents,
*projections);
// intepenetration value must be positive for contact mechanics
// model to work by default the gap value from detector is negative
std::for_each((*gaps).begin(), (*gaps).end(), [](Real & gap) { gap *= -1.; });
if (contact_elements.size() != 0) {
this->computeNodalAreas();
}
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::savePreviousState() {
AKANTU_DEBUG_IN();
// saving previous natural projections
(*previous_projections).copy(*projections);
// saving previous tangents
(*previous_tangents).copy(*tangents);
// saving previous tangential traction
(*previous_tangential_tractions).copy(*tangential_tractions);
previous_master_elements->clear();
previous_master_elements->resize(projections->size());
previous_master_elements->set(ElementNull);
for (auto & element : contact_elements) {
(*previous_master_elements)[element.slave] = element.master;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::computeNodalAreas(GhostType ghost_type) {
UInt nb_nodes = mesh.getNbNodes();
nodal_area->resize(nb_nodes);
nodal_area->zero();
external_force->resize(nb_nodes);
external_force->zero();
auto & fem_boundary =
getFEEngineClassBoundary<MyFEEngineType>("ContactMechanicsModel");
fem_boundary.initShapeFunctions(getPositions(), _not_ghost);
fem_boundary.initShapeFunctions(getPositions(), _ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
IntegrationPoint quad_point;
quad_point.ghost_type = ghost_type;
auto & group = mesh.getElementGroup("contact_surface");
UInt nb_degree_of_freedom = external_force->getNbComponent();
for (auto && type : group.elementTypes(spatial_dimension - 1, ghost_type)) {
const auto & element_ids = group.getElements(type, ghost_type);
UInt nb_quad_points = fem_boundary.getNbIntegrationPoints(type, ghost_type);
UInt nb_elements = element_ids.size();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> dual_before_integ(nb_elements * nb_quad_points,
nb_degree_of_freedom, 0.);
Array<Real> quad_coords(nb_elements * nb_quad_points, spatial_dimension);
const auto & normals_on_quad =
fem_boundary.getNormalsOnIntegrationPoints(type, ghost_type);
auto normals_begin = normals_on_quad.begin(spatial_dimension);
decltype(normals_begin) normals_iter;
auto quad_coords_iter = quad_coords.begin(spatial_dimension);
auto dual_iter = dual_before_integ.begin(nb_degree_of_freedom);
quad_point.type = type;
Element subelement;
subelement.type = type;
subelement.ghost_type = ghost_type;
for (auto el : element_ids) {
subelement.element = el;
const auto & element_to_subelement =
mesh.getElementToSubelement(type)(el);
Vector<Real> outside(spatial_dimension);
mesh.getBarycenter(subelement, outside);
Vector<Real> inside(spatial_dimension);
if (mesh.isMeshFacets()) {
mesh.getMeshParent().getBarycenter(element_to_subelement[0], inside);
} else {
mesh.getBarycenter(element_to_subelement[0], inside);
}
Vector<Real> inside_to_outside(spatial_dimension);
inside_to_outside = outside - inside;
normals_iter = normals_begin + el * nb_quad_points;
quad_point.element = el;
for (auto q : arange(nb_quad_points)) {
quad_point.num_point = q;
auto ddot = inside_to_outside.dot(*normals_iter);
Vector<Real> normal(*normals_iter);
if (ddot < 0)
normal *= -1.0;
(*dual_iter)
.mul<false>(Matrix<Real>::eye(spatial_dimension, 1), normal);
++dual_iter;
++quad_coords_iter;
++normals_iter;
}
}
Array<Real> dual_by_shapes(nb_elements * nb_quad_points,
nb_degree_of_freedom * nb_nodes_per_element);
fem_boundary.computeNtb(dual_before_integ, dual_by_shapes, type, ghost_type,
element_ids);
Array<Real> dual_by_shapes_integ(nb_elements, nb_degree_of_freedom *
nb_nodes_per_element);
fem_boundary.integrate(dual_by_shapes, dual_by_shapes_integ,
nb_degree_of_freedom * nb_nodes_per_element, type,
ghost_type, element_ids);
this->getDOFManager().assembleElementalArrayLocalArray(
dual_by_shapes_integ, *external_force, type, ghost_type, 1.,
element_ids);
}
for (auto && tuple :
zip(*nodal_area, make_view(*external_force, spatial_dimension))) {
auto & area = std::get<0>(tuple);
Vector<Real> force(std::get<1>(tuple));
area = force.norm();
}
this->external_force->clear();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Contact Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << Model::spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + resolutions [" << std::endl;
for (auto & resolution : resolutions) {
resolution->printself(stream, indent + 1);
}
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
MatrixType ContactMechanicsModel::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K")
return _symmetric;
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
}
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");
if (!this->getDOFManager().hasMatrix("K")) {
this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
}
for (auto & resolution : resolutions) {
resolution->assembleStiffnessMatrix(_not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::assembleLumpedMatrix(const ID & /*matrix_id*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::beforeSolveStep() {
for (auto & resolution : resolutions) {
resolution->beforeSolveStep();
}
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::afterSolveStep(bool converged) {
for (auto & resolution : resolutions) {
resolution->afterSolveStep(converged);
}
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
ContactMechanicsModel::createNodalFieldBool(const std::string &,
const std::string &, bool) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
ContactMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["contact_force"] = this->internal_force.get();
real_nodal_fields["normal_force"] = this->normal_force.get();
real_nodal_fields["tangential_force"] = this->tangential_force.get();
real_nodal_fields["blocked_dofs"] = this->blocked_dofs.get();
real_nodal_fields["normals"] = this->normals.get();
real_nodal_fields["tangents"] = this->tangents.get();
real_nodal_fields["gaps"] = this->gaps.get();
real_nodal_fields["areas"] = this->nodal_area.get();
real_nodal_fields["tangential_traction"] = this->tangential_tractions.get();
std::shared_ptr<dumpers::Field> field;
if (padding_flag) {
field = this->mesh.createNodalField(real_nodal_fields[field_name],
group_name, 3);
} else {
field =
this->mesh.createNodalField(real_nodal_fields[field_name], group_name);
}
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
ContactMechanicsModel::createNodalFieldUInt(const std::string & field_name,
const std::string & group_name,
bool /*padding_flag*/) {
std::shared_ptr<dumpers::Field> field;
if (field_name == "contact_state") {
auto && func =
std::make_unique<dumpers::ComputeUIntFromEnum<ContactState>>();
field = mesh.createNodalField(this->contact_state.get(), group_name);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, std::move(func));
}
return field;
}
#endif
/* -------------------------------------------------------------------------- */
UInt ContactMechanicsModel::getNbData(
const Array<Element> & elements, const SynchronizationTag & /*tag*/) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
for (const Element & el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::packData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::unpackData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt ContactMechanicsModel::getNbData(
const Array<UInt> & dofs, const SynchronizationTag & /*tag*/) const {
AKANTU_DEBUG_IN();
UInt size = 0;
AKANTU_DEBUG_OUT();
return size * dofs.size();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::packData(CommunicationBuffer & /*buffer*/,
const Array<UInt> & /*dofs*/,
const SynchronizationTag & /*tag*/) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ContactMechanicsModel::unpackData(CommunicationBuffer & /*buffer*/,
const Array<UInt> & /*dofs*/,
const SynchronizationTag & /*tag*/) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/contact_mechanics/contact_mechanics_model.hh b/src/model/contact_mechanics/contact_mechanics_model.hh
index f506fb631..201f93df0 100644
--- a/src/model/contact_mechanics/contact_mechanics_model.hh
+++ b/src/model/contact_mechanics/contact_mechanics_model.hh
@@ -1,372 +1,373 @@
/**
* @file contact_mechanics_model.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Jul 27 2010
- * @date last modification: Wed Feb 21 2018
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Thu Jun 24 2021
*
* @brief Model of Contact Mechanics
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "contact_detector.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_CONTACT_MECHANICS_MODEL_HH__
#define __AKANTU_CONTACT_MECHANICS_MODEL_HH__
namespace akantu {
class Resolution;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class ContactMechanicsModel : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<ContactMechanicsModel> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
public:
ContactMechanicsModel(
Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "contact_mechanics_model",
std::shared_ptr<DOFManager> dof_manager = nullptr,
const ModelType model_type = ModelType::_contact_mechanics_model);
~ContactMechanicsModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize completely the model
void initFullImpl(const ModelOptions & options) override;
/// allocate all vectors
void initSolver(TimeStepSolverType, NonLinearSolverType) override;
/// initialize all internal arrays for resolutions
void initResolutions();
/// initialize the modelType
void initModel() override;
/// call back for the solver, computes the force residual
void assembleResidual() override;
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep(bool converged = true) override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Contact Detection */
/* ------------------------------------------------------------------------ */
public:
void search();
void computeNodalAreas(GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Contact Resolution */
/* ------------------------------------------------------------------------ */
public:
/// register an empty contact resolution of a given type
Resolution & registerNewResolution(const ID & res_name, const ID & res_type,
const ID & opt_param);
protected:
/// register a resolution in the dynamic database
Resolution & registerNewResolution(const ParserSection & res_section);
/// read the resolution files to instantiate all the resolutions
void instantiateResolutions();
/// save the parameters from previous state
void savePreviousState();
/* ------------------------------------------------------------------------ */
/* Solver Interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the contact stiffness matrix
virtual void assembleStiffnessMatrix();
/// assembles the contant internal forces
virtual void assembleInternalForces();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
#if defined(AKANTU_USE_IOHELPER)
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldUInt(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
#endif
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
/// contact detection class
friend class ContactDetector;
/// contact resolution class
friend class Resolution;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the ContactMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement, Array<Real> &);
/// get the ContactMechanicsModel::increment vector \warn only consistent
/// if ContactMechanicsModel::setIncrementFlagOn has been called before
AKANTU_GET_MACRO(Increment, *displacement_increment, Array<Real> &);
/// get the ContactMechanics::internal_force vector (internal forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the ContactMechanicsModel::external_force vector (external forces)
AKANTU_GET_MACRO(ExternalForce, *external_force, Array<Real> &);
/// get the ContactMechanics::normal_force vector (normal forces)
AKANTU_GET_MACRO(NormalForce, *normal_force, Array<Real> &);
/// get the ContactMechanics::tangential_force vector (friction forces)
AKANTU_GET_MACRO(TangentialForce, *tangential_force, Array<Real> &);
/// get the ContactMechanics::traction vector (friction traction)
AKANTU_GET_MACRO(TangentialTractions, *tangential_tractions, Array<Real> &);
/// get the ContactMechanics::previous_tangential_tractions vector
AKANTU_GET_MACRO(PreviousTangentialTractions, *previous_tangential_tractions,
Array<Real> &);
/// get the ContactMechanicsModel::force vector (external forces)
Array<Real> & getForce() {
AKANTU_DEBUG_WARNING("getForce was maintained for backward compatibility, "
"use getExternalForce instead");
return *external_force;
}
/// get the ContactMechanics::blocked_dofs vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<Real> &);
/// get the ContactMechanics::gaps (contact gaps)
AKANTU_GET_MACRO(Gaps, *gaps, Array<Real> &);
/// get the ContactMechanics::normals (normals on slave nodes)
AKANTU_GET_MACRO(Normals, *normals, Array<Real> &);
/// get the ContactMechanics::tangents (tangents on slave nodes)
AKANTU_GET_MACRO(Tangents, *tangents, Array<Real> &);
/// get the ContactMechanics::previous_tangents (tangents on slave nodes)
AKANTU_GET_MACRO(PreviousTangents, *previous_tangents, Array<Real> &);
/// get the ContactMechanics::areas (nodal areas)
AKANTU_GET_MACRO(NodalArea, *nodal_area, Array<Real> &);
/// get the ContactMechanics::previous_projections (previous_projections)
AKANTU_GET_MACRO(PreviousProjections, *previous_projections, Array<Real> &);
/// get the ContactMechanics::projections (projections)
AKANTU_GET_MACRO(Projections, *projections, Array<Real> &);
/// get the ContactMechanics::contact_state vector (no_contact/stick/slip
/// state)
AKANTU_GET_MACRO(ContactState, *contact_state, Array<ContactState> &);
/// get the ContactMechanics::previous_master_elements
AKANTU_GET_MACRO(PreviousMasterElements, *previous_master_elements,
Array<Element> &);
/// get contact detector
AKANTU_GET_MACRO_NOT_CONST(ContactDetector, *detector, ContactDetector &);
/// get the contact elements
- inline Array<ContactElement> & getContactElements() {
+ inline const Array<ContactElement> & getContactElements() const {
return contact_elements;
}
/// get the current positions of the nodes
inline Array<Real> & getPositions() { return detector->getPositions(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// tells if the resolutions are instantiated
bool are_resolutions_instantiated;
/// displacements array
std::unique_ptr<Array<Real>> displacement;
/// increment of displacement
std::unique_ptr<Array<Real>> displacement_increment;
/// contact forces array
std::unique_ptr<Array<Real>> internal_force;
/// external forces array
std::unique_ptr<Array<Real>> external_force;
/// normal force array
std::unique_ptr<Array<Real>> normal_force;
/// friction force array
std::unique_ptr<Array<Real>> tangential_force;
/// friction traction array
std::unique_ptr<Array<Real>> tangential_tractions;
/// previous friction traction array
std::unique_ptr<Array<Real>> previous_tangential_tractions;
/// boundary vector
std::unique_ptr<Array<Real>> blocked_dofs;
/// array to store gap between slave and master
std::unique_ptr<Array<Real>> gaps;
/// array to store normals from master to slave
std::unique_ptr<Array<Real>> normals;
/// array to store tangents on the master element
std::unique_ptr<Array<Real>> tangents;
/// array to store previous tangents on the master element
std::unique_ptr<Array<Real>> previous_tangents;
/// array to store nodal areas
std::unique_ptr<Array<Real>> nodal_area;
/// array to store stick/slip state :
std::unique_ptr<Array<ContactState>> contact_state;
/// array to store previous projections in covariant basis
std::unique_ptr<Array<Real>> previous_projections;
// array to store projections in covariant basis
std::unique_ptr<Array<Real>> projections;
/// contact detection
std::unique_ptr<ContactDetector> detector;
/// list of contact resolutions
std::vector<std::unique_ptr<Resolution>> resolutions;
/// mapping between resolution name and resolution internal id
std::map<std::string, UInt> resolutions_names_to_id;
/// array to store contact elements
Array<ContactElement> contact_elements;
/// array to store previous master elements
std::unique_ptr<Array<Element>> previous_master_elements;
};
} // namespace akantu
/* ------------------------------------------------------------------------ */
/* inline functions */
/* ------------------------------------------------------------------------ */
#include "parser.hh"
#include "resolution.hh"
/* ------------------------------------------------------------------------ */
#endif /* __AKANTU_CONTACT_MECHANICS_MODEL_HH__ */
diff --git a/src/model/contact_mechanics/geometry_utils.cc b/src/model/contact_mechanics/geometry_utils.cc
index 9e8f82829..94a5b0554 100644
--- a/src/model/contact_mechanics/geometry_utils.cc
+++ b/src/model/contact_mechanics/geometry_utils.cc
@@ -1,730 +1,731 @@
/**
* @file geometry_utils.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Mmay 20 2019
- * @date last modification: Mon May 20 2019
+ * @date creation: Wed Oct 02 2019
+ * @date last modification: Thu Jun 24 2021
*
* @brief Implementation of various utilities needed for contact geometry
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "geometry_utils.hh"
#include "element_class_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void GeometryUtils::normal(const Mesh & mesh, const Array<Real> & positions,
const Element & element, Vector<Real> & normal,
bool outward) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt surface_dimension = spatial_dimension - 1;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(element.type);
Matrix<Real> coords(spatial_dimension, nb_nodes_per_element);
UInt * elem_val = mesh.getConnectivity(element.type, _not_ghost).storage();
mesh.extractNodalValuesFromElement(positions, coords.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
Matrix<Real> vectors(spatial_dimension, surface_dimension);
switch (spatial_dimension) {
case 1: {
normal[0] = 1;
break;
}
case 2: {
vectors(0) = Vector<Real>(coords(1)) - Vector<Real>(coords(0));
Math::normal2(vectors.storage(), normal.storage());
break;
}
case 3: {
vectors(0) = Vector<Real>(coords(1)) - Vector<Real>(coords(0));
vectors(1) = Vector<Real>(coords(2)) - Vector<Real>(coords(0));
Math::normal3(vectors(0).storage(), vectors(1).storage(), normal.storage());
break;
}
default: {
AKANTU_ERROR("Unknown dimension : " << spatial_dimension);
}
}
// to ensure that normal is always outwards from master surface
if (outward) {
const auto & element_to_subelement =
mesh.getElementToSubelement(element.type)(element.element);
Vector<Real> outside(spatial_dimension);
mesh.getBarycenter(element, outside);
// check if mesh facets exists for cohesive elements contact
Vector<Real> inside(spatial_dimension);
if (mesh.isMeshFacets()) {
mesh.getMeshParent().getBarycenter(element_to_subelement[0], inside);
} else {
mesh.getBarycenter(element_to_subelement[0], inside);
}
Vector<Real> inside_to_outside = outside - inside;
auto projection = inside_to_outside.dot(normal);
if (projection < 0) {
normal *= -1.0;
}
}
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::normal(const Mesh & mesh, const Element & element,
Matrix<Real> & tangents, Vector<Real> & normal,
bool outward) {
UInt spatial_dimension = mesh.getSpatialDimension();
// to ensure that normal is always outwards from master surface we
// compute a direction vector form inside of element attached to the
// suurface element
Vector<Real> inside_to_outside(spatial_dimension);
if (outward) {
const auto & element_to_subelement =
mesh.getElementToSubelement(element.type)(element.element);
Vector<Real> outside(spatial_dimension);
mesh.getBarycenter(element, outside);
// check if mesh facets exists for cohesive elements contact
Vector<Real> inside(spatial_dimension);
if (mesh.isMeshFacets()) {
mesh.getMeshParent().getBarycenter(element_to_subelement[0], inside);
} else {
mesh.getBarycenter(element_to_subelement[0], inside);
}
inside_to_outside = outside - inside;
// auto projection = inside_to_outside.dot(normal);
// if (projection < 0) {
// normal *= -1.0;
//}
}
// to ensure that direction of tangents are correct, cross product
// of tangents should give be in the same direction as of inside to outside
switch (spatial_dimension) {
case 2: {
normal[0] = -tangents(0, 1);
normal[1] = tangents(0, 0);
auto ddot = inside_to_outside.dot(normal);
if (ddot < 0) {
tangents *= -1.0;
normal *= -1.0;
}
break;
}
case 3: {
auto tang_trans = tangents.transpose();
auto tang1 = Vector<Real>(tang_trans(0));
auto tang2 = Vector<Real>(tang_trans(1));
auto tang1_cross_tang2 = tang1.crossProduct(tang2);
normal = tang1_cross_tang2 / tang1_cross_tang2.norm();
auto ddot = inside_to_outside.dot(normal);
if (ddot < 0) {
tang_trans(1) *= -1.0;
normal *= -1.0;
}
tangents = tang_trans.transpose();
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::covariantBasis(const Mesh & mesh,
const Array<Real> & positions,
const Element & element,
const Vector<Real> & normal,
Vector<Real> & natural_coord,
Matrix<Real> & tangents) {
UInt spatial_dimension = mesh.getSpatialDimension();
const ElementType type = element.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, nodes_coord.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
auto && dnds = ElementClassHelper<_ek_regular>::getDNDS(natural_coord, type);
tangents.mul<false, true>(dnds, nodes_coord);
auto temp_tangents = tangents.transpose();
for (UInt i = 0; i < spatial_dimension - 1; ++i) {
auto temp = Vector<Real>(temp_tangents(i));
temp_tangents(i) = temp.normalize();
}
tangents = temp_tangents.transpose();
// to ensure that direction of tangents are correct, cross product
// of tangents should give the normal vector computed earlier
switch (spatial_dimension) {
case 2: {
Vector<Real> e_z(3);
e_z[0] = 0.;
e_z[1] = 0.;
e_z[2] = 1.;
Vector<Real> tangent(3);
tangent[0] = tangents(0, 0);
tangent[1] = tangents(0, 1);
tangent[2] = 0.;
auto exp_normal = e_z.crossProduct(tangent);
auto ddot = normal.dot(exp_normal);
if (ddot < 0) {
tangents *= -1.0;
}
break;
}
case 3: {
auto tang_trans = tangents.transpose();
auto tang1 = Vector<Real>(tang_trans(0));
auto tang2 = Vector<Real>(tang_trans(1));
auto tang1_cross_tang2 = tang1.crossProduct(tang2);
auto exp_normal = tang1_cross_tang2 / tang1_cross_tang2.norm();
auto ddot = normal.dot(exp_normal);
if (ddot < 0) {
tang_trans(1) *= -1.0;
}
tangents = tang_trans.transpose();
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::covariantBasis(const Mesh & mesh,
const Array<Real> & positions,
const Element & element,
Vector<Real> & natural_coord,
Matrix<Real> & tangents) {
UInt spatial_dimension = mesh.getSpatialDimension();
const ElementType & type = element.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, nodes_coord.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
auto && dnds = ElementClassHelper<_ek_regular>::getDNDS(natural_coord, type);
tangents.mul<false, true>(dnds, nodes_coord);
auto temp_tangents = tangents.transpose();
for (UInt i = 0; i < spatial_dimension - 1; ++i) {
auto temp = Vector<Real>(temp_tangents(i));
temp_tangents(i) = temp.normalize();
}
tangents = temp_tangents.transpose();
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::curvature(const Mesh & mesh, const Array<Real> & positions,
const Element & element,
const Vector<Real> & natural_coord,
Matrix<Real> & curvature) {
UInt spatial_dimension = mesh.getSpatialDimension();
const ElementType & type = element.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
auto && d2nds2 =
ElementClassHelper<_ek_regular>::getD2NDS2(natural_coord, type);
Matrix<Real> coords(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, coords.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
curvature.mul<false, true>(coords, d2nds2);
}
/* -------------------------------------------------------------------------- */
UInt GeometryUtils::orthogonalProjection(
const Mesh & mesh, const Array<Real> & positions,
const Vector<Real> & slave, const Array<Element> & elements, Real & gap,
Vector<Real> & natural_projection, Vector<Real> & normal, Real alpha,
UInt max_iterations, Real projection_tolerance, Real extension_tolerance) {
UInt index = UInt(-1);
Real min_gap = std::numeric_limits<Real>::max();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt surface_dimension = spatial_dimension - 1;
UInt nb_same_sides{0};
UInt nb_boundary_elements{0};
UInt counter{0};
const auto & contact_group = mesh.getElementGroup("contact_surface");
for (const auto & element : elements) {
// filter out elements which are not there in the element group
// contact surface created by the surface selector and is stored
// in the mesh or mesh_facet, if a element is not there it
// returnas UInt(-1)
const auto & elements_of_type = contact_group.getElements(element.type);
if (elements_of_type.find(element.element) == UInt(-1)) {
continue;
}
nb_boundary_elements++;
// find the natural coordinate corresponding to the minimum gap
// between slave node and master element
Vector<Real> master(spatial_dimension);
Vector<Real> xi(natural_projection.size());
GeometryUtils::naturalProjection(mesh, positions, element, slave, master,
xi, max_iterations, projection_tolerance);
Matrix<Real> tangent_ele(surface_dimension, spatial_dimension);
GeometryUtils::covariantBasis(mesh, positions, element, xi, tangent_ele);
Vector<Real> normal_ele(spatial_dimension);
GeometryUtils::normal(mesh, element, tangent_ele, normal_ele);
// if gap between master projection and slave point is zero, then
// it means that slave point lies on the master element, hence the
// normal from master to slave cannot be computed in that case
auto master_to_slave = slave - master;
Real temp_gap = master_to_slave.norm();
if (temp_gap != 0) {
master_to_slave /= temp_gap;
}
// also the slave point should lie inside the master surface in
// case of explicit or outside in case of implicit, one way to
// check that is by checking the dot product of normal at each
// master element, if the values of all dot product is same then
// the slave point lies on the same side of each master element
// A alpha parameter is introduced which is 1 in case of explicit
// and -1 in case of implicit, therefor the variation (dot product
// + alpha) should be close to zero (within tolerance) for both
// cases
Real direction_tolerance = 1e-8;
auto product = master_to_slave.dot(normal_ele);
auto variation = std::abs(product + alpha);
if (variation <= direction_tolerance and temp_gap <= min_gap and
GeometryUtils::isValidProjection(xi, extension_tolerance)) {
gap = -temp_gap;
min_gap = temp_gap;
index = counter;
natural_projection = xi;
normal = normal_ele;
}
if (temp_gap == 0 or variation <= direction_tolerance) {
nb_same_sides++;
}
counter++;
}
// if point is not on the same side of all the boundary elements
// than it is not consider even if the closet master element is
// found
if (nb_same_sides != nb_boundary_elements) {
index = UInt(-1);
}
return index;
}
/* -------------------------------------------------------------------------- */
UInt GeometryUtils::orthogonalProjection(
const Mesh & mesh, const Array<Real> & positions,
const Vector<Real> & slave, const Array<Element> & elements, Real & gap,
Vector<Real> & natural_projection, Vector<Real> & normal,
Matrix<Real> & tangent, Real /*alpha*/, UInt max_iterations,
Real projection_tolerance, Real extension_tolerance) {
UInt index = UInt(-1);
Real min_gap = std::numeric_limits<Real>::max();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt surface_dimension = spatial_dimension - 1;
const auto & contact_group = mesh.getElementGroup("contact_surface");
for (auto && tuple : enumerate(elements)) {
auto & counter = std::get<0>(tuple);
const auto & element = std::get<1>(tuple);
// filter out elements which are not there in the element group
// contact surface created by the surface selector and is stored
// in the mesh or mesh_facet, if a element is not there it
// returnas UInt(-1)
const auto & elements_of_type = contact_group.getElements(element.type);
if (elements_of_type.find(element.element) == UInt(-1)) {
continue;
}
Vector<Real> master(spatial_dimension);
Vector<Real> xi_ele(natural_projection.size());
GeometryUtils::naturalProjection(mesh, positions, element, slave, master,
xi_ele, max_iterations,
projection_tolerance);
Matrix<Real> tangent_ele(surface_dimension, spatial_dimension);
GeometryUtils::covariantBasis(mesh, positions, element, xi_ele,
tangent_ele);
Vector<Real> normal_ele(spatial_dimension);
GeometryUtils::normal(mesh, element, tangent_ele, normal_ele);
// if gap between master projection and slave point is zero, then
// it means that slave point lies on the master element, hence the
// normal from master to slave cannot be computed in that case
auto master_to_slave = slave - master;
Real temp_gap = master_to_slave.norm();
if (temp_gap != 0) {
master_to_slave /= temp_gap;
}
// A alpha parameter is introduced which is 1 in case of explicit
// and -1 in case of implicit, therefor the variation (dot product
// + alpha) should be close to zero (within tolerance) for both
// cases
auto product = master_to_slave.dot(normal_ele);
if (product < 0 and temp_gap <= min_gap and
GeometryUtils::isValidProjection(xi_ele, extension_tolerance)) {
gap = -temp_gap;
min_gap = temp_gap;
index = counter;
natural_projection = xi_ele;
normal = normal_ele;
tangent = tangent_ele;
}
}
return index;
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::realProjection(const Mesh & mesh,
const Array<Real> & positions,
const Vector<Real> & slave,
const Element & element,
const Vector<Real> & normal,
Vector<Real> & projection) {
UInt spatial_dimension = mesh.getSpatialDimension();
const ElementType & type = element.type;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(element.type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, nodes_coord.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
Vector<Real> point(nodes_coord(0));
Real alpha = (slave - point).dot(normal);
projection = slave - alpha * normal;
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::realProjection(const Mesh & mesh,
const Array<Real> & positions,
const Element & element,
const Vector<Real> & natural_coord,
Vector<Real> & projection) {
auto spatial_dimension = mesh.getSpatialDimension();
const auto & type = element.type;
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(element.type);
auto shapes =
ElementClassHelper<_ek_regular>::getN(natural_coord, element.type);
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
mesh.extractNodalValuesFromElement(positions, nodes_coord.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
projection.mul<false>(nodes_coord, shapes);
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::naturalProjection(
const Mesh & mesh, const Array<Real> & positions, const Element & element,
const Vector<Real> & slave_coords, Vector<Real> & master_coords,
Vector<Real> & natural_projection, UInt max_iterations,
Real projection_tolerance) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt surface_dimension = spatial_dimension - 1;
const ElementType & type = element.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, nodes_coord.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
// initial guess
natural_projection.zero();
// obhjective function computed on the natural_guess
Matrix<Real> f(surface_dimension, 1);
// jacobian matrix computed on the natural_guess
Matrix<Real> J(surface_dimension, surface_dimension);
// Jinv = J^{-1}
Matrix<Real> Jinv(surface_dimension, surface_dimension);
// dxi = \xi_{k+1} - \xi_{k} in the iterative process
Matrix<Real> dxi(surface_dimension, 1);
// gradient at natural projection
Matrix<Real> gradient(surface_dimension, spatial_dimension);
// second derivative at natural peojection
Matrix<Real> double_gradient(surface_dimension, surface_dimension);
// second derivative of shape function at natural projection
Matrix<Real> d2nds2(surface_dimension * surface_dimension,
nb_nodes_per_element);
auto compute_double_gradient =
[&d2nds2, &nodes_coord, surface_dimension,
spatial_dimension](UInt & alpha, UInt & beta) {
auto index = alpha * surface_dimension + beta;
Vector<Real> d_alpha_beta(spatial_dimension);
auto d2nds2_transpose = d2nds2.transpose();
Vector<Real> d2nds2_alpha_beta(d2nds2_transpose(index));
d_alpha_beta.mul<false>(nodes_coord, d2nds2_alpha_beta);
return d_alpha_beta;
};
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
auto update_f = [&f, &master_coords, &natural_projection, &nodes_coord,
&slave_coords, &gradient, surface_dimension,
spatial_dimension, type]() {
// compute real coords on natural projection
auto && shapes =
ElementClassHelper<_ek_regular>::getN(natural_projection, type);
master_coords.mul<false>(nodes_coord, shapes);
auto distance = slave_coords - master_coords;
// first derivative of shape function at natural projection
auto && dnds =
ElementClassHelper<_ek_regular>::getDNDS(natural_projection, type);
gradient.mul<false, true>(dnds, nodes_coord);
// gradient transpose at natural projection
Matrix<Real> gradient_transpose(surface_dimension, spatial_dimension);
gradient_transpose = gradient.transpose();
// loop over surface dimensions
for (auto alpha : arange(surface_dimension)) {
Vector<Real> gradient_alpha(gradient_transpose(alpha));
f(alpha, 0) = -2. * gradient_alpha.dot(distance);
}
// compute initial error
auto error = f.norm<L_2>();
return error;
};
auto projection_error = update_f();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
UInt iterations{0};
while (projection_tolerance < projection_error and
iterations < max_iterations) {
// compute covariant components of metric tensor
auto a = GeometryUtils::covariantMetricTensor(gradient);
// computing second derivative at natural projection
d2nds2 =
ElementClassHelper<_ek_regular>::getD2NDS2(natural_projection, type);
// real coord - physical guess
auto distance = slave_coords - master_coords;
// computing Jacobian J
for (auto alpha : arange(surface_dimension)) {
for (auto beta : arange(surface_dimension)) {
auto dgrad_alpha_beta = compute_double_gradient(alpha, beta);
J(alpha, beta) = 2. * (a(alpha, beta) - dgrad_alpha_beta.dot(distance));
}
}
Jinv.inverse(J);
// compute increment
dxi.mul<false, false>(Jinv, f, -1.0);
// update our guess
natural_projection += Vector<Real>(dxi(0));
projection_error = update_f();
iterations++;
}
}
/* -------------------------------------------------------------------------- */
void GeometryUtils::contravariantBasis(const Matrix<Real> & covariant,
Matrix<Real> & contravariant) {
auto inv_A = GeometryUtils::contravariantMetricTensor(covariant);
contravariant.mul<false, false>(inv_A, covariant);
}
/* -------------------------------------------------------------------------- */
Matrix<Real>
GeometryUtils::covariantMetricTensor(const Matrix<Real> & covariant_bases) {
Matrix<Real> A(covariant_bases.rows(), covariant_bases.rows());
A.mul<false, true>(covariant_bases, covariant_bases);
return A;
}
/* -------------------------------------------------------------------------- */
Matrix<Real>
GeometryUtils::contravariantMetricTensor(const Matrix<Real> & covariant_bases) {
auto A = GeometryUtils::covariantMetricTensor(covariant_bases);
auto inv_A = A.inverse();
return inv_A;
}
/* -------------------------------------------------------------------------- */
Matrix<Real> GeometryUtils::covariantCurvatureTensor(
const Mesh & mesh, const Array<Real> & positions, const Element & element,
const Vector<Real> & natural_coord, const Vector<Real> & normal) {
UInt spatial_dimension = mesh.getSpatialDimension();
auto surface_dimension = spatial_dimension - 1;
const ElementType & type = element.type;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt * elem_val = mesh.getConnectivity(type, _not_ghost).storage();
auto && d2nds2 =
ElementClassHelper<_ek_regular>::getD2NDS2(natural_coord, type);
Matrix<Real> coords(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(positions, coords.storage(),
elem_val +
element.element * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
Matrix<Real> curvature(spatial_dimension,
surface_dimension * surface_dimension);
curvature.mul<false, true>(coords, d2nds2);
Matrix<Real> H(surface_dimension, surface_dimension);
UInt i = 0;
for (auto alpha : arange(surface_dimension)) {
for (auto beta : arange(surface_dimension)) {
Vector<Real> temp(curvature(i));
H(alpha, beta) = temp.dot(normal);
i++;
}
}
return H;
}
} // namespace akantu
diff --git a/src/model/contact_mechanics/geometry_utils.hh b/src/model/contact_mechanics/geometry_utils.hh
index 8765aec08..089f42b24 100644
--- a/src/model/contact_mechanics/geometry_utils.hh
+++ b/src/model/contact_mechanics/geometry_utils.hh
@@ -1,146 +1,147 @@
/**
* @file geometry_utils.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Sep 30 2019
- * @date last modification: Mon Sep 30 2019
+ * @date creation: Wed Oct 02 2019
+ * @date last modification: Sat Dec 12 2020
*
* @brief class to compute geometry related quantities
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GEOMETRY_UTILS_HH__
#define __AKANTU_GEOMETRY_UTILS_HH__
namespace akantu {
class GeometryUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the normal on an element (assuming elements is flat)
static void normal(const Mesh & mesh, const Array<Real> & positions,
const Element & element, Vector<Real> & normal,
bool outward = true);
// computes normal at given covariant basis
static void normal(const Mesh & mesh, const Element & element,
Matrix<Real> & covariant_basis, Vector<Real> & normal,
bool outward = true);
/// computes the orthogonal projection on a set of elements and
/// returns natural projection and normal gap and index of element
static UInt
orthogonalProjection(const Mesh & mesh, const Array<Real> & positions,
const Vector<Real> & slave,
const Array<Element> & elements, Real & gap,
Vector<Real> & natural_projection, Vector<Real> & normal,
Real alpha, UInt max_iterations = 100,
Real tolerance = 1e-10, Real extension_tolerance = 1e-5);
/// computes the orthogonal projection on a set of elements and
/// returns natural projection and normal gap and index of element
static UInt orthogonalProjection(
const Mesh & mesh, const Array<Real> & positions,
const Vector<Real> & slave, const Array<Element> & elements, Real & gap,
Vector<Real> & natural_projection, Vector<Real> & normal,
Matrix<Real> & tangent, Real alpha, UInt max_iterations = 100,
Real tolerance = 1e-10, Real extension_tolerance = 1e-5);
/// computes the natural projection on an element
static void
naturalProjection(const Mesh & mesh, const Array<Real> & positions,
const Element & element, const Vector<Real> & slave_coords,
Vector<Real> & master_coords,
Vector<Real> & natural_projection,
UInt max_iterations = 100, Real tolerance = 1e-10);
/// computes the real projection on an element
static void realProjection(const Mesh & mesh, const Array<Real> & positions,
const Vector<Real> & slave,
const Element & element,
const Vector<Real> & normal,
Vector<Real> & projection);
/// computes the real projection from a natural coordinate
static void realProjection(const Mesh & mesh, const Array<Real> & positions,
const Element & element,
const Vector<Real> & natural_coord,
Vector<Real> & projection);
/// computes the covariant basis/ local surface basis/ tangents on projection
/// point
static void covariantBasis(const Mesh & mesh, const Array<Real> & positions,
const Element & element,
Vector<Real> & natural_coord,
Matrix<Real> & basis);
/// computes the covariant basis/ local surface basis/ tangents on projection
/// point
static void covariantBasis(const Mesh & mesh, const Array<Real> & positions,
const Element & element,
const Vector<Real> & normal,
Vector<Real> & natural_coord,
Matrix<Real> & basis);
// computes the curvature on projection
static void curvature(const Mesh & mesh, const Array<Real> & positions,
const Element & element,
const Vector<Real> & natural_coord,
Matrix<Real> & curvature);
/// computes the contravariant basis on projection point
static void contravariantBasis(const Matrix<Real> & covariant,
Matrix<Real> & contravariant);
/// computes metric tesnor with covariant components
static Matrix<Real> covariantMetricTensor(const Matrix<Real> &);
/// computes metric tensor with contravariant components
static Matrix<Real> contravariantMetricTensor(const Matrix<Real> &);
// computes curvature tensor with convariant components
static Matrix<Real>
covariantCurvatureTensor(const Mesh &, const Array<Real> &, const Element &,
const Vector<Real> &, const Vector<Real> &);
/// checks if the element is truly a boundary element or not
inline static bool isBoundaryElement(const Mesh & mesh,
const Element & element);
/// checks if the natural projection is valid for not
inline static bool isValidProjection(const Vector<Real> & projection,
Real extension_tolerance = 1e-5);
};
} // namespace akantu
#include "geometry_utils_inline_impl.cc"
#endif /* __AKANTU_GEOMETRY_UTILS_HH__ */
diff --git a/src/model/contact_mechanics/geometry_utils_inline_impl.cc b/src/model/contact_mechanics/geometry_utils_inline_impl.cc
index d264b66ee..e41d380c2 100644
--- a/src/model/contact_mechanics/geometry_utils_inline_impl.cc
+++ b/src/model/contact_mechanics/geometry_utils_inline_impl.cc
@@ -1,70 +1,101 @@
+/**
+ * @file geometry_utils_inline_impl.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Sun Oct 06 2019
+ * @date last modification: Wed Sep 16 2020
+ *
+ * @brief Geometry utils
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#include "geometry_utils.hh"
#ifndef __AKANTU_GEOMETRY_UTILS_INLINE_IMPL_CC__
#define __AKANTU_GEOMETRY_UTILS_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool GeometryUtils::isBoundaryElement(const Mesh & mesh,
const Element & subelement) {
const auto & element_to_subelement =
mesh.getElementToSubelement(subelement.type)(subelement.element);
// for regular boundary elements when surfaceselector is set to
// physical surfaces, the mesh contains only 1 element attached to a
// boundary subelement
if (element_to_subelement.size() == 1 and
element_to_subelement[0].kind() == _ek_regular) {
return true;
}
// for cohesive interface elements when surfaceSelector is set
// either cohesive surface selector or all surface selector, in this
// case mesh passed is actually mesh_facet and for boundary or
// cohesive interface 2 elements are associated to a subelement
// we want only one regular element attached to the subelement
UInt nb_elements_regular = 0;
UInt nb_elements_cohesive = 0;
for (auto elem : element_to_subelement) {
if (elem == ElementNull)
continue;
if (elem.kind() == _ek_regular)
++nb_elements_regular;
if (elem.kind() == _ek_cohesive)
++nb_elements_cohesive;
}
auto nb_elements = element_to_subelement.size();
if (nb_elements_regular < nb_elements)
return true;
return false;
}
/* -------------------------------------------------------------------------- */
inline bool GeometryUtils::isValidProjection(const Vector<Real> & projection,
Real extension_tolerance) {
UInt nb_xi_inside = 0;
for (auto xi : projection) {
if (xi >= -1.0 - extension_tolerance and xi <= 1.0 + extension_tolerance)
nb_xi_inside++;
}
if (nb_xi_inside == projection.size())
return true;
return false;
}
} //namespace akantu
#endif
diff --git a/src/model/contact_mechanics/resolution.cc b/src/model/contact_mechanics/resolution.cc
index 1a422c603..443388573 100644
--- a/src/model/contact_mechanics/resolution.cc
+++ b/src/model/contact_mechanics/resolution.cc
@@ -1,221 +1,222 @@
/**
* @file resolution.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Jan 7 2019
- * @date last modification: Mon Jan 7 2019
+ * @date creation: Thu Jan 17 2019
+ * @date last modification: Wed Apr 07 2021
*
* @brief Implementation of common part of the contact resolution class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "resolution.hh"
#include "contact_mechanics_model.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Resolution::Resolution(ContactMechanicsModel & model, const ID & id)
: Parsable(ParserType::_contact_resolution, id), id(id),
fem(model.getFEEngine()), model(model) {
AKANTU_DEBUG_IN();
spatial_dimension = model.getMesh().getSpatialDimension();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Resolution::~Resolution() = default;
/* -------------------------------------------------------------------------- */
void Resolution::initialize() {
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("mu", mu, Real(0.), _pat_parsable | _pat_modifiable,
"Friction Coefficient");
registerParam("is_master_deformable", is_master_deformable, bool(false),
_pat_parsable | _pat_readable, "Is master surface deformable");
}
/* -------------------------------------------------------------------------- */
void Resolution::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::string type = getID().substr(getID().find_last_of(':') + 1);
stream << space << "Contact Resolution " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Resolution::assembleInternalForces(GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
this->assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Resolution::assembleInternalForces() {
AKANTU_DEBUG_IN();
for (auto & element : model.getContactElements()) {
auto nb_nodes = element.getNbNodes();
Vector<Real> local_fn(nb_nodes * spatial_dimension);
computeNormalForce(element, local_fn);
Vector<Real> local_ft(nb_nodes * spatial_dimension);
computeTangentialForce(element, local_ft);
Vector<Real> local_fc(nb_nodes * spatial_dimension);
local_fc = local_fn + local_ft;
assembleLocalToGlobalArray(element, local_fn, model.getNormalForce());
assembleLocalToGlobalArray(element, local_ft, model.getTangentialForce());
assembleLocalToGlobalArray(element, local_fc, model.getInternalForce());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Resolution::assembleLocalToGlobalArray(const ContactElement & element,
Vector<Real> & local, Array<Real> & global) {
auto get_connectivity = [&](auto & slave, auto & master) {
Vector<UInt> master_conn =
const_cast<const Mesh &>(model.getMesh()).getConnectivity(master);
Vector<UInt> elem_conn(master_conn.size() + 1);
elem_conn[0] = slave;
for (UInt i = 1; i < elem_conn.size(); ++i) {
elem_conn[i] = master_conn[i - 1];
}
return elem_conn;
};
auto & surface_selector = model.getContactDetector().getSurfaceSelector();
auto & slave_list = surface_selector.getSlaveList();
auto & master_list = surface_selector.getMasterList();
auto connectivity = get_connectivity(element.slave, element.master);
UInt nb_dofs = global.getNbComponent();
UInt nb_nodes = is_master_deformable ? connectivity.size() : 1;
Real alpha = is_master_deformable ? 0.5: 1.;
for (UInt i : arange(nb_nodes)) {
UInt n = connectivity[i];
auto slave_result = std::find(slave_list.begin(), slave_list.end(), n);
auto master_result = std::find(master_list.begin(), master_list.end(), n);
for (UInt j : arange(nb_dofs)) {
UInt offset_node = n * nb_dofs + j;
global[offset_node] += alpha*local[i * nb_dofs + j];
}
}
}
/* -------------------------------------------------------------------------- */
void Resolution::assembleStiffnessMatrix(GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
auto & global_stiffness =
const_cast<SparseMatrix &>(model.getDOFManager().getMatrix("K"));
for (auto & element : model.getContactElements()) {
auto nb_nodes = element.getNbNodes();
Matrix<Real> local_kn(nb_nodes * spatial_dimension, nb_nodes * spatial_dimension);
computeNormalModuli(element, local_kn);
assembleLocalToGlobalMatrix(element, local_kn, global_stiffness);
Matrix<Real> local_kt(nb_nodes * spatial_dimension, nb_nodes * spatial_dimension);
computeTangentialModuli(element, local_kt);
assembleLocalToGlobalMatrix(element, local_kt, global_stiffness);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Resolution::assembleLocalToGlobalMatrix(const ContactElement & element,
const Matrix<Real> & local, SparseMatrix & global) {
auto get_connectivity = [&](auto & slave, auto & master) {
Vector<UInt> master_conn =
const_cast<const Mesh &>(model.getMesh()).getConnectivity(master);
Vector<UInt> elem_conn(master_conn.size() + 1);
elem_conn[0] = slave;
for (UInt i = 1; i < elem_conn.size(); ++i) {
elem_conn[i] = master_conn[i - 1];
}
return elem_conn;
};
auto connectivity = get_connectivity(element.slave, element.master);
auto nb_dofs = spatial_dimension;
UInt nb_nodes = is_master_deformable ? connectivity.size() : 1;
UInt total_nb_dofs = nb_dofs * nb_nodes;
std::vector<UInt> equations;
for (UInt i : arange(connectivity.size())) {
UInt conn = connectivity[i];
for (UInt j : arange(nb_dofs)) {
equations.push_back(conn * nb_dofs + j);
}
}
for (UInt i : arange(total_nb_dofs)) {
UInt row = equations[i];
for (UInt j : arange(total_nb_dofs)) {
UInt col = equations[j];
global.add(row, col, local(i, j));
}
}
}
/* -------------------------------------------------------------------------- */
void Resolution::beforeSolveStep() {}
/* -------------------------------------------------------------------------- */
void Resolution::afterSolveStep(__attribute__((unused)) bool converged) {}
} // namespace akantu
diff --git a/src/model/contact_mechanics/resolution.hh b/src/model/contact_mechanics/resolution.hh
index c746ab842..ab5e5e42d 100644
--- a/src/model/contact_mechanics/resolution.hh
+++ b/src/model/contact_mechanics/resolution.hh
@@ -1,234 +1,235 @@
/**
* @file resolution.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Jan 7 2019
- * @date last modification: Mon Jan 7 2019
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Apr 07 2021
*
* @brief Mother class for all contact resolutions
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "parsable.hh"
#include "parser.hh"
#include "fe_engine.hh"
#include "contact_element.hh"
#include "resolution_utils.hh"
#include "geometry_utils.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RESOLUTION_HH__
#define __AKANTU_RESOLUTION_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class ContactMechanicsModel;
} // namespace akantu
namespace akantu {
/**
* Interface of all contact resolutions
* Prerequisites for a new resolution
* - inherit from this class
* - implement the following methods:
* \code
*
* virtual void computeNormalForce();
* virtual void computeTangentialForce();
* virtual void computeNormalModuli();
* virtual void computeTangentialModuli();
*
* \endcode
*
*/
class Resolution : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
/// instantiate contact resolution with defaults
Resolution(ContactMechanicsModel & model, const ID & id = "");
/// Destructor
~Resolution() override;
protected:
void initialize();
/// computes coordinates of a given element
void computeCoordinates(const Element & , Matrix<Real> &);
/* ------------------------------------------------------------------------ */
/* Functions that resolutions should reimplement for force */
/* ------------------------------------------------------------------------ */
public:
/// computes the force vector due to normal traction
virtual void computeNormalForce(__attribute__((unused)) const ContactElement &,
__attribute__((unused)) Vector<Real> &) {
AKANTU_TO_IMPLEMENT();
}
/// computes the tangential force vector due to frictional traction
virtual void computeTangentialForce(__attribute__((unused)) const ContactElement &,
__attribute__((unused)) Vector<Real> &) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Functions that resolutions should reimplement for stiffness */
/* ------------------------------------------------------------------------ */
public:
/// compute the normal moduli due to normal traction
virtual void computeNormalModuli(__attribute__((unused)) const ContactElement &,
__attribute__((unused)) Matrix<Real> & ) {
AKANTU_TO_IMPLEMENT();
}
/// compute the tangent moduli due to tangential traction
virtual void computeTangentialModuli(__attribute__((unused)) const ContactElement &,
__attribute__((unused)) Matrix<Real> & ) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// assemble the residual for this resolution
void assembleInternalForces(GhostType ghost_type);
/// assemble the stiffness matrix for this resolution
void assembleStiffnessMatrix(GhostType ghost_type);
private:
/// assemble the residual for this resolution
void assembleInternalForces();
/// assemble the local array to global array for a contact element
void assembleLocalToGlobalArray(const ContactElement & , Vector<Real> & , Array<Real> & );
/// assemble the local stiffness to global stiffness for a contact element
void assembleLocalToGlobalMatrix(const ContactElement &, const Matrix<Real> &, SparseMatrix &);
public:
virtual void beforeSolveStep();
virtual void afterSolveStep(bool converged = true);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(ID, id, const ID &);
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// friction coefficient : mu
Real mu;
/// spatial dimension
UInt spatial_dimension;
/// is master surface deformable
bool is_master_deformable;
/// Link to the fe engine object in the model
FEEngine & fem;
/// resolution name
std::string name;
/// model to which the resolution belong
ContactMechanicsModel & model;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Resolution & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
using ResolutionFactory =
Factory<Resolution, ID, UInt, const ID &, ContactMechanicsModel &, const ID &>;
/// macaulay bracket to convert positive gap to zero
template <typename T>
T macaulay(T var) {return var < 0 ? 0 : var; }
template <typename T>
T heaviside(T var) {return var < 0 ? 0 : 1.0; }
} // namespace akantu
#define INSTANTIATE_RESOLUTION_ONLY(res_name) \
class res_name
#define RESOLUTION_DEFAULT_PER_DIM_ALLOCATOR(id, res_name) \
[](UInt dim, const ID &, ContactMechanicsModel & model, \
const ID & id) -> std::unique_ptr<Resolution> { \
switch (dim) { \
case 1: \
return std::make_unique<res_name>(model, id); \
case 2: \
return std::make_unique<res_name>(model, id); \
case 3: \
return std::make_unique<res_name>(model, id); \
default: \
AKANTU_EXCEPTION("The dimension " \
<< dim << "is not a valid dimension for the contact resolution " \
<< #id); \
} \
}
#define INSTANTIATE_RESOLUTION(id, res_name) \
INSTANTIATE_RESOLUTION_ONLY(res_name); \
static bool resolution_is_alocated_##id[[gnu::unused]] = \
ResolutionFactory::getInstance().registerAllocator( \
#id, RESOLUTION_DEFAULT_PER_DIM_ALLOCATOR(id, res_name))
#endif /* __AKANTU_RESOLUTION_HH__ */
diff --git a/src/model/contact_mechanics/resolution_utils.cc b/src/model/contact_mechanics/resolution_utils.cc
index b32a6302d..528318aa4 100644
--- a/src/model/contact_mechanics/resolution_utils.cc
+++ b/src/model/contact_mechanics/resolution_utils.cc
@@ -1,70 +1,71 @@
/**
* @file resolution_utils.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Mmay 20 2019
- * @date last modification: Mon May 20 2019
+ * @date creation: Mon May 20 2019
+ * @date last modification: Sun Jun 06 2021
*
* @brief Implementation of various utilities neede for resolution class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "resolution_utils.hh"
#include "element_class_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void ResolutionUtils::computeShapeFunctionMatric(
const ContactElement & element, const Vector<Real> & projection,
Matrix<Real> & shape_matric) {
shape_matric.zero();
const ElementType & type = element.master.type;
auto surface_dimension = Mesh::getSpatialDimension(type);
auto spatial_dimension = surface_dimension + 1;
UInt nb_nodes_per_contact = element.getNbNodes();
AKANTU_DEBUG_ASSERT(spatial_dimension == shape_matric.rows() &&
spatial_dimension * nb_nodes_per_contact ==
shape_matric.cols(),
"Shape Matric dimensions are not correct");
auto && shapes =
ElementClassHelper<_ek_regular>::getN(projection, type);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
shape_matric(j, i * spatial_dimension + j) = 1;
continue;
}
shape_matric(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
}
} // namespace akantu
diff --git a/src/model/contact_mechanics/resolution_utils.hh b/src/model/contact_mechanics/resolution_utils.hh
index 26fa869b5..ba2a89101 100644
--- a/src/model/contact_mechanics/resolution_utils.hh
+++ b/src/model/contact_mechanics/resolution_utils.hh
@@ -1,62 +1,63 @@
/**
* @file resolution_utils.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
* @date creation: Mon May 20 2019
- * @date last modification: Mon May 20 2019
+ * @date last modification: Sun Jun 06 2021
*
* @brief All resolution utils necessary for various tasks
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "contact_mechanics_model.hh"
#include "contact_element.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RESOLUTION_UTILS_HH__
#define __AKANTU_RESOLUTION_UTILS_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class ResolutionUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the shape function matric for the contact element (@f$A
/// @f$) where row is equal to spatial dimension and cols is equal
/// to spatial dimension times number of nodes in contact element
static void computeShapeFunctionMatric(const ContactElement &,
const Vector<Real> &,
Matrix<Real> &);
};
} // namespace akantu
#endif /* __AKANTU_RESOLUTION_UTILS_HH__ */
diff --git a/src/model/contact_mechanics/resolutions/resolution_penalty.cc b/src/model/contact_mechanics/resolutions/resolution_penalty.cc
index 0c952233a..3c4e0bc86 100644
--- a/src/model/contact_mechanics/resolutions/resolution_penalty.cc
+++ b/src/model/contact_mechanics/resolutions/resolution_penalty.cc
@@ -1,839 +1,840 @@
/**
* @file resolution_penalty.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Jan 7 2019
- * @date last modification: Mon Jan 7 2019
+ * @date creation: Thu Jan 17 2019
+ * @date last modification: Wed Jun 09 2021
*
* @brief Specialization of the resolution class for the penalty method
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "resolution_penalty.hh"
#include "element_class_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ResolutionPenalty::ResolutionPenalty(ContactMechanicsModel & model,
const ID & id)
: Resolution(model, id) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::initialize() {
this->registerParam("epsilon_n", epsilon_n, Real(0.),
_pat_parsable | _pat_modifiable,
"Normal penalty parameter");
this->registerParam("epsilon_t", epsilon_t, Real(0.),
_pat_parsable | _pat_modifiable,
"Tangential penalty parameter");
}
/* -------------------------------------------------------------------------- */
Real ResolutionPenalty::computeNormalTraction(Real & gap) {
return epsilon_n * macaulay(gap);
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeNormalForce(const ContactElement & element,
Vector<Real> & force) {
force.zero();
auto & gaps = model.getGaps();
auto & projections = model.getProjections();
auto & normals = model.getNormals();
auto surface_dimension = spatial_dimension - 1;
Real gap(gaps.begin()[element.slave]);
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_area = const_cast<Array<Real> &>(model.getNodalArea());
// compute normal traction
Real p_n = computeNormalTraction(gap);
p_n *= nodal_area[element.slave];
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> shape_matric(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
ResolutionUtils::computeShapeFunctionMatric(element, projection,
shape_matric);
force.mul<true>(shape_matric, normal, p_n);
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeTangentialForce(const ContactElement & element,
Vector<Real> & force) {
if (mu == 0)
return;
force.zero();
UInt surface_dimension = spatial_dimension - 1;
// compute covariant basis
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
// check for no-contact to contact condition
// need a better way to check if new node added is not presnt in the
// previous master elemets
auto & previous_master_elements = model.getPreviousMasterElements();
if (element.slave >= previous_master_elements.size())
return;
auto & previous_element = previous_master_elements[element.slave];
if (previous_element.type == _not_defined)
return;
// compute tangential traction using return map algorithm
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
this->computeTangentialTraction(element, covariant_basis,
tangential_traction);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> shape_matric(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
ResolutionUtils::computeShapeFunctionMatric(element, projection,
shape_matric);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
auto & nodal_area = const_cast<Array<Real> &>(model.getNodalArea());
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
for (auto && values2 : enumerate(tangential_traction)) {
auto & beta = std::get<0>(values2);
auto & traction_beta = std::get<1>(values2);
Vector<Real> tmp(force.size());
tmp.mul<true>(shape_matric, tangent_alpha, traction_beta);
tmp *=
contravariant_metric_tensor(alpha, beta) * nodal_area[element.slave];
force += tmp;
}
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction_tangential) {
UInt surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
auto & gap = gaps.begin()[element.slave];
// Return map algorithm is employed
// compute trial traction
Vector<Real> traction_trial(surface_dimension);
this->computeTrialTangentialTraction(element, covariant_basis,
traction_trial);
// compute norm of trial traction
Real traction_trial_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto i : arange(surface_dimension)) {
for (auto j : arange(surface_dimension)) {
traction_trial_norm += traction_trial[i] * traction_trial[j] *
contravariant_metric_tensor(i, j);
}
}
traction_trial_norm = sqrt(traction_trial_norm);
// check stick or slip condition
auto & contact_state = model.getContactState();
auto & state = contact_state.begin()[element.slave];
Real p_n = computeNormalTraction(gap);
bool stick = (traction_trial_norm <= mu * p_n);
if (stick) {
state = ContactState::_stick;
computeStickTangentialTraction(element, traction_trial,
traction_tangential);
} else {
state = ContactState::_slip;
computeSlipTangentialTraction(element, covariant_basis, traction_trial,
traction_tangential);
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeTrialTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction) {
UInt surface_dimension = spatial_dimension - 1;
auto & projections = model.getProjections();
Vector<Real> current_projection(
projections.begin(surface_dimension)[element.slave]);
auto & previous_projections = model.getPreviousProjections();
Vector<Real> previous_projection(
previous_projections.begin(surface_dimension)[element.slave]);
// method from Laursen et. al.
/*auto covariant_metric_tensor =
GeometryUtils::covariantMetricTensor(covariant_basis); auto
increment_projection = current_projection - previous_projection;
traction.mul<false>(covariant_metric_tensor, increment_projection, epsilon_t);
auto & previous_tangential_tractions = model.getPreviousTangentialTractions();
Vector<Real>
previous_traction(previous_tangential_tractions.begin(surface_dimension)[element.slave]);
traction = previous_traction + traction;*/
// method from Schweizerhof
auto covariant_metric_tensor =
GeometryUtils::covariantMetricTensor(covariant_basis);
auto & previous_tangential_tractions = model.getPreviousTangentialTractions();
Vector<Real> previous_traction(
previous_tangential_tractions.begin(surface_dimension)[element.slave]);
auto & previous_tangents = model.getPreviousTangents();
Matrix<Real> previous_covariant_basis(previous_tangents.begin(
surface_dimension, spatial_dimension)[element.slave]);
auto previous_contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(previous_covariant_basis);
auto current_tangent = covariant_basis.transpose();
auto previous_tangent = previous_covariant_basis.transpose();
for (auto alpha : arange(surface_dimension)) {
Vector<Real> tangent_alpha(current_tangent(alpha));
for (auto gamma : arange(surface_dimension)) {
for (auto beta : arange(surface_dimension)) {
Vector<Real> tangent_beta(previous_tangent(beta));
auto t_alpha_t_beta = tangent_beta.dot(tangent_alpha);
traction[alpha] += previous_traction[gamma] *
previous_contravariant_metric_tensor(gamma, beta) *
t_alpha_t_beta;
}
}
}
auto & previous_master_elements = model.getPreviousMasterElements();
auto & previous_element = previous_master_elements[element.slave];
Vector<Real> previous_real_projection(spatial_dimension);
GeometryUtils::realProjection(
model.getMesh(), model.getContactDetector().getPositions(),
previous_element, previous_projection, previous_real_projection);
Vector<Real> current_real_projection(spatial_dimension);
GeometryUtils::realProjection(
model.getMesh(), model.getContactDetector().getPositions(),
element.master, current_projection, current_real_projection);
auto increment_real = current_real_projection - previous_real_projection;
Vector<Real> increment_xi(surface_dimension);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// increment in natural coordinate
for (auto beta : arange(surface_dimension)) {
for (auto gamma : arange(surface_dimension)) {
auto temp = increment_real.dot(current_tangent(gamma));
temp *= contravariant_metric_tensor(beta, gamma);
increment_xi[beta] += temp;
}
}
Vector<Real> temp(surface_dimension);
temp.mul<false>(covariant_metric_tensor, increment_xi, epsilon_t);
traction -= temp;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeStickTangentialTraction(
const ContactElement & /*element*/, Vector<Real> & traction_trial,
Vector<Real> & traction_tangential) {
traction_tangential = traction_trial;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeSlipTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction_trial, Vector<Real> & traction_tangential) {
UInt surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
auto & gap = gaps.begin()[element.slave];
// compute norm of trial traction
Real traction_trial_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto alpha : arange(surface_dimension)) {
for (auto beta : arange(surface_dimension)) {
traction_trial_norm += traction_trial[alpha] * traction_trial[beta] *
contravariant_metric_tensor(alpha, beta);
}
}
traction_trial_norm = sqrt(traction_trial_norm);
auto slip_direction = traction_trial;
slip_direction /= traction_trial_norm;
Real p_n = computeNormalTraction(gap);
traction_tangential = slip_direction;
traction_tangential *= mu * p_n;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeNormalModuli(const ContactElement & element,
Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
Real gap(gaps.begin()[element.slave]);
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// construct the main part of normal matrix
Matrix<Real> k_main(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
Matrix<Real> mat_n(normal.storage(), normal.size(), 1.);
n_outer_n.mul<false, true>(mat_n, mat_n);
Matrix<Real> tmp(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(n_outer_n, A);
k_main.mul<true, false>(A, tmp);
k_main *= epsilon_n * heaviside(gap) * nodal_area;
// construct the rotational part of the normal matrix
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
// consists of 2 rotational parts
Matrix<Real> k_rot1(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_rot2(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent = std::get<1>(values1);
Matrix<Real> n_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t(tangent.storage(), tangent.size(), 1.);
n_outer_t.mul<false, true>(mat_n, mat_t);
Matrix<Real> t_outer_n(spatial_dimension, spatial_dimension);
t_outer_n.mul<false, true>(mat_t, mat_n);
for (auto && values2 : enumerate(shape_derivatives.transpose())) {
auto & beta = std::get<0>(values2);
auto & dnds = std::get<1>(values2);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(n_outer_t, A);
tmp1.mul<true, false>(Aj, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_rot1 += tmp1;
tmp.mul<false, false>(t_outer_n, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_rot2 += tmp1;
}
}
k_rot1 *= -epsilon_n * heaviside(gap) * gap * nodal_area;
k_rot2 *= -epsilon_n * heaviside(gap) * gap * nodal_area;
stiffness += k_main + k_rot1 + k_rot2;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeTangentialModuli(const ContactElement & element,
Matrix<Real> & stiffness) {
if (mu == 0) {
return;
}
stiffness.zero();
auto & contact_state = model.getContactState();
auto state = contact_state.begin()[element.slave];
switch (state) {
case ContactState::_stick: {
computeStickModuli(element, stiffness);
break;
}
case ContactState::_slip: {
computeSlipModuli(element, stiffness);
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeStickModuli(const ContactElement & element,
Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
// tangents should have been calculated in normal modulii
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// construct 1st part of the stick modulii
Matrix<Real> k_main(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t_alpha(tangent_alpha.storage(), tangent_alpha.size(), 1.);
for (auto && values2 : enumerate(covariant_basis.transpose())) {
auto & beta = std::get<0>(values2);
auto & tangent_beta = std::get<1>(values2);
Matrix<Real> mat_t_beta(tangent_beta.storage(), tangent_beta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_alpha, mat_t_beta);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_main += tmp1;
}
}
k_main *= -epsilon_t;
// construct 2nd part of the stick modulii
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
Matrix<Real> k_second(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto alpha : arange(surface_dimension)) {
Matrix<Real> k_sum(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(shape_derivatives.transpose())) {
auto & beta = std::get<0>(values1);
auto & dnds = std::get<1>(values1);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
for (auto && values2 : enumerate(covariant_basis.transpose())) {
auto & gamma = std::get<0>(values2);
auto & tangent_gamma = std::get<1>(values2);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t_gamma(tangent_gamma.storage(), tangent_gamma.size(),
1.);
for (auto && values3 : enumerate(covariant_basis.transpose())) {
auto & theta = std::get<0>(values3);
auto & tangent_theta = std::get<1>(values3);
Matrix<Real> mat_t_theta(tangent_theta.storage(),
tangent_theta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_gamma, mat_t_theta);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_t, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, theta) *
contravariant_metric_tensor(beta, gamma);
Matrix<Real> tmp2(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp3(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp2.mul<false, false>(t_outer_t, A);
tmp3.mul<true, false>(Aj, tmp2);
tmp3 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
k_sum += tmp1 + tmp3;
}
}
}
k_second += tangential_traction[alpha] * k_sum;
}
stiffness += k_main * nodal_area - k_second * nodal_area;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::computeSlipModuli(const ContactElement & element,
Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
Real gap(gaps.begin()[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
// compute normal traction
Real p_n = computeNormalTraction(gap);
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
// restructure normal as a matrix for an outer product
Matrix<Real> mat_n(normal.storage(), normal.size(), 1.);
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
// tangents should have been calculated in normal modulii
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
// compute norm of trial traction
Real traction_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto i : arange(surface_dimension)) {
for (auto j : arange(surface_dimension)) {
traction_norm += tangential_traction[i] * tangential_traction[j] *
contravariant_metric_tensor(i, j);
}
}
traction_norm = sqrt(traction_norm);
// construct four parts of stick modulii (eq 107,107a-c)
Matrix<Real> k_first(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_second(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_third(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_fourth(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
Matrix<Real> mat_t_alpha(tangent_alpha.storage(), tangent_alpha.size(), 1.);
Matrix<Real> t_outer_n(spatial_dimension, spatial_dimension);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
for (auto && values2 :
zip(arange(surface_dimension), covariant_basis.transpose(),
shape_derivatives.transpose())) {
auto & beta = std::get<0>(values2);
auto & tangent_beta = std::get<1>(values2);
auto & dnds = std::get<2>(values2);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
// eq 107
Matrix<Real> mat_t_beta(tangent_beta.storage(), tangent_beta.size(), 1.);
t_outer_n.mul<false, true>(mat_t_beta, mat_n);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_n, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_n * mu * tangential_traction[alpha] *
contravariant_metric_tensor(alpha, beta);
tmp1 /= traction_norm;
k_first += tmp1 * nodal_area;
// eq 107a
t_outer_t.mul<false, true>(mat_t_alpha, mat_t_beta);
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_t * mu * p_n * contravariant_metric_tensor(alpha, beta);
tmp1 /= traction_norm;
k_second += tmp1 * nodal_area;
for (auto && values3 : enumerate(covariant_basis.transpose())) {
auto & gamma = std::get<0>(values3);
auto & tangent_gamma = std::get<1>(values3);
Matrix<Real> mat_t_gamma(tangent_gamma.storage(), tangent_gamma.size(),
1.);
for (auto && values4 : enumerate(covariant_basis.transpose())) {
auto & theta = std::get<0>(values4);
auto & tangent_theta = std::get<1>(values4);
Matrix<Real> mat_t_theta(tangent_theta.storage(),
tangent_theta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_gamma, mat_t_theta);
// eq 107b
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_t * mu * p_n * tangential_traction[alpha] *
tangential_traction[beta];
tmp1 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
tmp1 /= pow(traction_norm, 3);
k_third += tmp1 * nodal_area;
// eq 107c
tmp.mul<false, false>(t_outer_t, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, theta) *
contravariant_metric_tensor(beta, gamma);
tmp1 *= mu * p_n * tangential_traction[alpha];
tmp1 /= traction_norm;
Matrix<Real> tmp2(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp3(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp2.mul<false, false>(t_outer_t, A);
tmp3.mul<true, false>(Aj, tmp2);
tmp3 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
tmp3 *= mu * p_n * tangential_traction[alpha];
tmp3 /= traction_norm;
k_fourth += (tmp1 + tmp3) * nodal_area;
}
}
}
}
stiffness += k_third + k_fourth - k_first - k_second;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::beforeSolveStep() {}
/* -------------------------------------------------------------------------- */
void ResolutionPenalty::afterSolveStep(__attribute__((unused)) bool converged) {}
INSTANTIATE_RESOLUTION(penalty_linear, ResolutionPenalty);
} // namespace akantu
diff --git a/src/model/contact_mechanics/resolutions/resolution_penalty.hh b/src/model/contact_mechanics/resolutions/resolution_penalty.hh
index 61f7ba197..bb8e0d91d 100644
--- a/src/model/contact_mechanics/resolutions/resolution_penalty.hh
+++ b/src/model/contact_mechanics/resolutions/resolution_penalty.hh
@@ -1,122 +1,123 @@
/**
- * @file contact_resolution_penalty.hh
+ * @file resolution_penalty.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Wed Jun 09 2021
*
* @brief Linear Penalty Resolution for Contact Mechanics Model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "resolution.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RESOLUTION_PENALTY_HH__
#define __AKANTU_RESOLUTION_PENALTY_HH__
namespace akantu {
class ResolutionPenalty : public Resolution {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ResolutionPenalty(ContactMechanicsModel & model, const ID & id = "");
~ResolutionPenalty() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the resolution
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods for stiffness computation */
/* ------------------------------------------------------------------------ */
protected:
/// local computaion of stiffness matrix due to stick state
void computeStickModuli(const ContactElement &, Matrix<Real> &);
/// local computation of stiffness matrix due to slip state
void computeSlipModuli(const ContactElement &, Matrix<Real> &);
public:
/// local computation of tangent moduli due to normal traction
void computeNormalModuli(const ContactElement &, Matrix<Real> &) override;
/// local computation of tangent moduli due to tangential traction
void computeTangentialModuli(const ContactElement &, Matrix<Real> &) override;
/* ------------------------------------------------------------------------ */
/* Methods for force computation */
/* ------------------------------------------------------------------------ */
public:
/// local computation of normal force due to normal contact
void computeNormalForce(const ContactElement &, Vector<Real> &) override;
/// local computation of tangential force due to frictional traction
void computeTangentialForce(const ContactElement &, Vector<Real> &) override;
protected:
/// local computation of normal traction due to penetration
Real computeNormalTraction(Real &);
/// local computation of trial tangential traction due to friction
void computeTrialTangentialTraction(const ContactElement &,
const Matrix<Real> &, Vector<Real> &);
/// local computation of tangential traction due to stick
void computeStickTangentialTraction(const ContactElement &, Vector<Real> &,
Vector<Real> &);
/// local computation of tangential traction due to slip
void computeSlipTangentialTraction(const ContactElement &,
const Matrix<Real> &, Vector<Real> &,
Vector<Real> &);
/// local computation of tangential traction due to friction
void computeTangentialTraction(const ContactElement &, const Matrix<Real> &,
Vector<Real> &);
public:
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// penalty parameter for normal traction
Real epsilon_n;
/// penalty parameter for tangential traction
Real epsilon_t;
};
} // namespace akantu
#endif /* __AKANTU_RESOLUTION_PENALTY_HH__ */
diff --git a/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc b/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc
index 615d71fab..95f64dc3e 100644
--- a/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc
+++ b/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.cc
@@ -1,832 +1,833 @@
/**
* @file resolution_penalty_quadratic.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Aug 2 2020
- * @date last modification: Sun Aug 2 2020
+ * @date creation: Thu Jan 17 2019
+ * @date last modification: Wed Jun 09 2021
*
* @brief Specialization of the resolution class for the quadratic penalty
* method
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "resolution_penalty_quadratic.hh"
#include "element_class_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ResolutionPenaltyQuadratic::ResolutionPenaltyQuadratic(
ContactMechanicsModel & model, const ID & id)
: Parent(model, id) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::initialize() {}
/* -------------------------------------------------------------------------- */
Real ResolutionPenaltyQuadratic::computeNormalTraction(Real & gap) {
return epsilon_n * (macaulay(gap) * macaulay(gap) + macaulay(gap));
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeNormalForce(
const ContactElement & element, Vector<Real> & force) {
force.zero();
auto & gaps = model.getGaps();
auto & projections = model.getProjections();
auto & normals = model.getNormals();
auto surface_dimension = spatial_dimension - 1;
Real gap(gaps.begin()[element.slave]);
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_area = const_cast<Array<Real> &>(model.getNodalArea());
// compute normal traction
Real p_n = computeNormalTraction(gap);
p_n *= nodal_area[element.slave];
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> shape_matric(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
ResolutionUtils::computeShapeFunctionMatric(element, projection,
shape_matric);
force.mul<true>(shape_matric, normal, p_n);
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeTangentialForce(
const ContactElement & element, Vector<Real> & force) {
if (mu == 0)
return;
force.zero();
UInt surface_dimension = spatial_dimension - 1;
// compute tangents
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
// check for no-contact to contact condition
// need a better way to check if new node added is not presnt in the
// previous master elemets
auto & previous_master_elements = model.getPreviousMasterElements();
if (element.slave >= previous_master_elements.size())
return;
auto & previous_element = previous_master_elements[element.slave];
if (previous_element.type == _not_defined)
return;
// compute tangential traction using return map algorithm
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
this->computeTangentialTraction(element, covariant_basis,
tangential_traction);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> shape_matric(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
ResolutionUtils::computeShapeFunctionMatric(element, projection,
shape_matric);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
auto & nodal_area = const_cast<Array<Real> &>(model.getNodalArea());
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
for (auto && values2 : enumerate(tangential_traction)) {
auto & beta = std::get<0>(values2);
auto & traction_beta = std::get<1>(values2);
Vector<Real> tmp(force.size());
tmp.mul<true>(shape_matric, tangent_alpha, traction_beta);
tmp *=
contravariant_metric_tensor(alpha, beta) * nodal_area[element.slave];
force += tmp;
}
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction_tangential) {
UInt surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
auto & gap = gaps.begin()[element.slave];
// Return map algorithm is employed
// compute trial traction
Vector<Real> traction_trial(surface_dimension);
this->computeTrialTangentialTraction(element, covariant_basis,
traction_trial);
// compute norm of trial traction
Real traction_trial_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto i : arange(surface_dimension)) {
for (auto j : arange(surface_dimension)) {
traction_trial_norm += traction_trial[i] * traction_trial[j] *
contravariant_metric_tensor(i, j);
}
}
traction_trial_norm = sqrt(traction_trial_norm);
// check stick or slip condition
auto & contact_state = model.getContactState();
auto & state = contact_state.begin()[element.slave];
Real p_n = computeNormalTraction(gap);
bool stick = (traction_trial_norm <= mu * p_n) ? true : false;
if (stick) {
state = ContactState::_stick;
computeStickTangentialTraction(element, traction_trial,
traction_tangential);
} else {
state = ContactState::_slip;
computeSlipTangentialTraction(element, covariant_basis, traction_trial,
traction_tangential);
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeTrialTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction) {
UInt surface_dimension = spatial_dimension - 1;
auto & projections = model.getProjections();
Vector<Real> current_projection(
projections.begin(surface_dimension)[element.slave]);
auto & previous_projections = model.getPreviousProjections();
Vector<Real> previous_projection(
previous_projections.begin(surface_dimension)[element.slave]);
// method from Laursen et. al.
/*auto covariant_metric_tensor =
GeometryUtils::covariantMetricTensor(covariant_basis); auto
increment_projection = current_projection - previous_projection;
traction.mul<false>(covariant_metric_tensor, increment_projection, epsilon_t);
auto & previous_tangential_tractions = model.getPreviousTangentialTractions();
Vector<Real>
previous_traction(previous_tangential_tractions.begin(surface_dimension)[element.slave]);
traction = previous_traction + traction;*/
// method from Schweizerhof
auto covariant_metric_tensor =
GeometryUtils::covariantMetricTensor(covariant_basis);
auto & previous_tangential_tractions = model.getPreviousTangentialTractions();
Vector<Real> previous_traction(
previous_tangential_tractions.begin(surface_dimension)[element.slave]);
auto & previous_tangents = model.getPreviousTangents();
Matrix<Real> previous_covariant_basis(previous_tangents.begin(
surface_dimension, spatial_dimension)[element.slave]);
auto previous_contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(previous_covariant_basis);
auto current_tangent = covariant_basis.transpose();
auto previous_tangent = previous_covariant_basis.transpose();
for (auto alpha : arange(surface_dimension)) {
Vector<Real> tangent_alpha(current_tangent(alpha));
for (auto gamma : arange(surface_dimension)) {
for (auto beta : arange(surface_dimension)) {
Vector<Real> tangent_beta(previous_tangent(beta));
auto t_alpha_t_beta = tangent_beta.dot(tangent_alpha);
traction[alpha] += previous_traction[gamma] *
previous_contravariant_metric_tensor(gamma, beta) *
t_alpha_t_beta;
}
}
}
auto & previous_master_elements = model.getPreviousMasterElements();
auto & previous_element = previous_master_elements[element.slave];
Vector<Real> previous_real_projection(spatial_dimension);
GeometryUtils::realProjection(
model.getMesh(), model.getContactDetector().getPositions(),
previous_element, previous_projection, previous_real_projection);
Vector<Real> current_real_projection(spatial_dimension);
GeometryUtils::realProjection(
model.getMesh(), model.getContactDetector().getPositions(),
element.master, current_projection, current_real_projection);
auto increment_real = current_real_projection - previous_real_projection;
Vector<Real> increment_xi(surface_dimension);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// increment in natural coordinate
for (auto beta : arange(surface_dimension)) {
for (auto gamma : arange(surface_dimension)) {
auto temp = increment_real.dot(current_tangent(gamma));
temp *= contravariant_metric_tensor(beta, gamma);
increment_xi[beta] += temp;
}
}
Vector<Real> temp(surface_dimension);
temp.mul<false>(covariant_metric_tensor, increment_xi, epsilon_t);
traction -= temp;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeStickTangentialTraction(
const ContactElement & /*element*/, Vector<Real> & traction_trial,
Vector<Real> & traction_tangential) {
traction_tangential = traction_trial;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeSlipTangentialTraction(
const ContactElement & element, const Matrix<Real> & covariant_basis,
Vector<Real> & traction_trial, Vector<Real> & traction_tangential) {
UInt surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
auto & gap = gaps.begin()[element.slave];
// compute norm of trial traction
Real traction_trial_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto i : arange(surface_dimension)) {
for (auto j : arange(surface_dimension)) {
traction_trial_norm += traction_trial[i] * traction_trial[j] *
contravariant_metric_tensor(i, j);
}
}
traction_trial_norm = sqrt(traction_trial_norm);
auto slip_direction = traction_trial;
slip_direction /= traction_trial_norm;
Real p_n = computeNormalTraction(gap);
traction_tangential = slip_direction;
traction_tangential *= mu * p_n;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeNormalModuli(
const ContactElement & element, Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
Real gap(gaps.begin()[element.slave]);
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// construct the main part of normal matrix
Matrix<Real> k_main(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
Matrix<Real> mat_n(normal.storage(), normal.size(), 1.);
n_outer_n.mul<false, true>(mat_n, mat_n);
Matrix<Real> tmp(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(n_outer_n, A);
k_main.mul<true, false>(A, tmp);
k_main *= epsilon_n * heaviside(gap) * (2 * gap + 1) * nodal_area;
// construct the rotational part of the normal matrix
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
// consists of 2 rotational parts
Matrix<Real> k_rot1(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_rot2(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent = std::get<1>(values1);
Matrix<Real> n_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t(tangent.storage(), tangent.size(), 1.);
n_outer_t.mul<false, true>(mat_n, mat_t);
Matrix<Real> t_outer_n(spatial_dimension, spatial_dimension);
t_outer_n.mul<false, true>(mat_t, mat_n);
for (auto && values2 : enumerate(shape_derivatives.transpose())) {
auto & beta = std::get<0>(values2);
auto & dnds = std::get<1>(values2);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(n_outer_t, A);
tmp1.mul<true, false>(Aj, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_rot1 += tmp1;
tmp.mul<false, false>(t_outer_n, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_rot2 += tmp1;
}
}
k_rot1 *= -epsilon_n * heaviside(gap) * (gap * gap + gap) * nodal_area;
k_rot2 *= -epsilon_n * heaviside(gap) * (gap * gap + gap) * nodal_area;
stiffness += k_main + k_rot1 + k_rot2;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeTangentialModuli(
const ContactElement & element, Matrix<Real> & stiffness) {
if (mu == 0) {
return;
}
stiffness.zero();
auto & contact_state = model.getContactState();
auto state = contact_state.begin()[element.slave];
switch (state) {
case ContactState::_stick: {
computeStickModuli(element, stiffness);
break;
}
case ContactState::_slip: {
computeSlipModuli(element, stiffness);
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeStickModuli(
const ContactElement & element, Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
// tangents should have been calculated in normal modulii
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
// construct 1st part of the stick modulii
Matrix<Real> k_main(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t_alpha(tangent_alpha.storage(), tangent_alpha.size(), 1.);
for (auto && values2 : enumerate(covariant_basis.transpose())) {
auto & beta = std::get<0>(values2);
auto & tangent_beta = std::get<1>(values2);
Matrix<Real> mat_t_beta(tangent_beta.storage(), tangent_beta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_alpha, mat_t_beta);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, beta);
k_main += tmp1;
}
}
k_main *= -epsilon_t;
// construct 2nd part of the stick modulii
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
Matrix<Real> k_second(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto alpha : arange(surface_dimension)) {
Matrix<Real> k_sum(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(shape_derivatives.transpose())) {
auto & beta = std::get<0>(values1);
auto & dnds = std::get<1>(values1);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
for (auto && values2 : enumerate(covariant_basis.transpose())) {
auto & gamma = std::get<0>(values2);
auto & tangent_gamma = std::get<1>(values2);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
Matrix<Real> mat_t_gamma(tangent_gamma.storage(), tangent_gamma.size(),
1.);
for (auto && values3 : enumerate(covariant_basis.transpose())) {
auto & theta = std::get<0>(values3);
auto & tangent_theta = std::get<1>(values3);
Matrix<Real> mat_t_theta(tangent_theta.storage(),
tangent_theta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_gamma, mat_t_theta);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_t, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, theta) *
contravariant_metric_tensor(beta, gamma);
Matrix<Real> tmp2(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp3(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp2.mul<false, false>(t_outer_t, A);
tmp3.mul<true, false>(Aj, tmp2);
tmp3 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
k_sum += tmp1 + tmp3;
}
}
}
k_second += tangential_traction[alpha] * k_sum;
}
stiffness += k_main * nodal_area - k_second * nodal_area;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::computeSlipModuli(
const ContactElement & element, Matrix<Real> & stiffness) {
auto surface_dimension = spatial_dimension - 1;
auto & gaps = model.getGaps();
Real gap(gaps.begin()[element.slave]);
auto & nodal_areas = model.getNodalArea();
auto & nodal_area = nodal_areas.begin()[element.slave];
// compute normal traction
Real p_n = computeNormalTraction(gap);
auto & projections = model.getProjections();
Vector<Real> projection(projections.begin(surface_dimension)[element.slave]);
auto & normals = model.getNormals();
Vector<Real> normal(normals.begin(spatial_dimension)[element.slave]);
// restructure normal as a matrix for an outer product
Matrix<Real> mat_n(normal.storage(), normal.size(), 1.);
// method from Schweizerhof and A. Konyukhov, K. Schweizerhof
// DOI 10.1007/s00466-004-0616-7 and DOI 10.1007/s00466-003-0515-3
// construct A matrix
const ElementType & type = element.master.type;
auto && shapes = ElementClassHelper<_ek_regular>::getN(projection, type);
UInt nb_nodes_per_contact = element.getNbNodes();
Matrix<Real> A(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
A(j, i * spatial_dimension + j) = 1;
continue;
}
A(j, i * spatial_dimension + j) = -shapes[i - 1];
}
}
// computing shape derivatives
auto && shape_derivatives =
ElementClassHelper<_ek_regular>::getDNDS(projection, type);
Matrix<Real> Aj(spatial_dimension, spatial_dimension * nb_nodes_per_contact);
auto construct_Aj = [&](auto && dnds) {
for (auto i : arange(nb_nodes_per_contact)) {
for (auto j : arange(spatial_dimension)) {
if (i == 0) {
Aj(j, i * spatial_dimension + j) = 0;
continue;
}
Aj(j, i * spatial_dimension + j) = dnds(i - 1);
}
}
};
// tangents should have been calculated in normal modulii
auto & tangents = model.getTangents();
Matrix<Real> covariant_basis(
tangents.begin(surface_dimension, spatial_dimension)[element.slave]);
auto & tangential_tractions = model.getTangentialTractions();
Vector<Real> tangential_traction(
tangential_tractions.begin(surface_dimension)[element.slave]);
// compute norm of trial traction
Real traction_norm = 0;
auto contravariant_metric_tensor =
GeometryUtils::contravariantMetricTensor(covariant_basis);
for (auto i : arange(surface_dimension)) {
for (auto j : arange(surface_dimension)) {
traction_norm += tangential_traction[i] * tangential_traction[j] *
contravariant_metric_tensor(i, j);
}
}
traction_norm = sqrt(traction_norm);
// construct four parts of stick modulii (eq 107,107a-c)
Matrix<Real> k_first(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_second(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_third(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
Matrix<Real> k_fourth(nb_nodes_per_contact * spatial_dimension,
nb_nodes_per_contact * spatial_dimension);
for (auto && values1 : enumerate(covariant_basis.transpose())) {
auto & alpha = std::get<0>(values1);
auto & tangent_alpha = std::get<1>(values1);
Matrix<Real> mat_t_alpha(tangent_alpha.storage(), tangent_alpha.size(), 1.);
Matrix<Real> t_outer_n(spatial_dimension, spatial_dimension);
Matrix<Real> t_outer_t(spatial_dimension, spatial_dimension);
for (auto && values2 :
zip(arange(surface_dimension), covariant_basis.transpose(),
shape_derivatives.transpose())) {
auto & beta = std::get<0>(values2);
auto & tangent_beta = std::get<1>(values2);
auto & dnds = std::get<2>(values2);
// construct Aj from shape function wrt to jth natural
// coordinate
construct_Aj(dnds);
// eq 107
Matrix<Real> mat_t_beta(tangent_beta.storage(), tangent_beta.size(), 1.);
t_outer_n.mul<false, true>(mat_t_beta, mat_n);
Matrix<Real> tmp(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp1(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp.mul<false, false>(t_outer_n, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_n * mu * tangential_traction[alpha] *
contravariant_metric_tensor(alpha, beta);
tmp1 /= traction_norm;
k_first += tmp1 * nodal_area;
// eq 107a
t_outer_t.mul<false, true>(mat_t_alpha, mat_t_beta);
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_t * mu * p_n * contravariant_metric_tensor(alpha, beta);
tmp1 /= traction_norm;
k_second += tmp1 * nodal_area;
for (auto && values3 : enumerate(covariant_basis.transpose())) {
auto & gamma = std::get<0>(values3);
auto & tangent_gamma = std::get<1>(values3);
Matrix<Real> mat_t_gamma(tangent_gamma.storage(), tangent_gamma.size(),
1.);
for (auto && values4 : enumerate(covariant_basis.transpose())) {
auto & theta = std::get<0>(values4);
auto & tangent_theta = std::get<1>(values4);
Matrix<Real> mat_t_theta(tangent_theta.storage(),
tangent_theta.size(), 1.);
t_outer_t.mul<false, true>(mat_t_gamma, mat_t_theta);
// eq 107b
tmp.mul<false, false>(t_outer_t, A);
tmp1.mul<true, false>(A, tmp);
tmp1 *= epsilon_t * mu * p_n * tangential_traction[alpha] *
tangential_traction[beta];
tmp1 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
tmp1 /= pow(traction_norm, 3);
k_third += tmp1 * nodal_area;
// eq 107c
tmp.mul<false, false>(t_outer_t, Aj);
tmp1.mul<true, false>(A, tmp);
tmp1 *= contravariant_metric_tensor(alpha, theta) *
contravariant_metric_tensor(beta, gamma);
tmp1 *= mu * p_n * tangential_traction[alpha];
tmp1 /= traction_norm;
Matrix<Real> tmp2(spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
Matrix<Real> tmp3(nb_nodes_per_contact * spatial_dimension,
spatial_dimension * nb_nodes_per_contact);
tmp2.mul<false, false>(t_outer_t, A);
tmp3.mul<true, false>(Aj, tmp2);
tmp3 *= contravariant_metric_tensor(alpha, gamma) *
contravariant_metric_tensor(beta, theta);
tmp3 *= mu * p_n * tangential_traction[alpha];
tmp3 /= traction_norm;
k_fourth += (tmp1 + tmp3) * nodal_area;
}
}
}
}
stiffness += k_third + k_fourth - k_first - k_second;
}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::beforeSolveStep() {}
/* -------------------------------------------------------------------------- */
void ResolutionPenaltyQuadratic::afterSolveStep(
__attribute__((unused)) bool converged) {}
INSTANTIATE_RESOLUTION(penalty_quadratic, ResolutionPenaltyQuadratic);
} // namespace akantu
diff --git a/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh b/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh
index 8d9d6a3ac..16756ed47 100644
--- a/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh
+++ b/src/model/contact_mechanics/resolutions/resolution_penalty_quadratic.hh
@@ -1,124 +1,125 @@
/**
- * @file contact_resolution_penalty_quadratic.hh
+ * @file resolution_penalty_quadratic.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Aug 02 2020
- * @date last modification: Sun Aug 02 2020
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Mon Aug 10 2020
+ *
+ * @brief Quadratic Penalty Resolution for Contact Mechanics Model
*
- * @brief Quadratic Penalty Resolution for Contact Mechanics Model
*
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "resolution_penalty.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RESOLUTION_PENALTY_QUADRATIC_HH__
#define __AKANTU_RESOLUTION_PENALTY_QUADRATIC_HH__
namespace akantu {
class ResolutionPenaltyQuadratic : public ResolutionPenalty {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
using Parent = ResolutionPenalty;
public:
ResolutionPenaltyQuadratic(ContactMechanicsModel & model, const ID & id = "");
~ResolutionPenaltyQuadratic() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the resolution
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods for stiffness computation */
/* ------------------------------------------------------------------------ */
protected:
/// local computaion of stiffness matrix due to stick state
void computeStickModuli(const ContactElement &, Matrix<Real> &);
/// local computation of stiffness matrix due to slip state
void computeSlipModuli(const ContactElement &, Matrix<Real> &);
/* ------------------------------------------------------------------------ */
/* Methods for stiffness computation */
/* ------------------------------------------------------------------------ */
public:
/// local computation of tangent moduli due to normal traction
void computeNormalModuli(const ContactElement &, Matrix<Real> &) override;
/// local computation of tangent moduli due to tangential traction
void computeTangentialModuli(const ContactElement &, Matrix<Real> &) override;
/* ------------------------------------------------------------------------ */
/* Methods for force computation */
/* ------------------------------------------------------------------------ */
public:
/// local computation of normal force due to normal contact
void computeNormalForce(const ContactElement &, Vector<Real> &) override;
/// local computation of tangential force due to frictional traction
void computeTangentialForce(const ContactElement &, Vector<Real> &) override;
protected:
/// local computation of normal traction due to penetration
Real computeNormalTraction(Real &);
/// local computation of trial tangential traction due to friction
void computeTrialTangentialTraction(const ContactElement &, const Matrix<Real> &,
Vector<Real> &);
/// local computation of tangential traction due to stick
void computeStickTangentialTraction(const ContactElement &, Vector<Real> &,
Vector<Real> &);
/// local computation of tangential traction due to slip
void computeSlipTangentialTraction(const ContactElement &, const Matrix<Real> &,
Vector<Real> &, Vector<Real> &);
/// local computation of tangential traction due to friction
void computeTangentialTraction(const ContactElement &, const Matrix<Real> &,
Vector<Real> &);
public:
void beforeSolveStep() override;
void afterSolveStep(bool converged = true) override;
};
} // akantu
#endif /* __AKANTU_RESOLUTION_PENALTY_QUADRATIC_HH__ */
diff --git a/src/model/contact_mechanics/surface_selector.cc b/src/model/contact_mechanics/surface_selector.cc
index 59dcfad69..668c84d36 100644
--- a/src/model/contact_mechanics/surface_selector.cc
+++ b/src/model/contact_mechanics/surface_selector.cc
@@ -1,286 +1,287 @@
/**
* @file surface_selector.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Fri Jun 21 2019
- * @date last modification: Fri Jun 21 2019
+ * @date creation: Sun Jun 30 2019
+ * @date last modification: Fri Sep 18 2020
*
* @brief Surface selector for contact detector
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "surface_selector.hh"
#include "model.hh"
#include "geometry_utils.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SurfaceSelector::SurfaceSelector(Mesh & mesh)
: Parsable(ParserType::_contact_detector), mesh(mesh) {}
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from physical names
*/
PhysicalSurfaceSelector::PhysicalSurfaceSelector(Mesh & mesh)
: SurfaceSelector(mesh) {
const Parser & parser = getStaticParser();
const ParserSection & section =
*(parser.getSubSections(ParserType::_contact_detector).first);
master = section.getParameterValue<std::string>("master");
slave = section.getParameterValue<std::string>("slave");
UInt surface_dimension = mesh.getSpatialDimension() - 1;
auto & group = mesh.createElementGroup("contact_surface",
surface_dimension);
group.append(mesh.getElementGroup(master));
group.append(mesh.getElementGroup(slave));
group.optimize();
}
/* -------------------------------------------------------------------------- */
Array<UInt> & PhysicalSurfaceSelector::getMasterList() {
return mesh.getElementGroup(master).getNodeGroup().getNodes();
}
/* -------------------------------------------------------------------------- */
Array<UInt> & PhysicalSurfaceSelector::getSlaveList() {
return mesh.getElementGroup(slave).getNodeGroup().getNodes();
}
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from cohesive elements
*/
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
CohesiveSurfaceSelector::CohesiveSurfaceSelector(Mesh & mesh)
: SurfaceSelector(mesh), mesh_facets(mesh.getMeshFacets()) {
this->mesh.registerEventHandler(*this, _ehp_lowest);
UInt surface_dimension = mesh.getSpatialDimension() - 1;
mesh_facets.createElementGroup("contact_surface",
surface_dimension, true);
}
/* -------------------------------------------------------------------------- */
void CohesiveSurfaceSelector::onElementsAdded(const Array<Element> & element_list,
__attribute__((unused)) const NewElementsEvent & event) {
auto & group = mesh_facets.getElementGroup("contact_surface");
for(auto elem : element_list) {
if(elem.kind() != _ek_cohesive)
continue;
const auto & subelement_to_element =
mesh_facets.getSubelementToElement(elem.type);
auto && facets = Vector<Element>(
make_view(subelement_to_element,
subelement_to_element.getNbComponent())
.begin()[elem.element]);
for(auto facet : facets) {
group.add(facet, true);
}
}
group.optimize();
}
/* -------------------------------------------------------------------------- */
void CohesiveSurfaceSelector::onNodesAdded(__attribute__((unused)) const Array<UInt> & new_nodes,
const NewNodesEvent & event) {
if (not aka::is_of_type<CohesiveNewNodesEvent>(event))
return;
/*const auto & cohesive_event = aka::as_type<CohesiveNewNodesEvent>(event);
const auto & old_nodes = cohesive_event.getOldNodesList();
UInt nb_new_nodes = new_nodes.size();
UInt nb_old_nodes = old_nodes.size();
for (auto n : arange(nb_new_nodes)) {
new_nodes_list.push_back(new_nodes(n));
}
for (auto n : arange(nb_old_nodes)) {
new_nodes_list.push_back(old_nodes(n));
}*/
mesh_facets.fillNodesToElements(mesh.getSpatialDimension() - 1);
/*UInt surface_dimension = mesh.getSpatialDimension() - 1;
auto & group = mesh_facets.createElementGroup("contact_surface",
surface_dimension, true);
for (auto node : new_nodes_list) {
Array<Element> all_elements;
mesh_facets.getAssociatedElements(node, all_elements);
Array<Element> mesh_facet_elements;
this->filterBoundaryElements(all_elements, mesh_facet_elements);
for (auto nb_elem : arange(mesh_facet_elements.size()))
group.add(mesh_facet_elements[nb_elem], true);
}
group.optimize();*/
}
/* -------------------------------------------------------------------------- */
//void CohesiveSurfaceSelector::filterBoundaryElements(
// Array<Element> & subelements, Array<Element> & boundary_elements) {
// for (auto subelem : subelements) {
// if(GeometryUtils::isBoundaryElement(mesh_facets, subelem))
// boundary_elements.push_back(subelem);
// }
//}
/* -------------------------------------------------------------------------- */
Array<UInt> & CohesiveSurfaceSelector::getMasterList() {
return mesh_facets.getElementGroup("contact_surface").getNodeGroup().getNodes();
}
/* -------------------------------------------------------------------------- */
Array<UInt> & CohesiveSurfaceSelector::getSlaveList() {
return mesh_facets.getElementGroup("contact_surface").getNodeGroup().getNodes();
}
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from both cohesive elements and
* physical names
*/
AllSurfaceSelector::AllSurfaceSelector(Mesh & mesh)
: SurfaceSelector(mesh), mesh_facets(mesh.getMeshFacets()) {
this->mesh.registerEventHandler(*this, _ehp_lowest);
const Parser & parser = getStaticParser();
const ParserSection & section =
*(parser.getSubSections(ParserType::_contact_detector).first);
master = section.getParameterValue<std::string>("master");
slave = section.getParameterValue<std::string>("slave");
UInt surface_dimension = this->mesh.getSpatialDimension() - 1;
auto & group = mesh_facets.createElementGroup("contact_surface",
surface_dimension);
group.append(mesh_facets.getElementGroup(master));
group.append(mesh_facets.getElementGroup(slave));
group.optimize();
}
/* -------------------------------------------------------------------------- */
void AllSurfaceSelector::onElementsAdded(const Array<Element> & element_list,
__attribute__((unused)) const NewElementsEvent & event) {
auto & group = mesh_facets.getElementGroup("contact_surface");
for(auto elem : element_list) {
if(elem.kind() != _ek_cohesive)
continue;
const auto & subelement_to_element =
mesh_facets.getSubelementToElement(elem.type);
auto && facets = Vector<Element>(
make_view(subelement_to_element,
subelement_to_element.getNbComponent()).begin()[elem.element]);
for(auto facet : facets) {
group.add(facet, true);
}
}
group.optimize();
}
/* -------------------------------------------------------------------------- */
void AllSurfaceSelector::onNodesAdded(__attribute__((unused)) const Array<UInt> & new_nodes,
const NewNodesEvent & event) {
if (not aka::is_of_type<CohesiveNewNodesEvent>(event))
return;
/*const auto & cohesive_event = aka::as_type<CohesiveNewNodesEvent>(event);
const auto & old_nodes = cohesive_event.getOldNodesList();
UInt nb_new_nodes = new_nodes.size();
UInt nb_old_nodes = old_nodes.size();
for (auto n : arange(nb_new_nodes)) {
new_nodes_list.push_back(new_nodes(n));
}
for (auto n : arange(nb_old_nodes)) {
new_nodes_list.push_back(old_nodes(n));
}*/
mesh_facets.fillNodesToElements(mesh.getSpatialDimension() - 1);
/*auto & group = mesh_facets.getElementGroup("contact_surface");
for (auto node : new_nodes_list) {
Array<Element> all_elements;
mesh_facets.getAssociatedElements(node, all_elements);
Array<Element> mesh_facet_elements;
this->filterBoundaryElements(all_elements, mesh_facet_elements);
for (auto nb_elem : arange(mesh_facet_elements.size()))
group.add(mesh_facet_elements[nb_elem], true);
}
group.optimize();*/
}
/* -------------------------------------------------------------------------- */
Array<UInt> & AllSurfaceSelector::getMasterList() {
return mesh_facets.getElementGroup("contact_surface").getNodeGroup().getNodes();
}
/* -------------------------------------------------------------------------- */
Array<UInt> & AllSurfaceSelector::getSlaveList() {
return mesh_facets.getElementGroup("contact_surface").getNodeGroup().getNodes();
}
#endif
} // namespace akantu
diff --git a/src/model/contact_mechanics/surface_selector.hh b/src/model/contact_mechanics/surface_selector.hh
index 0e2feaf2c..e16759b32 100644
--- a/src/model/contact_mechanics/surface_selector.hh
+++ b/src/model/contact_mechanics/surface_selector.hh
@@ -1,149 +1,150 @@
/**
* @file surface_selector.hh
*
- * @author Mohit Pundir <pundir.pundir@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Fri Jun 21 2019
- * @date last modification: Fri Jun 21 2019
+ * @date creation: Sun Jun 30 2019
+ * @date last modification: Sun Jun 06 2021
*
* @brief Node selectors for contact detection
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
#include "mesh_utils.hh"
#include "parsable.hh"
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element_inserter.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SURFACE_SELECTOR_HH__
#define __AKANTU_SURFACE_SELECTOR_HH__
namespace akantu {
class Model;
class GlobalIdsUpdater;
} // namespace akantu
namespace akantu {
/**
* main class to assign surfaces for contact detection
*/
class SurfaceSelector : public MeshEventHandler, public Parsable {
public:
SurfaceSelector(Mesh & mesh);
virtual ~SurfaceSelector() = default;
public:
virtual Array<UInt> & getMasterList() { AKANTU_TO_IMPLEMENT();}
virtual Array<UInt> & getSlaveList() { AKANTU_TO_IMPLEMENT();}
protected:
Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from physical names
*/
class PhysicalSurfaceSelector : public SurfaceSelector {
public:
PhysicalSurfaceSelector(Mesh & mesh);
public:
Array<UInt> & getMasterList() override;
Array<UInt> & getSlaveList() override;
protected:
std::string master;
std::string slave;
};
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from cohesive elements
*/
#if defined(AKANTU_COHESIVE_ELEMENT)
class CohesiveSurfaceSelector : public SurfaceSelector {
public:
CohesiveSurfaceSelector(Mesh & mesh);
protected:
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
public:
Array<UInt> & getMasterList() override;
Array<UInt> & getSlaveList() override;
AKANTU_GET_MACRO_NOT_CONST(NewNodesList, new_nodes_list, Array<UInt> &);
AKANTU_GET_MACRO(NewNodesList, new_nodes_list, const Array<UInt> &);
protected:
Mesh & mesh_facets;
Array<UInt> new_nodes_list;
};
/* -------------------------------------------------------------------------- */
/**
* class that selects contact surface from both cohesive elements and
* physical names
*/
class AllSurfaceSelector : public SurfaceSelector {
public:
AllSurfaceSelector(Mesh & mesh);
protected:
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
public:
Array<UInt> & getMasterList() override;
Array<UInt> & getSlaveList() override;
AKANTU_GET_MACRO_NOT_CONST(NewNodesList, new_nodes_list, Array<UInt> &);
AKANTU_GET_MACRO(NewNodesList, new_nodes_list, const Array<UInt> &);
protected:
std::string master;
std::string slave;
Mesh & mesh_facets;
Array<UInt> new_nodes_list;
};
#endif
} // namespace akantu
#endif /* __AKANTU_SURFACE_SELECTOR_HH__ */
diff --git a/src/model/heat_transfer/heat_transfer_model.cc b/src/model/heat_transfer/heat_transfer_model.cc
index 8e3e0c920..87856f4ba 100644
--- a/src/model/heat_transfer/heat_transfer_model.cc
+++ b/src/model/heat_transfer/heat_transfer_model.cc
@@ -1,917 +1,919 @@
/**
* @file heat_transfer_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of HeatTransferModel class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
#include "dumpable_inline_impl.hh"
#include "element_synchronizer.hh"
#include "fe_engine_template.hh"
#include "generalized_trapezoidal.hh"
#include "group_manager_inline_impl.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "parser.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace heat_transfer {
namespace details {
class ComputeRhoFunctor {
public:
ComputeRhoFunctor(const HeatTransferModel & model) : model(model){};
void operator()(Matrix<Real> & rho, const Element & /*unused*/) {
rho.set(model.getCapacity() * model.getDensity());
}
private:
const HeatTransferModel & model;
};
} // namespace details
} // namespace heat_transfer
/* -------------------------------------------------------------------------- */
HeatTransferModel::HeatTransferModel(Mesh & mesh, UInt dim, const ID & id,
std::shared_ptr<DOFManager> dof_manager)
: Model(mesh, ModelType::_heat_transfer_model, dof_manager, dim, id),
temperature_gradient("temperature_gradient", id),
temperature_on_qpoints("temperature_on_qpoints", id),
conductivity_on_qpoints("conductivity_on_qpoints", id),
k_gradt_on_qpoints("k_gradt_on_qpoints", id) {
AKANTU_DEBUG_IN();
conductivity = Matrix<Real>(this->spatial_dimension, this->spatial_dimension);
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer,
SynchronizationTag::_htm_temperature);
this->registerSynchronizer(synchronizer,
SynchronizationTag::_htm_gradient_temperature);
}
registerFEEngineObject<FEEngineType>(id + ":fem", mesh, spatial_dimension);
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("heat_transfer", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
this->registerParam("conductivity", conductivity, _pat_parsmod);
this->registerParam("conductivity_variation", conductivity_variation, 0.,
_pat_parsmod);
this->registerParam("temperature_reference", T_ref, 0., _pat_parsmod);
this->registerParam("capacity", capacity, _pat_parsmod);
this->registerParam("density", density, _pat_parsmod);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initModel() {
auto & fem = this->getFEEngine();
fem.initShapeFunctions(_not_ghost);
fem.initShapeFunctions(_ghost);
temperature_on_qpoints.initialize(fem, _nb_component = 1);
temperature_gradient.initialize(fem, _nb_component = spatial_dimension);
conductivity_on_qpoints.initialize(fem, _nb_component = spatial_dimension *
spatial_dimension);
k_gradt_on_qpoints.initialize(fem, _nb_component = spatial_dimension);
}
/* -------------------------------------------------------------------------- */
FEEngine & HeatTransferModel::getFEEngineBoundary(const ID & name) {
return aka::as_type<FEEngine>(getFEEngineClassBoundary<FEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
HeatTransferModel::~HeatTransferModel() = default;
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor compute_rho(*this);
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldLumped(compute_rho, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType HeatTransferModel::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K" or matrix_id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleConductivityMatrix();
} else if (matrix_id == "M" and need_to_reassemble_capacity) {
this->assembleCapacity();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M" and need_to_reassemble_capacity) {
this->assembleCapacityLumped();
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleResidual() {
AKANTU_DEBUG_IN();
this->assembleInternalHeatRate();
this->getDOFManager().assembleToResidual("temperature",
*this->external_heat_rate, 1);
this->getDOFManager().assembleToResidual("temperature",
*this->internal_heat_rate, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::predictor() { ++temperature_release; }
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped() {
AKANTU_DEBUG_IN();
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
this->getDOFManager().zeroLumpedMatrix("M");
assembleCapacityLumped(_not_ghost);
assembleCapacityLumped(_ghost);
need_to_reassemble_capacity_lumped = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType /*unused*/) {
DOFManager & dof_manager = this->getDOFManager();
this->allocNodalField(this->temperature, 1, "temperature");
this->allocNodalField(this->external_heat_rate, 1, "external_heat_rate");
this->allocNodalField(this->internal_heat_rate, 1, "internal_heat_rate");
this->allocNodalField(this->blocked_dofs, 1, "blocked_dofs");
if (!dof_manager.hasDOFs("temperature")) {
dof_manager.registerDOFs("temperature", *this->temperature, _dst_nodal);
dof_manager.registerBlockedDOFs("temperature", *this->blocked_dofs);
}
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(this->temperature_rate, 1, "temperature_rate");
if (!dof_manager.hasDOFsDerivatives("temperature", 1)) {
dof_manager.registerDOFsDerivative("temperature", 1,
*this->temperature_rate);
}
}
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
HeatTransferModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions HeatTransferModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_forward_euler;
options.solution_type["temperature"] = IntegrationScheme::_temperature_rate;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["temperature"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_forward_euler;
options.solution_type["temperature"] =
IntegrationScheme::_temperature_rate;
} else {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["temperature"] =
IntegrationSchemeType::_backward_euler;
options.solution_type["temperature"] = IntegrationScheme::_temperature;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleConductivityMatrix() {
AKANTU_DEBUG_IN();
this->computeConductivityOnQuadPoints(_not_ghost);
if (conductivity_release[_not_ghost] == conductivity_matrix_release) {
return;
}
AKANTU_DEBUG_ASSERT(this->getDOFManager().hasMatrix("K"),
"The K matrix has not been initialized yet.");
this->getDOFManager().zeroMatrix("K");
auto & fem = this->getFEEngine();
for (auto && type : mesh.elementTypes(spatial_dimension)) {
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type);
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points,
nb_nodes_per_element * nb_nodes_per_element, "B^t*D*B");
fem.computeBtDB(conductivity_on_qpoints(type), *bt_d_b, 2, type);
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto K_e = std::make_unique<Array<Real>>(
nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_e");
fem.integrate(*bt_d_b, *K_e, nb_nodes_per_element * nb_nodes_per_element,
type);
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "temperature", *K_e, type, _not_ghost, _symmetric);
}
conductivity_matrix_release = conductivity_release[_not_ghost];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeConductivityOnQuadPoints(GhostType ghost_type) {
// if already computed once check if need to compute
if (not initial_conductivity[ghost_type]) {
// if temperature did not change, conductivity will not vary
if (temperature_release == conductivity_release[ghost_type]) {
return;
}
// if conductivity_variation is 0 no need to recompute
if (conductivity_variation == 0.) {
return;
}
}
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
auto & temperature_interpolated = temperature_on_qpoints(type, ghost_type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type, ghost_type);
auto & cond = conductivity_on_qpoints(type, ghost_type);
for (auto && tuple :
zip(make_view(cond, spatial_dimension, spatial_dimension),
temperature_interpolated)) {
auto & C = std::get<0>(tuple);
auto & T = std::get<1>(tuple);
C = conductivity;
Matrix<Real> variation(spatial_dimension, spatial_dimension,
conductivity_variation * (T - T_ref));
// @TODO: Guillaume are you sure ? why due you compute variation then ?
C += conductivity_variation;
}
}
conductivity_release[ghost_type] = temperature_release;
initial_conductivity[ghost_type] = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeKgradT(GhostType ghost_type) {
computeConductivityOnQuadPoints(ghost_type);
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
auto & gradient = temperature_gradient(type, ghost_type);
this->getFEEngine().gradientOnIntegrationPoints(*temperature, gradient, 1,
type, ghost_type);
for (auto && values :
zip(make_view(conductivity_on_qpoints(type, ghost_type),
spatial_dimension, spatial_dimension),
make_view(gradient, spatial_dimension),
make_view(k_gradt_on_qpoints(type, ghost_type),
spatial_dimension))) {
const auto & C = std::get<0>(values);
const auto & BT = std::get<1>(values);
auto & k_BT = std::get<2>(values);
k_BT.mul<false>(C, BT);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleInternalHeatRate() {
AKANTU_DEBUG_IN();
this->internal_heat_rate->zero();
this->synchronize(SynchronizationTag::_htm_temperature);
auto & fem = this->getFEEngine();
for (auto ghost_type : ghost_types) {
// compute k \grad T
computeKgradT(ghost_type);
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto & k_gradt_on_qpoints_vect = k_gradt_on_qpoints(type, ghost_type);
UInt nb_quad_points = k_gradt_on_qpoints_vect.size();
Array<Real> bt_k_gT(nb_quad_points, nb_nodes_per_element);
fem.computeBtD(k_gradt_on_qpoints_vect, bt_k_gT, type, ghost_type);
UInt nb_elements = mesh.getNbElement(type, ghost_type);
Array<Real> int_bt_k_gT(nb_elements, nb_nodes_per_element);
fem.integrate(bt_k_gT, int_bt_k_gT, nb_nodes_per_element, type,
ghost_type);
this->getDOFManager().assembleElementalArrayLocalArray(
int_bt_k_gT, *this->internal_heat_rate, type, ghost_type, -1);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real el_size;
Real min_el_size = std::numeric_limits<Real>::max();
Real conductivitymax = conductivity(0, 0);
// get the biggest parameter from k11 until k33//
for (UInt i = 0; i < spatial_dimension; i++) {
for (UInt j = 0; j < spatial_dimension; j++) {
conductivitymax = std::max(conductivity(i, j), conductivitymax);
}
}
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Array<Real> coord(0, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(mesh, mesh.getNodes(), coord, type,
_not_ghost);
auto el_coord = coord.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_element = mesh.getNbElement(type);
for (UInt el = 0; el < nb_element; ++el, ++el_coord) {
el_size = getFEEngine().getElementInradius(*el_coord, type);
min_el_size = std::min(min_el_size, el_size);
}
AKANTU_DEBUG_INFO("The minimum element size : "
<< min_el_size
<< " and the max conductivity is : " << conductivitymax);
}
Real min_dt = 2. * min_el_size * min_el_size / 4. * density * capacity /
conductivitymax;
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("heat_transfer").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::readMaterials() {
auto sect = this->getParserSection();
if (not std::get<1>(sect)) {
const auto & section = std::get<0>(sect);
this->parseSection(section);
}
conductivity_on_qpoints.set(conductivity);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
readMaterials();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacity() {
AKANTU_DEBUG_IN();
auto ghost_type = _not_ghost;
this->getDOFManager().zeroMatrix("M");
auto & fem = getFEEngineClass<FEEngineType>();
heat_transfer::details::ComputeRhoFunctor rho_functor(*this);
for (auto && type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldMatrix(rho_functor, "M", "temperature",
this->getDOFManager(), type, ghost_type);
}
need_to_reassemble_capacity = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->getFEEngine();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
rho.resize(nb_element * nb_quadrature_points);
rho.set(this->capacity);
// Real * rho_1_val = rho.storage();
// /// compute @f$ rho @f$ for each nodes of each element
// for (UInt el = 0; el < nb_element; ++el) {
// for (UInt n = 0; n < nb_quadrature_points; ++n) {
// *rho_1_val++ = this->capacity;
// }
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::computeThermalEnergyByNode() {
AKANTU_DEBUG_IN();
Real ethermal = 0.;
for (auto && pair : enumerate(make_view(
*internal_heat_rate, internal_heat_rate->getNbComponent()))) {
auto n = std::get<0>(pair);
auto & heat_rate = std::get<1>(pair);
Real heat = 0.;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool count_node = is_local_node;
for (UInt i = 0; i < heat_rate.size(); ++i) {
if (count_node) {
heat += heat_rate[i] * time_step;
}
}
ethermal += heat;
}
mesh.getCommunicator().allReduce(ethermal, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ethermal;
}
/* -------------------------------------------------------------------------- */
template <class iterator>
void HeatTransferModel::getThermalEnergy(
iterator Eth, Array<Real>::const_iterator<Real> T_it,
const Array<Real>::const_iterator<Real> & T_end) const {
for (; T_it != T_end; ++T_it, ++Eth) {
*Eth = capacity * density * *T_it;
}
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy(ElementType type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Vector<Real> Eth_on_quarature_points(nb_quadrature_points);
auto T_it = this->temperature_on_qpoints(type).begin();
T_it += index * nb_quadrature_points;
auto T_end = T_it + nb_quadrature_points;
getThermalEnergy(Eth_on_quarature_points.storage(), T_it, T_end);
return getFEEngine().integrate(Eth_on_quarature_points, type, index);
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy() {
Real Eth = 0;
auto & fem = getFEEngine();
for (auto && type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
auto nb_element = mesh.getNbElement(type, _not_ghost);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, _not_ghost);
Array<Real> Eth_per_quad(nb_element * nb_quadrature_points, 1);
auto & temperature_interpolated = temperature_on_qpoints(type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, type);
auto T_it = temperature_interpolated.begin();
auto T_end = temperature_interpolated.end();
getThermalEnergy(Eth_per_quad.begin(), T_it, T_end);
Eth += fem.integrate(Eth_per_quad, type);
}
return Eth;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
Real energy = 0;
if (id == "thermal") {
energy = getThermalEnergy();
}
// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id, ElementType type,
UInt index) {
AKANTU_DEBUG_IN();
Real energy = 0.;
if (id == "thermal") {
energy = getThermalEnergy(type, index);
}
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs.get();
auto field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createNodalFieldReal(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
if (field_name == "capacity_lumped") {
AKANTU_EXCEPTION(
"Capacity lumped is a nodal field now stored in the DOF manager."
"Therefore it cannot be used by a dumper anymore");
}
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["temperature"] = temperature.get();
real_nodal_fields["temperature_rate"] = temperature_rate.get();
real_nodal_fields["external_heat_rate"] = external_heat_rate.get();
real_nodal_fields["internal_heat_rate"] = internal_heat_rate.get();
real_nodal_fields["increment"] = increment.get();
std::shared_ptr<dumpers::Field> field =
mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createElementalField(
const std::string & field_name, const std::string & group_name,
bool /*padding_flag*/, UInt /*spatial_dimension*/,
ElementKind element_kind) {
std::shared_ptr<dumpers::Field> field;
if (field_name == "partitions") {
field = mesh.createElementalField<UInt, dumpers::ElementPartitionField>(
mesh.getConnectivities(), group_name, this->spatial_dimension,
element_kind);
} else if (field_name == "temperature_gradient") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(temperature_gradient);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
temperature_gradient, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
} else if (field_name == "conductivity") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(conductivity_on_qpoints);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
conductivity_on_qpoints, group_name, this->spatial_dimension,
element_kind, nb_data_per_elem);
}
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> HeatTransferModel::createElementalField(
const std::string & /* field_name*/, const std::string & /*group_name*/,
bool /*padding_flag*/, ElementKind /*element_kind*/) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
HeatTransferModel::createNodalFieldBool(const std::string & /*field_name*/,
const std::string & /*group_name*/,
bool /*padding_flag*/) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
HeatTransferModel::createNodalFieldReal(const std::string & /*field_name*/,
const std::string & /*group_name*/,
bool /*padding_flag*/) {
return nullptr;
}
#endif
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes = indexes.size();
switch (tag) {
case SynchronizationTag::_htm_temperature: {
size += nb_nodes * sizeof(Real);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
buffer << (*temperature)(index);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
buffer >> (*temperature)(index);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline UInt HeatTransferModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_htm_temperature: {
size += nb_nodes_per_element * sizeof(Real); // temperature
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
// temperature gradient
size += getNbIntegrationPoints(elements) * spatial_dimension * sizeof(Real);
size += nb_nodes_per_element * sizeof(Real); // nodal temperatures
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
packElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
packNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
/* -------------------------------------------------------------------------- */
inline void HeatTransferModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
switch (tag) {
case SynchronizationTag::_htm_temperature: {
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
case SynchronizationTag::_htm_gradient_temperature: {
unpackElementalDataHelper(temperature_gradient, buffer, elements, true,
getFEEngine());
unpackNodalDataHelper(*temperature, buffer, elements, mesh);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/heat_transfer/heat_transfer_model.hh b/src/model/heat_transfer/heat_transfer_model.hh
index 223c23105..ec41cbc8b 100644
--- a/src/model/heat_transfer/heat_transfer_model.hh
+++ b/src/model/heat_transfer/heat_transfer_model.hh
@@ -1,314 +1,316 @@
/**
* @file heat_transfer_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
- * @date last modification: Mon Feb 05 2018
+ * @date last modification: Mon Mar 15 2021
*
* @brief Model of Heat Transfer
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_HEAT_TRANSFER_MODEL_HH_
#define AKANTU_HEAT_TRANSFER_MODEL_HH_
namespace akantu {
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
namespace akantu {
class HeatTransferModel : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using FEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
HeatTransferModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "heat_transfer_model",
std::shared_ptr<DOFManager> dof_manager = nullptr);
~HeatTransferModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// generic function to initialize everything ready for explicit dynamics
void initFullImpl(const ModelOptions & options) override;
/// read one material file to instantiate all the materials
void readMaterials();
/// allocate all vectors
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
/// initialize the model
void initModel() override;
void predictor() override;
/// compute the heat flux
void assembleResidual() override;
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback to assemble a Matrix
void assembleMatrix(const ID & matrix_id) override;
/// callback to assemble a lumped Matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
/* ------------------------------------------------------------------------ */
/* Methods for explicit */
/* ------------------------------------------------------------------------ */
public:
/// compute and get the stable time step
Real getStableTimeStep();
/// set the stable timestep
void setTimeStep(Real time_step, const ID & solver_id = "") override;
// temporary protection to prevent bad usage: should check for bug
protected:
/// compute the internal heat flux \todo Need code review: currently not
/// public method
void assembleInternalHeatRate();
public:
/// calculate the lumped capacity vector for heat transfer problem
void assembleCapacityLumped();
public:
/// assemble the conductivity matrix
void assembleConductivityMatrix();
/// assemble the conductivity matrix
void assembleCapacity();
/// compute the capacity on quadrature points
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
private:
/// calculate the lumped capacity vector for heat transfer problem (w
/// ghost type)
void assembleCapacityLumped(GhostType ghost_type);
/// compute the conductivity tensor for each quadrature point in an array
void computeConductivityOnQuadPoints(GhostType ghost_type);
/// compute vector \f[k \grad T\f] for each quadrature point
void computeKgradT(GhostType ghost_type);
/// compute the thermal energy
Real computeThermalEnergyByNode();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
inline UInt getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension, ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Density, density, Real);
AKANTU_GET_MACRO(Capacity, capacity, Real);
/// get the current value of the time step
AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// get the assembled heat flux
AKANTU_GET_MACRO(InternalHeatRate, *internal_heat_rate, Array<Real> &);
/// get the boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
/// get the external heat rate vector
AKANTU_GET_MACRO(ExternalHeatRate, *external_heat_rate, Array<Real> &);
/// get the temperature gradient
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureGradient,
temperature_gradient, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ConductivityOnQpoints,
conductivity_on_qpoints, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureOnQpoints,
temperature_on_qpoints, Real);
/// internal variables
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(KgradT, k_gradt_on_qpoints, Real);
/// get the temperature
AKANTU_GET_MACRO(Temperature, *temperature, Array<Real> &);
/// get the temperature derivative
AKANTU_GET_MACRO(TemperatureRate, *temperature_rate, Array<Real> &);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id, ElementType type, UInt index);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id);
/// get the thermal energy for a given element
Real getThermalEnergy(ElementType type, UInt index);
/// get the thermal energy for a given element
Real getThermalEnergy();
protected:
/* ------------------------------------------------------------------------ */
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ----------------------------------------------------------------------- */
template <class iterator>
void getThermalEnergy(iterator Eth, Array<Real>::const_iterator<Real> T_it,
const Array<Real>::const_iterator<Real> & T_end) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// temperatures array
std::unique_ptr<Array<Real>> temperature;
/// temperatures derivatives array
std::unique_ptr<Array<Real>> temperature_rate;
/// increment array (@f$\delta \dot T@f$ or @f$\delta T@f$)
std::unique_ptr<Array<Real>> increment;
/// the density
Real density;
/// the speed of the changing temperature
ElementTypeMapArray<Real> temperature_gradient;
/// temperature field on quadrature points
ElementTypeMapArray<Real> temperature_on_qpoints;
/// conductivity tensor on quadrature points
ElementTypeMapArray<Real> conductivity_on_qpoints;
/// vector \f[k \grad T\f] on quad points
ElementTypeMapArray<Real> k_gradt_on_qpoints;
/// external flux vector
std::unique_ptr<Array<Real>> external_heat_rate;
/// residuals array
std::unique_ptr<Array<Real>> internal_heat_rate;
/// boundary vector
std::unique_ptr<Array<bool>> blocked_dofs;
// realtime
// Real time;
/// capacity
Real capacity;
// conductivity matrix
Matrix<Real> conductivity;
// linear variation of the conductivity (for temperature dependent
// conductivity)
Real conductivity_variation;
// reference temperature for the interpretation of temperature variation
Real T_ref;
// the biggest parameter of conductivity matrix
// Real conductivitymax;
bool need_to_reassemble_capacity{true};
bool need_to_reassemble_capacity_lumped{true};
UInt temperature_release{0};
UInt conductivity_matrix_release{UInt(-1)};
std::unordered_map<GhostType, bool> initial_conductivity{{_not_ghost, true},
{_ghost, true}};
std::unordered_map<GhostType, UInt> conductivity_release{{_not_ghost, 0},
{_ghost, 0}};
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model_inline_impl.hh"
#endif /* AKANTU_HEAT_TRANSFER_MODEL_HH_ */
diff --git a/src/model/heat_transfer/heat_transfer_model_inline_impl.hh b/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
index 672e0551d..928571565 100644
--- a/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
+++ b/src/model/heat_transfer/heat_transfer_model_inline_impl.hh
@@ -1,41 +1,43 @@
/**
* @file heat_transfer_model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Implementation of the inline functions of the HeatTransferModel class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_
#define AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_HEAT_TRANSFER_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/model.cc b/src/model/model.cc
index ab7e39ea9..d2765097c 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,365 +1,367 @@
/**
* @file model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief implementation of model common parts
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Model::Model(Mesh & mesh, const ModelType & type,
std::shared_ptr<DOFManager> dof_manager, UInt dim, const ID & id)
: ModelSolver(mesh, type, id, std::move(dof_manager)), mesh(mesh),
spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
: dim),
parser(getStaticParser()) {
this->mesh.registerEventHandler(*this, _ehp_model);
}
/* -------------------------------------------------------------------------- */
Model::Model(Mesh & mesh, const ModelType & type, UInt dim, const ID & id)
: ModelSolver(mesh, type, id), mesh(mesh),
spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
: dim),
parser(getStaticParser()) {
this->mesh.registerEventHandler(*this, _ehp_model);
}
/* -------------------------------------------------------------------------- */
Model::~Model() = default;
/* -------------------------------------------------------------------------- */
void Model::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
method = options.analysis_method;
if (!this->hasDefaultSolver()) {
this->initNewSolver(this->method);
}
initModel();
initFEEngineBoundary();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::initNewSolver(const AnalysisMethod & method) {
ID solver_name;
TimeStepSolverType tss_type;
std::tie(solver_name, tss_type) = this->getDefaultSolverID(method);
if (not this->hasSolver(solver_name)) {
ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);
for (auto && is_type : options.integration_scheme_type) {
if (!this->hasIntegrationScheme(solver_name, is_type.first)) {
this->setIntegrationScheme(solver_name, is_type.first, is_type.second,
options.solution_type[is_type.first]);
}
}
}
this->method = method;
this->setDefaultSolver(solver_name);
}
/* -------------------------------------------------------------------------- */
void Model::initFEEngineBoundary() {
try {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
} catch (debug::Exception & /*e*/) {
}
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump();
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name,
const std::string & dumper_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup() {
for (auto & group : mesh.iterateElementGroups()) {
group.dump();
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory) {
for (auto & group : mesh.iterateElementGroups()) {
group.setDirectory(directory);
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setGroupBaseName(const std::string & basename,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Model::getGroupDumper(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
return group.getDumper();
}
/* -------------------------------------------------------------------------- */
// DUMPER stuff
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & field_id,
std::shared_ptr<dumpers::Field> field,
DumperIOHelper & dumper) {
#ifdef AKANTU_USE_IOHELPER
dumper.registerField(field_id, std::move(field));
#endif
}
/* -------------------------------------------------------------------------- */
void Model::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseName(const std::string & field_id) {
mesh.setBaseName(field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
mesh.setBaseNameToDumper(dumper_name, basename);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all",
dumper_default_element_kind, false);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldToDumper(group.getDefaultDumperName(), field_id,
group_name, dumper_default_element_kind,
false);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->removeDumpGroupFieldFromDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.removeDumpFieldFromDumper(dumper_name, field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all",
dumper_default_element_kind, true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldVectorToDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
dumper_default_element_kind, true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all",
dumper_default_element_kind, true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
ElementKind element_kind,
bool padding_flag) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
this->spatial_dimension, element_kind,
padding_flag);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
ElementKind element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> field;
if (!field) {
field = this->createNodalFieldReal(field_id, group_name, padding_flag);
}
if (!field) {
field = this->createNodalFieldUInt(field_id, group_name, padding_flag);
}
if (!field) {
field = this->createNodalFieldBool(field_id, group_name, padding_flag);
}
if (!field) {
field = this->createElementalField(field_id, group_name, padding_flag,
spatial_dimension, element_kind);
}
if (!field) {
field = this->mesh.createFieldFromAttachedData<UInt>(field_id, group_name,
element_kind);
}
if (!field) {
field = this->mesh.createFieldFromAttachedData<Real>(field_id, group_name,
element_kind);
}
#ifndef AKANTU_NDEBUG
if (!field) {
AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
}
#endif
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
this->addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
/* -------------------------------------------------------------------------- */
void Model::dump(const std::string & dumper_name) { mesh.dump(dumper_name); }
/* -------------------------------------------------------------------------- */
void Model::dump(const std::string & dumper_name, UInt step) {
mesh.dump(dumper_name, step);
}
/* ------------------------------------------------------------------------- */
void Model::dump(const std::string & dumper_name, Real time, UInt step) {
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void Model::dump() {
auto default_dumper = mesh.getDefaultDumperName();
this->dump(default_dumper);
}
/* -------------------------------------------------------------------------- */
void Model::dump(UInt step) {
auto default_dumper = mesh.getDefaultDumperName();
this->dump(default_dumper, step);
}
/* -------------------------------------------------------------------------- */
void Model::dump(Real time, UInt step) {
auto default_dumper = mesh.getDefaultDumperName();
this->dump(default_dumper, time, step);
}
/* -------------------------------------------------------------------------- */
void Model::setDirectory(const std::string & directory) {
mesh.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
mesh.setDirectoryToDumper(dumper_name, directory);
}
/* -------------------------------------------------------------------------- */
void Model::setTextModeToDumper() { mesh.setTextModeToDumper(); }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/model.hh b/src/model/model.hh
index 56f61b1c0..c7b75fe07 100644
--- a/src/model/model.hh
+++ b/src/model/model.hh
@@ -1,389 +1,391 @@
/**
* @file model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Interface of a model
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_named_argument.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "model_options.hh"
#include "model_solver.hh"
/* -------------------------------------------------------------------------- */
#include <typeindex>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MODEL_HH_
#define AKANTU_MODEL_HH_
namespace akantu {
class SynchronizerRegistry;
class Parser;
class DumperIOHelper;
class DOFManager;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model : public ModelSolver, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Normal constructor where the DOFManager is created internally
Model(Mesh & mesh, const ModelType & type, UInt dim = _all_dimensions,
const ID & id = "model");
/// Model constructor the the dof manager is created externally, for example
/// in a ModelCoupler
Model(Mesh & mesh, const ModelType & type,
std::shared_ptr<DOFManager> dof_manager, UInt dim = _all_dimensions,
const ID & id = "model");
~Model() override;
using FEEngineMap = std::map<std::string, std::unique_ptr<FEEngine>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
virtual void initFullImpl(const ModelOptions & options);
public:
template <typename... pack>
std::enable_if_t<are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
switch (this->model_type) {
#ifdef AKANTU_SOLID_MECHANICS
case ModelType::_solid_mechanics_model:
this->initFullImpl(SolidMechanicsModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_COHESIVE_ELEMENT
case ModelType::_solid_mechanics_model_cohesive:
this->initFullImpl(SolidMechanicsModelCohesiveOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_HEAT_TRANSFER
case ModelType::_heat_transfer_model:
this->initFullImpl(HeatTransferModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_PHASE_FIELD
case ModelType::_phase_field_model:
this->initFullImpl(PhaseFieldModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_EMBEDDED
case ModelType::_embedded_model:
this->initFullImpl(EmbeddedInterfaceModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_CONTACT_MECHANICS
case ModelType::_contact_mechanics_model:
this->initFullImpl(ContactMechanicsModelOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
#ifdef AKANTU_MODEL_COUPLERS
case ModelType::_coupler_solid_contact:
this->initFullImpl(CouplerSolidContactOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
case ModelType::_coupler_solid_cohesive_contact:
this->initFullImpl(CouplerSolidCohesiveContactOptions{
use_named_args, std::forward<decltype(_pack)>(_pack)...});
break;
#endif
default:
this->initFullImpl(ModelOptions{use_named_args,
std::forward<decltype(_pack)>(_pack)...});
}
}
template <typename... pack>
std::enable_if_t<not are_named_argument<pack...>::value>
initFull(pack &&... _pack) {
this->initFullImpl(std::forward<decltype(_pack)>(_pack)...);
}
/// initialize a new solver if needed
void initNewSolver(const AnalysisMethod & method);
protected:
/// get some default values for derived classes
virtual std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) = 0;
virtual void initModel() {};
virtual void initFEEngineBoundary();
/// function to print the containt of the class
void printself(std::ostream & /*stream*/,
int /*indent*/ = 0) const override{};
public:
/* ------------------------------------------------------------------------ */
/* Access to the dumpable interface of the boundaries */
/* ------------------------------------------------------------------------ */
/// Dump the data for a given group
void dumpGroup(const std::string & group_name);
void dumpGroup(const std::string & group_name,
const std::string & dumper_name);
/// Dump the data for all boundaries
void dumpGroup();
/// Set the directory for a given group
void setGroupDirectory(const std::string & directory,
const std::string & group_name);
/// Set the directory for all boundaries
void setGroupDirectory(const std::string & directory);
/// Set the base name for a given group
void setGroupBaseName(const std::string & basename,
const std::string & group_name);
/// Get the internal dumper of a given group
DumperIOHelper & getGroupDumper(const std::string & group_name);
/* ------------------------------------------------------------------------ */
/* Function for non local capabilities */
/* ------------------------------------------------------------------------ */
virtual void updateDataForNonLocalCriterion(__attribute__((unused))
ElementTypeMapReal & criterion) {
AKANTU_TO_IMPLEMENT();
}
protected:
template <typename T>
void allocNodalField(std::unique_ptr<Array<T>> & array, UInt nb_component,
const ID & name) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get id of model
AKANTU_GET_MACRO(ID, id, const ID &)
/// get the number of surfaces
AKANTU_GET_MACRO(Mesh, mesh, Mesh &)
/// synchronize the boundary in case of parallel run
virtual void synchronizeBoundaries(){};
/// return the fem object associated with a provided name
inline FEEngine & getFEEngine(const ID & name = "") const;
/// return the fem boundary object associated with a provided name
virtual FEEngine & getFEEngineBoundary(const ID & name = "");
inline bool hasFEEngineBoundary(const ID & name = "");
/// register a fem object associated with name
template <typename FEEngineClass>
inline void registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension);
/// unregister a fem object associated with name
inline void unRegisterFEEngineObject(const std::string & name);
/// return the synchronizer registry
SynchronizerRegistry & getSynchronizerRegistry();
/// return the fem object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClass(std::string name = "") const;
/// return the fem boundary object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClassBoundary(std::string name = "");
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, Model::spatial_dimension, UInt);
/* ------------------------------------------------------------------------ */
/* Pack and unpack hexlper functions */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id = ID()) const;
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
void setTextModeToDumper();
virtual void addDumpGroupFieldToDumper(const std::string & field_id,
std::shared_ptr<dumpers::Field> field,
DumperIOHelper & dumper);
virtual void addDumpField(const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void setBaseName(const std::string & field_id);
virtual void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
virtual void addDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
ElementKind element_kind,
bool padding_flag);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
ElementKind element_kind,
bool padding_flag);
virtual void removeDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & /*field_name*/,
const std::string & /*group_name*/,
bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field>
createNodalFieldUInt(const std::string & /*field_name*/,
const std::string & /*group_name*/,
bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & /*field_name*/,
const std::string & /*group_name*/,
bool /*padding_flag*/) {
return nullptr;
}
virtual std::shared_ptr<dumpers::Field> createElementalField(
const std::string & /*field_name*/, const std::string & /*group_name*/,
bool /*padding_flag*/, UInt /*spatial_dimension*/, ElementKind /*kind*/) {
return nullptr;
}
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
/* ------------------------------------------------------------------------ */
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
/* ------------------------------------------------------------------------ */
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
friend std::ostream & operator<<(std::ostream & /*stream*/,
const Model & /*_this*/);
ID id;
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// Mesh
Mesh & mesh;
/// Spatial dimension of the problem
UInt spatial_dimension;
/// the main fem object present in all models
FEEngineMap fems;
/// the fem object present in all models for boundaries
FEEngineMap fems_boundary;
/// default fem object
std::string default_fem;
/// parser to the pointer to use
Parser & parser;
/// default ElementKind for dumper
ElementKind dumper_default_element_kind{_ek_regular};
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Model & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "model_inline_impl.hh"
#endif /* AKANTU_MODEL_HH_ */
diff --git a/src/model/model_couplers/cohesive_contact_solvercallback.cc b/src/model/model_couplers/cohesive_contact_solvercallback.cc
index e9dd98566..f38138028 100644
--- a/src/model/model_couplers/cohesive_contact_solvercallback.cc
+++ b/src/model/model_couplers/cohesive_contact_solvercallback.cc
@@ -1,140 +1,141 @@
/**
* @file cohesive_contact_solvercallback.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu May 22 2019
+ * @date creation: Sun Jun 06 2021
+ * @date last modification: Sun Jun 06 2021
*
* @brief class for coupling of solid mechanics cohesive and contact mechanics
* model via solvercallback
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_contact_solvercallback.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveContactSolverCallback::CohesiveContactSolverCallback(
SolidMechanicsModelCohesive & solid, ContactMechanicsModel & contact,
AnalysisMethod & method)
: SolverCallback(), solid(solid), contact(contact), method(method) {}
void CohesiveContactSolverCallback::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
solid.assembleStiffnessMatrix();
switch (method) {
case _static:
case _implicit_dynamic: {
contact.assembleStiffnessMatrix();
break;
}
default:
break;
}
} else if (matrix_id == "M") {
solid.assembleMass();
}
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
solid.assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::assembleResidual() {
// computes the internal forces
switch (method) {
case _explicit_lumped_mass: {
auto & current_positions = contact.getContactDetector().getPositions();
current_positions.copy(solid.getCurrentPosition());
contact.search();
break;
}
default:
break;
}
solid.assembleInternalForces();
contact.assembleInternalForces();
auto & internal_force = solid.getInternalForce();
auto & external_force = solid.getExternalForce();
auto & contact_force = contact.getInternalForce();
solid.getDOFManager().assembleToResidual("displacement", external_force, 1);
solid.getDOFManager().assembleToResidual("displacement", internal_force, 1);
solid.getDOFManager().assembleToResidual("displacement", contact_force, 1);
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::predictor() {
auto & solid_model_solver = aka::as_type<ModelSolver>(solid);
solid_model_solver.predictor();
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::beforeSolveStep() {
auto & solid_model_solver = aka::as_type<ModelSolver>(solid);
solid_model_solver.beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::afterSolveStep(bool converged) {
auto & solid_model_solver = aka::as_type<ModelSolver>(solid);
solid_model_solver.afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
void CohesiveContactSolverCallback::corrector() {
auto & solid_model_solver = aka::as_type<ModelSolver>(solid);
solid_model_solver.corrector();
switch (method) {
case _static:
case _implicit_dynamic: {
auto & current_positions = contact.getContactDetector().getPositions();
current_positions.copy(solid.getCurrentPosition());
contact.search();
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
MatrixType
CohesiveContactSolverCallback::getMatrixType(const ID & /*matrix_id*/) {
return _symmetric;
}
} // namespace akantu
diff --git a/src/model/model_couplers/cohesive_contact_solvercallback.hh b/src/model/model_couplers/cohesive_contact_solvercallback.hh
index 9618de102..02dcd7399 100644
--- a/src/model/model_couplers/cohesive_contact_solvercallback.hh
+++ b/src/model/model_couplers/cohesive_contact_solvercallback.hh
@@ -1,91 +1,92 @@
/**
* @file cohesive_contact_solvercallback.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu Jan 17 2019
+ * @date creation: Sun Jun 06 2021
+ * @date last modification: Wed Jul 28 2021
*
* @brief class for coupling of solid mechanics and conatct mechanics
* model via solvercallback
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_iterators.hh"
#include "non_linear_solver.hh"
#include "contact_mechanics_model.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_CONTACT_SOLVERCALLBACK_HH__
#define __AKANTU_COHESIVE_CONTACT_SOLVERCALLBACK_HH__
namespace akantu{
class CohesiveContactSolverCallback : public SolverCallback {
public:
CohesiveContactSolverCallback(SolidMechanicsModelCohesive &,
ContactMechanicsModel &, AnalysisMethod &);
public:
/// implementation of SolverCallback::assembleMatrix
void assembleMatrix(const ID &) override;
/// implementation of SolverCallback::assembleResidual
void assembleResidual() override;
/// implementation of SolverCallback::assembleLumpedMatrix
void assembleLumpedMatrix(const ID &) override;
/// implementation of SolverCallback::getMatrixType
MatrixType getMatrixType(const ID &) override;
/// implementation of SolverCallback::predictor
void predictor() override;
/// implementation of SolverCallback::corrector
void corrector() override;
/// implementation of SolverCallback::beforeSolveStep
void beforeSolveStep() override;
/// implementation of SolverCallback::afterSolveStep
void afterSolveStep(bool converged=true) override;
private:
/// model for the solid mechanics part of the coupling
SolidMechanicsModelCohesive & solid;
/// model for the contact resoluion of the coupling
ContactMechanicsModel & contact;
/// Method of resolution for the coupling solver
AnalysisMethod & method;
};
}
#endif
diff --git a/src/model/model_couplers/coupler_solid_cohesive_contact.cc b/src/model/model_couplers/coupler_solid_cohesive_contact.cc
index ad51d7e25..34953b99a 100644
--- a/src/model/model_couplers/coupler_solid_cohesive_contact.cc
+++ b/src/model/model_couplers/coupler_solid_cohesive_contact.cc
@@ -1,76 +1,78 @@
/**
* @file coupler_solid_cohesive_contact.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu May 22 2019
+ * @date creation: Mon Jan 21 2019
+ * @date last modification: Wed Jun 23 2021
*
* @brief class for coupling of solid mechanics cohesive and conatct mechanics
* model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_cohesive_contact.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <>
CouplerSolidContactTemplate<SolidMechanicsModelCohesive>::
CouplerSolidContactTemplate(Mesh & mesh, UInt dim, const ID & id,
std::shared_ptr<DOFManager> dof_manager,
ModelType model_type)
: Model(mesh, model_type, dof_manager, dim, id) {
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("coupler_solid_cohesive_contact",
id, true);
this->mesh.addDumpMeshToDumper("coupler_solid_cohesive_contact", mesh,
Model::spatial_dimension, _not_ghost,
_ek_cohesive);
#endif
this->registerDataAccessor(*this);
solid = std::make_unique<SolidMechanicsModelCohesive>(
mesh, Model::spatial_dimension, "solid_mechanics_model_cohesive",
this->dof_manager);
contact = std::make_unique<ContactMechanicsModel>(mesh.getMeshFacets(),
Model::spatial_dimension,
"contact_mechanics_model");
}
/* -------------------------------------------------------------------------- */
template <>
void CouplerSolidContactTemplate<SolidMechanicsModelCohesive>::initFullImpl(
const ModelOptions & options) {
Model::initFullImpl(options);
const auto & cscc_options =
aka::as_type<CouplerSolidCohesiveContactOptions>(options);
solid->initFull(_analysis_method = cscc_options.analysis_method,
_is_extrinsic = cscc_options.is_extrinsic);
contact->initFull(_analysis_method = cscc_options.analysis_method);
}
} // namespace akantu
diff --git a/src/model/model_couplers/coupler_solid_cohesive_contact.hh b/src/model/model_couplers/coupler_solid_cohesive_contact.hh
index dd59bc4ce..099a59b28 100644
--- a/src/model/model_couplers/coupler_solid_cohesive_contact.hh
+++ b/src/model/model_couplers/coupler_solid_cohesive_contact.hh
@@ -1,50 +1,52 @@
/**
* @file coupler_solid_cohesive_contact.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu Jan 17 2019
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Wed Jul 28 2021
*
* @brief class for coupling of solid mechanics and conatct mechanics
* model in explicit
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_contact.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COUPLER_SOLID_COHESIVE_CONTACT_HH__
#define __AKANTU_COUPLER_SOLID_COHESIVE_CONTACT_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
using CouplerSolidCohesiveContact =
CouplerSolidContactTemplate<SolidMechanicsModelCohesive>;
} // namespace akantu
#endif /* __COUPLER_SOLID_CONTACT_HH__ */
diff --git a/src/model/model_couplers/coupler_solid_contact.cc b/src/model/model_couplers/coupler_solid_contact.cc
index ccec4b4ba..37d11add6 100644
--- a/src/model/model_couplers/coupler_solid_contact.cc
+++ b/src/model/model_couplers/coupler_solid_contact.cc
@@ -1,69 +1,71 @@
/**
* @file coupler_solid_contact.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu May 22 2019
+ * @date creation: Mon Jan 21 2019
+ * @date last modification: Wed Jun 23 2021
*
* @brief class for coupling of solid mechanics and conatct mechanics
* model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_contact.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <>
CouplerSolidContactTemplate<SolidMechanicsModel>::CouplerSolidContactTemplate(
Mesh & mesh, UInt dim, const ID & id,
std::shared_ptr<DOFManager> dof_manager, ModelType model_type)
: Model(mesh, model_type, dof_manager, dim, id) {
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("coupler_solid_contact", id, true);
this->mesh.addDumpMeshToDumper("coupler_solid_contact", mesh,
Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
this->registerDataAccessor(*this);
solid = std::make_unique<SolidMechanicsModel>(mesh, Model::spatial_dimension,
"solid_mechanics_model",
this->dof_manager);
contact = std::make_unique<ContactMechanicsModel>(
mesh, Model::spatial_dimension, "contact_mechanics_model",
this->dof_manager);
}
/* -------------------------------------------------------------------------- */
template <>
void CouplerSolidContactTemplate<SolidMechanicsModel>::initFullImpl(
const ModelOptions & options) {
Model::initFullImpl(options);
solid->initFull(_analysis_method = this->method);
contact->initFull(_analysis_method = this->method);
}
} // namespace akantu
diff --git a/src/model/model_couplers/coupler_solid_contact.hh b/src/model/model_couplers/coupler_solid_contact.hh
index 58cbbbe7a..4fa8898a2 100644
--- a/src/model/model_couplers/coupler_solid_contact.hh
+++ b/src/model/model_couplers/coupler_solid_contact.hh
@@ -1,280 +1,282 @@
/**
- * @file coupler_solid_contact_explicit.hh
+ * @file coupler_solid_contact.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu Jan 17 2019
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Sat Jun 26 2021
*
* @brief class for coupling of solid mechanics and conatct mechanics
* model in explicit
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
#include "solid_mechanics_model.hh"
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive.hh"
#endif
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COUPLER_SOLID_CONTACT_HH__
#define __AKANTU_COUPLER_SOLID_CONTACT_HH__
/* ------------------------------------------------------------------------ */
/* Coupling : Solid Mechanics / Contact Mechanics */
/* ------------------------------------------------------------------------ */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
class CouplerSolidContactTemplate : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt> {
static_assert(
std::is_base_of<SolidMechanicsModel, SolidMechanicsModelType>::value,
"SolidMechanicsModelType should be derived from SolidMechanicsModel");
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
CouplerSolidContactTemplate(
Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "coupler_solid_contact",
std::shared_ptr<DOFManager> dof_manager = nullptr,
ModelType model_type = std::is_same<SolidMechanicsModelType,
SolidMechanicsModelCohesive>::value
? ModelType::_coupler_solid_cohesive_contact
: ModelType::_coupler_solid_contact);
~CouplerSolidContactTemplate() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize completely the model
void initFullImpl(const ModelOptions & options) override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver Interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the contact stiffness matrix
virtual void assembleStiffnessMatrix();
/// assembles the contant internal forces
virtual void assembleInternalForces();
#if defined(AKANTU_COHESIVE_ELEMENT)
template <class Model_ = SolidMechanicsModelType,
std::enable_if_t<std::is_same<
Model_, SolidMechanicsModelCohesive>::value> * = nullptr>
UInt checkCohesiveStress() {
return solid->checkCohesiveStress();
}
#endif
template <typename FunctorType>
inline void applyBC(const FunctorType & func) {
solid->applyBC(func);
}
template <class FunctorType>
inline void applyBC(const FunctorType & func,
const std::string & group_name) {
solid->applyBC(func, group_name);
}
template <class FunctorType>
inline void applyBC(const FunctorType & func,
const ElementGroup & element_group) {
solid->applyBC(func, element_group);
}
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// callback for the solver, this adds f_{ext} or f_{int} to the residual
void assembleResidual(const ID & residual_part) override;
bool canSplitResidual() override { return true; }
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep(bool converged = true) override;
/// callback for the model to instantiate the matricess when needed
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
/* ------------------------------------------------------------------------ */
/* Mass matrix for solid mechanics model */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
protected:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
protected:
/* ------------------------------------------------------------------------ */
TimeStepSolverType getDefaultSolverType() const override;
/* ------------------------------------------------------------------------ */
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() { return method == _explicit_lumped_mass; }
/* ------------------------------------------------------------------------ */
public:
// DataAccessor<Element>
UInt getNbData(const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override {
return 0;
}
void packData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override {}
void unpackData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) override {}
// DataAccessor<UInt> nodes
UInt getNbData(const Array<UInt> & /*nodes*/,
const SynchronizationTag & /*tag*/) const override {
return 0;
}
void packData(CommunicationBuffer & /*buffer*/, const Array<UInt> & /*nodes*/,
const SynchronizationTag & /*tag*/) const override {}
void unpackData(CommunicationBuffer & /*buffer*/,
const Array<UInt> & /*nodes*/,
const SynchronizationTag & /*tag*/) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the solid mechanics model
#if defined(AKANTU_COHESIVE_ELEMENT)
template <class Model_ = SolidMechanicsModelType,
std::enable_if_t<std::is_same<
Model_, SolidMechanicsModelCohesive>::value> * = nullptr>
SolidMechanicsModelCohesive & getSolidMechanicsModelCohesive() {
return *solid;
}
#endif
template <class Model_ = SolidMechanicsModelType,
std::enable_if_t<
std::is_same<Model_, SolidMechanicsModel>::value> * = nullptr>
SolidMechanicsModelType & getSolidMechanicsModel() {
return *solid;
}
/// get the contact mechanics model
AKANTU_GET_MACRO(ContactMechanicsModel, *contact, ContactMechanicsModel &)
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
#if defined(AKANTU_USE_IOHELPER)
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldUInt(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension, ElementKind kind) override;
#endif
void dump(const std::string & dumper_name) override;
void dump(const std::string & dumper_name, UInt step) override;
void dump(const std::string & dumper_name, Real time, UInt step) override;
void dump() override;
void dump(UInt step) override;
void dump(Real time, UInt step) override;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// solid mechanics model
std::unique_ptr<SolidMechanicsModelType> solid;
/// contact mechanics model
std::unique_ptr<ContactMechanicsModel> contact;
UInt step;
};
using CouplerSolidContact = CouplerSolidContactTemplate<SolidMechanicsModel>;
} // namespace akantu
#include "coupler_solid_contact_tmpl.hh"
#endif /* __COUPLER_SOLID_CONTACT_HH__ */
diff --git a/src/model/model_couplers/coupler_solid_contact_tmpl.hh b/src/model/model_couplers/coupler_solid_contact_tmpl.hh
index 225f7f5c5..dd349e195 100644
--- a/src/model/model_couplers/coupler_solid_contact_tmpl.hh
+++ b/src/model/model_couplers/coupler_solid_contact_tmpl.hh
@@ -1,398 +1,400 @@
/**
- * @file coupler_solid_contact.cc
+ * @file coupler_solid_contact_tmpl.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jan 17 2019
- * @date last modification: Thu May 22 2019
+ * @date creation: Mon Jan 21 2019
+ * @date last modification: Wed Jun 23 2021
*
* @brief class for coupling of solid mechanics and conatct mechanics
* model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_contact.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
CouplerSolidContactTemplate<
SolidMechanicsModelType>::~CouplerSolidContactTemplate() = default;
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::initSolver(
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
auto & solid_model_solver = aka::as_type<ModelSolver>(*solid);
solid_model_solver.initSolver(time_step_solver_type, non_linear_solver_type);
auto & contact_model_solver = aka::as_type<ModelSolver>(*contact);
contact_model_solver.initSolver(time_step_solver_type,
non_linear_solver_type);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
std::tuple<ID, TimeStepSolverType>
CouplerSolidContactTemplate<SolidMechanicsModelType>::getDefaultSolverID(
const AnalysisMethod & method) {
return solid->getDefaultSolverID(method);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
TimeStepSolverType
CouplerSolidContactTemplate<SolidMechanicsModelType>::getDefaultSolverType()
const {
return solid->getDefaultSolverType();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
ModelSolverOptions
CouplerSolidContactTemplate<SolidMechanicsModelType>::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
return solid->getDefaultSolverOptions(type);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleResidual() {
// computes the internal forces
switch (method) {
case _explicit_lumped_mass: {
auto & current_positions = contact->getContactDetector().getPositions();
current_positions.copy(solid->getCurrentPosition());
contact->search();
break;
}
default:
break;
}
this->assembleInternalForces();
auto & internal_force = solid->getInternalForce();
auto & external_force = solid->getExternalForce();
auto & contact_force = contact->getInternalForce();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement", external_force, 1);
this->getDOFManager().assembleToResidual("displacement", internal_force, 1);
this->getDOFManager().assembleToResidual("displacement", contact_force, 1);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleResidual(
const ID & residual_part) {
AKANTU_DEBUG_IN();
// contact->assembleInternalForces();
auto & internal_force = solid->getInternalForce();
auto & external_force = solid->getExternalForce();
auto & contact_force = contact->getInternalForce();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement", external_force, 1);
this->getDOFManager().assembleToResidual("displacement", contact_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->getDOFManager().assembleToResidual("displacement", internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::predictor() {
auto & solid_model_solver = aka::as_type<ModelSolver>(*solid);
solid_model_solver.predictor();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::corrector() {
auto & solid_model_solver = aka::as_type<ModelSolver>(*solid);
solid_model_solver.corrector();
switch (method) {
case _static:
case _implicit_dynamic: {
auto & current_positions = contact->getContactDetector().getPositions();
current_positions.copy(solid->getCurrentPosition());
contact->search();
break;
}
default:
break;
}
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
MatrixType CouplerSolidContactTemplate<SolidMechanicsModelType>::getMatrixType(
const ID & matrix_id) {
if (matrix_id == "K")
return _symmetric;
if (matrix_id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleMatrix(
const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else if (matrix_id == "M") {
solid->assembleMass();
}
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleLumpedMatrix(
const ID & matrix_id) {
if (matrix_id == "M") {
solid->assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::beforeSolveStep() {
auto & solid_solver_callback = aka::as_type<SolverCallback>(*solid);
solid_solver_callback.beforeSolveStep();
auto & contact_solver_callback = aka::as_type<SolverCallback>(*contact);
contact_solver_callback.beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::afterSolveStep(
bool converged) {
auto & solid_solver_callback = aka::as_type<SolverCallback>(*solid);
solid_solver_callback.afterSolveStep(converged);
auto & contact_solver_callback = aka::as_type<SolverCallback>(*contact);
contact_solver_callback.afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<
SolidMechanicsModelType>::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
solid->assembleInternalForces();
contact->assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<
SolidMechanicsModelType>::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");
solid->assembleStiffnessMatrix(true);
switch (method) {
case _static:
case _implicit_dynamic: {
contact->assembleStiffnessMatrix();
break;
}
default:
break;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<
SolidMechanicsModelType>::assembleMassLumped() {
solid->assembleMassLumped();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleMass() {
solid->assembleMass();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleMassLumped(
GhostType ghost_type) {
solid->assembleMassLumped(ghost_type);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::assembleMass(
GhostType ghost_type) {
solid->assembleMass(ghost_type);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
std::shared_ptr<dumpers::Field>
CouplerSolidContactTemplate<SolidMechanicsModelType>::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, UInt spatial_dimension, ElementKind kind) {
std::shared_ptr<dumpers::Field> field;
field = contact->createElementalField(field_name, group_name, padding_flag,
spatial_dimension, kind);
if (not field) {
field = solid->createElementalField(field_name, group_name, padding_flag,
spatial_dimension, kind);
}
return field;
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
std::shared_ptr<dumpers::Field>
CouplerSolidContactTemplate<SolidMechanicsModelType>::createNodalFieldReal(
const std::string & field_name, const std::string & group_name,
bool padding_flag) {
std::shared_ptr<dumpers::Field> field;
field = contact->createNodalFieldReal(field_name, group_name, padding_flag);
if (not field) {
field = solid->createNodalFieldReal(field_name, group_name, padding_flag);
}
return field;
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
std::shared_ptr<dumpers::Field>
CouplerSolidContactTemplate<SolidMechanicsModelType>::createNodalFieldUInt(
const std::string & field_name, const std::string & group_name,
bool padding_flag) {
std::shared_ptr<dumpers::Field> field;
field = contact->createNodalFieldUInt(field_name, group_name, padding_flag);
if (not field) {
field = solid->createNodalFieldUInt(field_name, group_name, padding_flag);
}
return field;
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
std::shared_ptr<dumpers::Field>
CouplerSolidContactTemplate<SolidMechanicsModelType>::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
bool padding_flag) {
std::shared_ptr<dumpers::Field> field;
field = contact->createNodalFieldBool(field_name, group_name, padding_flag);
if (not field) {
field = solid->createNodalFieldBool(field_name, group_name, padding_flag);
}
return field;
}
#endif
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump(
const std::string & dumper_name) {
solid->onDump();
Model::dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump(
const std::string & dumper_name, UInt step) {
solid->onDump();
Model::dump(dumper_name, step);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump(
const std::string & dumper_name, Real time, UInt step) {
solid->onDump();
Model::dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump() {
solid->onDump();
Model::dump();
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump(UInt step) {
solid->onDump();
Model::dump(step);
}
/* -------------------------------------------------------------------------- */
template <class SolidMechanicsModelType>
void CouplerSolidContactTemplate<SolidMechanicsModelType>::dump(Real time,
UInt step) {
solid->onDump();
Model::dump(time, step);
}
} // namespace akantu
diff --git a/src/model/model_couplers/coupler_solid_phasefield.cc b/src/model/model_couplers/coupler_solid_phasefield.cc
index 24b2da078..c6d05310e 100644
--- a/src/model/model_couplers/coupler_solid_phasefield.cc
+++ b/src/model/model_couplers/coupler_solid_phasefield.cc
@@ -1,641 +1,642 @@
/**
* @file coupler_solid_phasefield.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Fri Sep 28 2018
- * @date last modification: Thu Jun 20 2019
+ * @date creation: Mon Jun 24 2019
+ * @date last modification: Fri Apr 02 2021
*
* @brief class for coupling of solid mechancis and phase model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_phasefield.hh"
#include "dumpable_inline_impl.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "element_synchronizer.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
CouplerSolidPhaseField::CouplerSolidPhaseField(Mesh & mesh, UInt dim,
const ID & id,
const ModelType model_type)
: Model(mesh, model_type, dim, id) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("CouplerSolidPhaseField", mesh,
Model::spatial_dimension);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("coupler_solid_phasefield", id,
true);
this->mesh.addDumpMeshToDumper("coupler_solid_phasefield", mesh,
Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
this->registerDataAccessor(*this);
solid = new SolidMechanicsModel(mesh, Model::spatial_dimension,
"solid_mechanics_model");
phase = new PhaseFieldModel(mesh, Model::spatial_dimension,
"phase_field_model");
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, SynchronizationTag::_csp_damage);
this->registerSynchronizer(synchronizer, SynchronizationTag::_csp_strain);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
CouplerSolidPhaseField::~CouplerSolidPhaseField() {}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
this->initBC(*this, *displacement, *displacement_increment, *external_force);
solid->initFull( _analysis_method = this->method);
phase->initFull( _analysis_method = this->method);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::initModel() {
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
FEEngine & CouplerSolidPhaseField::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(
getFEEngineClassBoundary<MyFEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
auto & solid_model_solver =
aka::as_type<ModelSolver>(*solid);
solid_model_solver.initSolver(time_step_solver_type, non_linear_solver_type);
auto & phase_model_solver =
aka::as_type<ModelSolver>(*phase);
phase_model_solver.initSolver(time_step_solver_type, non_linear_solver_type);
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
CouplerSolidPhaseField::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", TimeStepSolverType::_dynamic);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolverType CouplerSolidPhaseField::getDefaultSolverType() const {
return TimeStepSolverType::_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions CouplerSolidPhaseField::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_dynamic: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_linear;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
break;
}
return options;
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleResidual() {
// computes the internal forces
this->assembleInternalForces();
auto & solid_internal_force = solid->getInternalForce();
auto & solid_external_force = solid->getExternalForce();
auto & phasefield_internal_force = phase->getInternalForce();
auto & phasefield_external_force = phase->getExternalForce();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement", solid_external_force,
1);
this->getDOFManager().assembleToResidual("displacement", solid_internal_force,
1);
this->getDOFManager().assembleToResidual("damage", phasefield_external_force,
1);
this->getDOFManager().assembleToResidual("damage", phasefield_internal_force,
1);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
auto & solid_internal_force = solid->getInternalForce();
auto & solid_external_force = solid->getExternalForce();
auto & phasefield_internal_force = phase->getInternalForce();
auto & phasefield_external_force = phase->getExternalForce();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
solid_external_force, 1);
this->getDOFManager().assembleToResidual("displacement",
solid_internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->getDOFManager().assembleToResidual("damage",
phasefield_external_force, 1);
this->getDOFManager().assembleToResidual("damage",
phasefield_internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::predictor() {
auto & solid_model_solver =
aka::as_type<ModelSolver>(*solid);
solid_model_solver.predictor();
auto & phase_model_solver =
aka::as_type<ModelSolver>(*phase);
phase_model_solver.predictor();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::corrector() {
auto & solid_model_solver =
aka::as_type<ModelSolver>(*solid);
solid_model_solver.corrector();
auto & phase_model_solver =
aka::as_type<ModelSolver>(*phase);
phase_model_solver.corrector();
}
/* -------------------------------------------------------------------------- */
MatrixType CouplerSolidPhaseField::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K")
return _symmetric;
if (matrix_id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else if (matrix_id == "M") {
solid->assembleMass();
}
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
solid->assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::beforeSolveStep() {
auto & solid_solver_callback =
aka::as_type<SolverCallback>(*solid);
solid_solver_callback.beforeSolveStep();
auto & phase_solver_callback =
aka::as_type<SolverCallback>(*phase);
phase_solver_callback.beforeSolveStep();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::afterSolveStep(bool converged) {
auto & solid_solver_callback =
aka::as_type<SolverCallback>(*solid);
solid_solver_callback.afterSolveStep(converged);
auto & phase_solver_callback =
aka::as_type<SolverCallback>(*phase);
phase_solver_callback.afterSolveStep(converged);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
solid->assembleInternalForces();
phase->assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");
solid->assembleStiffnessMatrix();
phase->assembleStiffnessMatrix();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleMassLumped() { solid->assembleMassLumped(); }
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleMass() { solid->assembleMass(); }
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleMassLumped(GhostType ghost_type) {
solid->assembleMassLumped(ghost_type);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::assembleMass(GhostType ghost_type) {
solid->assembleMass(ghost_type);
}
/* ------------------------------------------------------------------------- */
void CouplerSolidPhaseField::computeDamageOnQuadPoints(
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = phase->getFEEngine();
auto & mesh = phase->getMesh();
auto nb_materials = solid->getNbMaterials();
auto nb_phasefields = phase->getNbPhaseFields();
AKANTU_DEBUG_ASSERT(nb_phasefields == nb_materials,
"The number of phasefields and materials should be equal" );
for(auto index : arange(nb_materials)) {
auto & material = solid->getMaterial(index);
for(auto index2 : arange(nb_phasefields)) {
auto & phasefield = phase->getPhaseField(index2);
if(phasefield.getName() == material.getName()){
switch (spatial_dimension) {
case 1: {
auto & mat = static_cast<MaterialPhaseField<1> &>(material);
auto & damage = mat.getDamage();
for (auto & type :
mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
auto & damage_on_qpoints_vect = damage(type, ghost_type);
fem.interpolateOnIntegrationPoints(phase->getDamage(), damage_on_qpoints_vect,
1, type, ghost_type);
}
break;
}
case 2: {
auto & mat = static_cast<MaterialPhaseField<2> &>(material);
auto & damage = mat.getDamage();
for (auto & type :
mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
auto & damage_on_qpoints_vect = damage(type, ghost_type);
fem.interpolateOnIntegrationPoints(phase->getDamage(), damage_on_qpoints_vect,
1, type, ghost_type);
}
break;
}
default:
auto & mat = static_cast<MaterialPhaseField<3> &>(material);
auto & damage = mat.getDamage();
for (auto & type :
mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
auto & damage_on_qpoints_vect = damage(type, ghost_type);
fem.interpolateOnIntegrationPoints(phase->getDamage(), damage_on_qpoints_vect,
1, type, ghost_type);
}
break;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void CouplerSolidPhaseField::computeStrainOnQuadPoints(
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
auto & mesh = solid->getMesh();
auto nb_materials = solid->getNbMaterials();
auto nb_phasefields = phase->getNbPhaseFields();
AKANTU_DEBUG_ASSERT(nb_phasefields == nb_materials,
"The number of phasefields and materials should be equal" );
for(auto index : arange(nb_materials)) {
auto & material = solid->getMaterial(index);
for(auto index2 : arange(nb_phasefields)) {
auto & phasefield = phase->getPhaseField(index2);
if(phasefield.getName() == material.getName()){
auto & strain_on_qpoints = phasefield.getStrain();
auto & gradu_on_qpoints = material.getGradU();
for (auto & type: mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & strain_on_qpoints_vect = strain_on_qpoints(type, ghost_type);
auto & gradu_on_qpoints_vect = gradu_on_qpoints(type, ghost_type);
for (auto && values:
zip(make_view(strain_on_qpoints_vect, spatial_dimension, spatial_dimension),
make_view(gradu_on_qpoints_vect, spatial_dimension, spatial_dimension))) {
auto & strain = std::get<0>(values);
auto & grad_u = std::get<1>(values);
gradUToEpsilon(grad_u, strain);
}
}
break;
}
}
}
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void CouplerSolidPhaseField::solve(const ID & solid_solver_id, const ID & phase_solver_id) {
solid->solveStep(solid_solver_id);
this->computeStrainOnQuadPoints(_not_ghost);
phase->solveStep(phase_solver_id);
this->computeDamageOnQuadPoints(_not_ghost);
solid->assembleInternalForces();
}
/* ------------------------------------------------------------------------- */
void CouplerSolidPhaseField::gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
for (UInt j = 0; j < Model::spatial_dimension; ++j)
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
}
}
/* ------------------------------------------------------------------------- */
bool CouplerSolidPhaseField::checkConvergence(Array<Real> & u_new,
Array<Real> & u_old,
Array<Real> & d_new,
Array<Real> & d_old) {
const Array<bool> & blocked_dofs = solid->getBlockedDOFs();
UInt nb_degree_of_freedom = u_new.size();
auto u_n_it = u_new.begin();
auto u_o_it = u_old.begin();
auto bld_it = blocked_dofs.begin();
Real norm = 0;
for (UInt n = 0; n < nb_degree_of_freedom;
++n, ++u_n_it, ++u_o_it, ++bld_it) {
if ((!*bld_it)) {
norm += (*u_n_it - *u_o_it) * (*u_n_it - *u_o_it);
}
}
norm = std::sqrt(norm);
auto d_n_it = d_new.begin();
auto d_o_it = d_old.begin();
nb_degree_of_freedom = d_new.size();
Real norm2 = 0;
for (UInt i = 0; i < nb_degree_of_freedom; ++i) {
norm2 += (*d_n_it - *d_o_it);
}
norm2 = std::sqrt(norm2);
Real error = std::max(norm, norm2);
Real tolerance = 1e-8;
if (error < tolerance) {
return true;
}
return false;
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> CouplerSolidPhaseField::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, UInt spatial_dimension,
ElementKind kind) {
return solid->createElementalField(field_name, group_name, padding_flag,
spatial_dimension, kind);
std::shared_ptr<dumpers::Field> field;
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
CouplerSolidPhaseField::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return solid->createNodalFieldReal(field_name, group_name, padding_flag);
std::shared_ptr<dumpers::Field> field;
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
CouplerSolidPhaseField::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return solid->createNodalFieldBool(field_name, group_name, padding_flag);
std::shared_ptr<dumpers::Field> field;
return field;
}
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> CouplerSolidPhaseField::createElementalField(
const std::string &, const std::string &, bool, UInt ,
ElementKind) {
return nullptr;
}
/* ----------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
CouplerSolidPhaseField::createNodalFieldReal(const std::string &,
const std::string &, bool) {
return nullptr;
}
/*-------------------------------------------------------------------*/
std::shared_ptr<dumpers::Field>
CouplerSolidPhaseField::createNodalFieldBool(const std::string &,
const std::string &, bool) {
return nullptr;
}
#endif
/* -----------------------------------------------------------------------*/
void CouplerSolidPhaseField::dump(const std::string & dumper_name) {
solid->onDump();
mesh.dump(dumper_name);
}
/* ------------------------------------------------------------------------*/
void CouplerSolidPhaseField::dump(const std::string & dumper_name, UInt step) {
solid->onDump();
mesh.dump(dumper_name, step);
}
/* ----------------------------------------------------------------------- */
void CouplerSolidPhaseField::dump(const std::string & dumper_name, Real time,
UInt step) {
solid->onDump();
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::dump() {
solid->onDump();
mesh.dump();
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::dump(UInt step) {
solid->onDump();
mesh.dump(step);
}
/* -------------------------------------------------------------------------- */
void CouplerSolidPhaseField::dump(Real time, UInt step) {
solid->onDump();
mesh.dump(time, step);
}
} // namespace akantu
diff --git a/src/model/model_couplers/coupler_solid_phasefield.hh b/src/model/model_couplers/coupler_solid_phasefield.hh
index ba2e8694a..1726dfa94 100644
--- a/src/model/model_couplers/coupler_solid_phasefield.hh
+++ b/src/model/model_couplers/coupler_solid_phasefield.hh
@@ -1,288 +1,289 @@
/**
- * @file solid_phase_coupler.hh
+ * @file coupler_solid_phasefield.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Fri Sep 28 2018
- * @date last modification: Fri Sep 28 2018
+ * @date creation: Mon Jun 24 2019
+ * @date last modification: Wed Jun 23 2021
*
* @brief class for coupling of solid mechancis and phasefield model
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "material.hh"
#include "material_phasefield.hh"
#include "model.hh"
#include "phase_field_model.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COUPLER_SOLID_PHASEFIELD_HH__
#define __AKANTU_COUPLER_SOLID_PHASEFIELD_HH__
/* ------------------------------------------------------------------------ */
/* Coupling : Solid Mechanics / PhaseField */
/* ------------------------------------------------------------------------ */
namespace akantu {
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
class DOFManager;
} // namespace akantu
namespace akantu {
class CouplerSolidPhaseField
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<CouplerSolidPhaseField> {
/* ------------------------------------------------------------------------ */
/* Constructor/Destructors */
/* ------------------------------------------------------------------------ */
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
public:
CouplerSolidPhaseField(
Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "coupler_solid_phasefield",
const ModelType model_type = ModelType::_coupler_solid_phasefield);
~CouplerSolidPhaseField() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the complete model
void initFullImpl(const ModelOptions & options) override;
/// initialize the modelType
void initModel() override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver Interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the contact stiffness matrix
virtual void assembleStiffnessMatrix();
/// assembles the contant internal forces
virtual void assembleInternalForces();
public:
/// computes damage on quad points for solid mechanics model from
/// damage array from phasefield model
void computeDamageOnQuadPoints(const GhostType &);
/// computes strain on quadrature points for phasefield model from
/// displacement gradient from solid mechanics model
void computeStrainOnQuadPoints(const GhostType & ghost_type);
/// solve the coupled model
void solve(const ID & solid_solver_id = "", const ID & phase_solver_id = "");
private:
/// computes small strain from displacement gradient
void gradUToEpsilon(const Matrix<Real> & grad_u, Matrix<Real> & epsilon);
/// test the convergence criteria
bool checkConvergence(Array<Real> &, Array<Real> &, Array<Real> &,
Array<Real> &);
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// callback for the solver, this adds f_{ext} or f_{int} to the residual
void assembleResidual(const ID & residual_part) override;
bool canSplitResidual() override { return true; }
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the model to instantiate the matricess when needed
void initSolver(TimeStepSolverType, NonLinearSolverType) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep(bool converged = true) override;
/// solve the coupled model
//void solveStep(const ID & solver_id = "") override;
/// solve a step using a given pre instantiated time step solver and
/// non linear solver with a user defined callback instead of the
/// model itself /!\ This can mess up everything
//void solveStep(SolverCallback & callback, const ID & solver_id = "") override;
/* ------------------------------------------------------------------------ */
/* Mass matrix for solid mechanics model */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
protected:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
protected:
/* --------------------------------------------------------------------------
*/
TimeStepSolverType getDefaultSolverType() const override;
/* --------------------------------------------------------------------------
*/
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() { return method == _explicit_lumped_mass; }
/* ------------------------------------------------------------------------ */
public:
// DataAccessor<Element>
UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
UInt getNbData(__attribute__((unused)) const Array<UInt> & indexes,
__attribute__((unused)) const SynchronizationTag & tag) const override {
return 0;
}
void packData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<UInt> & dofs,
__attribute__((unused)) const SynchronizationTag & tag) const override{}
void unpackData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<UInt> & dofs,
__attribute__((unused)) const SynchronizationTag & tag) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the solid mechanics model
AKANTU_GET_MACRO(SolidMechanicsModel, *solid, SolidMechanicsModel &);
/// get the contact mechanics model
AKANTU_GET_MACRO(PhaseFieldModel, *phase, PhaseFieldModel &);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension,
ElementKind kind) override;
virtual void dump(const std::string & dumper_name) override;
virtual void dump(const std::string & dumper_name, UInt step) override;
virtual void dump(const std::string & dumper_name, Real time, UInt step) override;
void dump() override;
virtual void dump(UInt step) override;
virtual void dump(Real time, UInt step) override;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// solid mechanics model
SolidMechanicsModel * solid{nullptr};
/// phasefield model
PhaseFieldModel * phase{nullptr};
Array<Real> * displacement{nullptr};
///
Array<Real> * displacement_increment{nullptr};
/// external forces array
Array<Real> * external_force{nullptr};
};
} // namespace akantu
#endif /* __AKANTU_COUPLER_SOLID_PHASEFIELD_HH__ */
diff --git a/src/model/model_inline_impl.hh b/src/model/model_inline_impl.hh
index 7c3ed82c5..1563a3a2a 100644
--- a/src/model/model_inline_impl.hh
+++ b/src/model/model_inline_impl.hh
@@ -1,175 +1,177 @@
/**
* @file model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 25 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Mar 10 2021
*
* @brief inline implementation of the model class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MODEL_INLINE_IMPL_HH_
#define AKANTU_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClassBoundary(std::string name) {
if (name.empty()) {
name = default_fem;
}
auto it_boun = fems_boundary.find(name);
if (it_boun == fems_boundary.end()) {
AKANTU_DEBUG_INFO("Creating FEEngine boundary " << name);
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << name << " is not registered");
}
auto spatial_dimension = it->second->getElementDimension();
fems_boundary[name] = std::make_unique<FEEngineClass>(
it->second->getMesh(), spatial_dimension - 1,
id + ":fem_boundary:" + name);
}
return aka::as_type<FEEngineClass>(*fems_boundary[name]);
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClass(std::string name) const {
if (name.empty()) {
name = default_fem;
}
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << name << " is not registered");
}
return aka::as_type<FEEngineClass>(*(it->second));
}
/* -------------------------------------------------------------------------- */
inline void Model::unRegisterFEEngineObject(const std::string & name) {
auto it = fems.find(name);
if (it == fems.end()) {
AKANTU_EXCEPTION("FEEngine object with name " << name << " was not found");
}
fems.erase(it);
if (not fems.empty() and default_fem == name) {
default_fem = (*fems.begin()).first;
}
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline void Model::registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension) {
if (fems.empty()) {
default_fem = name;
}
auto it = fems.find(name);
if (it != fems.end()) {
AKANTU_EXCEPTION("FEEngine object with name " << name
<< " was already created");
}
fems[name] = std::make_unique<FEEngineClass>(
mesh, spatial_dimension, id + ":fem:" + name);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngine(const ID & name) const {
ID tmp_name = (name.empty()) ? default_fem : name;
auto it = fems.find(tmp_name);
if (it == fems.end()) {
AKANTU_EXCEPTION("The FEEngine " << tmp_name << " is not registered");
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngineBoundary(const ID & name) {
ID tmp_name = (name.empty()) ? default_fem : name;
auto it = fems_boundary.find(tmp_name);
if (it == fems_boundary.end()) {
AKANTU_EXCEPTION("The FEEngine boundary " << tmp_name
<< " is not registered");
}
AKANTU_DEBUG_ASSERT(it->second != nullptr, "The FEEngine boundary "
<< tmp_name
<< " was not created");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
inline bool Model::hasFEEngineBoundary(const ID & name) {
ID tmp_name = (name.empty()) ? default_fem : name;
auto it = fems_boundary.find(tmp_name);
return (it != fems_boundary.end());
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Model::allocNodalField(std::unique_ptr<Array<T>> & array,
UInt nb_component, const ID & name) const {
if (array) {
return;
}
UInt nb_nodes = mesh.getNbNodes();
array =
std::make_unique<Array<T>>(nb_nodes, nb_component, T(), id + ":" + name);
}
/* -------------------------------------------------------------------------- */
inline UInt Model::getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id) const {
UInt nb_quad = 0;
for (auto && el : elements) {
nb_quad +=
getFEEngine(fem_id).getNbIntegrationPoints(el.type, el.ghost_type);
}
return nb_quad;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/model_options.hh b/src/model/model_options.hh
index d33e89ecf..b9f462c99 100644
--- a/src/model/model_options.hh
+++ b/src/model/model_options.hh
@@ -1,200 +1,204 @@
/**
* @file model_options.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 04 2017
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Fri Jun 12 2020
*
- * @brief A Documented file.
+ * @brief Description of the model options
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_named_argument.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MODEL_OPTIONS_HH_
#define AKANTU_MODEL_OPTIONS_HH_
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(analysis_method);
}
struct ModelOptions {
explicit ModelOptions(AnalysisMethod analysis_method = _static)
: analysis_method(analysis_method) {}
template <typename... pack>
ModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: ModelOptions(OPTIONAL_NAMED_ARG(analysis_method, _static)) {}
virtual ~ModelOptions() = default;
AnalysisMethod analysis_method;
};
#ifdef AKANTU_SOLID_MECHANICS
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelOptions : public ModelOptions {
explicit SolidMechanicsModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
SolidMechanicsModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: SolidMechanicsModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_COHESIVE_ELEMENT
namespace {
DECLARE_NAMED_ARGUMENT(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelCohesiveOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelCohesiveOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false)
: SolidMechanicsModelOptions(analysis_method), is_extrinsic(extrinsic) {}
template <typename... pack>
SolidMechanicsModelCohesiveOptions(use_named_args_t /*unused*/,
pack &&... _pack)
: SolidMechanicsModelCohesiveOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(is_extrinsic, false)) {}
bool is_extrinsic{false};
};
#endif
#ifdef AKANTU_HEAT_TRANSFER
/* -------------------------------------------------------------------------- */
struct HeatTransferModelOptions : public ModelOptions {
explicit HeatTransferModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
HeatTransferModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: HeatTransferModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
#ifdef AKANTU_PHASE_FIELD
/* -------------------------------------------------------------------------- */
struct PhaseFieldModelOptions : public ModelOptions {
explicit PhaseFieldModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
PhaseFieldModelOptions(use_named_args_t, pack &&... _pack)
: PhaseFieldModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_EMBEDDED
namespace {
DECLARE_NAMED_ARGUMENT(init_intersections);
}
/* -------------------------------------------------------------------------- */
struct EmbeddedInterfaceModelOptions : SolidMechanicsModelOptions {
/**
* @brief Constructor for EmbeddedInterfaceModelOptions
* @param analysis_method see SolidMechanicsModelOptions
* @param init_intersections compute intersections
*/
EmbeddedInterfaceModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool init_intersections = true)
: SolidMechanicsModelOptions(analysis_method),
has_intersections(init_intersections) {}
template <typename... pack>
EmbeddedInterfaceModelOptions(use_named_args_t /*unused*/, pack &&... _pack)
: EmbeddedInterfaceModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(init_intersections, true)) {}
/// Should consider reinforcements
bool has_intersections;
};
#endif
#ifdef AKANTU_CONTACT_MECHANICS
/* -------------------------------------------------------------------------- */
struct ContactMechanicsModelOptions : public ModelOptions {
explicit ContactMechanicsModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
ContactMechanicsModelOptions(use_named_args_t, pack &&... _pack)
: ContactMechanicsModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
#endif
#ifdef AKANTU_MODEL_COUPLERS
/* -------------------------------------------------------------------------- */
struct CouplerSolidContactOptions : public ModelOptions {
explicit CouplerSolidContactOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass)
: ModelOptions(analysis_method) {}
template <typename... pack>
CouplerSolidContactOptions(use_named_args_t, pack &&... _pack)
: CouplerSolidContactOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass)) {}
};
/* -------------------------------------------------------------------------- */
struct CouplerSolidCohesiveContactOptions : public ModelOptions {
CouplerSolidCohesiveContactOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false)
: ModelOptions(analysis_method), is_extrinsic(extrinsic) {}
template<typename... pack>
CouplerSolidCohesiveContactOptions(use_named_args_t, pack &&... _pack)
: CouplerSolidCohesiveContactOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(is_extrinsic, false)) {}
bool is_extrinsic{false};
};
#endif
} // namespace akantu
#endif /* AKANTU_MODEL_OPTIONS_HH_ */
diff --git a/src/model/phase_field/phase_field_model.cc b/src/model/phase_field/phase_field_model.cc
index b4379b6cc..22465d450 100644
--- a/src/model/phase_field/phase_field_model.cc
+++ b/src/model/phase_field/phase_field_model.cc
@@ -1,632 +1,633 @@
/**
* @file phase_field_model.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Aug 01 2018
- * @date last modification: Wed Aug 01 2018
+ * @date creation: Tue Sep 04 2018
+ * @date last modification: Wed Jun 23 2021
*
* @brief Implementation of PhaseFieldModel class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "phase_field_model.hh"
#include "dumpable_inline_impl.hh"
#include "element_synchronizer.hh"
#include "fe_engine_template.hh"
#include "generalized_trapezoidal.hh"
#include "group_manager_inline_impl.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "parser.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PhaseFieldModel::PhaseFieldModel(Mesh & mesh, UInt dim, const ID & id,
ModelType model_type)
: Model(mesh, model_type, dim, id),
phasefield_index("phasefield index", id),
phasefield_local_numbering("phasefield local numbering", id) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<FEEngineType>("PhaseFieldFEEngine", mesh,
Model::spatial_dimension);
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("phase_field", id, true);
this->mesh.addDumpMesh(mesh, Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif // AKANTU_USE_IOHELPER
phasefield_selector =
std::make_shared<DefaultPhaseFieldSelector>(phasefield_index);
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_damage);
this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_driving);
this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_history);
this->registerSynchronizer(synchronizer, SynchronizationTag::_pfm_energy);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PhaseFieldModel::~PhaseFieldModel() = default;
/* -------------------------------------------------------------------------- */
MatrixType PhaseFieldModel::getMatrixType(const ID & matrix_id) {
if (matrix_id == "K") {
return _symmetric;
}
return _mt_not_defined;
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::initModel() {
auto & fem = this->getFEEngine();
fem.initShapeFunctions(_not_ghost);
fem.initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::initFullImpl(const ModelOptions & options) {
phasefield_index.initialize(mesh, _element_kind = _ek_not_defined,
_default_value = UInt(-1),
_with_nb_element = true);
phasefield_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true);
Model::initFullImpl(options);
// initialize the phasefields
if (this->parser.getLastParsedFile() != "") {
this->instantiatePhaseFields();
this->initPhaseFields();
}
this->initBC(*this, *damage, *external_force);
}
/* -------------------------------------------------------------------------- */
PhaseField &
PhaseFieldModel::registerNewPhaseField(const ParserSection & section) {
std::string phase_name;
std::string phase_type = section.getName();
std::string opt_param = section.getOption();
try {
std::string tmp = section.getParameter("name");
phase_name = tmp; /** this can seam weird, but there is an ambiguous
* operator overload that i couldn't solve. @todo remove
* the weirdness of this code
*/
} catch (debug::Exception &) {
AKANTU_ERROR("A phasefield of type \'"
<< phase_type
<< "\' in the input file has been defined without a name!");
}
PhaseField & phase =
this->registerNewPhaseField(phase_name, phase_type, opt_param);
phase.parseSection(section);
return phase;
}
/* -------------------------------------------------------------------------- */
PhaseField & PhaseFieldModel::registerNewPhaseField(const ID & phase_name,
const ID & phase_type,
const ID & opt_param) {
AKANTU_DEBUG_ASSERT(phasefields_names_to_id.find(phase_name) ==
phasefields_names_to_id.end(),
"A phasefield with this name '"
<< phase_name << "' has already been registered. "
<< "Please use unique names for phasefields");
UInt phase_count = phasefields.size();
phasefields_names_to_id[phase_name] = phase_count;
std::stringstream sstr_phase;
sstr_phase << this->id << ":" << phase_count << ":" << phase_type;
ID mat_id = sstr_phase.str();
std::unique_ptr<PhaseField> phase = PhaseFieldFactory::getInstance().allocate(
phase_type, opt_param, *this, mat_id);
phasefields.push_back(std::move(phase));
return *(phasefields.back());
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::instantiatePhaseFields() {
ParserSection model_section;
bool is_empty;
std::tie(model_section, is_empty) = this->getParserSection();
if (not is_empty) {
auto model_phasefields =
model_section.getSubSections(ParserType::_phasefield);
for (const auto & section : model_phasefields) {
this->registerNewPhaseField(section);
}
}
auto sub_sections = this->parser.getSubSections(ParserType::_phasefield);
for (const auto & section : sub_sections) {
this->registerNewPhaseField(section);
}
if (phasefields.empty())
AKANTU_EXCEPTION("No phasefields where instantiated for the model"
<< getID());
are_phasefields_instantiated = true;
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::initPhaseFields() {
AKANTU_DEBUG_ASSERT(phasefields.size() != 0, "No phasefield to initialize !");
if (!are_phasefields_instantiated)
instantiatePhaseFields();
this->assignPhaseFieldToElements();
for (auto & phasefield : phasefields) {
/// init internals properties
phasefield->initPhaseField();
}
this->synchronize(SynchronizationTag::_smm_init_mat);
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assignPhaseFieldToElements(
const ElementTypeMapArray<UInt> * filter) {
for_each_element(
mesh,
[&](auto && element) {
UInt phase_index = (*phasefield_selector)(element);
AKANTU_DEBUG_ASSERT(
phase_index < phasefields.size(),
"The phasefield selector returned an index that does not exists");
phasefield_index(element) = phase_index;
},
_element_filter = filter, _ghost_type = _not_ghost);
for_each_element(
mesh,
[&](auto && element) {
auto phase_index = phasefield_index(element);
auto index = phasefields[phase_index]->addElement(element);
phasefield_local_numbering(element) = index;
},
_element_filter = filter, _ghost_type = _not_ghost);
// synchronize the element phasefield arrays
this->synchronize(SynchronizationTag::_material_id);
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else {
AKANTU_ERROR("Unknown Matrix ID for PhaseFieldModel : " << matrix_id);
}
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::predictor() {
// AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::corrector() {
// AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType) {
DOFManager & dof_manager = this->getDOFManager();
this->allocNodalField(this->damage, 1, "damage");
this->allocNodalField(this->external_force, 1, "external_force");
this->allocNodalField(this->internal_force, 1, "internal_force");
this->allocNodalField(this->blocked_dofs, 1, "blocked_dofs");
this->allocNodalField(this->previous_damage, 1, "previous_damage");
if (!dof_manager.hasDOFs("damage")) {
dof_manager.registerDOFs("damage", *this->damage, _dst_nodal);
dof_manager.registerBlockedDOFs("damage", *this->blocked_dofs);
dof_manager.registerDOFsPrevious("damage", *this->previous_damage);
}
if (time_step_solver_type == TimeStepSolverType::_dynamic) {
AKANTU_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
FEEngine & PhaseFieldModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<FEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
PhaseFieldModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", TimeStepSolverType::_dynamic);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions PhaseFieldModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["damage"] =
IntegrationSchemeType::_central_difference;
options.solution_type["damage"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_linear;
options.integration_scheme_type["damage"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["damage"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["damage"] =
IntegrationSchemeType::_backward_euler;
options.solution_type["damage"] = IntegrationScheme::_damage;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::beforeSolveStep() {
for (auto & phasefield : phasefields) {
phasefield->beforeSolveStep();
}
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::afterSolveStep(bool converged) {
if (not converged)
return;
for (auto && values : zip(*damage, *previous_damage)) {
auto & dam = std::get<0>(values);
auto & prev_dam = std::get<1>(values);
dam -= prev_dam;
prev_dam = dam;
}
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");
if (!this->getDOFManager().hasMatrix("K")) {
this->getDOFManager().getNewMatrix("K", getMatrixType("K"));
}
this->getDOFManager().zeroMatrix("K");
for (auto & phasefield : phasefields) {
phasefield->assembleStiffnessMatrix(_not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assembleResidual() {
this->assembleInternalForces();
this->getDOFManager().assembleToResidual("damage", *this->external_force, 1);
this->getDOFManager().assembleToResidual("damage", *this->internal_force, 1);
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assembleInternalForces() {
AKANTU_DEBUG_INFO("Assemble the internal forces");
this->internal_force->zero();
// communicate the driving forces
AKANTU_DEBUG_INFO("Send data for residual assembly");
this->asynchronousSynchronize(SynchronizationTag::_pfm_driving);
// assemble the forces due to local driving forces
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for (auto & phasefield : phasefields) {
phasefield->assembleInternalForces(_not_ghost);
}
// finalize communications
AKANTU_DEBUG_INFO("Wait distant driving forces");
this->waitEndSynchronize(SynchronizationTag::_pfm_driving);
// assemble the residual due to ghost elements
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::assembleLumpedMatrix(const ID & /*matrix_id*/) {}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("phase_field").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
UInt PhaseFieldModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
UInt nb_nodes_per_element = 0;
for (const Element & el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_pfm_damage: {
size += nb_nodes_per_element * sizeof(Real); // damage
break;
}
case SynchronizationTag::_pfm_driving: {
size += getNbIntegrationPoints(elements) * sizeof(Real);
break;
}
case SynchronizationTag::_pfm_history: {
size += getNbIntegrationPoints(elements) * sizeof(Real);
break;
}
case SynchronizationTag::_pfm_energy: {
size += getNbIntegrationPoints(elements) * sizeof(Real);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
return size;
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::packData(__attribute__((unused))
CommunicationBuffer & buffer,
__attribute__((unused))
const Array<Element> & elements,
__attribute__((unused))
const SynchronizationTag & tag) const {}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::unpackData(__attribute__((unused))
CommunicationBuffer & buffer,
__attribute__((unused))
const Array<Element> & elements,
__attribute__((unused))
const SynchronizationTag & tag) {}
/* -------------------------------------------------------------------------- */
UInt PhaseFieldModel::getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
UInt size = 0;
UInt nb_nodes = indexes.size();
switch (tag) {
case SynchronizationTag::_pfm_damage: {
size += nb_nodes * sizeof(Real);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
return size;
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) const {
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_pfm_damage: {
buffer << (*damage)(index);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
}
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & indexes,
const SynchronizationTag & tag) {
for (auto index : indexes) {
switch (tag) {
case SynchronizationTag::_pfm_damage: {
buffer >> (*damage)(index);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
}
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name, bool) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs.get();
return mesh.createNodalField(uint_nodal_fields[field_name], group_name);
std::shared_ptr<dumpers::Field> field;
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name, bool) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["damage"] = damage.get();
real_nodal_fields["external_force"] = external_force.get();
real_nodal_fields["internal_force"] = internal_force.get();
return mesh.createNodalField(real_nodal_fields[field_name], group_name);
std::shared_ptr<dumpers::Field> field;
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createElementalField(const std::string & field_name,
const std::string & group_name, bool,
UInt, ElementKind element_kind) {
if (field_name == "partitions") {
return mesh.createElementalField<UInt, dumpers::ElementPartitionField>(
mesh.getConnectivities(), group_name, this->spatial_dimension,
element_kind);
}
std::shared_ptr<dumpers::Field> field;
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createElementalField(const std::string &, const std::string &,
bool, const UInt &, ElementKind) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createNodalFieldReal(const std::string &, const std::string &,
bool) {
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
PhaseFieldModel::createNodalFieldBool(const std::string &, const std::string &,
bool) {
return nullptr;
}
#endif
/* -------------------------------------------------------------------------- */
void PhaseFieldModel::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Phase Field Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << Model::spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + nodals information [" << std::endl;
damage->printself(stream, indent + 2);
external_force->printself(stream, indent + 2);
internal_force->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + phasefield information [" << std::endl;
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/model/phase_field/phase_field_model.hh b/src/model/phase_field/phase_field_model.hh
index 451a1de1a..28cdafa61 100644
--- a/src/model/phase_field/phase_field_model.hh
+++ b/src/model/phase_field/phase_field_model.hh
@@ -1,335 +1,336 @@
/**
* @file phase_field_model.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Jul 30 2018
- * @date last modification: Mon Feb 05 2018
+ * @date creation: Tue Sep 04 2018
+ * @date last modification: Wed Jun 23 2021
*
* @brief Model class for Phase Field problem
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASE_FIELD_MODEL_HH__
#define __AKANTU_PHASE_FIELD_MODEL_HH__
namespace akantu {
class PhaseField;
class PhaseFieldSelector;
template <ElementKind kind, class IntegrationOrderFuntor> class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class PhaseFieldModel : public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<PhaseFieldModel> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using FEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
PhaseFieldModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "phase_field_model",
ModelType model_type = ModelType::_phase_field_model);
~PhaseFieldModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// generic function to initialize everything ready for explicit dynamics
void initFullImpl(const ModelOptions & options) override;
/// initialize all internal array for phasefields
void initPhaseFields();
/// allocate all vectors
void initSolver(TimeStepSolverType, NonLinearSolverType) override;
/// initialize the model
void initModel() override;
/// predictor
void predictor() override;
/// corrector
void corrector() override;
/// compute the heat flux
void assembleResidual() override;
/// get the type of matrix needed
MatrixType getMatrixType(const ID &) override;
/// callback to assemble a Matrix
void assembleMatrix(const ID &) override;
/// callback to assemble a lumped Matrix
void assembleLumpedMatrix(const ID &) override;
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/* ------------------------------------------------------------------------ */
/* Materials (phase_field_model.cc) */
/* ------------------------------------------------------------------------ */
public:
/// register an empty phasefield of a given type
PhaseField & registerNewPhaseField(const ID & mat_name, const ID & mat_type,
const ID & opt_param);
/// reassigns phasefields depending on the phasefield selector
void reassignPhaseField();
protected:
/// register a phasefield in the dynamic database
PhaseField & registerNewPhaseField(const ParserSection & phase_section);
/// read the phasefield files to instantiate all the phasefields
void instantiatePhaseFields();
/// set the element_id_by_phasefield and add the elements to the good
/// phasefields
void assignPhaseFieldToElements(
const ElementTypeMapArray<UInt> * filter = nullptr);
/* ------------------------------------------------------------------------ */
/* Methods for static */
/* ------------------------------------------------------------------------ */
public:
/// assembles the phasefield stiffness matrix
virtual void assembleStiffnessMatrix();
/// compute the internal forces
virtual void assembleInternalForces();
// compute the internal forces
void assembleInternalForces(const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* Methods for dynamic */
/* ------------------------------------------------------------------------ */
public:
/// set the stable timestep
void setTimeStep(Real time_step, const ID & solver_id = "") override;
protected:
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep(bool converged = true) override;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & indexes,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the damage array
AKANTU_GET_MACRO_DEREF_PTR(Damage, damage);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Damage, damage);
/// get the PhaseFieldModel::internal_force vector (internal forces)
AKANTU_GET_MACRO_DEREF_PTR(InternalForce, internal_force);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(InternalForce, internal_force);
/// get the PhaseFieldModel::external_force vector (external forces)
AKANTU_GET_MACRO_DEREF_PTR(ExternalForce, external_force);
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(ExternalForce, external_force);
/// get the PhaseFieldModel::force vector (external forces)
Array<Real> & getForce() {
AKANTU_DEBUG_WARNING("getForce was maintained for backward compatibility, "
"use getExternalForce instead");
return *external_force;
}
/// get the PhaseFieldModel::blocked_dofs vector
AKANTU_GET_MACRO_DEREF_PTR(BlockedDOFs, blocked_dofs);
/// get an iterable on the phasefields
inline decltype(auto) getPhaseFields();
/// get an iterable on the phasefields
inline decltype(auto) getPhaseFields() const;
/// get a particular phasefield (by phasefield index)
inline PhaseField & getPhaseField(UInt mat_index);
/// get a particular phasefield (by phasefield index)
inline const PhaseField & getPhaseField(UInt mat_index) const;
/// get a particular phasefield (by phasefield name)
inline PhaseField & getPhaseField(const std::string & name);
/// get a particular phasefield (by phasefield name)
inline const PhaseField & getPhaseField(const std::string & name) const;
/// get a particular phasefield id from is name
inline UInt getPhaseFieldIndex(const std::string & name) const;
/// give the number of phasefields
inline UInt getNbPhaseFields() const { return phasefields.size(); }
/// give the phasefield internal index from its id
Int getInternalIndexFromID(const ID & id) const;
AKANTU_GET_MACRO(PhaseFieldByElement, phasefield_index,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(PhaseFieldLocalNumbering, phasefield_local_numbering,
const ElementTypeMapArray<UInt> &);
/// vectors containing local material element index for each global element
/// index
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PhaseFieldByElement, phasefield_index,
UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(PhaseFieldByElement, phasefield_index, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PhaseFieldLocalNumbering,
phasefield_local_numbering, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(PhaseFieldLocalNumbering,
phasefield_local_numbering, UInt);
AKANTU_GET_MACRO_NOT_CONST(PhaseFieldSelector, *phasefield_selector,
PhaseFieldSelector &);
AKANTU_SET_MACRO(PhaseFieldSelector, phasefield_selector,
std::shared_ptr<PhaseFieldSelector>);
FEEngine & getFEEngineBoundary(const ID & name = "") override;
/* ------------------------------------------------------------------------ */
/* Dumpable Interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension, ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// number of iterations
UInt n_iter;
/// damage array
std::unique_ptr<Array<Real>> damage;
/// damage array at the previous time step
std::unique_ptr<Array<Real>> previous_damage;
/// boundary vector
std::unique_ptr<Array<bool>> blocked_dofs;
/// external force vector
std::unique_ptr<Array<Real>> external_force;
/// residuals array
std::unique_ptr<Array<Real>> internal_force;
/// Arrays containing the phasefield index for each element
ElementTypeMapArray<UInt> phasefield_index;
/// Arrays containing the position in the element filter of the phasefield
/// (phasefield's local numbering)
ElementTypeMapArray<UInt> phasefield_local_numbering;
/// class defining of to choose a phasefield
std::shared_ptr<PhaseFieldSelector> phasefield_selector;
/// mapping between phasefield name and phasefield internal id
std::map<std::string, UInt> phasefields_names_to_id;
/// list of used phasefields
std::vector<std::unique_ptr<PhaseField>> phasefields;
/// tells if the phasefield are instantiated
bool are_phasefields_instantiated{false};
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "phasefield.hh"
#include "phase_field_model_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#endif
diff --git a/src/model/phase_field/phase_field_model_inline_impl.cc b/src/model/phase_field/phase_field_model_inline_impl.cc
index 8433875d7..5b06aadab 100644
--- a/src/model/phase_field/phase_field_model_inline_impl.cc
+++ b/src/model/phase_field/phase_field_model_inline_impl.cc
@@ -1,69 +1,100 @@
+/**
+ * @file phase_field_model_inline_impl.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Fri Jun 19 2020
+ *
+ * @brief Phase field implementation of inline functions
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "phasefield_selector.hh"
#include "phasefield_selector_tmpl.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASE_FIELD_MODEL_INLINE_IMPL_CC__
#define __AKANTU_PHASE_FIELD_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline decltype(auto) PhaseFieldModel::getPhaseFields() {
return make_dereference_adaptor(phasefields);
}
/* -------------------------------------------------------------------------- */
inline decltype(auto) PhaseFieldModel::getPhaseFields() const {
return make_dereference_adaptor(phasefields);
}
/* -------------------------------------------------------------------------- */
inline PhaseField & PhaseFieldModel::getPhaseField(UInt mat_index) {
AKANTU_DEBUG_ASSERT(mat_index < phasefields.size(),
"The model " << id << " has no phasefield no "
<< mat_index);
return *phasefields[mat_index];
}
/* -------------------------------------------------------------------------- */
inline const PhaseField & PhaseFieldModel::getPhaseField(UInt mat_index) const {
AKANTU_DEBUG_ASSERT(mat_index < phasefields.size(),
"The model " << id << " has no phasefield no "
<< mat_index);
return *phasefields[mat_index];
}
/* -------------------------------------------------------------------------- */
inline PhaseField & PhaseFieldModel::getPhaseField(const std::string & name) {
std::map<std::string, UInt>::const_iterator it =
phasefields_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != phasefields_names_to_id.end(),
"The model " << id << " has no phasefield named " << name);
return *phasefields[it->second];
}
/* -------------------------------------------------------------------------- */
inline UInt
PhaseFieldModel::getPhaseFieldIndex(const std::string & name) const {
auto it = phasefields_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != phasefields_names_to_id.end(),
"The model " << id << " has no phasefield named " << name);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline const PhaseField &
PhaseFieldModel::getPhaseField(const std::string & name) const {
auto it = phasefields_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != phasefields_names_to_id.end(),
"The model " << id << " has no phasefield named " << name);
return *phasefields[it->second];
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_PHASE_FIELD_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/phase_field/phasefield.cc b/src/model/phase_field/phasefield.cc
index 8ece183ec..f3fa89f96 100644
--- a/src/model/phase_field/phasefield.cc
+++ b/src/model/phase_field/phasefield.cc
@@ -1,298 +1,299 @@
/**
- * @file pahsefield.cc
+ * @file phasefield.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Mar 2 2020
- * @date last modification: Mon Mar 2 2020
+ * @date creation: Fri Jun 19 2020
+ * @date last modification: Fri May 14 2021
*
* @brief Implementation of the common part of the phasefield class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "phasefield.hh"
#include "phase_field_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PhaseField::PhaseField(PhaseFieldModel & model, const ID & id)
: Parsable(ParserType::_phasefield, id), id(id), fem(model.getFEEngine()),
model(model), spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id), damage("damage", *this),
phi("phi", *this), strain("strain", *this),
driving_force("driving_force", *this),
damage_energy("damage_energy", *this),
damage_energy_density("damage_energy_density", *this) {
AKANTU_DEBUG_IN();
/// for each connectivity types allocate the element filer array of the
/// material
element_filter.initialize(model.getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PhaseField::PhaseField(PhaseFieldModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: Parsable(ParserType::_phasefield, id), id(id), fem(fe_engine),
model(model), spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id),
damage("damage", *this, dim, fe_engine, this->element_filter),
phi("phi", *this, dim, fe_engine, this->element_filter),
strain("strain", *this, dim, fe_engine, this->element_filter),
driving_force("driving_force", *this, dim, fe_engine,
this->element_filter),
damage_energy("damage_energy", *this, dim, fe_engine,
this->element_filter),
damage_energy_density("damage_energy_density", *this, dim, fe_engine,
this->element_filter) {
AKANTU_DEBUG_IN();
/// for each connectivity types allocate the element filer array of the
/// material
element_filter.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PhaseField::~PhaseField() = default;
/* -------------------------------------------------------------------------- */
void PhaseField::initialize() {
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("l0", l0, Real(0.), _pat_parsable | _pat_readable,
"length scale parameter");
registerParam("gc", g_c, _pat_parsable | _pat_readable,
"critical local fracture energy density");
registerParam("E", E, _pat_parsable | _pat_readable, "Young's modulus");
registerParam("nu", nu, _pat_parsable | _pat_readable, "Poisson ratio");
damage.initialize(1);
phi.initialize(1);
driving_force.initialize(1);
strain.initialize(spatial_dimension * spatial_dimension);
damage_energy_density.initialize(1);
damage_energy.initialize(spatial_dimension * spatial_dimension);
}
/* -------------------------------------------------------------------------- */
void PhaseField::initPhaseField() {
AKANTU_DEBUG_IN();
this->phi.initializeHistory();
this->resizeInternals();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::resizeInternals() {
AKANTU_DEBUG_IN();
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it) {
it->second->resize();
}
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it) {
it->second->resize();
}
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it) {
it->second->resize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::updateInternalParameters() {
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
}
/* -------------------------------------------------------------------------- */
void PhaseField::computeAllDrivingForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (const auto & type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
auto & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
continue;
}
computeDrivingForce(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & internal_force = model.getInternalForce();
for (auto type : element_filter.elementTypes(_ghost_type = ghost_type)) {
auto & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
continue;
}
auto nb_element = elem_filter.size();
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
Array<Real> nt_driving_force(nb_quadrature_points, nb_nodes_per_element);
fem.computeNtb(driving_force(type, ghost_type), nt_driving_force, type,
ghost_type, elem_filter);
Array<Real> int_nt_driving_force(nb_element, nb_nodes_per_element);
fem.integrate(nt_driving_force, int_nt_driving_force, nb_nodes_per_element,
type, ghost_type, elem_filter);
model.getDOFManager().assembleElementalArrayLocalArray(
int_nt_driving_force, internal_force, type, ghost_type, 1, elem_filter);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix");
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
auto & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
AKANTU_DEBUG_OUT();
return;
}
auto nb_element = elem_filter.size();
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
auto nt_b_n = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points,
nb_nodes_per_element * nb_nodes_per_element, "N^t*b*N");
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points,
nb_nodes_per_element * nb_nodes_per_element, "B^t*D*B");
// damage_energy_density_on_qpoints = gc/l0 + phi = scalar
auto & damage_energy_density_vect = damage_energy_density(type, ghost_type);
// damage_energy_on_qpoints = gc*l0 = scalar
auto & damage_energy_vect = damage_energy(type, ghost_type);
fem.computeBtDB(damage_energy_vect, *bt_d_b, 2, type, ghost_type,
elem_filter);
fem.computeNtbN(damage_energy_density_vect, *nt_b_n, type, ghost_type,
elem_filter);
/// compute @f$ K_{\grad d} = \int_e \mathbf{N}^t * \mathbf{w} *
/// \mathbf{N}@f$
auto K_n = std::make_unique<Array<Real>>(
nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_n");
fem.integrate(*nt_b_n, *K_n, nb_nodes_per_element * nb_nodes_per_element,
type, ghost_type, elem_filter);
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "damage", *K_n, type, _not_ghost, _symmetric, elem_filter);
/// compute @f$ K_{\grad d} = \int_e \mathbf{B}^t * \mathbf{W} *
/// \mathbf{B}@f$
auto K_b = std::make_unique<Array<Real>>(
nb_element, nb_nodes_per_element * nb_nodes_per_element, "K_b");
fem.integrate(*bt_d_b, *K_b, nb_nodes_per_element * nb_nodes_per_element,
type, ghost_type, elem_filter);
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "damage", *K_b, type, _not_ghost, _symmetric, elem_filter);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::beforeSolveStep() {
this->savePreviousState();
this->computeAllDrivingForces(_not_ghost);
}
/* -------------------------------------------------------------------------- */
void PhaseField::afterSolveStep() {}
/* -------------------------------------------------------------------------- */
void PhaseField::savePreviousState() {
AKANTU_DEBUG_IN();
for (auto pair : internal_vectors_real) {
if (pair.second->hasHistory()) {
pair.second->saveCurrentValues();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PhaseField::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::string type = getID().substr(getID().find_last_of(':') + 1);
stream << space << "PhaseField Material " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/model/phase_field/phasefield.hh b/src/model/phase_field/phasefield.hh
index 27f442aa6..1b13f132d 100644
--- a/src/model/phase_field/phasefield.hh
+++ b/src/model/phase_field/phasefield.hh
@@ -1,299 +1,300 @@
/**
* @file phasefield.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Mar 2 2020
- * @date last modification: Mon Mar 2 2020
+ * @date creation: Fri Jun 19 2020
+ * @date last modification: Wed Jun 23 2021
*
* @brief Mother class for all phasefield laws
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "data_accessor.hh"
#include "parsable.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#include "random_internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASEFIELD_HH__
#define __AKANTU_PHASEFIELD_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class PhaseFieldModel;
class PhaseField;
} // namespace akantu
namespace akantu {
template <typename T>
using InternalPhaseField = InternalFieldTmpl<PhaseField, T>;
using PhaseFieldFactory =
Factory<PhaseField, ID, const ID &, PhaseFieldModel &, const ID &>;
class PhaseField : public DataAccessor<Element>, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PhaseField(const PhaseField & phase) = delete;
PhaseField & operator=(const PhaseField & phase) = delete;
/// Initialize phasefield with defaults
PhaseField(PhaseFieldModel & model, const ID & id = "");
/// Initialize phasefield with custom mesh & fe_engine
PhaseField(PhaseFieldModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
/// Destructor
~PhaseField() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
void registerInternal(InternalPhaseField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
template <typename T>
void unregisterInternal(InternalPhaseField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
/// initialize the phasefield computed parameter
virtual void initPhaseField();
///
virtual void beforeSolveStep();
///
virtual void afterSolveStep();
/// assemble the residual for this phasefield
virtual void assembleInternalForces(GhostType ghost_type);
/// assemble the stiffness matrix for this phasefield
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// compute the driving force for this phasefield
virtual void computeAllDrivingForces(GhostType ghost_type = _not_ghost);
/// save the phi in the phi internal field if needed
virtual void savePreviousState();
/// add an element to the local mesh filter
inline UInt addElement(const ElementType & type, UInt element,
const GhostType & ghost_type);
inline UInt addElement(const Element & element);
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
protected:
/// resize the internals arrrays
virtual void resizeInternals();
/// function called to updatet the internal parameters when the
/// modifiable parameters are modified
virtual void updateInternalParameters();
// constitutive law for driving force
virtual void computeDrivingForce(const ElementType & /* el_type */,
GhostType /* ghost_type */ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <typename T>
inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID()) const;
template <typename T>
inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID());
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Name, name, const std::string &);
AKANTU_GET_MACRO(Model, model, const PhaseFieldModel &)
AKANTU_GET_MACRO(ID, id, const ID &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Strain, strain, Real);
AKANTU_GET_MACRO(Strain, strain, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Strain, strain, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
AKANTU_GET_MACRO(ElementFilter, element_filter,
const ElementTypeMapArray<UInt> &);
template <typename T>
const InternalPhaseField<T> & getInternal(const ID & id) const;
template <typename T> InternalPhaseField<T> & getInternal(const ID & id);
template <typename T>
inline bool isInternal(const ID & id, const ElementKind & element_kind) const;
template <typename T> inline void setParam(const ID & param, T value);
inline const Parameter & getParam(const ID & param) const;
template <typename T>
void flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// boolean to know if the material has been initialized
bool is_init;
std::map<ID, InternalPhaseField<Real> *> internal_vectors_real;
std::map<ID, InternalPhaseField<UInt> *> internal_vectors_uint;
std::map<ID, InternalPhaseField<bool> *> internal_vectors_bool;
protected:
ID id;
/// Link to the fem object in the model
FEEngine & fem;
/// phasefield name
std::string name;
/// The model to whch the phasefield belong
PhaseFieldModel & model;
/// length scale parameter
Real l0;
/// critical energy release rate
Real g_c;
/// Young's modulus
Real E;
/// Poisson ratio
Real nu;
/// Lame's first parameter
Real lambda;
/// Lame's second paramter
Real mu;
/// spatial dimension
UInt spatial_dimension;
/// list of element handled by the phasefield
ElementTypeMapArray<UInt> element_filter;
/// damage arrays ordered by element types
InternalPhaseField<Real> damage;
/// phi arrays ordered by element types
InternalPhaseField<Real> phi;
/// strain arrays ordered by element types
InternalPhaseField<Real> strain;
/// driving force ordered by element types
InternalPhaseField<Real> driving_force;
/// damage energy ordered by element types
InternalPhaseField<Real> damage_energy;
/// damage energy density ordered by element types
InternalPhaseField<Real> damage_energy_density;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const PhaseField & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "phasefield_inline_impl.cc"
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
#define PHASEFIELD_DEFAULT_ALLOCATOR(id, phase_name) \
[](const ID &, PhaseFieldModel & model, \
const ID & id) -> std::unique_ptr<PhaseField> { \
return std::make_unique<phase_name>(model, id); \
}
#define INSTANTIATE_PHASEFIELD(id, phase_name) \
static bool phasefield_is_alocated_##id [[gnu::unused]] = \
PhaseFieldFactory::getInstance().registerAllocator( \
#id, PHASEFIELD_DEFAULT_ALLOCATOR(id, phase_name))
#endif
diff --git a/src/model/phase_field/phasefield_inline_impl.cc b/src/model/phase_field/phasefield_inline_impl.cc
index 84a6edec1..6f4f79413 100644
--- a/src/model/phase_field/phasefield_inline_impl.cc
+++ b/src/model/phase_field/phasefield_inline_impl.cc
@@ -1,128 +1,159 @@
+/**
+ * @file phasefield_inline_impl.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Jun 19 2020
+ * @date last modification: Fri Apr 02 2021
+ *
+ * @brief Phase field implementation of inline functions
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "phase_field_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASEFIELD_INLINE_IMPL_CC__
#define __AKANTU_PHASEFIELD_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt PhaseField::addElement(const ElementType & type, UInt element,
const GhostType & ghost_type) {
Array<UInt> & el_filter = this->element_filter(type, ghost_type);
el_filter.push_back(element);
return el_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
inline UInt PhaseField::addElement(const Element & element) {
return this->addElement(element.type, element.element, element.ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
inline void PhaseField::registerInternal<Real>(InternalPhaseField<Real> & vect) {
internal_vectors_real[vect.getID()] = &vect;
}
template <>
inline void PhaseField::registerInternal<UInt>(InternalPhaseField<UInt> & vect) {
internal_vectors_uint[vect.getID()] = &vect;
}
template <>
inline void PhaseField::registerInternal<bool>(InternalPhaseField<bool> & vect) {
internal_vectors_bool[vect.getID()] = &vect;
}
/* -------------------------------------------------------------------------- */
template <>
inline void PhaseField::unregisterInternal<Real>(InternalPhaseField<Real> & vect) {
internal_vectors_real.erase(vect.getID());
}
template <>
inline void PhaseField::unregisterInternal<UInt>(InternalPhaseField<UInt> & vect) {
internal_vectors_uint.erase(vect.getID());
}
template <>
inline void PhaseField::unregisterInternal<bool>(InternalPhaseField<bool> & vect) {
internal_vectors_bool.erase(vect.getID());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool PhaseField::isInternal(__attribute__((unused)) const ID & id,
__attribute__((unused))
const ElementKind & element_kind) const {
AKANTU_TO_IMPLEMENT();
}
template <>
inline bool PhaseField::isInternal<Real>(const ID & id,
const ElementKind & element_kind) const {
auto internal_array = internal_vectors_real.find(this->getID() + ":" + id);
if (internal_array == internal_vectors_real.end() ||
internal_array->second->getElementKind() != element_kind)
return false;
return true;
}
/* -------------------------------------------------------------------------- */
inline UInt PhaseField::getNbData(__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) const SynchronizationTag & tag) const {
return 0;
}
/* -------------------------------------------------------------------------- */
inline void PhaseField::packData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) const SynchronizationTag & tag) const {
}
/* -------------------------------------------------------------------------- */
inline void PhaseField::unpackData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) const SynchronizationTag & tag) {
}
/* -------------------------------------------------------------------------- */
inline const Parameter & PhaseField::getParam(const ID & param) const {
try {
return get(param);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void PhaseField::packElementDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) const {
DataAccessor::packElementalDataHelper<T>(data_to_pack, buffer, elements, true,
model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void PhaseField::unpackElementDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) {
DataAccessor::unpackElementalDataHelper<T>(data_to_unpack, buffer, elements,
true, model.getFEEngine(fem_id));
}
}
#endif
diff --git a/src/model/phase_field/phasefield_selector.hh b/src/model/phase_field/phasefield_selector.hh
index 511d986fa..ac46bb05c 100644
--- a/src/model/phase_field/phasefield_selector.hh
+++ b/src/model/phase_field/phasefield_selector.hh
@@ -1,168 +1,169 @@
/**
* @file phasefield_selector.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Mar 1 2020
- * @date last modification: Sun Mar 1 2020
+ * @date creation: Wed Nov 13 2013
+ * @date last modification: Fri May 14 2021
*
- * @brief class describing how to choose a phasefield variable
+ * @brief class describing how to choose a phasefield variable
* function for a given element
*
+ *
* @section LICENSE
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASEFIELD_SELECTOR_HH__
#define __AKANTU_PHASEFIELD_SELECTOR_HH__
namespace akantu {
class PhaseFieldModel;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* main class to assign same or different phasefield constitutive laws to
* different elements
*/
class PhaseFieldSelector
: public std::enable_shared_from_this<PhaseFieldSelector> {
public:
PhaseFieldSelector() = default;
virtual ~PhaseFieldSelector() = default;
virtual inline UInt operator()(const Element & element) {
if (fallback_selector) {
return (*fallback_selector)(element);
}
return fallback_value;
}
inline void setFallback(UInt f) { fallback_value = f; }
inline void
setFallback(const std::shared_ptr<PhaseFieldSelector> & fallback_selector) {
this->fallback_selector = fallback_selector;
}
inline void setFallback(PhaseFieldSelector & fallback_selector) {
this->fallback_selector = fallback_selector.shared_from_this();
}
inline std::shared_ptr<PhaseFieldSelector> & getFallbackSelector() {
return this->fallback_selector;
}
inline UInt getFallbackValue() const { return this->fallback_value; }
protected:
UInt fallback_value{0};
std::shared_ptr<PhaseFieldSelector> fallback_selector;
};
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first phasefield to regular elements by default
*/
class DefaultPhaseFieldSelector : public PhaseFieldSelector {
public:
explicit DefaultPhaseFieldSelector(
const ElementTypeMapArray<UInt> & phasefield_index)
: phasefield_index(phasefield_index) {}
UInt operator()(const Element & element) override {
if (not phasefield_index.exists(element.type, element.ghost_type)) {
return PhaseFieldSelector::operator()(element);
}
const auto & phase_indexes =
phasefield_index(element.type, element.ghost_type);
if (element.element < phase_indexes.size()) {
auto && tmp_phase = phase_indexes(element.element);
if (tmp_phase != UInt(-1)) {
return tmp_phase;
}
}
return PhaseFieldSelector::operator()(element);
}
private:
const ElementTypeMapArray<UInt> & phasefield_index;
};
/* -------------------------------------------------------------------------- */
/**
* Use elemental data to assign phasefields
*/
template <typename T>
class ElementDataPhaseFieldSelector : public PhaseFieldSelector {
public:
ElementDataPhaseFieldSelector(const ElementTypeMapArray<T> & element_data,
const PhaseFieldModel & model,
UInt first_index = 1)
: element_data(element_data), model(model), first_index(first_index) {}
inline T elementData(const Element & element) {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
T data = element_data(element.type, element.ghost_type)(element.element);
debug::setDebugLevel(dbl);
return data;
}
inline UInt operator()(const Element & element) override {
return PhaseFieldSelector::operator()(element);
}
protected:
/// list of element with the specified data (i.e. tag value)
const ElementTypeMapArray<T> & element_data;
/// the model that the materials belong
const PhaseFieldModel & model;
/// first phasefield index: equal to 1 if none specified
UInt first_index;
};
/* -------------------------------------------------------------------------- */
/**
* class to use mesh data information to assign different phasefields
* where name is the tag value: tag_0, tag_1
*/
template <typename T>
class MeshDataPhaseFieldSelector : public ElementDataPhaseFieldSelector<T> {
public:
MeshDataPhaseFieldSelector(const std::string & name,
const PhaseFieldModel & model,
UInt first_index = 1);
};
} // namespace akantu
#endif /* __AKANTU_PHASEFIELD_SELECTOR_HH__ */
diff --git a/src/model/phase_field/phasefield_selector_tmpl.hh b/src/model/phase_field/phasefield_selector_tmpl.hh
index 97fa56999..fca2db9eb 100644
--- a/src/model/phase_field/phasefield_selector_tmpl.hh
+++ b/src/model/phase_field/phasefield_selector_tmpl.hh
@@ -1,73 +1,74 @@
/**
* @file phasefield_selector_tmpl.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Mar 1 2020
- * @date last modification: Sun Mar 01 2020
+ * @date creation: Wed Nov 13 2013
+ * @date last modification: Fri Jun 19 2020
*
* @brief Implementation of the template PhaseFieldSelector
*
+ *
* @section LICENSE
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "phasefield_selector.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASEFIELD_SELECTOR_TMPL_HH__
#define __AKANTU_PHASEFIELD_SELECTOR_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataPhaseFieldSelector<std::string>::
operator()(const Element & element) {
try {
std::string material_name = this->elementData(element);
return model.getPhaseFieldIndex(material_name);
} catch (...) {
return PhaseFieldSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline UInt ElementDataPhaseFieldSelector<UInt>::
operator()(const Element & element) {
try {
return this->elementData(element) - first_index;
} catch (...) {
return PhaseFieldSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
MeshDataPhaseFieldSelector<T>::MeshDataPhaseFieldSelector(
const std::string & name, const PhaseFieldModel & model,
UInt first_index)
: ElementDataPhaseFieldSelector<T>(model.getMesh().getData<T>(name), model,
first_index) {}
} // namespace akantu
#endif /* __AKANTU_PHASEFIELD_SELECTOR_TMPL_HH__ */
diff --git a/src/model/phase_field/phasefields/phasefield_exponential.cc b/src/model/phase_field/phasefields/phasefield_exponential.cc
index e682a0dbd..e8def49b8 100644
--- a/src/model/phase_field/phasefields/phasefield_exponential.cc
+++ b/src/model/phase_field/phasefields/phasefield_exponential.cc
@@ -1,69 +1,70 @@
/**
* @file phasefield_exponential.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Mar 3 2020
- * @date last modification: Mon Mar 3 2020
+ * @date creation: Fri Jun 19 2020
+ * @date last modification: Wed Jun 23 2021
*
* @brief Specialization of the phasefield law class for exponential type
* law
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "phasefield_exponential.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
PhaseFieldExponential::PhaseFieldExponential(PhaseFieldModel & model,
const ID & id)
: PhaseField(model, id) {}
/* -------------------------------------------------------------------------- */
void PhaseFieldExponential::updateInternalParameters() {
PhaseField::updateInternalParameters();
Matrix<Real> d(spatial_dimension, spatial_dimension);
d.eye(this->g_c * this->l0);
damage_energy.set(d);
}
/* -------------------------------------------------------------------------- */
void PhaseFieldExponential::computeDrivingForce(const ElementType & el_type,
GhostType ghost_type) {
for (auto && tuple : zip(this->phi(el_type, ghost_type),
this->phi.previous(el_type, ghost_type),
this->driving_force(el_type, ghost_type),
this->damage_energy_density(el_type, ghost_type),
make_view(this->strain(el_type, ghost_type),
spatial_dimension, spatial_dimension))) {
computePhiOnQuad(std::get<4>(tuple), std::get<0>(tuple),
std::get<1>(tuple));
computeDamageEnergyDensityOnQuad(std::get<0>(tuple), std::get<3>(tuple));
computeDrivingForceOnQuad(std::get<0>(tuple), std::get<2>(tuple));
}
}
INSTANTIATE_PHASEFIELD(exponential, PhaseFieldExponential);
} // namespace akantu
diff --git a/src/model/phase_field/phasefields/phasefield_exponential.hh b/src/model/phase_field/phasefields/phasefield_exponential.hh
index 49c0285e0..77f1358ab 100644
--- a/src/model/phase_field/phasefields/phasefield_exponential.hh
+++ b/src/model/phase_field/phasefields/phasefield_exponential.hh
@@ -1,134 +1,135 @@
/**
* @file phasefield_exponential.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Fri Jun 18 2020
- * @date last modification: Mon Jan 29 2020
+ * @date creation: Fri Jun 19 2020
+ * @date last modification: Wed Jun 23 2021
*
* @brief Phasefield law for approximating discrete crack as an exponential
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "phasefield.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PHASEFIELD_EXPONENTIAL_HH__
#define __AKANTU_PHASEFIELD_EXPONENTIAL_HH__
namespace akantu {
class PhaseFieldExponential : public PhaseField {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PhaseFieldExponential(PhaseFieldModel & model, const ID & id = "");
~PhaseFieldExponential() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void computePhiOnQuad(const Matrix<Real> &, Real &, Real &);
void computeDrivingForce(const ElementType &, GhostType) override;
inline void computeDrivingForceOnQuad(const Real &, Real &);
inline void computeDamageEnergyDensityOnQuad(const Real &, Real &);
public:
void updateInternalParameters() override;
};
/* -------------------------------------------------------------------------- */
inline void
PhaseFieldExponential::computeDrivingForceOnQuad(const Real & phi_quad,
Real & driving_force_quad) {
driving_force_quad = 2.0 * phi_quad;
}
/* -------------------------------------------------------------------------- */
inline void PhaseFieldExponential::computeDamageEnergyDensityOnQuad(
const Real & phi_quad, Real & dam_energy_quad) {
dam_energy_quad = 2.0 * phi_quad + this->g_c / this->l0;
}
/* -------------------------------------------------------------------------- */
inline void
PhaseFieldExponential::computePhiOnQuad(const Matrix<Real> & strain_quad,
Real & phi_quad, Real & phi_hist_quad) {
Matrix<Real> strain_plus(spatial_dimension, spatial_dimension);
Matrix<Real> strain_minus(spatial_dimension, spatial_dimension);
Matrix<Real> strain_dir(spatial_dimension, spatial_dimension);
Matrix<Real> strain_diag_plus(spatial_dimension, spatial_dimension);
Matrix<Real> strain_diag_minus(spatial_dimension, spatial_dimension);
Vector<Real> strain_values(spatial_dimension);
Real trace_plus, trace_minus;
strain_plus.zero();
strain_minus.zero();
strain_dir.zero();
strain_values.zero();
strain_diag_plus.zero();
strain_diag_minus.zero();
strain_quad.eig(strain_values, strain_dir);
for (UInt i = 0; i < spatial_dimension; i++) {
strain_diag_plus(i, i) = std::max(Real(0.), strain_values(i));
strain_diag_minus(i, i) = std::min(Real(0.), strain_values(i));
}
Matrix<Real> mat_tmp(spatial_dimension, spatial_dimension);
Matrix<Real> sigma_plus(spatial_dimension, spatial_dimension);
Matrix<Real> sigma_minus(spatial_dimension, spatial_dimension);
mat_tmp.mul<false, true>(strain_diag_plus, strain_dir);
strain_plus.mul<false, false>(strain_dir, mat_tmp);
mat_tmp.mul<false, true>(strain_diag_minus, strain_dir);
strain_minus.mul<false, true>(strain_dir, mat_tmp);
trace_plus = std::max(Real(0.), strain_quad.trace());
trace_minus = std::min(Real(0.), strain_quad.trace());
for (UInt i = 0; i < spatial_dimension; i++) {
for (UInt j = 0; j < spatial_dimension; j++) {
sigma_plus(i, j) =
(i == j) * lambda * trace_plus + 2 * mu * strain_plus(i, j);
sigma_minus(i, j) =
(i == j) * lambda * trace_minus + 2 * mu * strain_minus(i, j);
}
}
phi_quad = 0.5 * sigma_plus.doubleDot(strain_quad);
if (phi_quad < phi_hist_quad)
phi_quad = phi_hist_quad;
}
} // namespace akantu
#endif
diff --git a/src/model/solid_mechanics/material.cc b/src/model/solid_mechanics/material.cc
index 1f9484c36..deb835bdf 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1209 +1,1214 @@
/**
* @file material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Fabian Barras <fabian.barras@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of the common part of the material class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
- * You should have received a copy of the GNU Lesser General Public License
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, const ID & id)
: Parsable(ParserType::_material, id), id(id), fem(model.getFEEngine()),
model(model), spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id), stress("stress", *this),
eigengradu("eigen_grad_u", *this), gradu("grad_u", *this),
green_strain("green_strain", *this),
piola_kirchhoff_2("piola_kirchhoff_2", *this),
potential_energy("potential_energy", *this),
interpolation_inverse_coordinates("interpolation inverse coordinates",
*this),
interpolation_points_matrices("interpolation points matrices", *this),
eigen_grad_u(model.getSpatialDimension(), model.getSpatialDimension(),
0.) {
AKANTU_DEBUG_IN();
this->registerParam("eigen_grad_u", eigen_grad_u, _pat_parsable,
"EigenGradU");
/// for each connectivity types allocate the element filer array of the
/// material
element_filter.initialize(model.getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: Parsable(ParserType::_material, id), id(id), fem(fe_engine), model(model),
spatial_dimension(dim), element_filter("element_filter", id),
stress("stress", *this, dim, fe_engine, this->element_filter),
eigengradu("eigen_grad_u", *this, dim, fe_engine, this->element_filter),
gradu("gradu", *this, dim, fe_engine, this->element_filter),
green_strain("green_strain", *this, dim, fe_engine, this->element_filter),
piola_kirchhoff_2("piola_kirchhoff_2", *this, dim, fe_engine,
this->element_filter),
potential_energy("potential_energy", *this, dim, fe_engine,
this->element_filter),
interpolation_inverse_coordinates("interpolation inverse_coordinates",
*this, dim, fe_engine,
this->element_filter),
interpolation_points_matrices("interpolation points matrices", *this, dim,
- fe_engine, this->element_filter) {
+ fe_engine, this->element_filter),
+ eigen_grad_u(dim, dim, 0.) {
AKANTU_DEBUG_IN();
element_filter.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() = default;
/* -------------------------------------------------------------------------- */
void Material::initialize() {
registerParam("rho", rho, Real(0.), _pat_parsable | _pat_modifiable,
"Density");
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("finite_deformation", finite_deformation, false,
_pat_parsable | _pat_readable, "Is finite deformation");
registerParam("inelastic_deformation", inelastic_deformation, false,
_pat_internal, "Is inelastic deformation");
/// allocate gradu stress for local elements
eigengradu.initialize(spatial_dimension * spatial_dimension);
gradu.initialize(spatial_dimension * spatial_dimension);
stress.initialize(spatial_dimension * spatial_dimension);
potential_energy.initialize(1);
this->model.registerEventHandler(*this);
}
/* -------------------------------------------------------------------------- */
void Material::initMaterial() {
AKANTU_DEBUG_IN();
if (finite_deformation) {
this->piola_kirchhoff_2.initialize(spatial_dimension * spatial_dimension);
if (use_previous_stress) {
this->piola_kirchhoff_2.initializeHistory();
}
this->green_strain.initialize(spatial_dimension * spatial_dimension);
}
if (use_previous_stress) {
this->stress.initializeHistory();
}
if (use_previous_gradu) {
this->gradu.initializeHistory();
}
this->resizeInternals();
- auto dim = model.getSpatialDimension();
+ auto dim = spatial_dimension;
for (const auto & type :
element_filter.elementTypes(_element_kind = _ek_regular)) {
for (auto & eigen_gradu : make_view(eigengradu(type), dim, dim)) {
eigen_gradu = eigen_grad_u;
}
}
is_init = true;
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::savePreviousState() {
AKANTU_DEBUG_IN();
for (auto pair : internal_vectors_real) {
if (pair.second->hasHistory()) {
pair.second->saveCurrentValues();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::restorePreviousState() {
AKANTU_DEBUG_IN();
for (auto pair : internal_vectors_real) {
if (pair.second->hasHistory()) {
pair.second->restorePreviousValues();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the internal forces by assembling @f$\int_{e} \sigma_e \frac{\partial
* \varphi}{\partial X} dX @f$
*
* @param[in] ghost_type compute the internal forces for _ghost or _not_ghost
* element
*/
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
if (!finite_deformation) {
auto & internal_force = const_cast<Array<Real> &>(model.getInternalForce());
// Mesh & mesh = fem.getMesh();
for (auto && type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0) {
continue;
}
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by
/// @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
auto * sigma_dphi_dx =
new Array<Real>(nb_element * nb_quadrature_points,
size_of_shapes_derivatives, "sigma_x_dphi_/_dX");
fem.computeBtD(stress(type, ghost_type), *sigma_dphi_dx, type, ghost_type,
elem_filter);
/**
* compute @f$\int \sigma * \frac{\partial \varphi}{\partial X}dX@f$ by
* @f$ \sum_q \mathbf{B}^t
* \mathbf{\sigma}_q \overline w_q J_q@f$
*/
auto * int_sigma_dphi_dx =
new Array<Real>(nb_element, nb_nodes_per_element * spatial_dimension,
"int_sigma_x_dphi_/_dX");
fem.integrate(*sigma_dphi_dx, *int_sigma_dphi_dx,
size_of_shapes_derivatives, type, ghost_type, elem_filter);
delete sigma_dphi_dx;
/// assemble
model.getDOFManager().assembleElementalArrayLocalArray(
*int_sigma_dphi_dx, internal_force, type, ghost_type, -1,
elem_filter);
delete int_sigma_dphi_dx;
}
} else {
switch (spatial_dimension) {
case 1:
this->assembleInternalForces<1>(ghost_type);
break;
case 2:
this->assembleInternalForces<2>(ghost_type);
break;
case 3:
this->assembleInternalForces<3>(ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (const auto & type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
continue;
}
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect,
spatial_dimension, type, ghost_type,
elem_filter);
gradu_vect -= eigengradu(type, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllCauchyStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(finite_deformation, "The Cauchy stress can only be "
"computed if you are working in "
"finite deformation.");
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
switch (spatial_dimension) {
case 1:
this->StoCauchy<1>(type, ghost_type);
break;
case 2:
this->StoCauchy<2>(type, ghost_type);
break;
case 3:
this->StoCauchy<3>(type, ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::StoCauchy(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto gradu_it = this->gradu(el_type, ghost_type).begin(dim, dim);
auto gradu_end = this->gradu(el_type, ghost_type).end(dim, dim);
auto piola_it = this->piola_kirchhoff_2(el_type, ghost_type).begin(dim, dim);
auto stress_it = this->stress(el_type, ghost_type).begin(dim, dim);
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
auto F_tensor = gradUToF<dim>(grad_u);
this->StoCauchy<dim>(F_tensor, piola, sigma);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::setToSteadyState(GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & displacement = model.getDisplacement();
// resizeInternalArray(gradu);
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(displacement, gradu_vect, spatial_dimension,
type, ghost_type, elem_filter);
setToSteadyState(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stiffness matrix by assembling @f$\int_{\omega} B^t \times D
* \times B d\omega @f$
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
if (finite_deformation) {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrixNL<1>(type, ghost_type);
assembleStiffnessMatrixL2<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrixNL<2>(type, ghost_type);
assembleStiffnessMatrixL2<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrixNL<3>(type, ghost_type);
assembleStiffnessMatrixL2<3>(type, ghost_type);
break;
}
}
} else {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrix<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrix<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrix<3>(type, ghost_type);
break;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrix(ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
AKANTU_DEBUG_OUT();
return;
}
// const Array<Real> & shapes_derivatives =
// fem.getShapesDerivatives(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
auto * tangent_stiffness_matrix =
new Array<Real>(nb_element * nb_quadrature_points,
tangent_size * tangent_size, "tangent_stiffness_matrix");
tangent_stiffness_matrix->zero();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
auto * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
bt_d_b_size * bt_d_b_size, "B^t*D*B");
fem.computeBtDB(*tangent_stiffness_matrix, *bt_d_b, 4, type, ghost_type,
elem_filter);
delete tangent_stiffness_matrix;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto * K_e = new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixNL(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
// Array<Real> & gradu_vect = delta_gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
auto * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
*shapes_derivatives_filtered, type, ghost_type,
elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_s_b_size = dim * nb_nodes_per_element;
auto * bt_s_b = new Array<Real>(nb_element * nb_quadrature_points,
bt_s_b_size * bt_s_b_size, "B^t*D*B");
UInt piola_matrix_size = getCauchyStressMatrixSize(dim);
Matrix<Real> B(piola_matrix_size, bt_s_b_size);
Matrix<Real> Bt_S(bt_s_b_size, piola_matrix_size);
Matrix<Real> S(piola_matrix_size, piola_matrix_size);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_S_B_it = bt_s_b->begin(bt_s_b_size, bt_s_b_size);
auto Bt_S_B_end = bt_s_b->end(bt_s_b_size, bt_s_b_size);
auto piola_it = piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
for (; Bt_S_B_it != Bt_S_B_end;
++Bt_S_B_it, ++shapes_derivatives_filtered_it, ++piola_it) {
auto & Bt_S_B = *Bt_S_B_it;
const auto & Piola_kirchhoff_matrix = *piola_it;
setCauchyStressMatrix<dim>(Piola_kirchhoff_matrix, S);
VoigtHelper<dim>::transferBMatrixToBNL(*shapes_derivatives_filtered_it, B,
nb_nodes_per_element);
Bt_S.template mul<true, false>(B, S);
Bt_S_B.template mul<false, false>(Bt_S, B);
}
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto * K_e = new Array<Real>(nb_element, bt_s_b_size * bt_s_b_size, "K_e");
fem.integrate(*bt_s_b, *K_e, bt_s_b_size * bt_s_b_size, type, ghost_type,
elem_filter);
delete bt_s_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixL2(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
auto * tangent_stiffness_matrix =
new Array<Real>(nb_element * nb_quadrature_points,
tangent_size * tangent_size, "tangent_stiffness_matrix");
tangent_stiffness_matrix->zero();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
auto * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
*shapes_derivatives_filtered, type, ghost_type,
elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
auto * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
bt_d_b_size * bt_d_b_size, "B^t*D*B");
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> B2(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
auto shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
auto Bt_D_B_it = bt_d_b->begin(bt_d_b_size, bt_d_b_size);
auto grad_u_it = gradu_vect.begin(dim, dim);
auto D_it = tangent_stiffness_matrix->begin(tangent_size, tangent_size);
auto D_end = tangent_stiffness_matrix->end(tangent_size, tangent_size);
for (; D_it != D_end;
++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it, ++grad_u_it) {
const auto & grad_u = *grad_u_it;
const auto & D = *D_it;
auto & Bt_D_B = *Bt_D_B_it;
// transferBMatrixToBL1<dim > (*shapes_derivatives_filtered_it, B,
// nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2, nb_nodes_per_element);
B += B2;
Bt_D.template mul<true, false>(B, D);
Bt_D_B.template mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto * K_e = new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & internal_force = model.getInternalForce();
Mesh & mesh = fem.getMesh();
for (auto type : element_filter.elementTypes(_ghost_type = ghost_type)) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.empty()) {
continue;
}
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
auto * shapesd_filtered = new Array<Real>(
nb_element, size_of_shapes_derivatives, "filtered shapesd");
FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
type, ghost_type, elem_filter);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
// Set stress vectors
UInt stress_size = getTangentStiffnessVoigtSize(dim);
// Set matrices B and BNL*
UInt bt_s_size = dim * nb_nodes_per_element;
auto * bt_s =
new Array<Real>(nb_element * nb_quadrature_points, bt_s_size, "B^t*S");
auto grad_u_it = this->gradu(type, ghost_type).begin(dim, dim);
auto grad_u_end = this->gradu(type, ghost_type).end(dim, dim);
auto stress_it = this->piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator bt_s_it = bt_s->begin(bt_s_size, 1);
Matrix<Real> B_tensor(stress_size, bt_s_size);
Matrix<Real> B2_tensor(stress_size, bt_s_size);
for (; grad_u_it != grad_u_end; ++grad_u_it, ++stress_it,
++shapes_derivatives_filtered_it,
++bt_s_it) {
auto & grad_u = *grad_u_it;
auto & r = *bt_s_it;
auto & S = *stress_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B_tensor, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2_tensor,
nb_nodes_per_element);
B_tensor += B2_tensor;
auto S_vect = Material::stressToVoigt<dim>(S);
Matrix<Real> S_voigt(S_vect.storage(), stress_size, 1);
r.template mul<true, false>(B_tensor, S_voigt);
}
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto * r_e = new Array<Real>(nb_element, bt_s_size, "r_e");
fem.integrate(*bt_s, *r_e, bt_s_size, type, ghost_type, elem_filter);
delete bt_s;
model.getDOFManager().assembleElementalArrayLocalArray(
*r_e, internal_force, type, ghost_type, -1., elem_filter);
delete r_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergyByElements() {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
computePotentialEnergy(type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergy(ElementType /*unused*/) {
AKANTU_DEBUG_IN();
AKANTU_TO_IMPLEMENT();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real epot = 0.;
computePotentialEnergyByElements();
/// integrate the potential energy for each type of elements
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot += fem.integrate(potential_energy(type, _not_ghost), type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy(ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real epot = 0.;
Vector<Real> epot_on_quad_points(fem.getNbIntegrationPoints(type));
computePotentialEnergyByElement(type, index, epot_on_quad_points);
epot = fem.integrate(epot_on_quad_points, type, element_filter(type)(index));
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & type) {
AKANTU_DEBUG_IN();
if (type == "potential") {
return getPotentialEnergy();
}
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(const std::string & energy_id, ElementType type,
UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "potential") {
return getPotentialEnergy(type, index);
}
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
void Material::initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
AKANTU_DEBUG_IN();
this->fem.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, &(this->element_filter));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
this->fem.interpolateElementalFieldFromIntegrationPoints(
this->stress, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, result, ghost_type,
&(this->element_filter));
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStressOnFacets(
ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result, const GhostType ghost_type) {
interpolateStress(by_elem_result, ghost_type);
UInt stress_size = this->stress.getNbComponent();
const Mesh & mesh = this->model.getMesh();
const Mesh & mesh_facets = mesh.getMeshFacets();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_fil = element_filter(type, ghost_type);
Array<Real> & by_elem_res = by_elem_result(type, ghost_type);
UInt nb_element = elem_fil.size();
UInt nb_element_full = this->model.getMesh().getNbElement(type, ghost_type);
UInt nb_interpolation_points_per_elem =
by_elem_res.size() / nb_element_full;
const Array<Element> & facet_to_element =
mesh_facets.getSubelementToElement(type, ghost_type);
ElementType type_facet = Mesh::getFacetType(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
UInt nb_quad_per_facet =
nb_interpolation_points_per_elem / nb_facet_per_elem;
Element element_for_comparison{type, 0, ghost_type};
const Array<std::vector<Element>> * element_to_facet = nullptr;
GhostType current_ghost_type = _casper;
Array<Real> * result_vec = nullptr;
Array<Real>::const_matrix_iterator result_it =
by_elem_res.begin_reinterpret(
stress_size, nb_interpolation_points_per_elem, nb_element_full);
for (UInt el = 0; el < nb_element; ++el) {
UInt global_el = elem_fil(el);
element_for_comparison.element = global_el;
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element facet_elem = facet_to_element(global_el, f);
UInt global_facet = facet_elem.element;
if (facet_elem.ghost_type != current_ghost_type) {
current_ghost_type = facet_elem.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
type_facet, current_ghost_type);
result_vec = &result(type_facet, current_ghost_type);
}
bool is_second_element =
(*element_to_facet)(global_facet)[0] != element_for_comparison;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
Vector<Real> result_local(result_vec->storage() +
(global_facet * nb_quad_per_facet + q) *
result_vec->getNbComponent() +
static_cast<UInt>(is_second_element) *
stress_size,
stress_size);
const Matrix<Real> & result_tmp(result_it[global_el]);
result_local = result_tmp(f * nb_quad_per_facet + q);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void Material::addElements(const Array<Element> & elements_to_add) {
AKANTU_DEBUG_IN();
UInt mat_id = model.getMaterialIndex(name);
for (const auto & element : elements_to_add) {
auto index = this->addElement(element);
model.material_index(element) = mat_id;
model.material_local_numbering(element) = index;
}
this->resizeInternals();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::removeElements(const Array<Element> & elements_to_remove) {
AKANTU_DEBUG_IN();
auto el_begin = elements_to_remove.begin();
auto el_end = elements_to_remove.end();
if (elements_to_remove.empty()) {
return;
}
auto & mesh = this->model.getMesh();
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", id);
material_local_new_numbering.initialize(
mesh, _element_filter = &element_filter, _element_kind = _ek_not_defined,
_with_nb_element = true);
ElementTypeMapArray<UInt> element_filter_tmp("element_filter_tmp", id);
element_filter_tmp.initialize(mesh, _element_filter = &element_filter,
_element_kind = _ek_not_defined);
ElementTypeMap<UInt> new_ids, element_ids;
for_each_element(
mesh,
[&](auto && el) {
if (not new_ids(el.type, el.ghost_type)) {
element_ids(el.type, el.ghost_type) = 0;
}
auto & element_id = element_ids(el.type, el.ghost_type);
auto l_el = Element{el.type, element_id, el.ghost_type};
if (std::find(el_begin, el_end, el) != el_end) {
material_local_new_numbering(l_el) = UInt(-1);
return;
}
element_filter_tmp(el.type, el.ghost_type).push_back(el.element);
if (not new_ids(el.type, el.ghost_type)) {
new_ids(el.type, el.ghost_type) = 0;
}
auto & new_id = new_ids(el.type, el.ghost_type);
material_local_new_numbering(l_el) = new_id;
model.material_local_numbering(el) = new_id;
++new_id;
++element_id;
},
_element_filter = &element_filter, _element_kind = _ek_not_defined);
for (auto ghost_type : ghost_types) {
for (const auto & type : element_filter.elementTypes(
_ghost_type = ghost_type, _element_kind = _ek_not_defined)) {
element_filter(type, ghost_type)
.copy(element_filter_tmp(type, ghost_type));
}
}
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::resizeInternals() {
AKANTU_DEBUG_IN();
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it) {
it->second->resize();
}
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it) {
it->second->resize();
}
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it) {
it->second->resize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsAdded(const Array<Element> & /*unused*/,
const NewElementsEvent & /*unused*/) {
this->resizeInternals();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
[[gnu::unused]] const RemovedElementsEvent & event) {
UInt my_num = model.getInternalIndexFromID(getID());
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", getID());
auto el_begin = element_list.begin();
auto el_end = element_list.end();
for (auto && gt : ghost_types) {
for (auto && type :
new_numbering.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
if (not element_filter.exists(type, gt) ||
element_filter(type, gt).empty()) {
continue;
}
auto & elem_filter = element_filter(type, gt);
auto & mat_indexes = this->model.material_index(type, gt);
auto & mat_loc_num = this->model.material_local_numbering(type, gt);
auto nb_element = this->model.getMesh().getNbElement(type, gt);
// all materials will resize of the same size...
mat_indexes.resize(nb_element);
mat_loc_num.resize(nb_element);
if (!material_local_new_numbering.exists(type, gt)) {
material_local_new_numbering.alloc(elem_filter.size(), 1, type, gt);
}
auto & mat_renumbering = material_local_new_numbering(type, gt);
const auto & renumbering = new_numbering(type, gt);
Array<UInt> elem_filter_tmp;
UInt ni = 0;
Element el{type, 0, gt};
for (UInt i = 0; i < elem_filter.size(); ++i) {
el.element = elem_filter(i);
if (std::find(el_begin, el_end, el) == el_end) {
UInt new_el = renumbering(el.element);
AKANTU_DEBUG_ASSERT(new_el != UInt(-1),
"A not removed element as been badly renumbered");
elem_filter_tmp.push_back(new_el);
mat_renumbering(i) = ni;
mat_indexes(new_el) = my_num;
mat_loc_num(new_el) = ni;
++ni;
} else {
mat_renumbering(i) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (auto it = internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
for (auto it = internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
for (auto it = internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it) {
it->second->removeIntegrationPoints(material_local_new_numbering);
}
}
/* -------------------------------------------------------------------------- */
void Material::beforeSolveStep() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::afterSolveStep(bool converged) {
if (not converged) {
this->restorePreviousState();
return;
}
for (const auto & type : element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
this->updateEnergies(type);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDamageIteration() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::onDamageUpdate() {
for (const auto & type : element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
this->updateEnergiesAfterDamage(type);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDump() {
if (this->isFiniteDeformation()) {
this->computeAllCauchyStresses(_not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void Material::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
std::string type = getID().substr(getID().find_last_of(':') + 1);
stream << space << "Material " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/// extrapolate internal values
void Material::extrapolateInternal(const ID & id, const Element & element,
[[gnu::unused]] const Matrix<Real> & point,
Matrix<Real> & extrapolated) {
if (this->isInternal<Real>(id, element.kind())) {
UInt nb_element =
this->element_filter(element.type, element.ghost_type).size();
const ID name = this->getID() + ":" + id;
UInt nb_quads =
this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
element.type, element.ghost_type);
const Array<Real> & internal =
this->getArray<Real>(id, element.type, element.ghost_type);
UInt nb_component = internal.getNbComponent();
Array<Real>::const_matrix_iterator internal_it =
internal.begin_reinterpret(nb_component, nb_quads, nb_element);
Element local_element = this->convertToLocalElement(element);
/// instead of really extrapolating, here the value of the first GP
/// is copied into the result vector. This works only for linear
/// elements
/// @todo extrapolate!!!!
AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");
const Matrix<Real> & values = internal_it[local_element.element];
UInt index = 0;
Vector<Real> tmp(nb_component);
for (UInt j = 0; j < values.cols(); ++j) {
tmp = values(j);
if (tmp.norm() > 0) {
index = j;
break;
}
}
for (UInt i = 0; i < extrapolated.size(); ++i) {
extrapolated(i) = values(index);
}
} else {
Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
extrapolated = default_values;
}
}
/* -------------------------------------------------------------------------- */
void Material::applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType ghost_type) {
for (auto && type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
if (element_filter(type, ghost_type).empty()) {
continue;
}
for (auto & eigengradu : make_view(this->eigengradu(type, ghost_type),
spatial_dimension, spatial_dimension)) {
eigengradu = prescribed_eigen_grad_u;
}
}
}
/* -------------------------------------------------------------------------- */
MaterialFactory & Material::getFactory() {
return MaterialFactory::getInstance();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index 4ae6f4b1c..4cc050413 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,706 +1,712 @@
/**
* @file material.hh
*
+ * @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Mother class for all materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_voigthelper.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "parsable.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#include "random_internal_field.hh"
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_HH_
#define AKANTU_MATERIAL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class SolidMechanicsModel;
class Material;
} // namespace akantu
namespace akantu {
using MaterialFactory =
Factory<Material, ID, UInt, const ID &, SolidMechanicsModel &, const ID &>;
/**
* Interface of all materials
* Prerequisites for a new material
* - inherit from this class
* - implement the following methods:
* \code
* virtual Real getStableTimeStep(Real h, const Element & element =
* ElementNull);
*
* virtual void computeStress(ElementType el_type,
* GhostType ghost_type = _not_ghost);
*
* virtual void computeTangentStiffness(ElementType el_type,
* Array<Real> & tangent_matrix,
* GhostType ghost_type = _not_ghost);
* \endcode
*
*/
class Material : public DataAccessor<Element>,
public Parsable,
public MeshEventHandler,
protected SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Material(const Material & mat) = delete;
Material & operator=(const Material & mat) = delete;
/// Initialize material with defaults
Material(SolidMechanicsModel & model, const ID & id = "");
/// Initialize material with custom mesh & fe_engine
Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
/// Destructor
~Material() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Function that materials can/should reimplement */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law
virtual void computeStress(ElementType /* el_type */,
GhostType /* ghost_type */ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the tangent stiffness matrix
virtual void computeTangentModuli(ElementType /*el_type*/,
Array<Real> & /*tangent_matrix*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the potential energy
virtual void computePotentialEnergy(ElementType el_type);
/// compute the potential energy for an element
virtual void
computePotentialEnergyByElement(ElementType /*type*/, UInt /*index*/,
Vector<Real> & /*epot_on_quad_points*/) {
AKANTU_TO_IMPLEMENT();
}
virtual void updateEnergies(ElementType /*el_type*/) {}
virtual void updateEnergiesAfterDamage(ElementType /*el_type*/) {}
/// set the material to steady state (to be implemented for materials that
/// need it)
virtual void setToSteadyState(ElementType /*el_type*/,
GhostType /*ghost_type*/ = _not_ghost) {}
/// function called to update the internal parameters when the modifiable
/// parameters are modified
virtual void updateInternalParameters() {}
public:
/// extrapolate internal values
virtual void extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & points,
Matrix<Real> & extrapolated);
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(const Element & /*element*/) const {
AKANTU_TO_IMPLEMENT();
}
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(const Element & /*element*/) const {
AKANTU_TO_IMPLEMENT();
}
/// get a material celerity to compute the stable time step (default: is the
/// push wave speed)
virtual Real getCelerity(const Element & element) const {
return getPushWaveSpeed(element);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T> void registerInternal(InternalField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
template <typename T> void unregisterInternal(InternalField<T> & /*vect*/) {
AKANTU_TO_IMPLEMENT();
}
/// initialize the material computed parameter
virtual void initMaterial();
/// compute the residual for this material
// virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// assemble the residual for this material
virtual void assembleInternalForces(GhostType ghost_type);
/// save the stress in the previous_stress if needed
virtual void savePreviousState();
/// restore the stress from previous_stress if needed
virtual void restorePreviousState();
/// compute the stresses for this material
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
// virtual void
// computeAllStressesFromTangentModuli(GhostType ghost_type = _not_ghost);
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost);
/// set material to steady state
void setToSteadyState(GhostType ghost_type = _not_ghost);
/// compute the stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// add an element to the local mesh filter
inline UInt addElement(ElementType type, UInt element, GhostType ghost_type);
inline UInt addElement(const Element & element);
/// add many elements at once
void addElements(const Array<Element> & elements_to_add);
/// remove many element at once
void removeElements(const Array<Element> & elements_to_remove);
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points
*/
void interpolateStress(ElementTypeMapArray<Real> & result,
GhostType ghost_type = _not_ghost);
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points and store the
* results per facet
*/
void interpolateStressOnFacets(ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result,
GhostType ghost_type = _not_ghost);
/**
* function to initialize the elemental field interpolation
* function by inverting the quadrature points' coordinates
*/
void initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates);
/* ------------------------------------------------------------------------ */
/* Common part */
/* ------------------------------------------------------------------------ */
protected:
/* ------------------------------------------------------------------------ */
static inline UInt getTangentStiffnessVoigtSize(UInt dim);
/// compute the potential energy by element
void computePotentialEnergyByElements();
/// resize the intenals arrays
virtual void resizeInternals();
/* ------------------------------------------------------------------------ */
/* Finite deformation functions */
/* This functions area implementing what is described in the paper of Bathe */
/* et al, in IJNME, Finite Element Formulations For Large Deformation */
/* Dynamic Analysis, Vol 9, 353-386, 1975 */
/* ------------------------------------------------------------------------ */
protected:
/// assemble the residual
template <UInt dim> void assembleInternalForces(GhostType ghost_type);
template <UInt dim>
void computeAllStressesFromTangentModuli(ElementType type,
GhostType ghost_type);
template <UInt dim>
void assembleStiffnessMatrix(ElementType type, GhostType ghost_type);
/// assembling in finite deformation
template <UInt dim>
void assembleStiffnessMatrixNL(ElementType type, GhostType ghost_type);
template <UInt dim>
void assembleStiffnessMatrixL2(ElementType type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Conversion functions */
/* ------------------------------------------------------------------------ */
public:
/// Size of the Stress matrix for the case of finite deformation see: Bathe et
/// al, IJNME, Vol 9, 353-386, 1975
static inline UInt getCauchyStressMatrixSize(UInt dim);
/// Sets the stress matrix according to Bathe et al, IJNME, Vol 9, 353-386,
/// 1975
template <UInt dim>
static inline void setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma);
/// write the stress tensor in the Voigt notation.
template <UInt dim>
static inline decltype(auto) stressToVoigt(const Matrix<Real> & stress) {
return VoigtHelper<dim>::matrixToVoigt(stress);
}
/// write the strain tensor in the Voigt notation.
template <UInt dim>
static inline decltype(auto) strainToVoigt(const Matrix<Real> & strain) {
return VoigtHelper<dim>::matrixToVoigtWithFactors(strain);
}
/// write a voigt vector to stress
template <UInt dim>
static inline void voigtToStress(const Vector<Real> & voigt,
Matrix<Real> & stress) {
VoigtHelper<dim>::voigtToMatrix(voigt, stress);
}
/// Computation of Cauchy stress tensor in the case of finite deformation from
/// the 2nd Piola-Kirchhoff for a given element type
template <UInt dim>
void StoCauchy(ElementType el_type, GhostType ghost_type = _not_ghost);
/// Computation the Cauchy stress the 2nd Piola-Kirchhoff and the deformation
/// gradient
template <UInt dim>
inline void StoCauchy(const Matrix<Real> & F, const Matrix<Real> & S,
Matrix<Real> & sigma, const Real & C33 = 1.0) const;
template <UInt dim>
static inline void gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F);
template <UInt dim>
static inline decltype(auto) gradUToF(const Matrix<Real> & grad_u);
static inline void rightCauchy(const Matrix<Real> & F, Matrix<Real> & C);
static inline void leftCauchy(const Matrix<Real> & F, Matrix<Real> & B);
template <UInt dim>
static inline void gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
template <UInt dim>
static inline decltype(auto) gradUToEpsilon(const Matrix<Real> & grad_u);
template <UInt dim>
static inline void gradUToE(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
template <UInt dim>
static inline decltype(auto) gradUToE(const Matrix<Real> & grad_u);
static inline Real stressToVonMises(const Matrix<Real> & stress);
protected:
/// converts global element to local element
inline Element convertToLocalElement(const Element & global_element) const;
/// converts local element to global element
inline Element convertToGlobalElement(const Element & local_element) const;
/// converts global quadrature point to local quadrature point
inline IntegrationPoint
convertToLocalPoint(const IntegrationPoint & global_point) const;
/// converts local quadrature point to global quadrature point
inline IntegrationPoint
convertToGlobalPoint(const IntegrationPoint & local_point) const;
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <typename T>
inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID()) const;
template <typename T>
inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID());
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
void onNodesAdded(const Array<UInt> & /*unused*/,
const NewNodesEvent & /*unused*/) override{};
void onNodesRemoved(const Array<UInt> & /*unused*/,
const Array<UInt> & /*unused*/,
const RemovedNodesEvent & /*unused*/) override{};
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsChanged(const Array<Element> & /*unused*/,
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) override{};
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void beforeSolveStep();
virtual void afterSolveStep(bool converged = true);
void onDamageIteration() override;
void onDamageUpdate() override;
void onDump() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Name, name, const std::string &);
AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &)
AKANTU_GET_MACRO(ID, id, const ID &);
AKANTU_GET_MACRO(Rho, rho, Real);
AKANTU_SET_MACRO(Rho, rho, Real);
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// return the potential energy for the subset of elements contained by the
/// material
Real getPotentialEnergy();
/// return the potential energy for the provided element
Real getPotentialEnergy(ElementType & type, UInt index);
/// return the energy (identified by id) for the subset of elements contained
/// by the material
virtual Real getEnergy(const std::string & type);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(const std::string & energy_id, ElementType type,
UInt index);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(GradU, gradu, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PotentialEnergy, potential_energy,
Real);
AKANTU_GET_MACRO(GradU, gradu, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Stress, stress, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(ElementFilter, element_filter,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(FEEngine, fem, FEEngine &);
bool isNonLocal() const { return is_non_local; }
template <typename T>
const Array<T> & getArray(const ID & id, ElementType type,
GhostType ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getArray(const ID & id, ElementType type,
GhostType ghost_type = _not_ghost);
template <typename T>
const InternalField<T> & getInternal(const ID & id) const;
template <typename T> InternalField<T> & getInternal(const ID & id);
template <typename T>
inline bool isInternal(const ID & id, ElementKind element_kind) const;
template <typename T>
ElementTypeMap<UInt> getInternalDataPerElem(const ID & id,
ElementKind element_kind) const;
bool isFiniteDeformation() const { return finite_deformation; }
bool isInelasticDeformation() const { return inelastic_deformation; }
template <typename T> inline void setParam(const ID & param, T value);
inline const Parameter & getParam(const ID & param) const;
template <typename T>
void flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) const;
/// apply a constant eigengrad_u everywhere in the material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
GhostType /*ghost_type*/ = _not_ghost);
bool hasMatrixChanged(const ID & id) {
if (id == "K") {
return hasStiffnessMatrixChanged() or finite_deformation;
}
return true;
}
MatrixType getMatrixType(const ID & id) {
if (id == "K") {
return getTangentType();
}
if (id == "M") {
return _symmetric;
}
return _mt_not_defined;
}
/// specify if the matrix need to be recomputed for this material
virtual bool hasStiffnessMatrixChanged() { return true; }
/// specify the type of matrix, if not overloaded the material is not valid
/// for static or implicit computations
virtual MatrixType getTangentType() { return _mt_not_defined; }
/// static method to reteive the material factory
static MaterialFactory & getFactory();
protected:
bool isInit() const { return is_init; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// boolean to know if the material has been initialized
bool is_init{false};
std::map<ID, InternalField<Real> *> internal_vectors_real;
std::map<ID, InternalField<UInt> *> internal_vectors_uint;
std::map<ID, InternalField<bool> *> internal_vectors_bool;
protected:
ID id;
/// Link to the fem object in the model
FEEngine & fem;
/// Finite deformation
bool finite_deformation{false};
/// Finite deformation
bool inelastic_deformation{false};
/// material name
std::string name;
/// The model to witch the material belong
SolidMechanicsModel & model;
/// density : rho
Real rho{0.};
/// spatial dimension
UInt spatial_dimension;
/// list of element handled by the material
ElementTypeMapArray<UInt> element_filter;
/// stresses arrays ordered by element types
InternalField<Real> stress;
/// eigengrad_u arrays ordered by element types
InternalField<Real> eigengradu;
/// grad_u arrays ordered by element types
InternalField<Real> gradu;
/// Green Lagrange strain (Finite deformation)
InternalField<Real> green_strain;
/// Second Piola-Kirchhoff stress tensor arrays ordered by element types
/// (Finite deformation)
InternalField<Real> piola_kirchhoff_2;
/// potential energy by element
InternalField<Real> potential_energy;
/// tell if using in non local mode or not
bool is_non_local{false};
/// tell if the material need the previous stress state
bool use_previous_stress{false};
/// tell if the material need the previous strain state
bool use_previous_gradu{false};
/// elemental field interpolation coordinates
InternalField<Real> interpolation_inverse_coordinates;
/// elemental field interpolation points
InternalField<Real> interpolation_points_matrices;
/// vector that contains the names of all the internals that need to
/// be transferred when material interfaces move
std::vector<ID> internals_to_transfer;
private:
/// eigen_grad_u for the parser
Matrix<Real> eigen_grad_u;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Material & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "material_inline_impl.hh"
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* Auto loop */
/* -------------------------------------------------------------------------- */
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeStress. This macro in addition to write the loop
/// provides two tensors (matrices) sigma and grad_u
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
auto && grad_u_view = \
make_view(this->gradu(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto stress_view = \
make_view(this->stress(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
if (this->isFiniteDeformation()) { \
stress_view = make_view(this->piola_kirchhoff_2(el_type, ghost_type), \
this->spatial_dimension, this->spatial_dimension); \
} \
\
for (auto && data : zip(grad_u_view, stress_view)) { \
[[gnu::unused]] Matrix<Real> & grad_u = std::get<0>(data); \
[[gnu::unused]] Matrix<Real> & sigma = std::get<1>(data)
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END }
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeTangentModuli. This macro in addition to write the
/// loop provides two tensors (matrices) sigma_tensor, grad_u, and a matrix
/// where the elemental tangent moduli should be stored in Voigt Notation
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
auto && grad_u_view = \
make_view(this->gradu(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto && stress_view = \
make_view(this->stress(el_type, ghost_type), this->spatial_dimension, \
this->spatial_dimension); \
\
auto tangent_size = \
this->getTangentStiffnessVoigtSize(this->spatial_dimension); \
\
auto && tangent_view = make_view(tangent_mat, tangent_size, tangent_size); \
\
for (auto && data : zip(grad_u_view, stress_view, tangent_view)) { \
[[gnu::unused]] Matrix<Real> & grad_u = std::get<0>(data); \
[[gnu::unused]] Matrix<Real> & sigma = std::get<1>(data); \
Matrix<Real> & tangent = std::get<2>(data);
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END }
/* -------------------------------------------------------------------------- */
#define INSTANTIATE_MATERIAL_ONLY(mat_name) \
template class mat_name<1>; /* NOLINT */ \
template class mat_name<2>; /* NOLINT */ \
template class mat_name<3> /* NOLINT */
#define MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name) \
[](UInt dim, const ID &, SolidMechanicsModel & model, \
const ID & id) /* NOLINT */ \
-> std::unique_ptr< \
Material> { /* NOLINT */ \
switch (dim) { \
case 1: \
return std::make_unique<mat_name<1>>(/* NOLINT */ \
model, id); \
case 2: \
return std::make_unique<mat_name<2>>(/* NOLINT */ \
model, id); \
case 3: \
return std::make_unique<mat_name<3>>(/* NOLINT */ \
model, id); \
default: \
AKANTU_EXCEPTION( \
"The dimension " \
<< dim \
<< "is not a valid dimension for the material " \
<< #id); \
} \
}
#define INSTANTIATE_MATERIAL(id, mat_name) \
INSTANTIATE_MATERIAL_ONLY(mat_name); \
static bool material_is_alocated_##id [[gnu::unused]] = \
MaterialFactory::getInstance().registerAllocator( \
#id, MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name))
#endif /* AKANTU_MATERIAL_HH_ */
diff --git a/src/model/solid_mechanics/material_inline_impl.hh b/src/model/solid_mechanics/material_inline_impl.hh
index 1a90222df..c9b47c3e4 100644
--- a/src/model/solid_mechanics/material_inline_impl.hh
+++ b/src/model/solid_mechanics/material_inline_impl.hh
@@ -1,545 +1,551 @@
/**
* @file material_inline_impl.hh
*
+ * @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of the inline functions of the class material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_INLINE_IMPL_HH_
#define AKANTU_MATERIAL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(ElementType type, UInt element,
GhostType ghost_type) {
Array<UInt> & el_filter = this->element_filter(type, ghost_type);
el_filter.push_back(element);
return el_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(const Element & element) {
return this->addElement(element.type, element.element, element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getTangentStiffnessVoigtSize(UInt dim) {
return (dim * (dim - 1) / 2 + dim);
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getCauchyStressMatrixSize(UInt dim) {
return (dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F) {
AKANTU_DEBUG_ASSERT(F.size() >= grad_u.size() && grad_u.size() == dim * dim,
"The dimension of the tensor F should be greater or "
"equal to the dimension of the tensor grad_u.");
F.eye();
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
F(i, j) += grad_u(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToF(const Matrix<Real> & grad_u) {
Matrix<Real> F(dim, dim);
gradUToF<dim>(grad_u, F);
return F;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::StoCauchy(const Matrix<Real> & F, const Matrix<Real> & S,
Matrix<Real> & sigma, const Real & C33) const {
Real J = F.det() * sqrt(C33);
Matrix<Real> F_S(dim, dim);
F_S = F * S;
Real constant = J ? 1. / J : 0;
sigma.mul<false, true>(F_S, F, constant);
}
/* -------------------------------------------------------------------------- */
inline void Material::rightCauchy(const Matrix<Real> & F, Matrix<Real> & C) {
C.mul<true, false>(F, F);
}
/* -------------------------------------------------------------------------- */
inline void Material::leftCauchy(const Matrix<Real> & F, Matrix<Real> & B) {
B.mul<false, true>(F, F);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToEpsilon(const Matrix<Real> & grad_u) {
Matrix<Real> epsilon(dim, dim);
Material::template gradUToEpsilon<dim>(grad_u, epsilon);
return epsilon;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToE(const Matrix<Real> & grad_u, Matrix<Real> & E) {
E.mul<true, false>(grad_u, grad_u, .5);
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
E(i, j) += 0.5 * (grad_u(i, j) + grad_u(j, i));
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline decltype(auto) Material::gradUToE(const Matrix<Real> & grad_u) {
Matrix<Real> E(dim, dim);
gradUToE<dim>(grad_u, E);
return E;
}
/* -------------------------------------------------------------------------- */
inline Real Material::stressToVonMises(const Matrix<Real> & stress) {
// compute deviatoric stress
UInt dim = stress.cols();
Matrix<Real> deviatoric_stress =
Matrix<Real>::eye(dim, -1. * stress.trace() / 3.);
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
deviatoric_stress(i, j) += stress(i, j);
}
}
// return Von Mises stress
return std::sqrt(3. * deviatoric_stress.doubleDot(deviatoric_stress) / 2.);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma) {
AKANTU_DEBUG_IN();
sigma.zero();
/// see Finite ekement formulations for large deformation dynamic analysis,
/// Bathe et al. IJNME vol 9, 1975, page 364 ^t \f$\tau\f$
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < dim; ++m) {
for (UInt n = 0; n < dim; ++n) {
sigma(i * dim + m, i * dim + n) = S_t(m, n);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToLocalElement(const Element & global_element) const {
UInt ge = global_element.element;
#ifndef AKANTU_NDEBUG
UInt model_mat_index = this->model.getMaterialByElement(
global_element.type, global_element.ghost_type)(ge);
UInt mat_index = this->model.getMaterialIndex(this->name);
AKANTU_DEBUG_ASSERT(model_mat_index == mat_index,
"Conversion of a global element in a local element for "
"the wrong material "
<< this->name << std::endl);
#endif
UInt le = this->model.getMaterialLocalNumbering(
global_element.type, global_element.ghost_type)(ge);
Element tmp_quad{global_element.type, le, global_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToGlobalElement(const Element & local_element) const {
UInt le = local_element.element;
UInt ge =
this->element_filter(local_element.type, local_element.ghost_type)(le);
Element tmp_quad{local_element.type, ge, local_element.ghost_type};
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToLocalPoint(const IntegrationPoint & global_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(global_point.type);
Element el =
this->convertToLocalElement(static_cast<const Element &>(global_point));
IntegrationPoint tmp_quad(el, global_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToGlobalPoint(const IntegrationPoint & local_point) const {
const FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(local_point.type);
Element el =
this->convertToGlobalElement(static_cast<const Element &>(local_point));
IntegrationPoint tmp_quad(el, local_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_smm_stress) {
return (this->isFiniteDeformation() ? 3 : 1) * spatial_dimension *
spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements);
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void Material::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_smm_stress) {
if (this->isFiniteDeformation()) {
packElementDataHelper(piola_kirchhoff_2, buffer, elements);
packElementDataHelper(gradu, buffer, elements);
}
packElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline void Material::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_smm_stress) {
if (this->isFiniteDeformation()) {
unpackElementDataHelper(piola_kirchhoff_2, buffer, elements);
unpackElementDataHelper(gradu, buffer, elements);
}
unpackElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline const Parameter & Material::getParam(const ID & param) const {
try {
return get(param);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::setParam(const ID & param, T value) {
try {
set<T>(param, value);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
updateInternalParameters();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::packElementDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) const {
DataAccessor::packElementalDataHelper<T>(data_to_pack, buffer, elements, true,
model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::unpackElementDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) {
DataAccessor::unpackElementalDataHelper<T>(data_to_unpack, buffer, elements,
true, model.getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::registerInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool[vect.getID()] = &vect;
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::unregisterInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool.erase(vect.getID());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool Material::isInternal(const ID & /*id*/,
ElementKind /*element_kind*/) const {
AKANTU_TO_IMPLEMENT();
}
template <>
inline bool Material::isInternal<Real>(const ID & id,
ElementKind element_kind) const {
auto internal_array = internal_vectors_real.find(this->getID() + ":" + id);
return not(internal_array == internal_vectors_real.end() ||
internal_array->second->getElementKind() != element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMap<UInt>
Material::getInternalDataPerElem(const ID & field_id,
ElementKind element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind)) {
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
}
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
UInt nb_data_per_quad = internal_field.getNbComponent();
ElementTypeMap<UInt> res;
for (auto ghost_type : ghost_types) {
for (auto & type : internal_field.elementTypes(ghost_type)) {
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(type, ghost_type);
res(type, ghost_type) = nb_data_per_quad * nb_quadrature_points;
}
}
return res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Material::flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type,
ElementKind element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind)) {
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
}
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
const Mesh & mesh = fe_engine.getMesh();
for (auto && type : internal_field.filterTypes(ghost_type)) {
const Array<Real> & src_vect = internal_field(type, ghost_type);
const Array<UInt> & filter = internal_field.getFilter(type, ghost_type);
// total number of elements in the corresponding mesh
UInt nb_element_dst = mesh.getNbElement(type, ghost_type);
// number of element in the internal field
UInt nb_element_src = filter.size();
// number of quadrature points per elem
UInt nb_quad_per_elem = fe_engine.getNbIntegrationPoints(type);
// number of data per quadrature point
UInt nb_data_per_quad = internal_field.getNbComponent();
if (!internal_flat.exists(type, ghost_type)) {
internal_flat.alloc(nb_element_dst * nb_quad_per_elem, nb_data_per_quad,
type, ghost_type);
}
if (nb_element_src == 0) {
continue;
}
// number of data per element
UInt nb_data = nb_quad_per_elem * nb_data_per_quad;
Array<Real> & dst_vect = internal_flat(type, ghost_type);
dst_vect.resize(nb_element_dst * nb_quad_per_elem);
auto it_dst = make_view(dst_vect, nb_data).begin();
for (auto && data : zip(filter, make_view(src_vect, nb_data))) {
it_dst[std::get<0>(data)] = std::get<1>(data);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const InternalField<T> &
Material::getInternal([[gnu::unused]] const ID & int_id) const {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline InternalField<T> &
Material::getInternal([[gnu::unused]] const ID & int_id) {
AKANTU_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <>
inline const InternalField<Real> &
Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
inline InternalField<Real> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
inline const InternalField<UInt> &
Material::getInternal(const ID & int_id) const {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
inline InternalField<UInt> & Material::getInternal(const ID & int_id) {
auto it = internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Material::getArray(const ID & vect_id, ElementType type,
GhostType ghost_type) const {
try {
return this->template getInternal<T>(vect_id)(type, ghost_type);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Material::getArray(const ID & vect_id, ElementType type,
GhostType ghost_type) {
try {
return this->template getInternal<T>(vect_id)(type, ghost_type);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << " [" << e << "]");
}
}
} // namespace akantu
#endif /* AKANTU_MATERIAL_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index 40d05bbb2..7c14637ad 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,157 +1,159 @@
/**
* @file material_selector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief class describing how to choose a material for a given element
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_SELECTOR_HH_
#define AKANTU_MATERIAL_SELECTOR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModel;
/**
* main class to assign same or different materials for different
* elements
*/
class MaterialSelector {
public:
MaterialSelector() = default;
virtual ~MaterialSelector() = default;
virtual inline UInt operator()(const Element & element) {
if (fallback_selector) {
return (*fallback_selector)(element);
}
return fallback_value;
}
inline void setFallback(UInt f) { fallback_value = f; }
inline void
setFallback(const std::shared_ptr<MaterialSelector> & fallback_selector) {
this->fallback_selector = fallback_selector;
}
inline std::shared_ptr<MaterialSelector> & getFallbackSelector() {
return this->fallback_selector;
}
inline UInt getFallbackValue() const { return this->fallback_value; }
protected:
UInt fallback_value{0};
std::shared_ptr<MaterialSelector> fallback_selector;
};
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first material to regular elements by default
*/
class DefaultMaterialSelector : public MaterialSelector {
public:
explicit DefaultMaterialSelector(
const ElementTypeMapArray<UInt> & material_index)
: material_index(material_index) {}
UInt operator()(const Element & element) override {
if (not material_index.exists(element.type, element.ghost_type)) {
return MaterialSelector::operator()(element);
}
const auto & mat_indexes = material_index(element.type, element.ghost_type);
if (element.element < mat_indexes.size()) {
auto && tmp_mat = mat_indexes(element.element);
if (tmp_mat != UInt(-1)) {
return tmp_mat;
}
}
return MaterialSelector::operator()(element);
}
private:
const ElementTypeMapArray<UInt> & material_index;
};
/* -------------------------------------------------------------------------- */
/**
* Use elemental data to assign materials
*/
template <typename T>
class ElementDataMaterialSelector : public MaterialSelector {
public:
ElementDataMaterialSelector(const ElementTypeMapArray<T> & element_data,
const SolidMechanicsModel & model,
UInt first_index = 1)
: element_data(element_data), model(model), first_index(first_index) {}
inline T elementData(const Element & element) {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
T data = element_data(element.type, element.ghost_type)(element.element);
debug::setDebugLevel(dbl);
return data;
}
inline UInt operator()(const Element & element) override;
protected:
/// list of element with the specified data (i.e. tag value)
const ElementTypeMapArray<T> & element_data;
/// the model that the materials belong
const SolidMechanicsModel & model;
/// first material index: equal to 1 if none specified
UInt first_index;
};
/* -------------------------------------------------------------------------- */
/**
* class to use mesh data information to assign different materials
* where name is the tag value: tag_0, tag_1
*/
template <typename T>
class MeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
MeshDataMaterialSelector(const std::string & name,
const SolidMechanicsModel & model,
UInt first_index = 1);
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_SELECTOR_HH_ */
diff --git a/src/model/solid_mechanics/material_selector_tmpl.hh b/src/model/solid_mechanics/material_selector_tmpl.hh
index 10815691e..7ed2c9f28 100644
--- a/src/model/solid_mechanics/material_selector_tmpl.hh
+++ b/src/model/solid_mechanics/material_selector_tmpl.hh
@@ -1,80 +1,82 @@
/**
* @file material_selector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of the template MaterialSelector
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_SELECTOR_TMPL_HH_
#define AKANTU_MATERIAL_SELECTOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline UInt
ElementDataMaterialSelector<std::string>::operator()(const Element & element) {
try {
std::string material_name = this->elementData(element);
return model.getMaterialIndex(material_name);
} catch (std::exception & e) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline UInt
ElementDataMaterialSelector<UInt>::operator()(const Element & element) {
try {
return this->elementData(element) - first_index;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline UInt
ElementDataMaterialSelector<T>::operator()(const Element & element) {
return MaterialSelector::operator()(element);
}
/* -------------------------------------------------------------------------- */
template <typename T>
MeshDataMaterialSelector<T>::MeshDataMaterialSelector(
const std::string & name, const SolidMechanicsModel & model,
UInt first_index)
: ElementDataMaterialSelector<T>(model.getMesh().getData<T>(name), model,
first_index) {}
} // namespace akantu
#endif /* AKANTU_MATERIAL_SELECTOR_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/internal_field.hh b/src/model/solid_mechanics/materials/internal_field.hh
index 7743d195d..9b6bd112c 100644
--- a/src/model/solid_mechanics/materials/internal_field.hh
+++ b/src/model/solid_mechanics/materials/internal_field.hh
@@ -1,283 +1,286 @@
/**
* @file internal_field.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Feb 08 2018
+ * @date last modification: Fri Mar 26 2021
*
* @brief Material internal properties
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTERNAL_FIELD_HH_
#define AKANTU_INTERNAL_FIELD_HH_
namespace akantu {
class Material;
class FEEngine;
/**
* class for the internal fields of materials
* to store values for each quadrature
*/
template <class Material, typename T> class InternalFieldTmpl : public ElementTypeMapArray<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InternalFieldTmpl(const ID & id, Material & material);
~InternalFieldTmpl() override;
/// This constructor is only here to let cohesive elements compile
InternalFieldTmpl(const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
/// More general constructor
InternalFieldTmpl(const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
InternalFieldTmpl(const ID & id, const InternalFieldTmpl<Material, T> & other);
private:
InternalFieldTmpl operator=(const InternalFieldTmpl &) = delete;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to reset the FEEngine for the internal field
virtual void setFEEngine(FEEngine & fe_engine);
/// function to reset the element kind for the internal
virtual void setElementKind(ElementKind element_kind);
/// initialize the field to a given number of component
virtual void initialize(UInt nb_component);
/// activate the history of this field
virtual void initializeHistory();
/// resize the arrays and set the new element to 0
virtual void resize();
/// set the field to a given value v
virtual void setDefaultValue(const T & v);
/// reset all the fields to the default value
virtual void reset();
/// save the current values in the history
virtual void saveCurrentValues();
/// restore the previous values from the history
virtual void restorePreviousValues();
/// remove the quadrature points corresponding to suppressed elements
virtual void
removeIntegrationPoints(const ElementTypeMapArray<UInt> & new_numbering);
/// print the content
void printself(std::ostream & stream, int /*indent*/ = 0) const override;
/// get the default value
inline operator T() const;
virtual FEEngine & getFEEngine() { return *fem; }
virtual const FEEngine & getFEEngine() const { return *fem; }
/// AKANTU_GET_MACRO(FEEngine, *fem, FEEngine &);
protected:
/// initialize the arrays in the ElementTypeMapArray<T>
void internalInitialize(UInt nb_component);
/// set the values for new internals
virtual void setArrayValues(T * begin, T * end);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
// using type_iterator = typename ElementTypeMapArray<T>::type_iterator;
// using filter_type_iterator =
// typename ElementTypeMapArray<UInt>::type_iterator;
// /// get the type iterator on all types contained in the internal field
// type_iterator firstType(GhostType ghost_type = _not_ghost) const {
// return ElementTypeMapArray<T>::firstType(this->spatial_dimension,
// ghost_type, this->element_kind);
// }
// /// get the type iterator on the last type contained in the internal field
// type_iterator lastType(GhostType ghost_type = _not_ghost) const {
// return ElementTypeMapArray<T>::lastType(this->spatial_dimension,
// ghost_type,
// this->element_kind);
// }
// /// get the type iterator on all types contained in the internal field
// filter_type_iterator
// filterFirstType(GhostType ghost_type = _not_ghost) const {
// return this->element_filter.firstType(this->spatial_dimension,
// ghost_type,
// this->element_kind);
// }
// /// get the type iterator on the last type contained in the internal field
// filter_type_iterator
// filterLastType(GhostType ghost_type = _not_ghost) const {
// return this->element_filter.lastType(this->spatial_dimension, ghost_type,
// this->element_kind);
// }
/// get filter types for range loop
decltype(auto) elementTypes(GhostType ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::elementTypes(
_spatial_dimension = this->spatial_dimension,
_element_kind = this->element_kind, _ghost_type = ghost_type);
}
/// get filter types for range loop
decltype(auto) filterTypes(GhostType ghost_type = _not_ghost) const {
return this->element_filter.elementTypes(
_spatial_dimension = this->spatial_dimension,
_element_kind = this->element_kind, _ghost_type = ghost_type);
}
/// get the array for a given type of the element_filter
const Array<UInt> &
getFilter(ElementType type,
GhostType ghost_type = _not_ghost) const {
return this->element_filter(type, ghost_type);
}
/// get the Array corresponding to the type en ghost_type specified
virtual Array<T> & operator()(ElementType type,
GhostType ghost_type = _not_ghost) {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual const Array<T> &
operator()(ElementType type,
GhostType ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual Array<T> & previous(ElementType type,
GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual const Array<T> &
previous(ElementType type,
GhostType ghost_type = _not_ghost) const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual InternalFieldTmpl<Material, T> & previous() {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
virtual const InternalFieldTmpl<Material, T> & previous() const {
AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
/// check if the history is used or not
bool hasHistory() const { return (previous_values != nullptr); }
/// get the kind treated by the internal
ElementKind getElementKind() const { return element_kind; }
/// return the number of components
UInt getNbComponent() const { return nb_component; }
/// return the spatial dimension corresponding to the internal element type
/// loop filter
UInt getSpatialDimension() const { return this->spatial_dimension; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the material for which this is an internal parameter
Material & material;
/// the fem containing the mesh and the element informations
FEEngine * fem{nullptr};
/// Element filter if needed
const ElementTypeMapArray<UInt> & element_filter;
/// default value
T default_value{};
/// spatial dimension of the element to consider
UInt spatial_dimension{0};
/// ElementKind of the element to consider
ElementKind element_kind{_ek_regular};
/// Number of component of the internal field
UInt nb_component{0};
/// Is the field initialized
bool is_init{false};
/// previous values
std::unique_ptr<InternalFieldTmpl<Material, T>> previous_values;
};
/// standard output stream operator
template <class Material, typename T>
inline std::ostream & operator<<(std::ostream & stream,
const InternalFieldTmpl<Material, T> & _this) {
_this.printself(stream);
return stream;
}
template<typename T>
using InternalField = InternalFieldTmpl<Material, T>;
} // namespace akantu
#endif /* AKANTU_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/materials/internal_field_tmpl.hh b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
index 14e66bdb8..4d9e2e6da 100644
--- a/src/model/solid_mechanics/materials/internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
@@ -1,331 +1,334 @@
/**
* @file internal_field_tmpl.hh
*
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 02 2021
*
* @brief Material internal properties
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_INTERNAL_FIELD_TMPL_HH_
#define AKANTU_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
InternalFieldTmpl<Material, T>::InternalFieldTmpl(const ID & id, Material & material)
: ElementTypeMapArray<T>(id, material.getID()),
material(material), fem(&(material.getModel().getFEEngine())),
element_filter(material.getElementFilter()),
spatial_dimension(material.getModel().getSpatialDimension()) {}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
InternalFieldTmpl<Material, T>::InternalFieldTmpl(
const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID()),
material(material), fem(&fem), element_filter(element_filter),
spatial_dimension(material.getSpatialDimension()) {}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
InternalFieldTmpl<Material, T>::InternalFieldTmpl(
const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID()),
material(material), fem(&fem), element_filter(element_filter),
spatial_dimension(dim) {}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
InternalFieldTmpl<Material, T>::InternalFieldTmpl(const ID & id,
const InternalFieldTmpl<Material, T> & other)
: ElementTypeMapArray<T>(id, other.material.getID()),
material(other.material), fem(other.fem),
element_filter(other.element_filter), default_value(other.default_value),
spatial_dimension(other.spatial_dimension),
element_kind(other.element_kind), nb_component(other.nb_component) {
AKANTU_DEBUG_ASSERT(other.is_init,
"Cannot create a copy of a non initialized field");
this->internalInitialize(this->nb_component);
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
InternalFieldTmpl<Material, T>::~InternalFieldTmpl() {
if (this->is_init) {
this->material.unregisterInternal(*this);
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::setFEEngine(FEEngine & fe_engine) {
this->fem = &fe_engine;
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::setElementKind(ElementKind element_kind) {
this->element_kind = element_kind;
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::initialize(UInt nb_component) {
internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::initializeHistory() {
if (!previous_values)
previous_values =
std::make_unique<InternalFieldTmpl<Material, T>>("previous_" + this->getID(), *this);
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::resize() {
if (!this->is_init){
return;
}
for (auto ghost : ghost_types) {
for (const auto & type : this->filterTypes(ghost)) {
UInt nb_element = this->element_filter(type, ghost).size();
UInt nb_quadrature_points =
this->fem->getNbIntegrationPoints(type, ghost);
UInt new_size = nb_element * nb_quadrature_points;
UInt old_size = 0;
Array<T> * vect = nullptr;
if (this->exists(type, ghost)) {
vect = &(this->operator()(type, ghost));
old_size = vect->size();
vect->resize(new_size);
} else {
vect = &(this->alloc(nb_element * nb_quadrature_points, nb_component,
type, ghost));
}
this->setArrayValues(vect->storage() + old_size * vect->getNbComponent(),
vect->storage() + new_size * vect->getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::setDefaultValue(const T & value) {
this->default_value = value;
this->reset();
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::reset() {
for (auto ghost_type : ghost_types){
for (const auto & type : this->elementTypes(ghost_type)) {
Array<T> & vect = (*this)(type, ghost_type);
//vect.zero();
this->setArrayValues(
vect.storage(), vect.storage() + vect.size() * vect.getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::internalInitialize(UInt nb_component) {
if (!this->is_init) {
this->nb_component = nb_component;
for (auto ghost : ghost_types) {
for (const auto & type : this->filterTypes(ghost)) {
UInt nb_element = this->element_filter(type, ghost).size();
UInt nb_quadrature_points =
this->fem->getNbIntegrationPoints(type, ghost);
if (this->exists(type, ghost)) {
this->operator()(type, ghost)
.resize(nb_element * nb_quadrature_points);
} else {
this->alloc(nb_element * nb_quadrature_points, nb_component, type,
ghost);
}
}
}
this->material.registerInternal(*this);
this->is_init = true;
}
this->reset();
if (this->previous_values) {
this->previous_values->internalInitialize(nb_component);
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::setArrayValues(T * begin, T * end) {
for (; begin < end; ++begin){
*begin = this->default_value;
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::saveCurrentValues() {
AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
if (not this->is_init) {
return;
}
for (auto ghost_type : ghost_types) {
for (const auto & type : this->elementTypes(ghost_type)) {
(*this->previous_values)(type, ghost_type)
.copy((*this)(type, ghost_type));
}
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::restorePreviousValues() {
AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
if (not this->is_init) {
return;
}
for (auto ghost_type : ghost_types) {
for (const auto & type : this->elementTypes(ghost_type)) {
(*this)(type, ghost_type)
.copy((*this->previous_values)(type, ghost_type));
}
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::removeIntegrationPoints(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto ghost_type : ghost_types) {
for (auto type : new_numbering.elementTypes(_all_dimensions, ghost_type,
_ek_not_defined)) {
if (not this->exists(type, ghost_type)) {
continue;
}
Array<T> & vect = (*this)(type, ghost_type);
if (vect.empty()) {
continue;
}
const Array<UInt> & renumbering = new_numbering(type, ghost_type);
UInt nb_quad_per_elem = fem->getNbIntegrationPoints(type, ghost_type);
UInt nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size() << "!=" << tmp.size()
<< ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(T));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
void InternalFieldTmpl<Material, T>::printself(std::ostream & stream,
int indent [[gnu::unused]]) const {
stream << "InternalField [ " << this->getID();
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
ElementTypeMapArray<T>::printself(stream, indent + 3);
} else {
#endif
stream << " {" << this->getData(_not_ghost).size() << " types - "
<< this->getData(_ghost).size() << " ghost types"
<< "}";
#if !defined(AKANTU_NDEBUG)
}
#endif
stream << " ]";
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<InternalField<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
/* -------------------------------------------------------------------------- */
template <class Material, typename T>
inline InternalFieldTmpl<Material, T>::operator T() const {
return default_value;
}
} // namespace akantu
#endif /* AKANTU_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_core_includes.hh b/src/model/solid_mechanics/materials/material_core_includes.hh
index 4b6bf873e..e595aeeba 100644
--- a/src/model/solid_mechanics/materials/material_core_includes.hh
+++ b/src/model/solid_mechanics/materials/material_core_includes.hh
@@ -1,80 +1,82 @@
/**
* @file material_core_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Thu Mar 11 2021
*
* @brief List of materials for core package
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_CORE_INCLUDES_HH_
#define AKANTU_MATERIAL_CORE_INCLUDES_HH_
/* -------------------------------------------------------------------------- */
/* Material list */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
// elastic materials
#include "material_elastic.hh"
#include "material_elastic_linear_anisotropic.hh"
#include "material_elastic_orthotropic.hh"
#include "material_neohookean.hh"
// visco-elastic materials
#include "material_standard_linear_solid_deviatoric.hh"
// damage laws
#include "material_marigo.hh"
#include "material_mazars.hh"
// phasefield laws
#include "material_phasefield.hh"
// small-deformation plasticity
#include "material_linear_isotropic_hardening.hh"
// Drucker-Prager plasticity
#include "material_drucker_prager.hh"
// von-mises plasticity with damage
#include "material_von_mises_mazars.hh"
#endif
#define AKANTU_CORE_MATERIAL_LIST \
((2, (elastic, MaterialElastic))) \
((2, (neohookean, MaterialNeohookean))) \
((2, (elastic_orthotropic, MaterialElasticOrthotropic))) \
((2, (elastic_anisotropic, MaterialElasticLinearAnisotropic))) \
((2, (sls_deviatoric, MaterialStandardLinearSolidDeviatoric))) \
((2, (marigo, MaterialMarigo)))((2, (mazars, MaterialMazars))) \
((2, (plastic_linear_isotropic_hardening, \
MaterialLinearIsotropicHardening))) \
((2, (plastic_drucker_prager, MaterialDruckerPrager))) \
((2, (plastic_mazars, MaterialVonMisesMazars))) \
((2, (phasefield, MaterialPhaseField)))
#endif /* AKANTU_MATERIAL_CORE_INCLUDES_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
index b5c897168..9e3da3aba 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.cc
@@ -1,80 +1,84 @@
/**
* @file material_anisotropic_damage.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mer jun 26 2019
+ * @date creation: Wed Jul 03 2019
+ * @date last modification: Fri Jul 24 2020
*
- * @brief A Documented file.
+ * @brief Base class for anisotropic damage materials
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_anisotropic_damage.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace {
template <UInt dim>
std::unique_ptr<Material>
materialAnisotropicDamage(std::integral_constant<UInt, dim> /*unused*/,
const ID & option, SolidMechanicsModel & model,
const ID & id) {
if (option.empty() or option == "mazars") {
return std::make_unique<MaterialAnisotropicDamage<
dim, EquivalentStrainMazars, DamageThresholdTan>>(model, id);
}
if (option == "mazars-drucker-prager") {
return std::make_unique<MaterialAnisotropicDamage<
dim, EquivalentStrainMazarsDruckerPrager, DamageThresholdTan>>(model,
id);
}
AKANTU_EXCEPTION("The option " << option
<< " is not valid for the material " << id);
}
template <class... Args>
decltype(auto) dimensionDispatch(UInt dim, Args &&... args) {
switch (dim) {
case 1:
return materialAnisotropicDamage(std::integral_constant<UInt, 1>{},
std::forward<Args>(args)...);
case 2:
return materialAnisotropicDamage(std::integral_constant<UInt, 2>{},
std::forward<Args>(args)...);
case 3:
return materialAnisotropicDamage(std::integral_constant<UInt, 3>{},
std::forward<Args>(args)...);
default: {
AKANTU_EXCEPTION("In what dimension are you leaving ?");
}
}
}
} // namespace
static bool material_is_alocated_anisotropic_damage [[gnu::unused]] =
MaterialFactory::getInstance().registerAllocator(
"anisotropic_damage",
[](UInt dim, const ID & option, SolidMechanicsModel & model,
const ID & id) -> std::unique_ptr<Material> {
return dimensionDispatch(dim, option, model, id);
});
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
index 7583b31f0..54c87919d 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage.hh
@@ -1,87 +1,91 @@
/**
* @file material_anisotropic_damage.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mar jun 25 2019
+ * @date creation: Sat Feb 03 2018
+ * @date last modification: Fri Jul 24 2020
*
- * @brief A Documented file.
+ * @brief Base class for anisotropic damage materials
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_
#define AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_
namespace akantu {
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold,
template <UInt> class Parent = MaterialElastic>
class MaterialAnisotropicDamage : public Parent<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialAnisotropicDamage(SolidMechanicsModel & model, const ID & id = "");
~MaterialAnisotropicDamage() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void computeStress(ElementType el_type, GhostType ghost_type) override;
private:
void damageStress(Matrix<double> & sigma, const Matrix<double> & sigma_el,
const Matrix<double> & D, Real TrD);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Real Dc{0.99};
/// damage internal variable
InternalField<Real> damage;
/// elastic stress
InternalField<Real> elastic_stress;
/// equivalent strain
InternalField<Real> equivalent_strain;
/// trace of the damageThreshold
InternalField<Real> trace_damage;
/// damage criteria
EquivalentStrain<dim> equivalent_strain_function;
/// damage evolution
DamageThreshold<dim> damage_threshold_function;
};
} // namespace akantu
#include "material_anisotropic_damage_tmpl.hh"
#endif /* AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
index b48dbac7d..3c8516d07 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_anisotropic_damage_tmpl.hh
@@ -1,375 +1,380 @@
/**
* @file material_anisotropic_damage_tmpl.hh
*
- * @author Nicolas Richart
+ * @author Emil Gallyamov <emil.gallyamov@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mar jun 25 2019
+ * @date creation: Wed Jul 03 2019
+ * @date last modification: Fri Jul 24 2020
*
- * @brief A Documented file.
+ * @brief Base class for anisotropic damage materials
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "material_anisotropic_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_
#define AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_
namespace akantu {
struct EmptyIteratorContainer {
struct iterator {
auto & operator++() { return *this; }
Real operator*() { return 0; }
bool operator!=(const iterator & /*unused*/) const { return true; }
bool operator==(const iterator & /*unused*/) const { return false; }
};
auto begin() const // NOLINT(readability-convert-member-functions-to-static)
{
return iterator();
}
auto end() const // NOLINT(readability-convert-member-functions-to-static)
{
return iterator();
}
};
} // namespace akantu
namespace std {
template <> struct iterator_traits<::akantu::EmptyIteratorContainer::iterator> {
using iterator_category = forward_iterator_tag;
using value_type = akantu::Real;
using difference_type = std::ptrdiff_t;
using pointer = akantu::Real *;
using reference = akantu::Real &;
};
} // namespace std
namespace akantu {
namespace {
template <UInt dim, class Op>
void tensorPlus_(const Matrix<Real> & A, Op && oper) {
Vector<Real> A_eigs(dim);
A.eig(A_eigs);
for (auto & ap : A_eigs) {
oper(ap);
}
}
template <UInt dim> auto tensorPlus2(const Matrix<Real> & A) {
Real square = 0;
tensorPlus_<dim>(A, [&](Real eig) {
eig = std::max(eig, 0.);
square += eig * eig;
});
return square;
}
template <UInt dim> auto tensorPlusTrace(const Matrix<Real> & A) {
Real trace_plus = 0;
Real trace_minus = 0;
tensorPlus_<dim>(A, [&](Real eig) {
trace_plus += std::max(eig, 0.);
trace_minus += std::min(eig, 0.);
});
return std::make_pair(trace_plus, trace_minus);
}
template <UInt dim, class Op>
auto tensorPlusOp(const Matrix<Real> & A, Matrix<Real> & A_directions,
Op && oper, bool sorted = false) {
Vector<Real> A_eigs(dim);
Matrix<Real> A_diag(dim, dim);
A.eig(A_eigs, A_directions, sorted);
for (auto && data : enumerate(A_eigs)) {
auto i = std::get<0>(data);
A_diag(i, i) = oper(std::max(std::get<1>(data), 0.), i);
}
return A_directions * A_diag * A_directions.transpose();
}
template <UInt dim, class Op>
auto tensorPlus(const Matrix<Real> & A, Matrix<Real> & A_directions,
bool sorted = false) {
return tensorPlusOp<dim>(
A, A_directions, [](Real x, Real /*unused*/) { return x; }, sorted);
}
template <UInt dim, class Op>
auto tensorPlusOp(const Matrix<Real> & A, Op && oper) {
Matrix<Real> A_directions(dim, dim);
return tensorPlusOp<dim>(A, A_directions, std::forward<Op>(oper));
}
template <UInt dim> auto tensorPlus(const Matrix<Real> & A) {
return tensorPlusOp<dim>(A, [](Real x, Real /*unused*/) { return x; });
}
template <UInt dim> auto tensorSqrt(const Matrix<Real> & A) {
return tensorPlusOp<dim>(
A, [](Real x, UInt /*unused*/) { return std::sqrt(x); });
}
} // namespace
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold, Parent>::
MaterialAnisotropicDamage(SolidMechanicsModel & model, const ID & id)
: Parent<dim>(model, id), damage("damage_tensor", *this),
elastic_stress("elastic_stress", *this),
equivalent_strain("equivalent_strain", *this),
trace_damage("trace_damage", *this), equivalent_strain_function(*this),
damage_threshold_function(*this) {
this->registerParam("Dc", Dc, _pat_parsable, "Critical damage");
this->damage.initialize(dim * dim);
this->elastic_stress.initialize(dim * dim);
this->equivalent_strain.initialize(1);
this->trace_damage.initialize(1);
this->trace_damage.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
void MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold, Parent>::
damageStress(Matrix<Real> & sigma, const Matrix<Real> & sigma_el,
const Matrix<Real> & D, Real TrD) {
// σ_(n + 1) = (1 − D_(n + 1))^(1/2) σ~_(n + 1) (1 − D_(n + 1))^(1 / 2)
// - ((1 − D_(n + 1)) : σ~_(n + 1))/ (3 - Tr(D_(n+1))) (1 − D_(n + 1))
// + 1/3 (1 - Tr(D_(n+1)) <Tr(σ~_(n + 1))>_+ + <Tr(σ~_(n + 1))>_-) I
auto one_D = Matrix<Real>::eye(dim) - D;
auto sqrt_one_D = tensorSqrt<dim>(one_D);
Real Tr_sigma_plus;
Real Tr_sigma_minus;
std::tie(Tr_sigma_plus, Tr_sigma_minus) = tensorPlusTrace<dim>(sigma_el);
auto I = Matrix<Real>::eye(dim);
sigma = sqrt_one_D * sigma_el * sqrt_one_D -
(one_D.doubleDot(sigma_el) / (dim - TrD) * one_D) +
1. / dim * ((1 - TrD) * Tr_sigma_plus - Tr_sigma_minus) * I;
}
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class EquivalentStrain,
template <UInt> class DamageThreshold, template <UInt> class Parent>
void MaterialAnisotropicDamage<dim, EquivalentStrain, DamageThreshold,
Parent>::computeStress(ElementType type,
GhostType ghost_type) {
for (auto && data :
zip(make_view(this->stress(type, ghost_type), dim, dim),
make_view(this->gradu(type, ghost_type), dim, dim),
make_view(this->sigma_th(type, ghost_type)),
make_view(this->elastic_stress(type, ghost_type), dim, dim),
make_view(this->equivalent_strain(type, ghost_type)),
make_view(this->damage(type, ghost_type), dim, dim),
make_view(this->trace_damage(type, ghost_type)),
make_view(this->trace_damage.previous(type, ghost_type)),
equivalent_strain_function, damage_threshold_function)) {
auto & sigma = std::get<0>(data);
auto & grad_u = std::get<1>(data);
auto & sigma_th = std::get<2>(data);
auto & sigma_el = std::get<3>(data);
auto & epsilon_hat = std::get<4>(data);
auto & D = std::get<5>(data);
auto & TrD_n_1 = std::get<6>(data);
auto & TrD = std::get<7>(data);
auto & equivalent_strain_data = std::get<8>(data);
auto & damage_threshold_data = std::get<9>(data);
Matrix<Real> Dtmp(dim, dim);
Real TrD_n_1_tmp;
Matrix<Real> epsilon(dim, dim);
// yes you read properly this is a label for a goto
auto computeDamage = [&]() {
MaterialElastic<dim>::computeStressOnQuad(grad_u, sigma_el, sigma_th);
this->template gradUToEpsilon<dim>(grad_u, epsilon);
// evaluate the damage criteria
epsilon_hat = equivalent_strain_function(epsilon, equivalent_strain_data);
// evolve the damage if needed
auto K_TrD = damage_threshold_function.K(TrD, damage_threshold_data);
auto f = epsilon_hat - K_TrD;
// if test function > 0 evolve the damage
if (f > 0) {
TrD_n_1_tmp =
damage_threshold_function.K_inv(epsilon_hat, damage_threshold_data);
auto epsilon_plus = tensorPlus<dim>(epsilon);
auto delta_lambda = (TrD_n_1_tmp - TrD) / (epsilon_hat * epsilon_hat);
Dtmp = D + delta_lambda * epsilon_plus;
return true;
}
return false;
};
// compute a temporary version of the new damage
auto is_damage_updated = computeDamage();
if (is_damage_updated) {
/// Check and correct for broken case
if (Dtmp.trace() > Dc) {
if (epsilon.trace() > 0) { // tensile loading
auto kpa = this->kpa;
auto lambda = this->lambda;
// change kappa to Kappa_broken = (1-Dc) Kappa
kpa = (1 - Dc) * kpa;
this->E = 9 * kpa * (kpa - lambda) / (3 * kpa - lambda);
this->nu = lambda / (3 * kpa - lambda);
this->updateInternalParameters();
computeDamage();
} else if (std::abs(epsilon.trace()) < 1e-10) { // deviatoric case
Matrix<Real> n(dim, dim);
std::vector<UInt> ns;
tensorPlusOp<dim>(
Dtmp, n,
[&](Real x, UInt i) {
if (x > this->Dc) {
ns.push_back(i);
return this->Dc;
}
return x;
},
true);
}
}
TrD_n_1 = TrD_n_1_tmp;
D = Dtmp;
} else {
TrD_n_1 = TrD;
}
// apply the damage to the stress
damageStress(sigma, sigma_el, D, TrD_n_1);
}
}
/* -------------------------------------------------------------------------- */
/* EquivalentStrain functions */
/* -------------------------------------------------------------------------- */
template <UInt dim>
class EquivalentStrainMazars : public EmptyIteratorContainer {
public:
EquivalentStrainMazars(Material & /*mat*/) {}
template <class... Other>
Real operator()(const Matrix<Real> & epsilon, Other &&... /*other*/) {
Real epsilon_hat = 0.;
std::tie(epsilon_hat, std::ignore) = tensorPlusTrace<dim>(epsilon);
return std::sqrt(epsilon_hat);
}
};
template <UInt dim>
class EquivalentStrainMazarsDruckerPrager : public EquivalentStrainMazars<dim> {
public:
EquivalentStrainMazarsDruckerPrager(Material & mat)
: EquivalentStrainMazars<dim>(mat) {
mat.registerParam("k", k, _pat_parsable, "k");
}
template <class... Other>
Real operator()(const Matrix<Real> & epsilon, Real /*unused*/) {
Real epsilon_hat = EquivalentStrainMazars<dim>::operator()(epsilon);
epsilon_hat += k * epsilon.trace();
return epsilon_hat;
}
protected:
Real k;
};
/* -------------------------------------------------------------------------- */
/* DamageThreshold functions */
/* -------------------------------------------------------------------------- */
template <UInt dim>
class DamageThresholdLinear : public EmptyIteratorContainer {
public:
DamageThresholdLinear(Material & mat) : mat(mat) {
mat.registerParam("A", A, _pat_parsable, "A");
mat.registerParam("K0", K0, _pat_parsable, "K0");
}
template <class... Other> Real K(Real x, Other &&... /*other*/) {
return 1. / A * x + K0;
}
template <class... Other> Real K_inv(Real x, Other &&... /*other*/) {
return A * (x - K0);
}
private:
Material & mat;
Real A;
Real K0;
};
template <UInt dim> class DamageThresholdTan : public EmptyIteratorContainer {
public:
DamageThresholdTan(Material & mat) : mat(mat) {
mat.registerParam("a", a, _pat_parsable, "a");
mat.registerParam("A", A, _pat_parsable, "A");
mat.registerParam("K0", K0, _pat_parsable, "K0");
}
template <class... Other> Real K(Real x, Other &&... /*other*/) {
return a * std::tan(std::atan2(x, a) - std::atan2(K0, a));
}
template <class... Other> Real K_inv(Real x, Other &&... /*other*/) {
return a * A * (std::atan2(x, a) - std::atan2(K0, a));
}
private:
Material & mat;
Real a{2.93e-4};
Real A{5e3};
Real K0{5e-5};
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_ANISOTROPIC_DAMAGE_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
index 8649e41f3..9264dc164 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
@@ -1,108 +1,110 @@
/**
* @file material_damage.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material isotropic elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_DAMAGE_HH_
#define AKANTU_MATERIAL_DAMAGE_HH_
namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialElastic>
class MaterialDamage : public Parent<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamage(SolidMechanicsModel & model, const ID & id = "");
~MaterialDamage() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
bool hasStiffnessMatrixChanged() override { return true; }
protected:
/// update the dissipated energy, must be called after the stress have been
/// computed
void updateEnergies(ElementType el_type) override;
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getEnergy(const std::string & type) override;
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real)
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage internal variable
InternalField<Real> damage;
/// dissipated energy
InternalField<Real> dissipated_energy;
/// contain the current value of @f$ \int_0^{\epsilon}\sigma(\omega)d\omega
/// @f$ the dissipated energy
InternalField<Real> int_sigma;
};
} // namespace akantu
#include "material_damage_tmpl.hh"
#endif /* AKANTU_MATERIAL_DAMAGE_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
index ce9d1dba1..e002a0774 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
@@ -1,73 +1,75 @@
/**
* @file material_damage_non_local.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 23 2012
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief interface for non local damage material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_
#define AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_
namespace akantu {
template <UInt dim, class MaterialDamageLocal>
class MaterialDamageNonLocal
: public MaterialNonLocal<dim, MaterialDamageLocal> {
public:
using MaterialParent = MaterialNonLocal<dim, MaterialDamageLocal>;
MaterialDamageNonLocal(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id){};
protected:
/* ------------------------------------------------------------------------ */
virtual void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) = 0;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) override {
AKANTU_DEBUG_IN();
for (auto type : this->element_filter.elementTypes(dim, ghost_type)) {
auto & elem_filter = this->element_filter(type, ghost_type);
if (elem_filter.empty()) {
continue;
}
computeNonLocalStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
index dd7719106..635c0307e 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
@@ -1,172 +1,174 @@
/**
* @file material_damage_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
- * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Specialization of the material class for the damage material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
MaterialDamage<spatial_dimension, Parent>::MaterialDamage(
SolidMechanicsModel & model, const ID & id)
: Parent<spatial_dimension>(model, id), damage("damage", *this),
dissipated_energy("damage dissipated energy", *this),
int_sigma("integral of sigma", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = false;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->damage.initialize(1);
this->dissipated_energy.initialize(1);
this->int_sigma.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::initMaterial() {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the dissipated energy in each element by a trapezoidal approximation
* of
* @f$ Ed = \int_0^{\epsilon}\sigma(\omega)d\omega -
* \frac{1}{2}\sigma:\epsilon@f$
*/
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::updateEnergies(
ElementType el_type) {
Parent<spatial_dimension>::updateEnergies(el_type);
this->computePotentialEnergy(el_type);
auto epsilon_p =
this->gradu.previous(el_type).begin(spatial_dimension, spatial_dimension);
auto sigma_p = this->stress.previous(el_type).begin(spatial_dimension,
spatial_dimension);
auto epot = this->potential_energy(el_type).begin();
auto ints = this->int_sigma(el_type).begin();
auto ed = this->dissipated_energy(el_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> delta_gradu(grad_u);
delta_gradu -= *epsilon_p;
Matrix<Real> sigma_h(sigma);
sigma_h += *sigma_p;
Real dint = .5 * sigma_h.doubleDot(delta_gradu);
*ints += dint;
*ed = *ints - *epot;
++epsilon_p;
++sigma_p;
++epot;
++ints;
++ed;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuli(
ElementType el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::computeTangentModuli(el_type, tangent_matrix,
ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, *dam);
++dam;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Real & dam) {
tangent *= (1 - dam);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getEnergy(
const std::string & type) {
if (type == "dissipated") {
return getDissipatedEnergy();
}
return Parent<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
index c95d35cf4..621273af9 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
@@ -1,102 +1,104 @@
/**
* @file material_marigo.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Jul 09 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Specialization of the material class for the marigo material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMarigo<spatial_dimension>::MaterialMarigo(SolidMechanicsModel & model,
const ID & id)
: MaterialDamage<spatial_dimension>(model, id), Yd("Yd", *this),
damage_in_y(false), yc_limit(false) {
AKANTU_DEBUG_IN();
this->registerParam("Sd", Sd, Real(5000.), _pat_parsable | _pat_modifiable);
this->registerParam("epsilon_c", epsilon_c, Real(0.), _pat_parsable,
"Critical strain");
this->registerParam("Yc limit", yc_limit, false, _pat_internal,
"As the material a critical Y");
this->registerParam("damage_in_y", damage_in_y, false, _pat_parsable,
"Use threshold (1-D)Y");
this->registerParam("Yd", Yd, _pat_parsable, "Damaging energy threshold");
this->Yd.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamage<spatial_dimension>::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::updateInternalParameters() {
MaterialDamage<spatial_dimension>::updateInternalParameters();
Yc = .5 * epsilon_c * this->E * epsilon_c;
yc_limit = (std::abs(epsilon_c) > std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto dam = this->damage(el_type, ghost_type).begin();
auto Yd_q = this->Yd(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Y = 0.;
computeStressOnQuad(grad_u, sigma, *dam, Y, *Yd_q);
++dam;
++Yd_q;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(marigo, MaterialMarigo);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
index 6663304d2..7102ac5f3 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
@@ -1,122 +1,124 @@
/**
* @file material_marigo.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Marigo damage law
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_MARIGO_HH_
#define AKANTU_MATERIAL_MARIGO_HH_
namespace akantu {
/**
* Material marigo
*
* parameters in the material files :
* - Yd : (default: 50)
* - Sd : (default: 5000)
* - Ydrandomness : (default:0)
*/
template <UInt spatial_dimension>
class MaterialMarigo : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMarigo(SolidMechanicsModel & model, const ID & id = "");
~MaterialMarigo() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & dam, Real & Y, Real & Ydq);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & Y, Real & Ydq);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Yd;
/// damage threshold
Real Sd;
/// critical epsilon when the material is considered as broken
Real epsilon_c;
Real Yc;
bool damage_in_y;
bool yc_limit;
};
} // namespace akantu
#include "material_marigo_inline_impl.hh"
#endif /* AKANTU_MATERIAL_MARIGO_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
index b67f5af9e..2eaebd93a 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_inline_impl.hh
@@ -1,133 +1,135 @@
/**
* @file material_marigo_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Fri Dec 02 2016
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of the inline functions of the material marigo
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo.hh"
#ifndef AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_
#define AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_
namespace akantu {
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeStressOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam, Real & Y,
Real & Ydq) {
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
}
Y *= 0.5;
if (damage_in_y) {
Y *= (1 - dam);
}
if (yc_limit) {
Y = std::min(Y, Yc);
}
if (!this->is_non_local) {
computeDamageAndStressOnQuad(sigma, dam, Y, Ydq);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::computeDamageAndStressOnQuad(
Matrix<Real> & sigma, Real & dam, Real & Y, Real & Ydq) {
Real Fd = Y - Ydq - Sd * dam;
if (Fd > 0) {
dam = (Y - Ydq) / Sd;
}
dam = std::min(dam, Real(1.));
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline UInt MaterialMarigo<spatial_dimension>::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == SynchronizationTag::_smm_init_mat) {
size += sizeof(Real) * this->getModel().getNbIntegrationPoints(elements);
}
size += MaterialDamage<spatial_dimension>::getNbData(elements, tag);
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMarigo<spatial_dimension>::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_smm_init_mat) {
this->packElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::packData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void
MaterialMarigo<spatial_dimension>::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == SynchronizationTag::_smm_init_mat) {
this->unpackElementDataHelper(Yd, buffer, elements);
}
MaterialDamage<spatial_dimension>::unpackData(buffer, elements, tag);
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_MATERIAL_MARIGO_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
index d71fa1cc2..557563d85 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.cc
@@ -1,105 +1,107 @@
/**
* @file material_marigo_non_local.cc
*
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Marigo non-local inline function implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_marigo_non_local.hh"
#include "non_local_neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMarigoNonLocal<spatial_dimension>::MaterialMarigoNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialMarigoNonLocalParent(model, id), Y("Y", *this),
Ynl("Y non local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Y.initialize(1);
this->Ynl.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::registerNonLocalVariables() {
this->model.getNonLocalManager().registerNonLocalVariable(this->Y.getName(),
Ynl.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(Ynl.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
Real * Yt = this->Y(el_type, ghost_type).storage();
Real * Ydq = this->Yd(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMarigo<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *dam,
*Yt, *Ydq);
++dam;
++Yt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(type, ghost_type).storage();
Real * Ydq = this->Yd(type, ghost_type).storage();
Real * Ynlt = this->Ynl(type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(type, ghost_type);
this->computeDamageAndStressOnQuad(sigma, *dam, *Ynlt, *Ydq);
++dam;
++Ynlt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(marigo_non_local, MaterialMarigoNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
index 0e91c567b..5dddcec10 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
@@ -1,91 +1,93 @@
/**
* @file material_marigo_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Marigo non-local description
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_marigo.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_
#define AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* Material Marigo
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMarigoNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMarigo<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MaterialMarigoNonLocalParent = MaterialDamageNonLocal<spatial_dimension,
MaterialMarigo<spatial_dimension>>;
MaterialMarigoNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void registerNonLocalVariables() override;
/// constitutive law
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) override;
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Y, Y, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> Y;
InternalField<Real> Ynl;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
index a516a138f..26a9d3ed2 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
@@ -1,80 +1,82 @@
/**
* @file material_mazars.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Jul 09 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Specialization of the material class for the damage material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazars<spatial_dimension>::MaterialMazars(SolidMechanicsModel & model,
const ID & id)
: MaterialDamage<spatial_dimension>(model, id), K0("K0", *this),
damage_in_compute_stress(true) {
AKANTU_DEBUG_IN();
this->registerParam("K0", K0, _pat_parsable, "K0");
this->registerParam("At", At, Real(0.8), _pat_parsable, "At");
this->registerParam("Ac", Ac, Real(1.4), _pat_parsable, "Ac");
this->registerParam("Bc", Bc, Real(1900.), _pat_parsable, "Bc");
this->registerParam("Bt", Bt, Real(12000.), _pat_parsable, "Bt");
this->registerParam("beta", beta, Real(1.06), _pat_parsable, "beta");
this->K0.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazars<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Ehat = 0;
computeStressOnQuad(grad_u, sigma, *dam, Ehat);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(mazars, MaterialMazars);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
index 8f332e749..8d22b97af 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
@@ -1,124 +1,126 @@
/**
* @file material_mazars.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Material Following the Mazars law for damage evolution
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_MAZARS_HH_
#define AKANTU_MATERIAL_MAZARS_HH_
namespace akantu {
/**
* Material Mazars
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - K0 : Damage threshold
* - At : Parameter damage traction 1
* - Bt : Parameter damage traction 2
* - Ac : Parameter damage compression 1
* - Bc : Parameter damage compression 2
* - beta : Parameter for shear
*/
template <UInt spatial_dimension>
class MaterialMazars : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMazars(SolidMechanicsModel & model, const ID & id = "");
~MaterialMazars() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageAndStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageOnQuad(const Real & epsilon_equ,
const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ,
Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage threshold
RandomInternalField<Real> K0;
/// parameter damage traction 1
Real At;
/// parameter damage traction 2
Real Bt;
/// parameter damage compression 1
Real Ac;
/// parameter damage compression 2
Real Bc;
/// parameter for shear
Real beta;
/// specify the variable to average false = ehat, true = damage (only valid
/// for non local version)
bool damage_in_compute_stress;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_mazars_inline_impl.hh"
#endif /* AKANTU_MATERIAL_MAZARS_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
index 296593f8d..abd814732 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_inline_impl.hh
@@ -1,162 +1,165 @@
/**
* @file material_mazars_inline_impl.hh
*
- * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
+ * @author Marion Estelle Chambart <mchambart@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 06 2011
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of the material damage
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_mazars.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
Matrix<Real> epsilon(3, 3);
epsilon.zero();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
}
}
Vector<Real> Fdiag(3);
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
Ehat = 0.;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_p = std::max(Real(0.), Fdiag(i));
Ehat += epsilon_p * epsilon_p;
}
Ehat = sqrt(Ehat);
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
if (damage_in_compute_stress) {
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
if (not this->is_non_local) {
computeDamageAndStressOnQuad(grad_u, sigma, dam, Ehat);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageAndStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
if (!damage_in_compute_stress) {
Vector<Real> Fdiag(3);
Fdiag.zero();
Matrix<Real> epsilon(3, 3);
epsilon.zero();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
}
}
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialMazars<spatial_dimension>::computeDamageOnQuad(
const Real & epsilon_equ,
__attribute__((unused)) const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ, Real & dam) {
Real Fs = epsilon_equ - K0;
if (Fs > 0.) {
Real dam_t;
Real dam_c;
dam_t =
1 - K0 * (1 - At) / epsilon_equ - At * (exp(-Bt * (epsilon_equ - K0)));
dam_c =
1 - K0 * (1 - Ac) / epsilon_equ - Ac * (exp(-Bc * (epsilon_equ - K0)));
Real Cdiag;
Cdiag = this->E * (1 - this->nu) / ((1 + this->nu) * (1 - 2 * this->nu));
Vector<Real> sigma_princ(3);
sigma_princ(0) = Cdiag * epsilon_princ(0) +
this->lambda * (epsilon_princ(1) + epsilon_princ(2));
sigma_princ(1) = Cdiag * epsilon_princ(1) +
this->lambda * (epsilon_princ(0) + epsilon_princ(2));
sigma_princ(2) = Cdiag * epsilon_princ(2) +
this->lambda * (epsilon_princ(1) + epsilon_princ(0));
Vector<Real> sigma_p(3);
for (UInt i = 0; i < 3; i++) {
sigma_p(i) = std::max(Real(0.), sigma_princ(i));
}
// sigma_p *= 1. - dam;
Real trace_p = this->nu / this->E * (sigma_p(0) + sigma_p(1) + sigma_p(2));
Real alpha_t = 0;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_t = (1 + this->nu) / this->E * sigma_p(i) - trace_p;
Real epsilon_p = std::max(Real(0.), epsilon_princ(i));
alpha_t += epsilon_t * epsilon_p;
}
alpha_t /= epsilon_equ * epsilon_equ;
alpha_t = std::min(alpha_t, Real(1.));
Real alpha_c = 1. - alpha_t;
alpha_t = std::pow(alpha_t, beta);
alpha_c = std::pow(alpha_c, beta);
Real damtemp;
damtemp = alpha_t * dam_t + alpha_c * dam_c;
dam = std::max(damtemp, dam);
dam = std::min(dam, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
// template<UInt spatial_dimension>
// inline void
// MaterialMazars<spatial_dimension>::computeTangentModuliOnQuad(Matrix<Real> &
// tangent) {
// MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(tangent);
// tangent *= (1-dam);
// }
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
index f046b3079..a9331b17a 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
@@ -1,123 +1,126 @@
/**
* @file material_mazars_non_local.cc
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Specialization of the material class for the non-local mazars
* material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_mazars_non_local.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazarsNonLocal<spatial_dimension>::MaterialMazarsNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialNonLocalParent(model, id), Ehat("epsilon_equ", *this),
non_local_variable("mazars_non_local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Ehat.initialize(1);
this->non_local_variable.initialize(1);
this->registerParam("average_on_damage", this->damage_in_compute_stress,
false, _pat_parsable | _pat_modifiable,
"Is D the non local variable");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::registerNonLocalVariables() {
ID local;
if (this->damage_in_compute_stress) {
local = this->damage.getName();
} else {
local = this->Ehat.getName();
}
this->model.getNonLocalManager().registerNonLocalVariable(
local, non_local_variable.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(non_local_variable.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage = this->damage(el_type, ghost_type).storage();
Real * epsilon_equ = this->Ehat(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMazars<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *damage,
*epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & non_loc_var = non_local_variable(el_type, ghost_type);
Real * damage;
Real * epsilon_equ;
if (this->damage_in_compute_stress) {
damage = non_loc_var.storage();
epsilon_equ = this->Ehat(el_type, ghost_type).storage();
} else {
damage = this->damage(el_type, ghost_type).storage();
epsilon_equ = non_loc_var.storage();
}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(grad_u, sigma, *damage, *epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(mazars_non_local, MaterialMazarsNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
index 5168b3730..a326996ae 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
@@ -1,90 +1,92 @@
/**
* @file material_mazars_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Mazars non-local description
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_mazars.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_
#define AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_
namespace akantu {
/**
* Material Mazars Non local
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialMazarsNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MaterialNonLocalParent =
MaterialDamageNonLocal<spatial_dimension,
MaterialMazars<spatial_dimension>>;
MaterialMazarsNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the ehat per quadrature points to perform the averaging
InternalField<Real> Ehat;
InternalField<Real> non_local_variable;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_phasefield.cc b/src/model/solid_mechanics/materials/material_damage/material_phasefield.cc
index 011de19ef..c55d48a0a 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_phasefield.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_phasefield.cc
@@ -1,107 +1,108 @@
/**
* @file material_phasefield.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Oct 02 2018
- * @date last modification: Tue Oct 02 2018
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Fri Apr 02 2021
*
* @brief Specialization of the material class for the phasefield material
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_phasefield.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialPhaseField<spatial_dimension>::MaterialPhaseField(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("eta", eta, Real(0.), _pat_parsable, "eta");
this->damage.initialize(0);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPhaseField<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto dam = this->damage(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPhaseField<spatial_dimension>::computeTangentModuli(
ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeTangentModuli(el_type, tangent_matrix,
ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, *dam);
++dam;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPhaseField<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Real & dam) {
tangent *= (1 - dam)*(1 - dam) + eta;
}
INSTANTIATE_MATERIAL(phasefield, MaterialPhaseField);
} // akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_phasefield.hh b/src/model/solid_mechanics/materials/material_damage/material_phasefield.hh
index adb654699..54ac83922 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_phasefield.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_phasefield.hh
@@ -1,96 +1,97 @@
/**
* @file material_phasefield.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Oct 2 2018
- * @date last modification: Tue Oct 02 2018
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Fri Apr 02 2021
*
* @brief Phasefield damage law
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_PHASEFIELD_HH__
#define __AKANTU_MATERIAL_PHASEFIELD_HH__
namespace akantu {
template <UInt spatial_dimension>
class MaterialPhaseField : public MaterialDamage<spatial_dimension> {
using Parent = MaterialDamage<spatial_dimension>;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPhaseField(SolidMechanicsModel & model, const ID & id = "");
~MaterialPhaseField() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & dam);
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
Real eta;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_phasefield_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MATERIAL_PHASEFIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_phasefield_inline_impl.cc b/src/model/solid_mechanics/materials/material_damage/material_phasefield_inline_impl.cc
index 90acfeb4a..1a20942fd 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_phasefield_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_phasefield_inline_impl.cc
@@ -1,85 +1,86 @@
/**
* @file material_phasefield_inline_impl.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Oct 02 2018
- * @date last modification: Wed Oct 02 2018
+ * @date creation: Mon Dec 13 2010
+ * @date last modification: Fri Apr 02 2021
*
* @brief Implementation of the inline functions of the material phasefield
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
inline void MaterialPhaseField<spatial_dimension>::computeStressOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam) {
MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
Matrix<Real> strain( spatial_dimension, spatial_dimension);
Matrix<Real> strain_plus( spatial_dimension, spatial_dimension);
Matrix<Real> strain_minus( spatial_dimension, spatial_dimension);
Matrix<Real> strain_dir( spatial_dimension, spatial_dimension);
Matrix<Real> strain_diag_plus( spatial_dimension, spatial_dimension);
Matrix<Real> strain_diag_minus(spatial_dimension, spatial_dimension);
Vector<Real> strain_values(spatial_dimension);
Real trace_plus, trace_minus;
this->template gradUToEpsilon<spatial_dimension>(grad_u, strain);
strain.eig(strain_values, strain_dir);
for (UInt i=0; i < spatial_dimension; i++) {
strain_diag_plus(i, i) = std::max(Real(0.), strain_values(i));
strain_diag_minus(i, i) = std::min(Real(0.), strain_values(i));
}
Matrix<Real> mat_tmp( spatial_dimension, spatial_dimension);
Matrix<Real> sigma_plus( spatial_dimension, spatial_dimension);
Matrix<Real> sigma_minus(spatial_dimension, spatial_dimension);
mat_tmp.mul<false,true>(strain_diag_plus, strain_dir);
strain_plus.mul<false, false>(strain_dir, mat_tmp);
mat_tmp.mul<false, true>(strain_diag_minus, strain_dir);
strain_minus.mul<false, true>(strain_dir, mat_tmp);
trace_plus = std::max(Real(0.), strain.trace());
trace_minus = std::min(Real(0.), strain.trace());
Real lambda = MaterialElastic<spatial_dimension>::getLambda();
Real mu = MaterialElastic<spatial_dimension>::getMu();
for (UInt i=0; i < spatial_dimension; i++) {
for (UInt j=0; j < spatial_dimension; j++) {
sigma_plus(i, j) = (i==j) * lambda * trace_plus
+ 2 * mu * strain_plus(i, j);
sigma_minus(i, j) = (i==j) * lambda * trace_minus
+ 2 * mu * strain_minus(i, j);
}
}
//sigma = (1 - dam) * sigma_plus + sigma_minus;
sigma *= (1- dam)*(1-dam) + eta;
}
diff --git a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc
index c10f2c624..8914a034e 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.cc
@@ -1,155 +1,186 @@
+/**
+ * @file material_von_mises_mazars.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Mon Apr 07 2014
+ * @date last modification: Fri Dec 04 2020
+ *
+ * @brief Mazars damage with Von Misses criteria
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "material_von_mises_mazars.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim, template <UInt> class Parent>
MaterialVonMisesMazars<dim, Parent>::MaterialVonMisesMazars(
SolidMechanicsModel & model, const ID & id)
: MaterialDamage<dim, Parent>(model, id), K0("K0", *this),
damage_in_compute_stress(true) {
AKANTU_DEBUG_IN();
this->registerParam("K0", K0, _pat_parsable, "K0");
this->registerParam("At", At, Real(0.8), _pat_parsable, "At");
this->registerParam("Ac", Ac, Real(1.4), _pat_parsable, "Ac");
this->registerParam("Bc", Bc, Real(1900.), _pat_parsable, "Bc");
this->registerParam("Bt", Bt, Real(12000.), _pat_parsable, "Bt");
this->registerParam("beta", beta, Real(1.06), _pat_parsable, "beta");
this->K0.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
void MaterialVonMisesMazars<spatial_dimension, Parent>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening_it = this->iso_hardening(el_type, ghost_type).begin();
auto previous_iso_hardening_it =
this->iso_hardening.previous(el_type, ghost_type).begin();
Real * dam = this->damage(el_type, ghost_type).storage();
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToE<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToE<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
MaterialLinearIsotropicHardening<spatial_dimension>::computeStressOnQuad(
green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Ehat = 0;
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
MaterialLinearIsotropicHardening<spatial_dimension>::computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it, *previous_sigma_th_it);
Matrix<Real> grad_u_elastic(grad_u);
grad_u_elastic -= inelastic_strain_tensor;
computeStressOnQuad(grad_u_elastic, sigma, *dam, Ehat);
++dam;
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(plastic_mazars, MaterialVonMisesMazars);
}
diff --git a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh
index 69f736bbc..8866a4972 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars.hh
@@ -1,87 +1,116 @@
-
+/**
+ * @file material_von_mises_mazars.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Fri Dec 04 2020
+ *
+ * @brief Mazars damage with Von Misses criteria
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_linear_isotropic_hardening.hh"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_VONMISES_MAZARS_HH__
#define __AKANTU_MATERIAL_VONMISES_MAZARS_HH__
namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialLinearIsotropicHardening>
class MaterialVonMisesMazars
: public MaterialDamage<spatial_dimension, Parent> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialVonMisesMazars(SolidMechanicsModel & model,
const ID & id = "");
MaterialVonMisesMazars(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageAndStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & damage,
Real & Ehat);
inline void computeDamageOnQuad(const Real & epsilon_equ,
const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ,
Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage threshold
RandomInternalField<Real> K0;
/// parameter damage traction 1
Real At;
/// parameter damage traction 2
Real Bt;
/// parameter damage compression 1
Real Ac;
/// parameter damage compression 2
Real Bc;
/// parameter for shear
Real beta;
/// specify the variable to average false = ehat, true = damage (only valid
/// for non local version)
bool damage_in_compute_stress;
};
} // namespace akantu
#include "material_von_mises_mazars_inline_impl.hh"
#endif /* __AKANTU_MATERIAL_VONMISES_MAZARS_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh
index 8a9e28ed3..9b90ca95b 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_inline_impl.hh
@@ -1,125 +1,156 @@
+/**
+ * @file material_von_mises_mazars_inline_impl.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Wed Apr 06 2011
+ * @date last modification: Wed Dec 23 2020
+ *
+ * @brief Mazars damage with Von Misses criteria
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "material_von_mises_mazars.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialVonMisesMazars<spatial_dimension, Parent>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
Matrix<Real> epsilon(3, 3);
epsilon.zero();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
}
}
Vector<Real> Fdiag(3);
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
Ehat = 0.;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_p = std::max(Real(0.), Fdiag(i));
Ehat += epsilon_p * epsilon_p;
}
Ehat = sqrt(Ehat);
// MaterialElastic<spatial_dimension>::computeStressOnQuad(grad_u, sigma);
if (damage_in_compute_stress) {
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
if (not this->is_non_local) {
computeDamageAndStressOnQuad(grad_u, sigma, dam, Ehat);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialVonMisesMazars<spatial_dimension, Parent>::computeDamageAndStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & dam,
Real & Ehat) {
if (!damage_in_compute_stress) {
Vector<Real> Fdiag(3);
Fdiag.zero();
Matrix<Real> epsilon(3, 3);
epsilon.zero();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
epsilon(i, j) = .5 * (grad_u(i, j) + grad_u(j, i));
}
}
Math::matrixEig(3, epsilon.storage(), Fdiag.storage());
computeDamageOnQuad(Ehat, sigma, Fdiag, dam);
}
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension, template <UInt> class Parent>
inline void
MaterialVonMisesMazars<spatial_dimension, Parent>::computeDamageOnQuad(
const Real & epsilon_equ,
__attribute__((unused)) const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ, Real & dam) {
Real Fs = epsilon_equ - K0;
if (Fs > 0.) {
Real dam_t;
Real dam_c;
dam_t =
1 - K0 * (1 - At) / epsilon_equ - At * (exp(-Bt * (epsilon_equ - K0)));
dam_c =
1 - K0 * (1 - Ac) / epsilon_equ - Ac * (exp(-Bc * (epsilon_equ - K0)));
Real Cdiag;
Cdiag = this->E * (1 - this->nu) / ((1 + this->nu) * (1 - 2 * this->nu));
Vector<Real> sigma_princ(3);
sigma_princ(0) = Cdiag * epsilon_princ(0) +
this->lambda * (epsilon_princ(1) + epsilon_princ(2));
sigma_princ(1) = Cdiag * epsilon_princ(1) +
this->lambda * (epsilon_princ(0) + epsilon_princ(2));
sigma_princ(2) = Cdiag * epsilon_princ(2) +
this->lambda * (epsilon_princ(1) + epsilon_princ(0));
Vector<Real> sigma_p(3);
for (UInt i = 0; i < 3; i++) {
sigma_p(i) = std::max(Real(0.), sigma_princ(i));
}
// sigma_p *= 1. - dam;
Real trace_p = this->nu / this->E * (sigma_p(0) + sigma_p(1) + sigma_p(2));
Real alpha_t = 0;
for (UInt i = 0; i < 3; ++i) {
Real epsilon_t = (1 + this->nu) / this->E * sigma_p(i) - trace_p;
Real epsilon_p = std::max(Real(0.), epsilon_princ(i));
alpha_t += epsilon_t * epsilon_p;
}
alpha_t /= epsilon_equ * epsilon_equ;
alpha_t = std::min(alpha_t, Real(1.));
Real alpha_c = 1. - alpha_t;
alpha_t = std::pow(alpha_t, beta);
alpha_c = std::pow(alpha_c, beta);
Real damtemp;
damtemp = alpha_t * dam_t + alpha_c * dam_c;
dam = std::max(damtemp, dam);
dam = std::min(dam, Real(1.));
}
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc
index dc402739e..6b65cec3d 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.cc
@@ -1,94 +1,123 @@
-
+/**
+ * @file material_von_mises_mazars_non_local.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Thu Dec 17 2020
+ *
+ * @brief Mazars damage with Von Misses criteria
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
/* -------------------------------------------------------------------------- */
#include "material_von_mises_mazars_non_local.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialVonMisesMazarsNonLocal<spatial_dimension>::MaterialVonMisesMazarsNonLocal(
SolidMechanicsModel & model, const ID & id)
: MaterialNonLocalParent(model, id), Ehat("epsilon_equ", *this),
non_local_variable("mazars_non_local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Ehat.initialize(1);
this->non_local_variable.initialize(1);
this->registerParam("average_on_damage", this->damage_in_compute_stress,
false, _pat_parsable | _pat_modifiable,
"Is D the non local variable");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialVonMisesMazarsNonLocal<spatial_dimension>::registerNonLocalVariables() {
ID local;
if (this->damage_in_compute_stress) {
local = this->damage.getName();
} else {
local = this->Ehat.getName();
}
this->model.getNonLocalManager().registerNonLocalVariable(
local, non_local_variable.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(non_local_variable.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialVonMisesMazarsNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage = this->damage(el_type, ghost_type).storage();
Real * epsilon_equ = this->Ehat(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialVonMisesMazars<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *damage,
*epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialVonMisesMazarsNonLocal<spatial_dimension>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & non_loc_var = non_local_variable(el_type, ghost_type);
Real * damage;
Real * epsilon_equ;
if (this->damage_in_compute_stress) {
damage = non_loc_var.storage();
epsilon_equ = this->Ehat(el_type, ghost_type).storage();
} else {
damage = this->damage(el_type, ghost_type).storage();
epsilon_equ = non_loc_var.storage();
}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(grad_u, sigma, *damage, *epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(von_mises_mazars_non_local, MaterialVonMisesMazarsNonLocal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh
index e8904d367..3275af4c1 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_von_mises_mazars_non_local.hh
@@ -1,63 +1,91 @@
-
-
+/**
+ * @file material_von_mises_mazars_non_local.hh
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Thu Dec 17 2020
+ *
+ * @brief Mazars damage with Von Misses criteria
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_damage_non_local.hh"
#include "material_von_mises_mazars.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_VON_MISES_MAZARS_NON_LOCAL_HH_
#define AKANTU_MATERIAL_VON_MISES_MAZARS_NON_LOCAL_HH_
namespace akantu {
/**
* Material Mazars Non local + Von Mises plasticity
*
* parameters in the material files :
*/
template <UInt spatial_dimension>
class MaterialVonMisesMazarsNonLocal
: public MaterialDamageNonLocal<spatial_dimension,
MaterialVonMisesMazars<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MaterialNonLocalParent =
MaterialDamageNonLocal<spatial_dimension,
MaterialVonMisesMazars<spatial_dimension>>;
MaterialVonMisesMazarsNonLocal(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void computeNonLocalStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the ehat per quadrature points to perform the averaging
InternalField<Real> Ehat;
InternalField<Real> non_local_variable;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_VON_MISES_MAZARS_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic.cc b/src/model/solid_mechanics/materials/material_elastic.cc
index af46e94b5..5fd3fae00 100644
--- a/src/model/solid_mechanics/materials/material_elastic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic.cc
@@ -1,257 +1,260 @@
/**
* @file material_elastic.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Specialization of the material class for the elastic material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
UInt /*a_dim*/,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: Parent(model, dim, mesh, fe_engine, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initialize() {
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
if (dim == 1) {
this->nu = 0.;
}
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::updateInternalParameters() {
MaterialThermal<dim>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <> void MaterialElastic<2>::updateInternalParameters() {
MaterialThermal<2>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
if (this->plane_stress) {
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - this->nu));
}
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator sigma_th_it =
this->sigma_th(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
const Real & sigma_th = *sigma_th_it;
this->computeStressOnQuad(grad_u, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
/// finite gradus
Matrix<Real> E(dim, dim);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// compute E
this->template gradUToE<dim>(grad_u, E);
const Real & sigma_th = *sigma_th_it;
/// compute second Piola-Kirchhoff stress tensor
this->computeStressOnQuad(E, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElastic<dim>::getPushWaveSpeed(const Element & /*unused*/) const {
return sqrt((lambda + 2 * mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElastic<dim>::getShearWaveSpeed(const Element & /*unused*/) const {
return sqrt(mu / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computePotentialEnergy(ElementType el_type) {
AKANTU_DEBUG_IN();
// MaterialThermal<dim>::computePotentialEnergy(ElementType)
// needs to be implemented
// MaterialThermal<dim>::computePotentialEnergy(el_type);
auto epot = this->potential_energy(el_type, _not_ghost).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
this->computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
auto E = this->template gradUToE<dim>(grad_u);
this->computePotentialEnergyOnQuad(E, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElastic<dim>::computePotentialEnergyByElement(
ElementType type, UInt index, Vector<Real> & epot_on_quad_points) {
auto gradu_it = this->gradu(type).begin(dim, dim);
auto gradu_end = this->gradu(type).begin(dim, dim);
auto stress_it = this->stress(type).begin(dim, dim);
if (this->finite_deformation) {
stress_it = this->piola_kirchhoff_2(type).begin(dim, dim);
}
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(dim, dim);
if (this->finite_deformation) {
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
auto E = this->template gradUToE<dim>(*gradu_it);
this->computePotentialEnergyOnQuad(E, *stress_it, *epot_quad);
}
} else {
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
this->computePotentialEnergyOnQuad(*gradu_it, *stress_it, *epot_quad);
}
}
}
/* -------------------------------------------------------------------------- */
template <>
Real MaterialElastic<1>::getPushWaveSpeed(const Element & /*element*/) const {
return std::sqrt(this->E / this->rho);
}
template <>
Real MaterialElastic<1>::getShearWaveSpeed(const Element & /*element*/) const {
AKANTU_EXCEPTION("There is no shear wave speed in 1D");
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic, MaterialElastic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic.hh b/src/model/solid_mechanics/materials/material_elastic.hh
index dcde5ccbe..1214316dc 100644
--- a/src/model/solid_mechanics/materials/material_elastic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic.hh
@@ -1,158 +1,160 @@
/**
* @file material_elastic.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Nov 17 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material isotropic elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_thermal.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ELASTIC_HH_
#define AKANTU_MATERIAL_ELASTIC_HH_
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialElastic
: public PlaneStressToolbox<spatial_dimension,
MaterialThermal<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
using Parent =
PlaneStressToolbox<spatial_dimension, MaterialThermal<spatial_dimension>>;
public:
MaterialElastic(SolidMechanicsModel & model, const ID & id = "");
MaterialElastic(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialElastic() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real sigma_th = 0) const;
/// compute the tangent stiffness matrix for an element
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
static inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
bool hasStiffnessMatrixChanged() override {
return (not was_stiffness_assembled);
}
MatrixType getTangentType() override {
return _symmetric;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get first Lame constant
AKANTU_GET_MACRO(Lambda, lambda, Real);
/// get second Lame constant
AKANTU_GET_MACRO(Mu, mu, Real);
/// get bulk modulus
AKANTU_GET_MACRO(Kappa, kpa, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // namespace akantu
#include "material_elastic_inline_impl.hh"
#endif /* AKANTU_MATERIAL_ELASTIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh b/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
index be93c1d7a..7e94d01b1 100644
--- a/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_inline_impl.hh
@@ -1,120 +1,122 @@
/**
* @file material_elastic_inline_impl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Fri Dec 16 2016
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of the material elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_
#define AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real sigma_th) const {
Real trace = grad_u.trace(); // trace = (\nabla u)_{kk}
// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
// u_{ij} + \nabla u_{ji})
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
sigma(i, j) = Math::kronecker(i, j) * lambda * trace +
mu * (grad_u(i, j) + grad_u(j, i)) + Math::kronecker(i, j) * sigma_th;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void MaterialElastic<1>::computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real sigma_th) const {
sigma(0, 0) = this->E * grad_u(0, 0) + sigma_th;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
inline void MaterialElastic<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
UInt n = tangent.cols();
// Real Ep = E/((1+nu)*(1-2*nu));
Real Miiii = lambda + 2 * mu;
Real Miijj = lambda;
Real Mijij = mu;
if (spatial_dimension == 1) {
tangent(0, 0) = this->E;
} else {
tangent(0, 0) = Miiii;
}
// test of dimension should by optimized out by the compiler due to the
// template
if (spatial_dimension >= 2) {
tangent(1, 1) = Miiii;
tangent(0, 1) = Miijj;
tangent(1, 0) = Miijj;
tangent(n - 1, n - 1) = Mijij;
}
if (spatial_dimension == 3) {
tangent(2, 2) = Miiii;
tangent(0, 2) = Miijj;
tangent(1, 2) = Miijj;
tangent(2, 0) = Miijj;
tangent(2, 1) = Miijj;
tangent(3, 3) = Mijij;
tangent(4, 4) = Mijij;
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElastic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
epot = .5 * sigma.doubleDot(grad_u);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
MaterialElastic<1>::computeTangentModuliOnQuad(Matrix<Real> & tangent) const {
tangent(0, 0) = E;
}
} // namespace akantu
#endif /* AKANTU_MATERIAL_ELASTIC_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
index 9f0c796c2..e065dc3f7 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
@@ -1,260 +1,262 @@
/**
* @file material_elastic_linear_anisotropic.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 25 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Anisotropic elastic material
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
#include <sstream>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElasticLinearAnisotropic<dim>::MaterialElasticLinearAnisotropic(
SolidMechanicsModel & model, const ID & id, bool symmetric)
: Material(model, id), rot_mat(dim, dim), Cprime(dim * dim, dim * dim),
C(voigt_h::size, voigt_h::size), eigC(voigt_h::size),
symmetric(symmetric), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[0] = 1.;
this->registerParam("n1", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of main material axis");
if (dim > 1) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[1] = 1.;
this->registerParam("n2", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of secondary material axis");
}
if (dim > 2) {
this->dir_vecs.push_back(std::make_unique<Vector<Real>>(dim));
(*this->dir_vecs.back())[2] = 1.;
this->registerParam("n3", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of tertiary material axis");
}
for (UInt i = 0; i < voigt_h::size; ++i) {
UInt start = 0;
if (this->symmetric) {
start = i;
}
for (UInt j = start; j < voigt_h::size; ++j) {
std::stringstream param("C");
param << "C" << i + 1 << j + 1;
this->registerParam(param.str(), this->Cprime(i, j), Real(0.),
_pat_parsmod, "Coefficient " + param.str());
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElasticLinearAnisotropic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::updateInternalParameters() {
Material::updateInternalParameters();
if (this->symmetric) {
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = i + 1; j < voigt_h::size; ++j) {
this->Cprime(j, i) = this->Cprime(i, j);
}
}
}
this->rotateCprime();
this->C.eig(this->eigC);
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticLinearAnisotropic<Dim>::rotateCprime() {
// start by filling the empty parts fo Cprime
UInt diff = Dim * Dim - voigt_h::size;
for (UInt i = voigt_h::size; i < Dim * Dim; ++i) {
for (UInt j = 0; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i - diff, j);
}
}
for (UInt i = 0; i < Dim * Dim; ++i) {
for (UInt j = voigt_h::size; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i, j - diff);
}
}
// construction of rotator tensor
// normalise rotation matrix
for (UInt j = 0; j < Dim; ++j) {
Vector<Real> rot_vec = this->rot_mat(j);
rot_vec = *this->dir_vecs[j];
rot_vec.normalize();
}
// make sure the vectors form a right-handed base
Vector<Real> test_axis(3);
Vector<Real> v1(3);
Vector<Real> v2(3);
Vector<Real> v3(3, 0.);
if (Dim == 2) {
for (UInt i = 0; i < Dim; ++i) {
v1[i] = this->rot_mat(0, i);
v2[i] = this->rot_mat(1, i);
}
v3.crossProduct(v1, v2);
if (v3.norm() < 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_ERROR("The axis vectors parallel.");
}
v3.normalize();
} else if (Dim == 3) {
v1 = this->rot_mat(0);
v2 = this->rot_mat(1);
v3 = this->rot_mat(2);
}
test_axis.crossProduct(v1, v2);
test_axis -= v3;
if (test_axis.norm() > 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_ERROR("The axis vectors do not form a right-handed coordinate "
<< "system. I. e., ||n1 x n2 - n3|| should be zero, but "
<< "it is " << test_axis.norm() << ".");
}
// create the rotator and the reverse rotator
Matrix<Real> rotator(Dim * Dim, Dim * Dim);
Matrix<Real> revrotor(Dim * Dim, Dim * Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
for (UInt k = 0; k < Dim; ++k) {
for (UInt l = 0; l < Dim; ++l) {
UInt I = voigt_h::mat[i][j];
UInt J = voigt_h::mat[k][l];
rotator(I, J) = this->rot_mat(k, i) * this->rot_mat(l, j);
revrotor(I, J) = this->rot_mat(i, k) * this->rot_mat(j, l);
}
}
}
}
// create the full rotated matrix
Matrix<Real> Cfull(Dim * Dim, Dim * Dim);
Cfull = rotator * Cprime * revrotor;
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = 0; j < voigt_h::size; ++j) {
this->C(i, j) = Cfull(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeTangentModuli(
ElementType el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(!this->finite_deformation,
"finite deformation not possible in material anisotropic "
"(TO BE IMPLEMENTED)");
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, _not_ghost).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElasticLinearAnisotropic<dim>::getCelerity(
__attribute__((unused)) const Element & element) const {
return std::sqrt(this->eigC(0) / rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_anisotropic, MaterialElasticLinearAnisotropic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
index 002370c08..1ff23a0dd 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
@@ -1,139 +1,141 @@
/**
* @file material_elastic_linear_anisotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 16 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Orthotropic elastic material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_
#define AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_
namespace akantu {
/**
* General linear anisotropic elastic material
* The only constraint on the elastic tensor is that it can be represented
* as a symmetric 6x6 matrix (3D) or 3x3 (2D).
*
* parameters in the material files :
* - rho : density (default: 0)
* - C_ij : entry on the stiffness
*/
template <UInt Dim> class MaterialElasticLinearAnisotropic : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticLinearAnisotropic(SolidMechanicsModel & model,
const ID & id = "", bool symmetric = true);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
void updateInternalParameters() override;
bool hasStiffnessMatrixChanged() override {
return (not was_stiffness_assembled);
}
MatrixType getTangentType() override {
return _symmetric;
}
protected:
// compute C from Cprime
void rotateCprime();
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma) const;
/// tangent matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute max wave celerity
Real getCelerity(const Element & element) const override;
AKANTU_GET_MACRO(VoigtStiffness, C, Matrix<Real>);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using voigt_h = VoigtHelper<Dim>;
/// direction matrix and vectors
std::vector<std::unique_ptr<Vector<Real>>> dir_vecs;
Matrix<Real> rot_mat;
/// Elastic stiffness tensor in material frame and full vectorised notation
Matrix<Real> Cprime;
/// Elastic stiffness tensor in voigt notation
Matrix<Real> C;
/// eigenvalues of stiffness tensor
Vector<Real> eigC;
bool symmetric;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // namespace akantu
#include "material_elastic_linear_anisotropic_inline_impl.hh"
#endif /* AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
index 3f0204d5f..9fc848098 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic_inline_impl.hh
@@ -1,72 +1,74 @@
/**
* @file material_elastic_linear_anisotropic_inline_impl.hh
*
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 16 2018
- * @date last modification: Fri Feb 16 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of the material elastic linear
* anisotropic
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_
#define AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, Matrix<Real> & sigma) const {
auto voigt_strain = strainToVoigt<dim>(gradUToEpsilon<dim>(grad_u));
auto voigt_stress = this->C * voigt_strain;
voigtToStress<dim>(voigt_stress, sigma);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) const {
tangent.copy(this->C);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialElasticLinearAnisotropic<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & sigma, Real & epot) {
AKANTU_DEBUG_ASSERT(this->symmetric,
"The elastic constants matrix is not symmetric,"
"energy is not path independent.");
epot = .5 * sigma.doubleDot(grad_u);
}
} // namespace akantu
#endif /* AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
index 12c24f420..bbddfdd3c 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
@@ -1,175 +1,177 @@
/**
* @file material_elastic_orthotropic.cc
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Orthotropic elastic material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_orthotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt Dim>
MaterialElasticOrthotropic<Dim>::MaterialElasticOrthotropic(
SolidMechanicsModel & model, const ID & id)
: MaterialElasticLinearAnisotropic<Dim>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E1", E1, Real(0.), _pat_parsmod, "Young's modulus (n1)");
this->registerParam("E2", E2, Real(0.), _pat_parsmod, "Young's modulus (n2)");
this->registerParam("nu12", nu12, Real(0.), _pat_parsmod,
"Poisson's ratio (12)");
this->registerParam("G12", G12, Real(0.), _pat_parsmod, "Shear modulus (12)");
if (Dim > 2) {
this->registerParam("E3", E3, Real(0.), _pat_parsmod,
"Young's modulus (n3)");
this->registerParam("nu13", nu13, Real(0.), _pat_parsmod,
"Poisson's ratio (13)");
this->registerParam("nu23", nu23, Real(0.), _pat_parsmod,
"Poisson's ratio (23)");
this->registerParam("G13", G13, Real(0.), _pat_parsmod,
"Shear modulus (13)");
this->registerParam("G23", G23, Real(0.), _pat_parsmod,
"Shear modulus (23)");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticOrthotropic<Dim>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialElasticLinearAnisotropic<Dim>::initMaterial();
AKANTU_DEBUG_ASSERT(not this->finite_deformation,
"finite deformation not possible in material orthotropic "
"(TO BE IMPLEMENTED)");
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt Dim>
void MaterialElasticOrthotropic<Dim>::updateInternalParameters() {
this->C.zero();
this->Cprime.zero();
/* 1) construction of temporary material frame stiffness tensor------------ */
// http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
// Full (i.e. dim^2 by dim^2) stiffness tensor in material frame
if (Dim == 1) {
AKANTU_ERROR("Dimensions 1 not implemented: makes no sense to have "
"orthotropy for 1D");
}
Real Gamma;
if (Dim == 3) {
Gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
}
if (Dim == 2) {
Gamma = 1 / (1 - nu12 * nu21);
}
// Lamé's first parameters
this->Cprime(0, 0) = E1 * (1 - nu23 * nu32) * Gamma;
this->Cprime(1, 1) = E2 * (1 - nu13 * nu31) * Gamma;
if (Dim == 3) {
this->Cprime(2, 2) = E3 * (1 - nu12 * nu21) * Gamma;
}
// normalised poisson's ratio's
this->Cprime(1, 0) = this->Cprime(0, 1) = E1 * (nu21 + nu31 * nu23) * Gamma;
if (Dim == 3) {
this->Cprime(2, 0) = this->Cprime(0, 2) = E1 * (nu31 + nu21 * nu32) * Gamma;
this->Cprime(2, 1) = this->Cprime(1, 2) = E2 * (nu32 + nu12 * nu31) * Gamma;
}
// Lamé's second parameters (shear moduli)
if (Dim == 3) {
this->Cprime(3, 3) = G23;
this->Cprime(4, 4) = G13;
this->Cprime(5, 5) = G12;
} else {
this->Cprime(2, 2) = G12;
}
/* 1) rotation of C into the global frame */
this->rotateCprime();
this->C.eig(this->eigC);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElasticOrthotropic<spatial_dimension>::
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) {
Array<Real>::matrix_iterator gradu_it =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator gradu_end =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator stress_it =
this->stress(type).begin(spatial_dimension, spatial_dimension);
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
grad_u.copy(*gradu_it);
this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(elastic_orthotropic, MaterialElasticOrthotropic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
index c0a1fe800..473dd869b 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
@@ -1,135 +1,137 @@
/**
* @file material_elastic_orthotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Fri Feb 16 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Orthotropic elastic material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_
#define AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_
namespace akantu {
/**
* Orthotropic elastic material
*
* parameters in the material files :
* - n1 : direction of x-axis in material base, normalisation not necessary
* (default: {1, 0, 0})
* - n2 : direction of y-axis in material base, normalisation not necessary
* (default: {0, 1, 0})
* - n3 : direction of z-axis in material base, normalisation not necessary
* (default: {0, 0, 1})
* - rho : density (default: 0)
* - E1 : Young's modulus along n1 (default: 0)
* - E2 : Young's modulus along n2 (default: 0)
* - E3 : Young's modulus along n3 (default: 0)
* - nu12 : Poisson's ratio along 12 (default: 0)
* - nu13 : Poisson's ratio along 13 (default: 0)
* - nu23 : Poisson's ratio along 23 (default: 0)
* - G12 : Shear modulus along 12 (default: 0)
* - G13 : Shear modulus along 13 (default: 0)
* - G23 : Shear modulus along 23 (default: 0)
*/
template <UInt Dim>
class MaterialElasticOrthotropic
: public MaterialElasticLinearAnisotropic<Dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticOrthotropic(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
void updateInternalParameters() override;
void
computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(E1, E1, Real);
AKANTU_GET_MACRO(E2, E2, Real);
AKANTU_GET_MACRO(E3, E3, Real);
AKANTU_GET_MACRO(Nu12, nu12, Real);
AKANTU_GET_MACRO(Nu13, nu13, Real);
AKANTU_GET_MACRO(Nu23, nu23, Real);
AKANTU_GET_MACRO(G12, G12, Real);
AKANTU_GET_MACRO(G13, G13, Real);
AKANTU_GET_MACRO(G23, G23, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the n1 young modulus
Real E1{0.};
/// the n2 young modulus
Real E2{0.};
/// the n3 young modulus
Real E3{0.};
/// 12 Poisson coefficient
Real nu12{0.};
/// 13 Poisson coefficient
Real nu13{0.};
/// 23 Poisson coefficient
Real nu23{0.};
/// 12 shear modulus
Real G12{0.};
/// 13 shear modulus
Real G13{0.};
/// 23 shear modulus
Real G23{0.};
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh b/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
index a95ac65ef..2d9466aa5 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
@@ -1,40 +1,42 @@
/**
* @file material_embedded_includes.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Fri Feb 09 2018
*
* @brief List of includes for embedded elements
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_reinforcement.hh"
#endif
#define AKANTU_MATERIAL_REINFORCEMENT_LAW_TMPL_LIST \
((elastic, (MaterialElastic<1>)))( \
(plastic, (MaterialLinearIsotropicHardening<1>)))
#define AKANTU_EMBEDDED_MATERIAL_LIST \
((2, (reinforcement, MaterialReinforcement)))
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
index ae493cc19..0ec5f9d0f 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
@@ -1,208 +1,210 @@
/**
* @file material_reinforcement.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Fri Feb 09 2018
*
* @brief Reinforcement material
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_REINFORCEMENT_HH_
#define AKANTU_MATERIAL_REINFORCEMENT_HH_
#include "aka_common.hh"
#include "embedded_interface_model.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Material used to represent embedded reinforcements
*
* This class is used for computing the reinforcement stiffness matrix
* along with the reinforcement residual. Room is made for constitutive law,
* but actual use of contitutive laws is made in MaterialReinforcementTemplate.
*
* Be careful with the dimensions in this class :
* - this->spatial_dimension is always 1
* - the template parameter dim is the dimension of the problem
*/
template <class Mat, UInt dim> class MaterialReinforcement : public Mat {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcement(EmbeddedInterfaceModel & model, const ID & id = "");
/// Destructor
~MaterialReinforcement() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Init the material
void initMaterial() override;
/// Init the filters for background elements
void initFilters();
/// Init the background shape derivatives
void initBackgroundShapeDerivatives();
/// Init the cosine matrices
void initDirectingCosines();
/// Assemble stiffness matrix
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// Compute all the stresses !
void computeAllStresses(GhostType ghost_type) override;
/// Compute energy
Real getEnergy(const std::string & id) override;
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Protected methods */
/* ------------------------------------------------------------------------ */
protected:
/// Allocate the background shape derivatives
void allocBackgroundShapeDerivatives();
/// Compute the directing cosines matrix for one element type
void computeDirectingCosines(ElementType type, GhostType ghost_type);
/// Compute the directing cosines matrix on quadrature points.
inline void computeDirectingCosinesOnQuad(const Matrix<Real> & nodes,
Matrix<Real> & cosines);
/// Add the prestress to the computed stress
void addPrestress(ElementType type, GhostType ghost_type);
/// Compute displacement gradient in reinforcement
void computeGradU(ElementType interface_type, GhostType ghost_type);
/// Assemble the stiffness matrix for an element type (typically _segment_2)
void assembleStiffnessMatrix(ElementType type, GhostType ghost_type);
/// Assemble the stiffness matrix for background & interface types
void assembleStiffnessMatrixInterface(ElementType interface_type,
ElementType background_type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type
void computeBackgroundShapeDerivatives(ElementType type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type pair
void computeBackgroundShapeDerivatives(ElementType interface_type,
ElementType bg_type,
GhostType ghost_type,
const Array<UInt> & filter);
/// Filter elements crossed by interface of a type
void filterInterfaceBackgroundElements(Array<UInt> & foreground,
Array<UInt> & background,
ElementType type,
ElementType interface_type,
GhostType ghost_type);
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(ElementType type, GhostType ghost_type);
/// Assemble the residual for a pair of elements
void assembleInternalForcesInterface(ElementType interface_type,
ElementType background_type,
GhostType ghost_type);
// TODO figure out why voigt size is 4 in 2D
inline void stressTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
inline void strainTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
/// Get background filter
Array<UInt> & getBackgroundFilter(ElementType fg_type,
ElementType bg_type,
GhostType ghost_type) {
return (*background_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/// Get foreground filter
Array<UInt> & getForegroundFilter(ElementType fg_type,
ElementType bg_type,
GhostType ghost_type) {
return (*foreground_filter(fg_type, ghost_type))(bg_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Embedded model
EmbeddedInterfaceModel & emodel;
/// Gradu of concrete on reinforcement
InternalField<Real> gradu_embedded;
/// C matrix on quad
InternalField<Real> directing_cosines;
/// Prestress on quad
InternalField<Real> pre_stress;
/// Cross-sectional area
Real area;
template <typename T>
using CrossMap = ElementTypeMap<std::unique_ptr<ElementTypeMapArray<T>>>;
/// Background mesh shape derivatives
CrossMap<Real> shape_derivatives;
/// Foreground mesh filter (contains segment ids)
CrossMap<UInt> foreground_filter;
/// Background element filter (contains bg ids)
CrossMap<UInt> background_filter;
};
} // namespace akantu
#include "material_reinforcement_tmpl.hh"
#endif // AKANTU_MATERIAL_REINFORCEMENT_HH_
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
index d3dcd411b..973db45b8 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_tmpl.hh
@@ -1,780 +1,777 @@
/**
* @file material_reinforcement_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Reinforcement material
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_reinforcement.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::MaterialReinforcement(
EmbeddedInterfaceModel & model, const ID & id)
: Mat(model, 1, model.getInterfaceMesh(),
model.getFEEngine("EmbeddedInterfaceFEEngine"), id),
emodel(model),
gradu_embedded("gradu_embedded", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
directing_cosines("directing_cosines", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
pre_stress("pre_stress", *this, 1,
model.getFEEngine("EmbeddedInterfaceFEEngine"),
this->element_filter),
area(1.0) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initialize() {
AKANTU_DEBUG_IN();
this->registerParam("area", area, _pat_parsable | _pat_modifiable,
"Reinforcement cross-sectional area");
this->registerParam("pre_stress", pre_stress, _pat_parsable | _pat_modifiable,
"Uniform pre-stress");
- // this->unregisterInternal(this->stress);
-
- // Fool the AvgHomogenizingFunctor
- // stress.initialize(dim * dim);
-
// Reallocate the element filter
this->element_filter.initialize(this->emodel.getInterfaceMesh(),
_spatial_dimension = 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
MaterialReinforcement<Mat, dim>::~MaterialReinforcement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initMaterial() {
Mat::initMaterial();
gradu_embedded.initialize(dim * dim);
pre_stress.initialize(1);
/// We initialise the stuff that is not going to change during the simulation
this->initFilters();
this->allocBackgroundShapeDerivatives();
this->initBackgroundShapeDerivatives();
this->initDirectingCosines();
}
/* -------------------------------------------------------------------------- */
/// Initialize the filter for background elements
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initFilters() {
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "filter";
if (gt == _ghost) {
shaped_id += ":ghost";
}
auto & background =
background_filter(std::make_unique<ElementTypeMapArray<UInt>>(
"bg_" + shaped_id, this->name),
type, gt);
auto & foreground = foreground_filter(
std::make_unique<ElementTypeMapArray<UInt>>(shaped_id, this->name),
type, gt);
foreground->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
background->initialize(emodel.getMesh(), _nb_component = 1,
_ghost_type = gt);
// Computing filters
for (auto && bg_type : background->elementTypes(dim, gt)) {
filterInterfaceBackgroundElements(
(*foreground)(bg_type), (*background)(bg_type), bg_type, type, gt);
}
}
}
}
/* -------------------------------------------------------------------------- */
/// Construct a filter for a (interface_type, background_type) pair
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::filterInterfaceBackgroundElements(
Array<UInt> & foreground, Array<UInt> & background, ElementType type,
ElementType interface_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
foreground.resize(0);
background.resize(0);
Array<Element> & elements =
emodel.getInterfaceAssociatedElements(interface_type, ghost_type);
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
for (auto & elem_id : elem_filter) {
Element & elem = elements(elem_id);
if (elem.type == type) {
background.push_back(elem.element);
foreground.push_back(elem_id);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
namespace detail {
class BackgroundShapeDInitializer : public ElementTypeMapArrayInitializer {
public:
BackgroundShapeDInitializer(UInt spatial_dimension, FEEngine & engine,
ElementType foreground_type,
const ElementTypeMapArray<UInt> & filter,
GhostType ghost_type)
: ElementTypeMapArrayInitializer(
[](ElementType bgtype, GhostType /*unused*/) {
return ShapeFunctions::getShapeDerivativesSize(bgtype);
},
spatial_dimension, ghost_type, _ek_regular) {
auto nb_quad = engine.getNbIntegrationPoints(foreground_type);
// Counting how many background elements are affected by elements of
// interface_type
for (auto type : filter.elementTypes(this->spatial_dimension)) {
// Inserting size
array_size_per_bg_type(filter(type).size() * nb_quad, type,
this->ghost_type);
}
}
auto elementTypes() const -> decltype(auto) {
return array_size_per_bg_type.elementTypes();
}
UInt size(ElementType bgtype) const {
return array_size_per_bg_type(bgtype, this->ghost_type);
}
protected:
ElementTypeMap<UInt> array_size_per_bg_type;
};
} // namespace detail
/**
* Background shape derivatives need to be stored per background element
* types but also per embedded element type, which is why they are stored
* in an ElementTypeMap<ElementTypeMapArray<Real> *>. The outer ElementTypeMap
* refers to the embedded types, and the inner refers to the background types.
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::allocBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto gt : ghost_types) {
for (auto && type : emodel.getInterfaceMesh().elementTypes(1, gt)) {
std::string shaped_id = "embedded_shape_derivatives";
if (gt == _ghost) {
shaped_id += ":ghost";
}
auto & shaped_etma = shape_derivatives(
std::make_unique<ElementTypeMapArray<Real>>(shaped_id, this->name),
type, gt);
shaped_etma->initialize(
detail::BackgroundShapeDInitializer(
emodel.getSpatialDimension(),
emodel.getFEEngine("EmbeddedInterfaceFEEngine"), type,
*background_filter(type, gt), gt),
0, true);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
for (auto interface_type :
this->element_filter.elementTypes(this->spatial_dimension)) {
for (auto type : background_filter(interface_type)->elementTypes(dim)) {
computeBackgroundShapeDerivatives(interface_type, type, _not_ghost,
this->element_filter(interface_type));
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeBackgroundShapeDerivatives(
ElementType interface_type, ElementType bg_type, GhostType ghost_type,
const Array<UInt> & filter) {
auto & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
auto & engine = emodel.getFEEngine();
auto & interface_mesh = emodel.getInterfaceMesh();
const auto nb_nodes_elem_bg = Mesh::getNbNodesPerElement(bg_type);
// const auto nb_strss = VoigtHelper<dim>::size;
const auto nb_quads_per_elem =
interface_engine.getNbIntegrationPoints(interface_type);
Array<Real> quad_pos(0, dim, "interface_quad_pos");
interface_engine.interpolateOnIntegrationPoints(interface_mesh.getNodes(),
quad_pos, dim, interface_type,
ghost_type, filter);
auto & background_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & background_elements =
(*background_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto & foreground_elements =
(*foreground_filter(interface_type, ghost_type))(bg_type, ghost_type);
auto shapesd_begin =
background_shapesd.begin(dim, nb_nodes_elem_bg, nb_quads_per_elem);
auto quad_begin = quad_pos.begin(dim, nb_quads_per_elem);
for (auto && tuple : zip(background_elements, foreground_elements)) {
auto bg = std::get<0>(tuple);
auto fg = std::get<1>(tuple);
for (UInt i = 0; i < nb_quads_per_elem; ++i) {
Matrix<Real> shapesd = Tensor3<Real>(shapesd_begin[fg])(i);
Vector<Real> quads = Matrix<Real>(quad_begin[fg])(i);
engine.computeShapeDerivatives(quads, bg, bg_type, shapesd, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::initDirectingCosines() {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getInterfaceMesh();
const UInt voigt_size = VoigtHelper<dim>::size;
directing_cosines.initialize(voigt_size);
for (auto && type : mesh.elementTypes(1, _not_ghost)) {
computeDirectingCosines(type, _not_ghost);
// computeDirectingCosines(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(1, _not_ghost)) {
assembleStiffnessMatrix(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(1, _not_ghost)) {
this->assembleInternalForces(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
for (auto && type : interface_mesh.elementTypes(_ghost_type = ghost_type)) {
computeGradU(type, ghost_type);
this->computeStress(type, ghost_type);
addPrestress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::addPrestress(ElementType type,
GhostType ghost_type) {
auto & stress = this->stress(type, ghost_type);
auto & sigma_p = this->pre_stress(type, ghost_type);
for (auto && tuple : zip(stress, sigma_p)) {
std::get<0>(tuple) += std::get<1>(tuple);
}
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForces(
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getMesh();
for (auto && mesh_type : mesh.elementTypes(dim, ghost_type)) {
assembleInternalForcesInterface(type, mesh_type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes and assemble the residual. Residual in reinforcement is computed as:
*
* \f[
* \vec{r} = A_s \int_S{\mathbf{B}^T\mathbf{C}^T \vec{\sigma_s}\,\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleInternalForcesInterface(
ElementType interface_type, ElementType background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt back_dof = dim * nodes_per_background_e;
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_quadrature_points * nb_element, back_dof,
"integrant");
auto integrant_it = integrant.begin(back_dof);
auto integrant_end = integrant.end(back_dof);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
auto C_it = directing_cosines(interface_type, ghost_type).begin(voigt_size);
auto sigma_it = this->stress(interface_type, ghost_type).begin();
Matrix<Real> Bvoigt(voigt_size, back_dof);
for (; integrant_it != integrant_end;
++integrant_it, ++B_it, ++C_it, ++sigma_it) {
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*B_it, Bvoigt,
nodes_per_background_e);
Vector<Real> & C = *C_it;
Vector<Real> & BtCt_sigma = *integrant_it;
BtCt_sigma.mul<true>(Bvoigt, C);
BtCt_sigma *= *sigma_it * area;
}
Array<Real> residual_interface(nb_element, back_dof, "residual_interface");
interface_engine.integrate(integrant, residual_interface, back_dof,
interface_type, ghost_type, elem_filter);
integrant.resize(0);
Array<UInt> background_filter(nb_element, 1, "background_filter");
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalArrayLocalArray(
residual_interface, emodel.getInternalForce(), background_type,
ghost_type, -1., filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeDirectingCosines(
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = emodel.getInterfaceMesh();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt steel_dof = dim * nb_nodes_per_element;
const UInt voigt_size = VoigtHelper<dim>::size;
const UInt nb_quad_points = emodel.getFEEngine("EmbeddedInterfaceFEEngine")
.getNbIntegrationPoints(type, ghost_type);
Array<Real> node_coordinates(this->element_filter(type, ghost_type).size(),
steel_dof);
this->emodel.getFEEngine().template extractNodalToElementField<Real>(
interface_mesh, interface_mesh.getNodes(), node_coordinates, type,
ghost_type, this->element_filter(type, ghost_type));
Array<Real>::matrix_iterator directing_cosines_it =
directing_cosines(type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator node_coordinates_it =
node_coordinates.begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator node_coordinates_end =
node_coordinates.end(dim, nb_nodes_per_element);
for (; node_coordinates_it != node_coordinates_end; ++node_coordinates_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++directing_cosines_it) {
Matrix<Real> & nodes = *node_coordinates_it;
Matrix<Real> & cosines = *directing_cosines_it;
computeDirectingCosinesOnQuad(nodes, cosines);
}
}
// Mauro: the directing_cosines internal is defined on the quadrature points
// of each element
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrix(
ElementType type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = emodel.getMesh();
for (auto && mesh_type : mesh.elementTypes(dim, ghost_type)) {
assembleStiffnessMatrixInterface(type, mesh_type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes the reinforcement stiffness matrix (Gomes & Awruch, 2001)
* \f[
* \mathbf{K}_e = \sum_{i=1}^R{A_i\int_{S_i}{\mathbf{B}^T
* \mathbf{C}_i^T \mathbf{D}_{s, i} \mathbf{C}_i \mathbf{B}\,\mathrm{d}s}}
* \f]
*/
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::assembleStiffnessMatrixInterface(
ElementType interface_type, ElementType background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = VoigtHelper<dim>::size;
FEEngine & interface_engine = emodel.getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = this->element_filter(interface_type, ghost_type);
Array<Real> & grad_u = gradu_embedded(interface_type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt back_dof = dim * nodes_per_background_e;
UInt integrant_size = back_dof;
grad_u.resize(nb_quadrature_points * nb_element);
Array<Real> tangent_moduli(nb_element * nb_quadrature_points, 1,
"interface_tangent_moduli");
this->computeTangentModuli(interface_type, tangent_moduli, ghost_type);
Array<Real> & shapesd = (*shape_derivatives(interface_type, ghost_type))(
background_type, ghost_type);
Array<Real> integrant(nb_element * nb_quadrature_points,
integrant_size * integrant_size, "B^t*C^t*D*C*B");
/// Temporary matrices for integrant product
Matrix<Real> Bvoigt(voigt_size, back_dof);
Matrix<Real> DCB(1, back_dof);
Matrix<Real> CtDCB(voigt_size, back_dof);
Array<Real>::scalar_iterator D_it = tangent_moduli.begin();
Array<Real>::scalar_iterator D_end = tangent_moduli.end();
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, ghost_type).begin(1, voigt_size);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator integrant_it =
integrant.begin(integrant_size, integrant_size);
for (; D_it != D_end; ++D_it, ++C_it, ++B_it, ++integrant_it) {
Real & D = *D_it;
Matrix<Real> & C = *C_it;
Matrix<Real> & B = *B_it;
Matrix<Real> & BtCtDCB = *integrant_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(B, Bvoigt,
nodes_per_background_e);
DCB.mul<false, false>(C, Bvoigt);
DCB *= D * area;
CtDCB.mul<true, false>(C, DCB);
BtCtDCB.mul<true, false>(Bvoigt, CtDCB);
}
tangent_moduli.resize(0);
Array<Real> K_interface(nb_element, integrant_size * integrant_size,
"K_interface");
interface_engine.integrate(integrant, K_interface,
integrant_size * integrant_size, interface_type,
ghost_type, elem_filter);
integrant.resize(0);
// Mauro: Here K_interface contains the local stiffness matrices,
// directing_cosines contains the information about the orientation
// of the reinforcements, any rotation of the local stiffness matrix
// can be done here
auto & filter =
getBackgroundFilter(interface_type, background_type, ghost_type);
emodel.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", K_interface, background_type, ghost_type, _symmetric,
filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
Real MaterialReinforcement<Mat, dim>::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
if (id == "potential") {
Real epot = 0.;
this->computePotentialEnergyByElements();
for (auto && type :
this->element_filter.elementTypes(this->spatial_dimension)) {
FEEngine & interface_engine =
emodel.getFEEngine("EmbeddedInterfaceFEEngine");
epot += interface_engine.integrate(
this->potential_energy(type, _not_ghost), type, _not_ghost,
this->element_filter(type, _not_ghost));
epot *= area;
}
return epot;
}
AKANTU_DEBUG_OUT();
return 0;
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
void MaterialReinforcement<Mat, dim>::computeGradU(ElementType interface_type,
GhostType ghost_type) {
// Looping over background types
for (auto && bg_type :
background_filter(interface_type, ghost_type)->elementTypes(dim)) {
const UInt nodes_per_background_e = Mesh::getNbNodesPerElement(bg_type);
const UInt voigt_size = VoigtHelper<dim>::size;
auto & bg_shapesd =
(*shape_derivatives(interface_type, ghost_type))(bg_type, ghost_type);
auto & filter = getBackgroundFilter(interface_type, bg_type, ghost_type);
Array<Real> disp_per_element(0, dim * nodes_per_background_e, "disp_elem");
FEEngine::extractNodalToElementField(
emodel.getMesh(), emodel.getDisplacement(), disp_per_element, bg_type,
ghost_type, filter);
Matrix<Real> concrete_du(dim, dim);
Matrix<Real> epsilon(dim, dim);
Vector<Real> evoigt(voigt_size);
for (auto && tuple :
zip(make_view(disp_per_element, dim, nodes_per_background_e),
make_view(bg_shapesd, dim, nodes_per_background_e),
this->gradu(interface_type, ghost_type),
make_view(this->directing_cosines(interface_type, ghost_type),
voigt_size))) {
auto & u = std::get<0>(tuple);
auto & B = std::get<1>(tuple);
auto & du = std::get<2>(tuple);
auto & C = std::get<3>(tuple);
concrete_du.mul<false, true>(u, B);
auto epsilon = 0.5 * (concrete_du + concrete_du.transpose());
strainTensorToVoigtVector(epsilon, evoigt);
du = C.dot(evoigt);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* The structure of the directing cosines matrix is :
* \f{eqnarray*}{
* C_{1,\cdot} & = & (l^2, m^2, n^2, mn, ln, lm) \\
* C_{i,j} & = & 0
* \f}
*
* with :
* \f[
* (l, m, n) = \frac{1}{\|\frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}\|} \cdot
* \frac{\mathrm{d}\vec{r}(s)}{\mathrm{d}s}
* \f]
*/
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::computeDirectingCosinesOnQuad(
const Matrix<Real> & nodes, Matrix<Real> & cosines) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(nodes.cols() == 2,
"Higher order reinforcement elements not implemented");
const Vector<Real> a = nodes(0);
const Vector<Real> b = nodes(1);
Vector<Real> delta = b - a;
Real sq_length = 0.;
for (UInt i = 0; i < dim; i++) {
sq_length += delta(i) * delta(i);
}
if (dim == 2) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(0) * delta(1); // lm
} else if (dim == 3) {
cosines(0, 0) = delta(0) * delta(0); // l^2
cosines(0, 1) = delta(1) * delta(1); // m^2
cosines(0, 2) = delta(2) * delta(2); // n^2
cosines(0, 3) = delta(1) * delta(2); // mn
cosines(0, 4) = delta(0) * delta(2); // ln
cosines(0, 5) = delta(0) * delta(1); // lm
}
cosines /= sq_length;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::stressTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = tensor(0, 1);
} else if (dim == 3) {
vector(3) = tensor(1, 2);
vector(4) = tensor(0, 2);
vector(5) = tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Mat, UInt dim>
inline void MaterialReinforcement<Mat, dim>::strainTensorToVoigtVector(
const Matrix<Real> & tensor, Vector<Real> & vector) {
AKANTU_DEBUG_IN();
for (UInt i = 0; i < dim; i++) {
vector(i) = tensor(i, i);
}
if (dim == 2) {
vector(2) = 2 * tensor(0, 1);
} else if (dim == 3) {
vector(3) = 2 * tensor(1, 2);
vector(4) = 2 * tensor(0, 2);
vector(5) = 2 * tensor(0, 1);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
index cd288dcbf..d886085a2 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
@@ -1,272 +1,275 @@
/**
* @file material_neohookean.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 08 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Specialization of the material class for finite deformation
* neo-hookean material
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialNeohookean<spatial_dimension>::MaterialNeohookean(
SolidMechanicsModel & model, const ID & id)
: PlaneStressToolbox<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->finite_deformation = true;
this->initialize_third_axis_deformation = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<spatial_dimension>::initMaterial();
if (spatial_dimension == 1) {
nu = 0.;
}
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <> void MaterialNeohookean<2>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<2>::initMaterial();
this->updateInternalParameters();
if (this->plane_stress) {
this->third_axis_deformation.setDefaultValue(1.);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::updateInternalParameters() {
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
PlaneStressToolbox<dim>::computeCauchyStressPlaneStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto gradu_it = this->gradu(el_type, ghost_type).begin(2, 2);
auto gradu_end = this->gradu(el_type, ghost_type).end(2, 2);
auto piola_it = this->piola_kirchhoff_2(el_type, ghost_type).begin(2, 2);
auto stress_it = this->stress(el_type, ghost_type).begin(2, 2);
auto c33_it = this->third_axis_deformation(el_type, ghost_type).begin();
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it, ++c33_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
StoCauchy<2>(gradUToF<2>(grad_u), piola, sigma, *c33_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
auto c33_it = this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeThirdAxisDeformation(
ElementType /*el_type*/, GhostType /*ghost_type*/) {}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->plane_stress, "The third component of the strain "
"can only be computed for 2D "
"problems in Plane Stress!!");
Array<Real>::scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeThirdAxisDeformationOnQuad(grad_u, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type);
Array<Real>::scalar_iterator epot = this->potential_energy(el_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computeTangentModuli(
__attribute__((unused)) ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeTangentModuli(__attribute__((unused))
ElementType el_type,
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *c33_it);
++c33_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getPushWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt((this->lambda + 2 * this->mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getShearWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt(this->mu / this->rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(neohookean, MaterialNeohookean);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
index 0bca79512..3b9e1480d 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
@@ -1,169 +1,171 @@
/**
* @file material_neohookean.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 29 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Material isotropic elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_NEOHOOKEAN_HH_
#define AKANTU_MATERIAL_NEOHOOKEAN_HH_
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialNeohookean : public PlaneStressToolbox<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialNeohookean(SolidMechanicsModel & model, const ID & id = "");
~MaterialNeohookean() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Computation of the cauchy stress for plane strain materials
void
computeCauchyStressPlaneStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// Non linear computation of the third direction strain in 2D plane stress
/// case
void computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
Real getShearWaveSpeed(const Element & element) const override;
MatrixType getTangentType() override {
return _symmetric;
}
protected:
/// constitutive law for a given quadrature point
inline void computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S);
/// constitutive law for a given quadrature point (first piola)
inline void computeFirstPiolaKirchhoffOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & S,
Matrix<Real> & P);
/// constitutive law for a given quadrature point
inline void computeDeltaStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & grad_delta_u,
Matrix<Real> & delta_S);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & S,
const Real & C33 = 1.0);
/// constitutive law for a given quadrature point
inline void computeThirdAxisDeformationOnQuad(Matrix<Real> & grad_u,
Real & c33_value);
/// constitutive law for a given quadrature point
// inline void updateStressOnQuad(const Matrix<Real> & sigma,
// Matrix<Real> & cauchy_sigma);
/// compute the potential energy for a quadrature point
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
Real & epot);
/// compute the tangent stiffness matrix for an element
void computeTangentModuliOnQuad(Matrix<Real> & tangent, Matrix<Real> & grad_u,
const Real & C33 = 1.0);
/// recompute the lame coefficient if E or nu changes
void updateInternalParameters() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_neohookean_inline_impl.hh"
#endif /* AKANTU_MATERIAL_NEOHOOKEAN_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
index 8a0b473ea..2c2375613 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean_inline_impl.hh
@@ -1,197 +1,200 @@
/**
* @file material_neohookean_inline_impl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of the material elastic
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <iostream>
#include <utility>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeDeltaStressOnQuad(
__attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & grad_delta_u,
__attribute__((unused)) Matrix<Real> & delta_S) {}
//! computes the second piola kirchhoff stress, called S
template <UInt dim>
inline void MaterialNeohookean<dim>::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & S,
const Real & C33) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
Matrix<Real> Cminus(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33); // the term sqrt(C33) corresponds to the off
// plane strain (2D plane stress)
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
S(i, j) = Math::kronecker(i, j) * mu + (lambda * log(J) - mu) * Cminus(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
class C33_NR : public Math::NewtonRaphsonFunctor {
public:
C33_NR(std::string name, const Real & lambda, const Real & mu,
const Matrix<Real> & C)
: NewtonRaphsonFunctor(std::move(name)), lambda(lambda), mu(mu), C(C) {}
inline Real f(Real x) const override {
return (this->lambda / 2. *
(std::log(x) + std::log(this->C(0, 0) * this->C(1, 1) -
Math::pow<2>(this->C(0, 1)))) +
this->mu * (x - 1.));
}
inline Real f_prime(Real x) const override {
AKANTU_DEBUG_ASSERT(std::abs(x) > Math::getTolerance(),
"x is zero (x should be the off plane right Cauchy"
<< " measure in this function so you made a mistake"
<< " somewhere else that lead to a zero here!!!");
return (this->lambda / (2. * x) + this->mu);
}
private:
const Real & lambda;
const Real & mu;
const Matrix<Real> & C;
};
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeThirdAxisDeformationOnQuad(
Matrix<Real> & grad_u, Real & c33_value) {
// Neo hookean book
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Math::NewtonRaphson nr(1e-5, 100);
c33_value = nr.solve(
C33_NR("Neohookean_plan_stress", this->lambda, this->mu, C), c33_value);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void
MaterialNeohookean<dim>::computePiolaKirchhoffOnQuad(const Matrix<Real> & E,
Matrix<Real> & S) {
Real trace = E.trace(); /// \f$ trace = (\nabla u)_{kk} \f$
/// \f$ \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji}) \f$
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
S(i, j) = Math::kronecker(i, j) * lambda * trace + 2.0 * mu * E(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeFirstPiolaKirchhoffOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & S, Matrix<Real> & P) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
// first Piola-Kirchhoff is computed as the product of the deformation
// gracient
// tensor and the second Piola-Kirchhoff stress tensor
P = F * S;
}
/**************************************************************************************/
/* Computation of the potential energy for a this neo hookean material */
template <UInt dim>
inline void MaterialNeohookean<dim>::computePotentialEnergyOnQuad(
const Matrix<Real> & grad_u, Real & epot) {
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim); // Right green
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det();
// std::cout<<"det(F) -> "<<J<<std::endl;
epot =
0.5 * lambda * pow(log(J), 2.) + mu * (-log(J) + 0.5 * (C.trace() - dim));
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialNeohookean<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, Matrix<Real> & grad_u, const Real & C33) {
// Neo hookean book
UInt cols = tangent.cols();
UInt rows = tangent.rows();
Matrix<Real> F(dim, dim);
Matrix<Real> C(dim, dim);
Matrix<Real> Cminus(dim, dim);
this->template gradUToF<dim>(grad_u, F);
this->rightCauchy(F, C);
Real J = F.det() * sqrt(C33);
// std::cout<<"det(F) -> "<<J<<std::endl;
Cminus.inverse(C);
for (UInt m = 0; m < rows; m++) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; n++) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
// book belytchko
tangent(m, n) = lambda * Cminus(i, j) * Cminus(k, l) +
(mu - lambda * log(J)) * (Cminus(i, k) * Cminus(j, l) +
Cminus(i, l) * Cminus(k, j));
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_non_local.hh b/src/model/solid_mechanics/materials/material_non_local.hh
index fb983cb5a..60b4d8e23 100644
--- a/src/model/solid_mechanics/materials/material_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_non_local.hh
@@ -1,118 +1,120 @@
/**
* @file material_non_local.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material class that handle the non locality of a law for example
* damage.
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_NON_LOCAL_HH_
#define AKANTU_MATERIAL_NON_LOCAL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class MaterialNonLocalInterface {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material the non local parts of the material
void initMaterialNonLocal() {
this->registerNeighborhood();
this->registerNonLocalVariables();
};
/// insert the quadrature points in the neighborhoods of the non-local manager
virtual void insertIntegrationPointsInNeighborhoods(
GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) = 0;
/// update the values in the non-local internal fields
virtual void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
GhostType ghost_type,
ElementKind kind) = 0;
/// constitutive law
virtual void computeNonLocalStresses(GhostType ghost_type = _not_ghost) = 0;
protected:
/// get the name of the neighborhood for this material
virtual ID getNeighborhoodName() = 0;
/// register the neighborhoods for the material
virtual void registerNeighborhood() = 0;
/// register the non local internal variable
virtual void registerNonLocalVariables() = 0;
virtual inline void onElementsAdded(const Array<Element> & /*unused*/,
const NewElementsEvent & /*unused*/) {}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
class MaterialNonLocal : public MaterialNonLocalInterface, public LocalParent {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit MaterialNonLocal(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// insert the quadrature points in the neighborhoods of the non-local manager
void insertIntegrationPointsInNeighborhoods(
GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) override;
/// update the values in the non-local internal fields
void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id,
GhostType ghost_type,
ElementKind kind) override;
/// register the neighborhoods for the material
void registerNeighborhood() override;
protected:
/// get the name of the neighborhood for this material
ID getNeighborhoodName() override { return this->name; }
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "material_non_local_tmpl.hh"
#endif /* AKANTU_MATERIAL_NON_LOCAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_non_local_includes.hh b/src/model/solid_mechanics/materials/material_non_local_includes.hh
index 2def30dab..d21efc5b0 100644
--- a/src/model/solid_mechanics/materials/material_non_local_includes.hh
+++ b/src/model/solid_mechanics/materials/material_non_local_includes.hh
@@ -1,40 +1,42 @@
/**
* @file material_non_local_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 31 2012
- * @date last modification: Thu Jul 06 2017
+ * @date last modification: Thu Dec 17 2020
*
* @brief Non local materials includes
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_CMAKE_LIST_MATERIALS
#include "material_marigo_non_local.hh"
#include "material_mazars_non_local.hh"
#include "material_von_mises_mazars_non_local.hh"
#endif
#define AKANTU_DAMAGE_NON_LOCAL_MATERIAL_LIST \
((2, (marigo_non_local, MaterialMarigoNonLocal)))( \
(2, (mazars_non_local, MaterialMazarsNonLocal)))( \
(2, (von_mises_mazars_non_local, MaterialVonMisesMazarsNonLocal)))
diff --git a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
index 241f63a2b..67cddbb15 100644
--- a/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_non_local_tmpl.hh
@@ -1,127 +1,129 @@
/**
* @file material_non_local_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 06 2017
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Mar 26 2021
*
* @brief Implementation of material non-local
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "material_non_local.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
MaterialNonLocal<dim, LocalParent>::MaterialNonLocal(
SolidMechanicsModel & model, const ID & id)
: LocalParent(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::insertIntegrationPointsInNeighborhoods(
GhostType ghost_type,
const ElementTypeMapReal & quadrature_points_coordinates) {
IntegrationPoint q;
q.ghost_type = ghost_type;
auto & neighborhood = this->model.getNonLocalManager().getNeighborhood(
this->getNeighborhoodName());
for (auto & type :
this->element_filter.elementTypes(dim, ghost_type, _ek_regular)) {
q.type = type;
const auto & elem_filter = this->element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element != 0U) {
UInt nb_quad =
this->getFEEngine().getNbIntegrationPoints(type, ghost_type);
const auto & quads = quadrature_points_coordinates(type, ghost_type);
auto nb_total_element =
this->model.getMesh().getNbElement(type, ghost_type);
auto quads_it = quads.begin_reinterpret(dim, nb_quad, nb_total_element);
for (auto & elem : elem_filter) {
Matrix<Real> quads = quads_it[elem];
q.element = elem;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
neighborhood.insertIntegrationPoint(q, quads(nq));
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::updateNonLocalInternals(
ElementTypeMapReal & non_local_flattened, const ID & field_id,
GhostType ghost_type, ElementKind kind) {
/// loop over all types in the material
for (auto & el_type :
this->element_filter.elementTypes(dim, ghost_type, kind)) {
Array<Real> & internal =
this->template getInternal<Real>(field_id)(el_type, ghost_type);
auto & internal_flat = non_local_flattened(el_type, ghost_type);
auto nb_component = internal_flat.getNbComponent();
auto internal_it = internal.begin(nb_component);
auto internal_flat_it = internal_flat.begin(nb_component);
/// loop all elements for the given type
const auto & filter = this->element_filter(el_type, ghost_type);
UInt nb_quads =
this->getFEEngine().getNbIntegrationPoints(el_type, ghost_type);
for (auto & elem : filter) {
for (UInt q = 0; q < nb_quads; ++q, ++internal_it) {
UInt global_quad = elem * nb_quads + q;
*internal_it = internal_flat_it[global_quad];
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class LocalParent>
void MaterialNonLocal<dim, LocalParent>::registerNeighborhood() {
ID name = this->getNeighborhoodName();
this->model.getNonLocalManager().registerNeighborhood(name, name);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc
index 7d40076a9..f0bb0ad1f 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.cc
@@ -1,193 +1,195 @@
/**
- * @file material_plastic.cc
+ * @file material_drucker_prager.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 09 2020
- * @date last modification: Wed Sep 09 2020
+ * @date creation: Mon Apr 07 2014
+ * @date last modification: Tue Apr 06 2021
*
* @brief Implementation of the akantu::MaterialDruckerPrager class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_drucker_prager.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
template <UInt spatial_dimension>
MaterialDruckerPrager<spatial_dimension>::MaterialDruckerPrager(
SolidMechanicsModel & model, const ID & id)
: MaterialPlastic<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialDruckerPrager<spatial_dimension>::MaterialDruckerPrager(
SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: MaterialPlastic<spatial_dimension>(model, dim, mesh, fe_engine, id) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDruckerPrager<spatial_dimension>::initialize() {
this->registerParam("phi", phi, Real(0.), _pat_parsable | _pat_modifiable,
"Internal friction angle in degrees");
this->registerParam("fc", fc, Real(1.), _pat_parsable | _pat_modifiable,
"Compressive strength");
this->registerParam("radial_return", radial_return_mapping, bool(true),
_pat_parsable | _pat_modifiable, "Radial return mapping");
this->updateInternalParameters();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDruckerPrager<spatial_dimension>::updateInternalParameters() {
MaterialElastic<spatial_dimension>::updateInternalParameters();
// compute alpha and k parameters for Drucker-Prager
Real phi_radian = this->phi * M_PI / 180.;
this->alpha = (6. * sin(phi_radian)) / (3. - sin(phi_radian));
Real cohesion = this->fc * (1. - sin(phi_radian)) / (2. * cos(phi_radian));
this->k = (6. * cohesion * cos(phi_radian)) / (3. - sin(phi_radian));
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDruckerPrager<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToE<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToE<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
computeStressOnQuad(green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *sigma_th_it, *previous_sigma_th_it);
++sigma_th_it;
++inelastic_strain_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialDruckerPrager<spatial_dimension>::computeTangentModuli(
ElementType /*el_type*/, Array<Real> & /*tangent_matrix*/,
GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(plastic_drucker_prager, MaterialDruckerPrager);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh
index b44efa9b6..0b4f6ed4b 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager.hh
@@ -1,145 +1,147 @@
/**
- * @file material_drucker_pruger.hh
+ * @file material_drucker_prager.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 09 2020
- * @date last modification: Wed Sep 09 2020
+ * @date creation: Fri Jun 18 2010
+ * @date last modification: Tue Apr 06 2021
*
* @brief Specialization of the material class for isotropic
* plasticity with Drucker-Pruger yield criterion
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_DRUCKER_PRAGER_HH__
#define __AKANTU_MATERIAL_DRUCKER_PRAGER_HH__
namespace akantu {
/**
* Material plastic with a Drucker-pruger yield criterion
*/
template<UInt spatial_dimension>
class MaterialDruckerPrager
: public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDruckerPrager(SolidMechanicsModel & model,
const ID & id = "");
MaterialDruckerPrager(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
protected:
using voigt_h = VoigtHelper<spatial_dimension>;
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
protected:
/// Infinitesimal deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
const Real & sigma_th, const Real & previous_sigma_th);
/// Finite deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain, const Matrix<Real> & previous_inelas_strain,
const Real & sigma_th, const Real & previous_sigma_th,
const Matrix<Real> & F_tensor);
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u, const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor) const;
inline Real computeYieldFunction(const Matrix<Real> & sigma);
inline Real computeYieldStress(const Matrix<Real> & sigma);
inline void computeDeviatoricStress(const Matrix<Real> & sigma,
Matrix<Real> & sigma_dev);
/// rcompute the alpha and k parameters
void updateInternalParameters() override;
public:
// closet point projection method to compute stress state on the
// yield surface
inline void computeGradientAndPlasticMultplier(
const Matrix<Real> & sigma_tr, Real & plastic_multiplier_guess,
Vector<Real> & gradient_f, Vector<Real> & delta_inelastic_strain,
UInt max_iterations = 100, Real tolerance = 1e-10);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// Internal friction angle of the material
Real phi;
// Compressive strength of the material
Real fc;
// modified friction angle for Drucker-Prager
Real alpha;
// modified compressive strength for Drucker-Prager
Real k;
// radial return mapping
bool radial_return_mapping;
};
} // namespace akantu
#include "material_drucker_prager_inline_impl.hh"
#endif /*__AKANTU_MATERIAL_DRUCKER_PRAGER_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh
index 6e0bb33b9..553af07d5 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_drucker_prager_inline_impl.hh
@@ -1,468 +1,470 @@
/**
- * @file material_linear_isotropic_hardening_inline_impl.hh
+ * @file material_drucker_prager_inline_impl.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Wed Sep 09 2020
- * @date last modification: Wed Sep 09 2020
+ * @date creation: Sat Sep 12 2020
+ * @date last modification: Tue Apr 06 2021
*
* @brief Implementation of the inline functions of the material
* Drucker-Prager
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "material_drucker_prager.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Deviatoric Stress
template<UInt dim>
inline void MaterialDruckerPrager<dim>::computeDeviatoricStress(const Matrix<Real> & sigma,
Matrix<Real> & sigma_dev){
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_dev(i, j) = sigma(i, j);
sigma_dev -= Matrix<Real>::eye(dim, sigma.trace() / dim);
}
/* -------------------------------------------------------------------------- */
/// Yield Stress
template<UInt dim>
inline Real MaterialDruckerPrager<dim>::computeYieldStress(const Matrix<Real> &
sigma) {
return this->alpha * sigma.trace() - this->k;
}
/* -------------------------------------------------------------------------- */
/// Yield function
template<UInt dim>
inline Real MaterialDruckerPrager<dim>::computeYieldFunction(const Matrix<Real> &
sigma) {
Matrix<Real> sigma_dev(dim, dim, 0);
this->computeDeviatoricStress(sigma, sigma_dev);
// compute deviatoric invariant J2
Real j2 = (1./ 2.) * sigma_dev.doubleDot(sigma_dev);
Real sigma_dev_eff = std::sqrt(3. * j2);
Real modified_yield_stress = computeYieldStress(sigma);
return sigma_dev_eff + modified_yield_stress;
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
inline void MaterialDruckerPrager<dim>::computeGradientAndPlasticMultplier(
const Matrix<Real> & sigma_trial, Real & plastic_multiplier_guess,
Vector<Real> & gradient_f, Vector<Real> & delta_inelastic_strain,
UInt max_iterations,
Real tolerance) {
UInt size = voigt_h::size;
// guess stress state at each iteration, initial guess is the trial state
Matrix<Real> sigma_guess(sigma_trial);
// plastic multiplier guess at each iteration, initial guess is zero
plastic_multiplier_guess = 0.;
// gradient of yield surface in voigt notation
gradient_f.zero();
// plastic strain increment at each iteration
delta_inelastic_strain.zero();
// variation in sigma at each iteration
Vector<Real> delta_sigma(size, 0.);
// krocker delta vector in voigt notation
Vector<Real> kronecker_delta(size, 0.);
for(auto i : arange(dim))
kronecker_delta[i] = 1.;
// hessian matrix of yield surface
Matrix<Real> hessian_f(size, size, 0.);
// scaling matrix for computing gradient and hessian from voigt notation
Matrix<Real> scaling_matrix(size, size, 0.);
scaling_matrix.eye(1.);
for(auto i : arange(dim, size))
for(auto j : arange(dim, size))
scaling_matrix(i, j) *= 2.;
// elastic stifnness tensor
Matrix<Real> De(size, size, 0.);
MaterialElastic<dim>::computeTangentModuliOnQuad(De);
// elastic compliance tensor
Matrix<Real> Ce(size, size, 0.);
Ce.inverse(De);
// objective function to be computed
Vector<Real> f(size, 0.);
// yield function value at each iteration
Real yield_function;
// if sigma is above the threshold value
auto above_threshold = [&sigma_guess](Real & k, Real & alpha) {
Real I1 = sigma_guess.trace();
return I1 >= k/alpha;
};
// to project stress state at origin of yield function if first
// invariant is greater than the threshold
if(above_threshold(k, alpha) and this->alpha > 0) {
auto update_first_obj = [&sigma_guess]() {
//const UInt dimension = sigma_guess.cols();
Matrix<Real> sigma_dev(dim, dim, 0);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_dev(i, j) = sigma_guess(i, j);
sigma_dev -= Matrix<Real>::eye(dim, sigma_guess.trace() / dim);
auto error = (1./2) *sigma_dev.doubleDot(sigma_dev);
return error;
};
auto update_sec_obj = [&sigma_guess](Real & k, Real & alpha) {
auto error = alpha*sigma_guess.trace() - k;
return error;
};
auto projection_error = update_first_obj();
while(tolerance < projection_error) {
Matrix<Real> delta_sigma(dim, dim);
Matrix<Real> jacobian(dim, dim);
Matrix<Real> jacobian_inv(dim, dim);
Matrix<Real> sigma_dev(dim, dim, 0);
this->computeDeviatoricStress(sigma_guess, sigma_dev);
jacobian_inv.inverse(sigma_dev);
delta_sigma = -projection_error * jacobian_inv;
sigma_guess += delta_sigma;
projection_error = update_first_obj();
}
projection_error = update_sec_obj(k, alpha);
while(tolerance < projection_error) {
Matrix<Real> delta_sigma(dim, dim);
Matrix<Real> jacobian(dim, dim);
Matrix<Real> jacobian_inv(dim, dim);
jacobian = this->alpha * Matrix<Real>::eye(dim, dim);
jacobian_inv.inverse(jacobian);
delta_sigma += -projection_error * jacobian_inv;
sigma_guess += delta_sigma;
projection_error = update_sec_obj(k, alpha);
}
auto delta_sigma_final = sigma_trial - sigma_guess;
auto delta_sigma_voigt = voigt_h::matrixToVoigt(delta_sigma_final);
delta_inelastic_strain.mul<false>(Ce, delta_sigma_voigt);
return;
}
// lambda function to compute gradient of yield surface in voigt notation
auto compute_gradient_f = [&sigma_guess, &scaling_matrix, &kronecker_delta,
&gradient_f](Real & alpha){
//const UInt dimension = sigma_guess.cols();
Matrix<Real> sigma_dev(dim, dim, 0);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_dev(i, j) = sigma_guess(i, j);
sigma_dev -= Matrix<Real>::eye(dim, sigma_guess.trace() / dim);
Vector<Real> sigma_dev_voigt = voigt_h::matrixToVoigt(sigma_dev);
// compute deviatoric invariant
Real j2 = (1./2.) * sigma_dev.doubleDot(sigma_dev);
gradient_f.mul<false>(scaling_matrix, sigma_dev_voigt, 3./ (2. * std::sqrt(3. * j2)) );
gradient_f += alpha * kronecker_delta;
};
// lambda function to compute hessian matrix of yield surface
auto compute_hessian_f = [&sigma_guess, &hessian_f, &scaling_matrix,
&kronecker_delta](){
Matrix<Real> sigma_dev(dim, dim, 0);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_dev(i, j) = sigma_guess(i, j);
sigma_dev -= Matrix<Real>::eye(dim, sigma_guess.trace() / dim);
auto sigma_dev_voigt = voigt_h::matrixToVoigt(sigma_dev);
// compute deviatoric invariant J2
Real j2 = (1./2.) * sigma_dev.doubleDot(sigma_dev);
Vector<Real> temp(sigma_dev_voigt.size());
temp.mul<false>(scaling_matrix, sigma_dev_voigt);
Matrix<Real> id(kronecker_delta.size(), kronecker_delta.size());
id.outerProduct(kronecker_delta, kronecker_delta);
id *= -1./3.;
id += Matrix<Real>::eye(kronecker_delta.size(), 1.);
Matrix<Real> tmp3(kronecker_delta.size(), kronecker_delta.size());
tmp3.mul<false, false>(scaling_matrix, id);
hessian_f.outerProduct(temp, temp);
hessian_f *= -9./(4.* pow(3.*j2, 3./2.));
hessian_f += (3./(2.* pow(3.*j2, 1./2.)))*tmp3;
};
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
auto update_f = [&f, &sigma_guess, &sigma_trial, &plastic_multiplier_guess, &Ce, &De,
&yield_function, &gradient_f, &delta_inelastic_strain,
&compute_gradient_f](Real & k, Real & alpha){
// compute gradient
compute_gradient_f(alpha);
// compute yield function
Matrix<Real> sigma_dev(dim, dim, 0);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
sigma_dev(i, j) = sigma_guess(i, j);
sigma_dev -= Matrix<Real>::eye(dim, sigma_guess.trace() / dim);
Real j2 = (1./ 2.) * sigma_dev.doubleDot(sigma_dev);
Real sigma_dev_eff = std::sqrt(3. * j2);
Real modified_yield_stress = alpha * sigma_guess.trace() - k;
yield_function = sigma_dev_eff + modified_yield_stress;
// compute increment strain
auto sigma_trial_voigt = voigt_h::matrixToVoigt(sigma_trial);
auto sigma_guess_voigt = voigt_h::matrixToVoigt(sigma_guess);
auto tmp = sigma_trial_voigt - sigma_guess_voigt;
delta_inelastic_strain.mul<false>(Ce, tmp);
// compute objective function
f.mul<false>(De, gradient_f, plastic_multiplier_guess);
f = tmp - f;
// compute error
auto error = std::max(f.norm<L_2>(), std::abs(yield_function));
return error;
};
Real alpha_tmp{alpha};
Real k_tmp{k};
if(radial_return_mapping){
alpha_tmp = 0;
k_tmp = std::abs(alpha*sigma_guess.trace() - k);
}
auto projection_error = update_f(k_tmp , alpha_tmp);
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
Matrix<Real> xi(size, size);
Matrix<Real> xi_inv(size, size);
Vector<Real> tmp(size);
Vector<Real> tmp1(size);
Matrix<Real> tmp2(size, size);
UInt iterations{0};
while(tolerance < projection_error and iterations < max_iterations) {
// compute hessian at previous step
compute_hessian_f();
// compute inverse matrix Xi
xi = Ce + plastic_multiplier_guess * hessian_f;
// compute inverse matrix Xi
xi_inv.inverse(xi);
tmp.mul<false>(xi_inv, gradient_f);
auto denominator = gradient_f.dot(tmp);
// compute plastic multplier guess
tmp1.mul<false>(xi_inv, delta_inelastic_strain);
plastic_multiplier_guess = gradient_f.dot(tmp1);
plastic_multiplier_guess += yield_function;
plastic_multiplier_guess /= denominator;
// compute delta sigma
tmp2.outerProduct(tmp, tmp);
tmp2 /= denominator;
tmp2 = xi_inv - tmp2;
delta_sigma.mul<false>(tmp2, delta_inelastic_strain);
delta_sigma -= tmp*yield_function/denominator;
// compute sigma_guess
Matrix<Real> delta_sigma_mat(dim, dim);
voigt_h::voigtToMatrix(delta_sigma, delta_sigma_mat);
sigma_guess += delta_sigma_mat;
projection_error = update_f(k_tmp, alpha_tmp);
iterations++;
}
}
/* -------------------------------------------------------------------------- */
/// Infinitesimal deformations
template <UInt dim>
inline void MaterialDruckerPrager<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain, const Matrix<Real> & previous_inelastic_strain,
const Real & sigma_th, const Real & previous_sigma_th) {
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// Compute the yielding sress
/*Real yield_stress = computeYieldStress(sigma_tr);
Matrix<Real> sigma_tr_dev(dim, dim, 0);
this->computeDeviatoricStress(sigma_tr, sigma_tr_dev);
Real j2 = (1./ 2.) * sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. * j2);
bool initial_yielding = ((sigma_tr_dev_eff + yield_stress) > 0);*/
bool initial_yielding =
(this->computeYieldFunction(sigma_tr) > 0);
// use closet point projection to compute the plastic multiplier and
// gradient and inealstic strain at the surface for the given trial stress state
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if(initial_yielding) {
UInt size = voigt_h::size;
// plastic multiplier
Real dp{0.};
// gradient of yield surface in voigt notation
Vector<Real> gradient_f(size, 0.);
// inelastic strain in voigt notation
Vector<Real> delta_inelastic_strain_voigt(size, 0.);
// compute using closet-point projection
this->computeGradientAndPlasticMultplier(sigma_tr, dp, gradient_f,
delta_inelastic_strain_voigt);
for(auto i: arange(dim, size))
delta_inelastic_strain_voigt[i] /= 2.;
voigt_h::voigtToMatrix(delta_inelastic_strain_voigt,
delta_inelastic_strain);
}
// Compute the increment in inelastic strain
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
/// Finite deformations
template <UInt dim>
inline void MaterialDruckerPrager<dim>::computeStressOnQuad(
__attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & previous_grad_u,
__attribute__((unused)) Matrix<Real> & sigma,
__attribute__((unused)) const Matrix<Real> & previous_sigma,
__attribute__((unused)) Matrix<Real> & inelastic_strain,
__attribute__((unused)) const Matrix<Real> & previous_inelastic_strain,
__attribute__((unused)) const Real & sigma_th,
__attribute__((unused)) const Real & previous_sigma_th,
__attribute__((unused)) const Matrix<Real> & F_tensor) {
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialDruckerPrager<dim>::computeTangentModuliOnQuad(
__attribute__((unused)) Matrix<Real> & tangent,
__attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & previous_grad_u,
__attribute__((unused)) const Matrix<Real> & sigma_tensor,
__attribute__((unused)) const Matrix<Real> & previous_sigma_tensor) const {
}
}
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
index 7d5b4bc9f..afeb80be3 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
@@ -1,203 +1,205 @@
/**
* @file material_linear_isotropic_hardening.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Sat Dec 02 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_linear_isotropic_hardening.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialLinearIsotropicHardening<dim>::MaterialLinearIsotropicHardening(
SolidMechanicsModel & model, const ID & id)
: MaterialPlastic<dim>(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialLinearIsotropicHardening<spatial_dimension>::
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: MaterialPlastic<spatial_dimension>(model, dim, mesh, fe_engine, id) {}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
// NOLINTNEXTLINE(bugprone-parent-virtual-call)
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening_it = this->iso_hardening(el_type, ghost_type).begin();
auto previous_iso_hardening_it =
this->iso_hardening.previous(el_type, ghost_type).begin();
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToE<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToE<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
computeStressOnQuad(green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it, *previous_sigma_th_it);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeTangentModuli(
ElementType el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening = this->iso_hardening(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *previous_gradu_it, sigma,
*previous_stress_it, *iso_hardening);
++previous_gradu_it;
++previous_stress_it;
++iso_hardening;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(plastic_linear_isotropic_hardening,
MaterialLinearIsotropicHardening);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
index 9f9d9f920..bd330ea7c 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
@@ -1,114 +1,116 @@
/**
* @file material_linear_isotropic_hardening.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sat Dec 02 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_
#define AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_
namespace akantu {
/**
* Material plastic with a linear evolution of the yielding stress
*/
template <UInt spatial_dimension>
class MaterialLinearIsotropicHardening
: public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialLinearIsotropicHardening(SolidMechanicsModel & model,
const ID & id = "");
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
protected:
/// Infinitesimal deformations
inline void
computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
Real & iso_hardening, const Real & previous_iso_hardening,
const Real & sigma_th, const Real & previous_sigma_th);
/// Finite deformations
inline void computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th, const Matrix<Real> & F_tensor);
inline void computeTangentModuliOnQuad(
Matrix<Real> & tangent, const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u, const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor,
const Real & iso_hardening) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_linear_isotropic_hardening_inline_impl.hh"
#endif /* AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
index f4cdaf146..d5ae4a2a9 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening_inline_impl.hh
@@ -1,300 +1,302 @@
/**
* @file material_linear_isotropic_hardening_inline_impl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Thu Nov 30 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of the material plasticity
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "material_linear_isotropic_hardening.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// Infinitesimal deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th) {
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// We need a full stress tensor, otherwise the VM stress is messed up
Matrix<Real> sigma_tr_dev(3, 3, 0);
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
sigma_tr_dev(i, j) = sigma_tr(i, j);
}
}
sigma_tr_dev -= Matrix<Real>::eye(3, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
bool initial_yielding =
((sigma_tr_dev_eff - iso_hardening - this->sigma_y) > 0);
Real dp = (initial_yielding)
? (sigma_tr_dev_eff - this->sigma_y - previous_iso_hardening) /
(3 * this->mu + this->h)
: 0;
iso_hardening = previous_iso_hardening + this->h * dp;
// Compute inelastic strain (ignore last components in 1-2D)
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
delta_inelastic_strain(i, j) = sigma_tr_dev(i, j);
}
}
delta_inelastic_strain *= 3. / 2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
/// Finite deformations
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain, Real & iso_hardening,
const Real & previous_iso_hardening, const Real & sigma_th,
const Real & previous_sigma_th, const Matrix<Real> & F_tensor) {
// Finite plasticity
Real dp = 0.0;
Real d_dp = 0.0;
UInt n = 0;
Real delta_sigma_th = sigma_th - previous_sigma_th;
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
// Compute trial stress, sigma_tr
Matrix<Real> sigma_tr(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr,
delta_sigma_th);
sigma_tr += previous_sigma;
// Compute deviatoric trial stress, sigma_tr_dev
Matrix<Real> sigma_tr_dev(sigma_tr);
sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// Compute effective deviatoric trial stress
Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
Real sigma_tr_dev_eff = std::sqrt(3. / 2. * s);
// compute the cauchy stress to apply the Von-Mises criterion
Matrix<Real> cauchy_stress(dim, dim);
Material::StoCauchy<dim>(F_tensor, sigma_tr, cauchy_stress);
Matrix<Real> cauchy_stress_dev(cauchy_stress);
cauchy_stress_dev -= Matrix<Real>::eye(dim, cauchy_stress.trace() / 3.0);
Real c = cauchy_stress_dev.doubleDot(cauchy_stress_dev);
Real cauchy_stress_dev_eff = std::sqrt(3. / 2. * c);
const Real iso_hardening_t = previous_iso_hardening;
iso_hardening = iso_hardening_t;
// Loop for correcting stress based on yield function
// F is written in terms of S
// bool initial_yielding = ( (sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > 0) ;
// while ( initial_yielding && std::abs(sigma_tr_dev_eff - iso_hardening -
// this->sigma_y) > Math::getTolerance() ) {
// d_dp = (sigma_tr_dev_eff - 3. * this->mu *dp - iso_hardening -
// this->sigma_y)
// / (3. * this->mu + this->h);
// //r = r + h * dp;
// dp = dp + d_dp;
// iso_hardening = iso_hardening_t + this->h * dp;
// ++n;
// /// TODO : explicit this criterion with an error message
// if ((std::abs(d_dp) < 1e-9) || (n>50)){
// AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
// << d_dp << "\tNumber of iteration:"<<n);
// break;
// }
// }
// F is written in terms of cauchy stress
bool initial_yielding =
((cauchy_stress_dev_eff - iso_hardening - this->sigma_y) > 0);
while (initial_yielding && std::abs(cauchy_stress_dev_eff - iso_hardening -
this->sigma_y) > Math::getTolerance()) {
d_dp = (cauchy_stress_dev_eff - 3. * this->mu * dp - iso_hardening -
this->sigma_y) /
(3. * this->mu + this->h);
// r = r + h * dp;
dp = dp + d_dp;
iso_hardening = iso_hardening_t + this->h * dp;
++n;
/// TODO : explicit this criterion with an error message
if ((d_dp < 1e-5) || (n > 50)) {
AKANTU_DEBUG_INFO("convergence of increment of plastic strain. d_dp:"
<< d_dp << "\tNumber of iteration:" << n);
break;
}
}
// Update internal variable
Matrix<Real> delta_inelastic_strain(dim, dim, 0.);
if (std::abs(sigma_tr_dev_eff) >
sigma_tr_dev.norm<L_inf>() * Math::getTolerance()) {
// /// compute the direction of the plastic strain as \frac{\partial
// F}{\partial S} = \frac{3}{2J\sigma_{effective}}} Ft \sigma_{dev} F
Matrix<Real> cauchy_dev_F(dim, dim);
cauchy_dev_F.mul<false, false>(F_tensor, cauchy_stress_dev);
Real J = F_tensor.det();
Real constant = not Math::are_float_equal(J, 0.) ? 1. / J : 0;
constant *= 3. * dp / (2. * cauchy_stress_dev_eff);
delta_inelastic_strain.mul<true, false>(F_tensor, cauchy_dev_F, constant);
// Direction given by the piola kirchhoff deviatoric tensor \frac{\partial
// F}{\partial S} = \frac{3}{2\sigma_{effective}}}S_{dev}
// delta_inelastic_strain.copy(sigma_tr_dev);
// delta_inelastic_strain *= 3./2. * dp / sigma_tr_dev_eff;
}
MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
grad_delta_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialLinearIsotropicHardening<dim>::computeTangentModuliOnQuad(
Matrix<Real> & tangent, __attribute__((unused)) const Matrix<Real> & grad_u,
__attribute__((unused)) const Matrix<Real> & previous_grad_u,
__attribute__((unused)) const Matrix<Real> & sigma_tensor,
__attribute__((unused)) const Matrix<Real> & previous_sigma_tensor,
__attribute__((unused)) const Real & iso_hardening) const {
// Real r=iso_hardening;
// Matrix<Real> grad_delta_u(grad_u);
// grad_delta_u -= previous_grad_u;
// //Compute trial stress, sigma_tr
// Matrix<Real> sigma_tr(dim, dim);
// MaterialElastic<dim>::computeStressOnQuad(grad_delta_u, sigma_tr);
// sigma_tr += previous_sigma_tensor;
// // Compute deviatoric trial stress, sigma_tr_dev
// Matrix<Real> sigma_tr_dev(sigma_tr);
// sigma_tr_dev -= Matrix<Real>::eye(dim, sigma_tr.trace() / 3.0);
// // Compute effective deviatoric trial stress
// Real s = sigma_tr_dev.doubleDot(sigma_tr_dev);
// Real sigma_tr_dev_eff=std::sqrt(3./2. * s);
// // Compute deviatoric stress, sigma_dev
// Matrix<Real> sigma_dev(sigma_tensor);
// sigma_dev -= Matrix<Real>::eye(dim, sigma_tensor.trace() / 3.0);
// // Compute effective deviatoric stress
// s = sigma_dev.doubleDot(sigma_dev);
// Real sigma_dev_eff = std::sqrt(3./2. * s);
// Real xr = 0.0;
// if(sigma_tr_dev_eff > sigma_dev_eff * Math::getTolerance())
// xr = sigma_dev_eff / sigma_tr_dev_eff;
// Real __attribute__((unused)) q = 1.5 * (1. / (1. + 3. * this->mu /
// this->h) - xr);
/*
UInt cols = tangent.cols();
UInt rows = tangent.rows();
for (UInt m = 0; m < rows; ++m) {
UInt i = VoigtHelper<dim>::vec[m][0];
UInt j = VoigtHelper<dim>::vec[m][1];
for (UInt n = 0; n < cols; ++n) {
UInt k = VoigtHelper<dim>::vec[n][0];
UInt l = VoigtHelper<dim>::vec[n][1];
*/
// This section of the code is commented
// There were some problems with the convergence of plastic-coupled
// simulations with thermal expansion
// XXX: DO NOT REMOVE
/*if (((sigma_tr_dev_eff-iso_hardening-sigmay) > 0) && (xr > 0)) {
tangent(m,n) =
2. * this->mu * q * (sigma_tr_dev (i,j) / sigma_tr_dev_eff) * (sigma_tr_dev
(k,l) / sigma_tr_dev_eff) +
(i==k) * (j==l) * 2. * this->mu * xr +
(i==j) * (k==l) * (this->kpa - 2./3. * this->mu * xr);
if ((m == n) && (m>=dim))
tangent(m, n) = tangent(m, n) - this->mu * xr;
} else {*/
/*
tangent(m,n) = (i==k) * (j==l) * 2. * this->mu +
(i==j) * (k==l) * this->lambda;
tangent(m,n) -= (m==n) * (m>=dim) * this->mu;
*/
//}
// correct tangent stiffness for shear component
//}
//}
MaterialElastic<dim>::computeTangentModuliOnQuad(tangent);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
index 059a710d5..73bf43b23 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
@@ -1,199 +1,202 @@
/**
* @file material_plastic.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implemantation of the akantu::MaterialPlastic class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
iso_hardening("iso_hardening", *this),
inelastic_strain("inelastic_strain", *this),
plastic_energy("plastic_energy", *this),
d_plastic_energy("d_plastic_energy", *this) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template <UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
UInt dim, const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: MaterialElastic<spatial_dimension>(model, dim, mesh, fe_engine, id),
iso_hardening("iso_hardening", *this, dim, fe_engine,
this->element_filter),
inelastic_strain("inelastic_strain", *this, dim, fe_engine,
this->element_filter),
plastic_energy("plastic_energy", *this, dim, fe_engine,
this->element_filter),
d_plastic_energy("d_plastic_energy", *this, dim, fe_engine,
this->element_filter) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::initialize() {
this->registerParam("h", h, Real(0.), _pat_parsable | _pat_modifiable,
"Hardening modulus");
this->registerParam("sigma_y", sigma_y, Real(0.),
_pat_parsable | _pat_modifiable, "Yield stress");
this->iso_hardening.initialize(1);
this->iso_hardening.initializeHistory();
this->plastic_energy.initialize(1);
this->d_plastic_energy.initialize(1);
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->inelastic_strain.initialize(spatial_dimension * spatial_dimension);
this->inelastic_strain.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getEnergy(const std::string & type) {
if (type == "plastic") {
return getPlasticEnergy();
}
return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getPlasticEnergy() {
AKANTU_DEBUG_IN();
Real penergy = 0.;
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
penergy +=
this->fem.integrate(plastic_energy(type, _not_ghost), type, _not_ghost,
this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return penergy;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
Array<Real>::scalar_iterator epot = this->potential_energy(el_type).begin();
Array<Real>::const_iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type).begin(spatial_dimension,
spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> elastic_strain(spatial_dimension, spatial_dimension);
elastic_strain.copy(grad_u);
elastic_strain -= *inelastic_strain_it;
MaterialElastic<spatial_dimension>::computePotentialEnergyOnQuad(
elastic_strain, sigma, *epot);
++epot;
++inelastic_strain_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::updateEnergies(ElementType el_type) {
AKANTU_DEBUG_IN();
MaterialElastic<spatial_dimension>::updateEnergies(el_type);
Array<Real>::iterator<> pe_it = this->plastic_energy(el_type).begin();
Array<Real>::iterator<> wp_it = this->d_plastic_energy(el_type).begin();
Array<Real>::iterator<Matrix<Real>> inelastic_strain_it =
this->inelastic_strain(el_type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::iterator<Matrix<Real>> previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::matrix_iterator previous_sigma =
this->stress.previous(el_type).begin(spatial_dimension,
spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
Matrix<Real> delta_strain_it(*inelastic_strain_it);
delta_strain_it -= *previous_inelastic_strain_it;
Matrix<Real> sigma_h(sigma);
sigma_h += *previous_sigma;
*wp_it = .5 * sigma_h.doubleDot(delta_strain_it);
*pe_it += *wp_it;
++pe_it;
++wp_it;
++inelastic_strain_it;
++previous_inelastic_strain_it;
++previous_sigma;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL_ONLY(MaterialPlastic);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
index c40cd1142..5e908bc97 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
@@ -1,132 +1,134 @@
/**
* @file material_plastic.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Thu Dec 07 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Common interface for plastic materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_PLASTIC_HH_
#define AKANTU_MATERIAL_PLASTIC_HH_
namespace akantu {
/**
* Parent class for the plastic constitutive laws
* parameters in the material files :
* - h : Hardening parameter (default: 0)
* - sigmay : Yield stress
*/
template <UInt dim> class MaterialPlastic : public MaterialElastic<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPlastic(SolidMechanicsModel & model, const ID & id = "");
MaterialPlastic(SolidMechanicsModel & model, UInt a_dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief Return potential or plastic energy
*
* Plastic dissipated energy is integrated over time.
*/
Real getEnergy(const std::string & type) override;
/// Update the plastic energy for the current timestep
void updateEnergies(ElementType el_type) override;
/// Compute the true potential energy (w/ elastic strain)
void computePotentialEnergy(ElementType el_type) override;
protected:
/// compute the stress and inelastic strain for the quadrature point
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const;
inline void computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & delta_grad_u, Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma, Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const;
/// Get the integrated plastic energy for the time step
Real getPlasticEnergy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Yield stresss
Real sigma_y;
/// hardening modulus
Real h;
/// isotropic hardening, r
InternalField<Real> iso_hardening;
/// inelastic strain arrays ordered by element types (inelastic deformation)
InternalField<Real> inelastic_strain;
/// Plastic energy
InternalField<Real> plastic_energy;
/// @todo : add a coefficient beta that will multiply the plastic energy
/// increment
/// to compute the energy converted to heat
/// Plastic energy increment
InternalField<Real> d_plastic_energy;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_plastic_inline_impl.hh"
#endif /* AKANTU_MATERIAL_PLASTIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.hh b/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.hh
index d2471ac32..e1361c09b 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic_inline_impl.hh
@@ -1,75 +1,77 @@
/**
* @file material_plastic_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
- * @date last modification: Wed Jan 24 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Implementation of the inline functions of akantu::MaterialPlastic
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef MATERIAL_PLASTIC_INLINE_IMPL_H
#define MATERIAL_PLASTIC_INLINE_IMPL_H
#include "material_plastic.hh"
namespace akantu {
template <UInt dim>
inline void MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & delta_grad_u, Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma, Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const {
Matrix<Real> grad_u_elastic(dim, dim);
grad_u_elastic.copy(delta_grad_u);
grad_u_elastic -= delta_inelastic_strain;
Matrix<Real> sigma_elastic(dim, dim);
MaterialElastic<dim>::computeStressOnQuad(grad_u_elastic, sigma_elastic);
sigma.copy(previous_sigma);
sigma += sigma_elastic;
inelastic_strain.copy(previous_inelastic_strain);
inelastic_strain += delta_inelastic_strain;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialPlastic<dim>::computeStressAndInelasticStrainOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, const Matrix<Real> & previous_sigma,
Matrix<Real> & inelastic_strain,
const Matrix<Real> & previous_inelastic_strain,
const Matrix<Real> & delta_inelastic_strain) const {
Matrix<Real> delta_grad_u(grad_u);
delta_grad_u -= previous_grad_u;
computeStressAndInelasticStrainOnQuad(
delta_grad_u, sigma, previous_sigma, inelastic_strain,
previous_inelastic_strain, delta_inelastic_strain);
}
} // namespace akantu
#endif /* MATERIAL_PLASTIC_INLINE_IMPL_H */
diff --git a/src/model/solid_mechanics/materials/material_thermal.cc b/src/model/solid_mechanics/materials/material_thermal.cc
index bda853570..4de1e3844 100644
--- a/src/model/solid_mechanics/materials/material_thermal.cc
+++ b/src/model/solid_mechanics/materials/material_thermal.cc
@@ -1,118 +1,97 @@
/**
* @file material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Specialization of the material class for the thermal material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
- * You should have received a copy of the GNU Lesser General Public License
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_thermal.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
-template <UInt spatial_dimension>
-MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
- const ID & id)
+template <UInt dim>
+MaterialThermal<dim>::MaterialThermal(SolidMechanicsModel & model,
+ const ID & id)
: Material(model, id), delta_T("delta_T", *this),
sigma_th("sigma_th", *this), use_previous_stress_thermal(false) {
- AKANTU_DEBUG_IN();
this->initialize();
- AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-template <UInt spatial_dimension>
-MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
- UInt dim, const Mesh & mesh,
- FEEngine & fe_engine,
- const ID & id)
- : Material(model, dim, mesh, fe_engine, id),
+template <UInt dim>
+MaterialThermal<dim>::MaterialThermal(SolidMechanicsModel & model,
+ UInt spatial_dimension, const Mesh & mesh,
+ FEEngine & fe_engine, const ID & id)
+ : Material(model, spatial_dimension, mesh, fe_engine, id),
delta_T("delta_T", *this, dim, fe_engine, this->element_filter),
sigma_th("sigma_th", *this, dim, fe_engine, this->element_filter),
use_previous_stress_thermal(false) {
- AKANTU_DEBUG_IN();
this->initialize();
- AKANTU_DEBUG_OUT();
}
-template <UInt spatial_dimension>
-void MaterialThermal<spatial_dimension>::initialize() {
+/* -------------------------------------------------------------------------- */
+template <UInt dim> void MaterialThermal<dim>::initialize() {
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("alpha", alpha, Real(0.), _pat_parsable | _pat_modifiable,
"Thermal expansion coefficient");
this->registerParam("delta_T", delta_T, _pat_parsable | _pat_modifiable,
"Uniform temperature field");
delta_T.initialize(1);
}
/* -------------------------------------------------------------------------- */
-template <UInt spatial_dimension>
-void MaterialThermal<spatial_dimension>::initMaterial() {
- AKANTU_DEBUG_IN();
-
+template <UInt dim> void MaterialThermal<dim>::initMaterial() {
sigma_th.initialize(1);
if (use_previous_stress_thermal) {
sigma_th.initializeHistory();
}
Material::initMaterial();
-
- AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialThermal<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
- AKANTU_DEBUG_IN();
-
for (auto && tuple : zip(this->delta_T(el_type, ghost_type),
this->sigma_th(el_type, ghost_type))) {
computeStressOnQuad(std::get<1>(tuple), std::get<0>(tuple));
}
-
- AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-
-template <UInt dim>
-void MaterialThermal<dim>::computePotentialEnergy(ElementType /*el_type*/) {
- AKANTU_DEBUG_IN();
- AKANTU_TO_IMPLEMENT();
- AKANTU_DEBUG_OUT();
-}
-
-/* -------------------------------------------------------------------------- */
-
INSTANTIATE_MATERIAL_ONLY(MaterialThermal);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_thermal.hh b/src/model/solid_mechanics/materials/material_thermal.hh
index 1a1c26884..f6a303e42 100644
--- a/src/model/solid_mechanics/materials/material_thermal.hh
+++ b/src/model/solid_mechanics/materials/material_thermal.hh
@@ -1,112 +1,110 @@
/**
* @file material_thermal.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Jan 29 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material isotropic thermo-elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_THERMAL_HH_
#define AKANTU_MATERIAL_THERMAL_HH_
namespace akantu {
template <UInt spatial_dimension> class MaterialThermal : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialThermal(SolidMechanicsModel & model, const ID & id = "");
MaterialThermal(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~MaterialThermal() override = default;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type) override;
/// local computation of thermal stress
inline void computeStressOnQuad(Real & sigma, const Real & deltaT);
- /// local computation of thermal stress
- void computePotentialEnergy(ElementType el_type) override;
-
- /* --------------------------------------------------------------------------
- */
+ /* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Young modulus
Real E;
/// Poisson ratio
Real nu;
/// Thermal expansion coefficient
/// TODO : implement alpha as a matrix
Real alpha;
/// Temperature field
InternalField<Real> delta_T;
/// Current thermal stress
InternalField<Real> sigma_th;
/// Tell if we need to use the previous thermal stress
bool use_previous_stress_thermal;
};
/* ------------------------------------------------------------------------ */
/* Inline impl */
/* ------------------------------------------------------------------------ */
template <UInt dim>
inline void MaterialThermal<dim>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E / (1. - 2. * this->nu) * this->alpha * deltaT;
}
template <>
inline void MaterialThermal<1>::computeStressOnQuad(Real & sigma,
const Real & deltaT) {
sigma = -this->E * this->alpha * deltaT;
}
} // namespace akantu
#endif /* AKANTU_MATERIAL_THERMAL_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
index 594535c7f..a9db37ec7 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
@@ -1,316 +1,318 @@
/**
* @file material_standard_linear_solid_deviatoric.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Wed May 04 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material Visco-elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_standard_linear_solid_deviatoric.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialStandardLinearSolidDeviatoric<
dim>::MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id)
: MaterialElastic<dim>(model, id), stress_dev("stress_dev", *this),
history_integral("history_integral", *this),
dissipated_energy("dissipated_energy", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Eta", eta, Real(1.), _pat_parsable | _pat_modifiable,
"Viscosity");
this->registerParam("Ev", Ev, Real(1.), _pat_parsable | _pat_modifiable,
"Stiffness of the viscous element");
this->registerParam("Einf", E_inf, Real(1.), _pat_readable,
"Stiffness of the elastic element");
UInt stress_size = dim * dim;
this->stress_dev.initialize(stress_size);
this->history_integral.initialize(stress_size);
this->dissipated_energy.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::initMaterial() {
AKANTU_DEBUG_IN();
updateInternalParameters();
MaterialElastic<dim>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::updateInternalParameters() {
MaterialElastic<dim>::updateInternalParameters();
E_inf = this->E - this->Ev;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::setToSteadyState(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
Real Theta = grad_u.trace();
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
dev_s(i, j) = 2 * this->mu *
(.5 * (grad_u(i, j) + grad_u(j, i)) -
1. / 3. * Theta * Math::kronecker(i, j));
h(i, j) = 0.;
}
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real tau = 0.;
// if(std::abs(Ev) > std::numeric_limits<Real>::epsilon())
tau = eta / Ev;
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
Matrix<Real> s(dim, dim);
Real dt = this->model.getTimeStep();
Real exp_dt_tau = exp(-dt / tau);
Real exp_dt_tau_2 = exp(-.5 * dt / tau);
Matrix<Real> epsilon_v(dim, dim);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
s.zero();
sigma.zero();
/// Compute the first invariant of strain
Real gamma_inf = E_inf / this->E;
Real gamma_v = Ev / this->E;
auto epsilon_d = this->template gradUToEpsilon<dim>(grad_u);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
Matrix<Real> U_rond_prim(dim, dim);
U_rond_prim.eye(gamma_inf * this->kpa * Theta);
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
s(i, j) = 2 * this->mu * epsilon_d(i, j);
h(i, j) = exp_dt_tau * h(i, j) + exp_dt_tau_2 * (s(i, j) - dev_s(i, j));
dev_s(i, j) = s(i, j);
sigma(i, j) = U_rond_prim(i, j) + gamma_inf * s(i, j) + gamma_v * h(i, j);
}
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
this->updateDissipatedEnergy(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialStandardLinearSolidDeviatoric<dim>::updateDissipatedEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
// if(ghost_type == _ghost) return 0.;
Real tau = 0.;
tau = eta / Ev;
Real * dis_energy = dissipated_energy(el_type, ghost_type).storage();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(dim, dim);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(dim, dim);
Matrix<Real> q(dim, dim);
Matrix<Real> q_rate(dim, dim);
Matrix<Real> epsilon_d(dim, dim);
Matrix<Real> epsilon_v(dim, dim);
Real dt = this->model.getTimeStep();
Real gamma_v = Ev / this->E;
Real alpha = 1. / (2. * this->mu * gamma_v);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
this->template gradUToEpsilon<dim>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
q.copy(dev_s);
q -= h;
q *= gamma_v;
q_rate.copy(dev_s);
q_rate *= gamma_v;
q_rate -= q;
q_rate /= tau;
for (UInt i = 0; i < dim; ++i) {
for (UInt j = 0; j < dim; ++j) {
*dis_energy += (epsilon_d(i, j) - alpha * q(i, j)) * q_rate(i, j) * dt;
}
}
/// Save the deviator of stress
++stress_d;
++history_int;
++dis_energy;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type : this->element_filter.elementTypes(dim, _not_ghost)) {
de +=
this->fem.integrate(dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getDissipatedEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getEnergy(
const std::string & type) {
if (type == "dissipated") {
return getDissipatedEnergy();
}
if (type == "dissipated_sls_deviatoric") {
return getDissipatedEnergy();
}
return MaterialElastic<dim>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialStandardLinearSolidDeviatoric<dim>::getEnergy(
const std::string & energy_id, ElementType type, UInt index) {
if (energy_id == "dissipated") {
return getDissipatedEnergy(type, index);
}
if (energy_id == "dissipated_sls_deviatoric") {
return getDissipatedEnergy(type, index);
}
return MaterialElastic<dim>::getEnergy(energy_id, type, index);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(sls_deviatoric, MaterialStandardLinearSolidDeviatoric);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
index 855f78c32..2a6df1f97 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
@@ -1,136 +1,138 @@
/**
* @file material_standard_linear_solid_deviatoric.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Material Visco-elastic, based on Standard Solid rheological model,
* see
* [] J.C. Simo, T.J.R. Hughes, "Computational Inelasticity", Springer (1998),
* see Sections 10.2 and 10.3
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_
#define AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_
namespace akantu {
/**
* Material standard linear solid deviatoric
*
*
* @verbatim
E_\inf
------|\/\/\|------
| |
---| |---
| |
----|\/\/\|--[|----
E_v \eta
@endverbatim
*
* keyword : sls_deviatoric
*
* parameters in the material files :
* - E : Initial Young's modulus @f$ E = E_i + E_v @f$
* - eta : viscosity
* - Ev : stiffness of the viscous element
*/
template <UInt spatial_dimension>
class MaterialStandardLinearSolidDeviatoric
: public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model,
const ID & id = "");
~MaterialStandardLinearSolidDeviatoric() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// update the internal parameters (for modifiable parameters)
void updateInternalParameters() override;
/// set material to steady state
void setToSteadyState(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
protected:
/// update the dissipated energy, is called after the stress have been
/// computed
void updateDissipatedEnergy(ElementType el_type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// viscosity, viscous elastic modulus
Real eta, Ev, E_inf;
Vector<Real> etas;
/// history of deviatoric stress
InternalField<Real> stress_dev;
/// Internal variable: history integral
InternalField<Real> history_integral;
/// Dissipated energy
InternalField<Real> dissipated_energy;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH_ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
index 49cc92d7f..f0aac9836 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.cc
@@ -1,737 +1,736 @@
/**
- * @file material_viscoelastic_maxwell.hh
+ * @file material_viscoelastic_maxwell.cc
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
- * @date creation: Tue May 08 2018
- * @date last modification: Tue May 08 2018
+ * @date creation: Mon Jun 04 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material Visco-elastic, based on Maxwell chain,
* see
* [] R. de Borst and A.H. van den Boogaard "Finite-element modeling of
* deformation and cracking in early-age concrete", J.Eng.Mech., 1994
* as well as
* [] Manual of DIANA FEA Theory manual v.10.2 Section 37.6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_viscoelastic_maxwell.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialViscoelasticMaxwell<spatial_dimension>::MaterialViscoelasticMaxwell(
SolidMechanicsModel & model, const ID & id)
: MaterialElastic<spatial_dimension>(model, id),
C(voigt_h::size, voigt_h::size), D(voigt_h::size, voigt_h::size),
sigma_v("sigma_v", *this), epsilon_v("epsilon_v", *this),
dissipated_energy("dissipated_energy", *this),
mechanical_work("mechanical_work", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Einf", Einf, Real(1.), _pat_parsable | _pat_modifiable,
"Stiffness of the elastic element");
this->registerParam("previous_dt", previous_dt, Real(0.), _pat_readable,
"Time step of previous solveStep");
this->registerParam("Eta", Eta, _pat_parsable | _pat_modifiable,
"Viscosity of a Maxwell element");
this->registerParam("Ev", Ev, _pat_parsable | _pat_modifiable,
"Stiffness of a Maxwell element");
this->update_variable_flag = true;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->dissipated_energy.initialize(1);
this->mechanical_work.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->E = Einf + Ev.norm<L_1>();
// this->E = std::min(this->Einf, this->Ev(0));
MaterialElastic<spatial_dimension>::initMaterial();
AKANTU_DEBUG_ASSERT(this->Eta.size() == this->Ev.size(),
"Eta and Ev have different dimensions! Please correct.");
AKANTU_DEBUG_ASSERT(
!this->finite_deformation,
"Current material works only in infinitesimal deformations.");
UInt stress_size = spatial_dimension * spatial_dimension;
this->sigma_v.initialize(stress_size * this->Ev.size());
this->epsilon_v.initialize(stress_size * this->Ev.size());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<
spatial_dimension>::updateInternalParameters() {
MaterialElastic<spatial_dimension>::updateInternalParameters();
Real pre_mult = 1 / (1 + this->nu) / (1 - 2 * this->nu);
UInt n = voigt_h::size;
Real Miiii = pre_mult * (1 - this->nu);
Real Miijj = pre_mult * this->nu;
Real Mijij = pre_mult * 0.5 * (1 - 2 * this->nu);
Real Diiii = 1;
Real Diijj = -this->nu;
Real Dijij = (2 + 2 * this->nu);
if (spatial_dimension == 1) {
C(0, 0) = 1;
D(0, 0) = 1;
} else {
C(0, 0) = Miiii;
D(0, 0) = Diiii;
}
if (spatial_dimension >= 2) {
C(1, 1) = Miiii;
C(0, 1) = Miijj;
C(1, 0) = Miijj;
C(n - 1, n - 1) = Mijij;
D(1, 1) = Diiii;
D(0, 1) = Diijj;
D(1, 0) = Diijj;
D(n - 1, n - 1) = Dijij;
}
if (spatial_dimension == 3) {
C(2, 2) = Miiii;
C(0, 2) = Miijj;
C(1, 2) = Miijj;
C(2, 0) = Miijj;
C(2, 1) = Miijj;
C(3, 3) = Mijij;
C(4, 4) = Mijij;
D(2, 2) = Diiii;
D(0, 2) = Diijj;
D(1, 2) = Diijj;
D(2, 0) = Diijj;
D(2, 1) = Diijj;
D(3, 3) = Dijij;
D(4, 4) = Dijij;
}
}
/* -------------------------------------------------------------------------- */
template <> void MaterialViscoelasticMaxwell<2>::updateInternalParameters() {
MaterialElastic<2>::updateInternalParameters();
Real pre_mult = 1 / (1 + this->nu) / (1 - 2 * this->nu);
UInt n = voigt_h::size;
Real Miiii = pre_mult * (1 - this->nu);
Real Miijj = pre_mult * this->nu;
Real Mijij = pre_mult * 0.5 * (1 - 2 * this->nu);
Real Diiii = 1;
Real Diijj = -this->nu;
Real Dijij = (2 + 2 * this->nu);
C(0, 0) = Miiii;
C(1, 1) = Miiii;
C(0, 1) = Miijj;
C(1, 0) = Miijj;
C(n - 1, n - 1) = Mijij;
D(0, 0) = Diiii;
D(1, 1) = Diiii;
D(0, 1) = Diijj;
D(1, 0) = Diijj;
D(n - 1, n - 1) = Dijij;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
// NOLINTNEXTLINE(bugprone-parent-virtual-call)
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, *previous_gradu_it, sigma, *sigma_v_it,
*sigma_th_it);
++sigma_th_it;
++previous_gradu_it;
++sigma_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeStressOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, Tensor3<Real> & sigma_v, const Real & sigma_th) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
Vector<Real> voigt_current_strain(voigt_h::size);
Vector<Real> voigt_previous_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
Vector<Real> voigt_sigma_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_current_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
voigt_previous_strain(I) =
voigt_factor * (previous_grad_u(i, j) + previous_grad_u(j, i)) / 2.;
}
voigt_stress = this->Einf * this->C * voigt_current_strain;
Real dt = this->model.getTimeStep();
for (UInt k = 0; k < Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
Real E_additional;
if (exp_dt_lambda == 1) {
E_additional = this->Ev(k);
} else {
E_additional = (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_sigma_v(I) = sigma_v(i, j, k);
}
voigt_stress += E_additional * this->C *
(voigt_current_strain - voigt_previous_strain) +
exp_dt_lambda * voigt_sigma_v;
}
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
sigma(i, j) = sigma(j, i) =
voigt_stress(I) + Math::kronecker(i, j) * sigma_th;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computePotentialEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
- // NOLINTNEXTLINE(bugprone-parent-virtual-call)
- MaterialThermal<spatial_dimension>::computePotentialEnergy(el_type);
-
auto epot = this->potential_energy(el_type).begin();
auto sigma_v_it = this->sigma_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it = this->epsilon_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
this->computePotentialEnergyOnQuad(grad_u, *epot, *sigma_v_it, *epsilon_v_it);
++epot;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::
computePotentialEnergyOnQuad(const Matrix<Real> & grad_u, Real & epot,
Tensor3<Real> & sigma_v,
Tensor3<Real> & epsilon_v) {
Vector<Real> voigt_strain(voigt_h::size);
Vector<Real> voigt_stress(voigt_h::size);
Vector<Real> voigt_sigma_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strain(I) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
voigt_stress = this->Einf * this->C * voigt_strain;
epot = 0.5 * voigt_stress.dot(voigt_strain);
for (UInt k = 0; k < this->Eta.size(); ++k) {
Matrix<Real> stress_v = sigma_v(k);
Matrix<Real> strain_v = epsilon_v(k);
epot += 0.5 * stress_v.doubleDot(strain_v);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::afterSolveStep(
bool converged) {
Material::afterSolveStep(converged);
if (not converged) {
return;
}
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
if (this->update_variable_flag) {
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it =
this->epsilon_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateIntVarOnQuad(grad_u, *previous_gradu_it, *sigma_v_it,
*epsilon_v_it);
++previous_gradu_it;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
this->updateDissipatedEnergy(el_type);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateIntVarOnQuad(
const Matrix<Real> & grad_u, const Matrix<Real> & previous_grad_u,
Tensor3<Real> & sigma_v, Tensor3<Real> & epsilon_v) {
Matrix<Real> grad_delta_u(grad_u);
grad_delta_u -= previous_grad_u;
Real dt = this->model.getTimeStep();
Vector<Real> voigt_delta_strain(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_delta_strain(I) =
voigt_factor * (grad_delta_u(i, j) + grad_delta_u(j, i)) / 2.;
}
for (UInt k = 0; k < this->Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
Real E_ef_v;
if (exp_dt_lambda == 1) {
E_ef_v = this->Ev(k);
} else {
E_ef_v = (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
Vector<Real> voigt_sigma_v(voigt_h::size);
Vector<Real> voigt_epsilon_v(voigt_h::size);
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_sigma_v(I) = sigma_v(i, j, k);
}
voigt_sigma_v =
exp_dt_lambda * voigt_sigma_v + E_ef_v * this->C * voigt_delta_strain;
voigt_epsilon_v = 1 / Ev(k) * this->D * voigt_sigma_v;
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
sigma_v(i, j, k) = sigma_v(j, i, k) = voigt_sigma_v(I);
epsilon_v(i, j, k) = epsilon_v(j, i, k) = voigt_epsilon_v(I);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeTangentModuli(
ElementType el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real dt = this->model.getTimeStep();
Real E_ef = this->Einf;
for (UInt k = 0; k < Eta.size(); ++k) {
Real lambda = this->Eta(k) / this->Ev(k);
Real exp_dt_lambda = exp(-dt / lambda);
if (exp_dt_lambda == 1) {
E_ef += this->Ev(k);
} else {
E_ef += (1 - exp_dt_lambda) * this->Ev(k) * lambda / dt;
}
}
this->previous_dt = dt;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
tangent_matrix *= E_ef;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::computeTangentModuliOnQuad(
Matrix<Real> & tangent) {
tangent.copy(C);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::savePreviousState() {
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
auto sigma_th_it = this->sigma_th(el_type, _not_ghost).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, _not_ghost).begin();
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_sigma_it;
previous_grad_u.copy(grad_u);
previous_sigma.copy(sigma);
*previous_sigma_th_it = *sigma_th_it;
++previous_gradu_it, ++previous_sigma_it, ++previous_sigma_th_it,
++sigma_v_it, ++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateIntVariables() {
for (auto & el_type : this->element_filter.elementTypes(
_all_dimensions, _not_ghost, _ek_not_defined)) {
auto previous_gradu_it = this->gradu.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension);
auto sigma_v_it =
this->sigma_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it =
this->epsilon_v(el_type, _not_ghost)
.begin(spatial_dimension, spatial_dimension, this->Eta.size());
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateIntVarOnQuad(grad_u, *previous_gradu_it, *sigma_v_it, *epsilon_v_it);
++previous_gradu_it;
++sigma_v_it;
++epsilon_v_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::updateDissipatedEnergy(
ElementType el_type) {
AKANTU_DEBUG_IN();
this->computePotentialEnergy(el_type);
auto epot = this->potential_energy(el_type).begin();
auto dis_energy = this->dissipated_energy(el_type).begin();
auto mech_work = this->mechanical_work(el_type).begin();
auto sigma_v_it = this->sigma_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto epsilon_v_it = this->epsilon_v(el_type).begin(
spatial_dimension, spatial_dimension, this->Eta.size());
auto previous_gradu_it =
this->gradu.previous(el_type).begin(spatial_dimension, spatial_dimension);
auto previous_sigma_it = this->stress.previous(el_type).begin(
spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
updateDissipatedEnergyOnQuad(grad_u, *previous_gradu_it, sigma,
*previous_sigma_it, *dis_energy, *mech_work,
*epot);
++previous_gradu_it;
++previous_sigma_it;
++dis_energy;
++mech_work;
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::
updateDissipatedEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
const Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Real & dis_energy, Real & mech_work,
const Real & pot_energy) {
Real dt = this->model.getTimeStep();
Matrix<Real> strain_rate = grad_u;
strain_rate -= previous_grad_u;
strain_rate /= dt;
Matrix<Real> av_stress = sigma;
av_stress += previous_sigma;
av_stress /= 2;
mech_work += av_stress.doubleDot(strain_rate) * dt;
dis_energy = mech_work - pot_energy;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getDissipatedEnergy()
const {
AKANTU_DEBUG_IN();
Real de = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
de +=
this->fem.integrate(this->dissipated_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getDissipatedEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getMechanicalWork() const {
AKANTU_DEBUG_IN();
Real mw = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
mw +=
this->fem.integrate(this->mechanical_work(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return mw;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getMechanicalWork(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it = this->mechanical_work(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getPotentialEnergy()
const {
AKANTU_DEBUG_IN();
Real epot = 0.;
/// integrate the dissipated energy for each type of elements
for (auto & type :
this->element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot +=
this->fem.integrate(this->potential_energy(type, _not_ghost), type,
_not_ghost, this->element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getPotentialEnergy(
ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->fem.getNbIntegrationPoints(type);
auto it =
this->potential_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->fem.integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getEnergy(
const std::string & type) {
if (type == "dissipated") {
return getDissipatedEnergy();
}
if (type == "potential") {
return getPotentialEnergy();
}
if (type == "work") {
return getMechanicalWork();
}
return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialViscoelasticMaxwell<spatial_dimension>::getEnergy(
const std::string & energy_id, ElementType type, UInt index) {
if (energy_id == "dissipated") {
return getDissipatedEnergy(type, index);
}
if (energy_id == "potential") {
return getPotentialEnergy(type, index);
}
if (energy_id == "work") {
return getMechanicalWork(type, index);
}
return MaterialElastic<spatial_dimension>::getEnergy(energy_id, type, index);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::forceUpdateVariable() {
update_variable_flag = true;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialViscoelasticMaxwell<spatial_dimension>::forceNotUpdateVariable() {
update_variable_flag = false;
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(viscoelastic_maxwell, MaterialViscoelasticMaxwell);
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
index 693bee468..d8ef5fb17 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_viscoelastic_maxwell.hh
@@ -1,229 +1,231 @@
/**
* @file material_viscoelastic_maxwell.hh
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
- * @date creation: Tue May 08 2018
- * @date last modification: Tue May 08 2018
+ * @date creation: Mon Jun 04 2018
+ * @date last modification: Wed Dec 09 2020
*
* @brief Material Visco-elastic, based on Maxwell chain,
* see
* [] R. de Borst and A.H. van den Boogaard "Finite-element modeling of
* deformation and cracking in early-age concrete", J.Eng.Mech., 1994
* as well as
* [] Manual of DIANA FEA Theory manual v.10.2 Section 37.6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_voigthelper.hh"
#include "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_
#define AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_
namespace akantu {
/**
* Material Viscoelastic based on Maxwell chain
*
*
* @verbatim
E_0
------|\/\/\|-------
| |
---| |---
| |
----|\/\/\|--[|-----
| E_v1 \Eta_1|
---| |---
| |
----|\/\/\|--[|-----
| E_v2 \Eta_2 |
---| |---
| |
----|\/\/\|--[|----
E_vN \Eta_N
@endverbatim
*
* keyword : viscoelastic_maxwell
*
* parameters in the material files :
* - N : number of Maxwell elements
* - Einf : one spring element stiffness
* - Ev1 : stiffness of the 1st viscous element
* - Eta1: viscosity of the 1st Maxwell element
* ...
* - Ev<N> : stiffness of the Nst viscous element
* - Eta<N>: viscosity of the Nst Maxwell element
*/
template <UInt spatial_dimension>
class MaterialViscoelasticMaxwell : public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialViscoelasticMaxwell(SolidMechanicsModel & model, const ID & id = "");
~MaterialViscoelasticMaxwell() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// recompute the lame coefficient and effective tangent moduli
void updateInternalParameters() override;
/// update internal variable on a converged Newton
void afterSolveStep(bool converged) override;
/// update internal variable based on previous and current strain values
void updateIntVariables();
/// update the internal variable sigma_v on quadrature point
void updateIntVarOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Tensor3<Real> & sigma_v, Tensor3<Real> & epsilon_v);
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(ElementType el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// save previous stress and strain values into "previous" arrays
void savePreviousState() override;
/// change flag of updateIntVar to true
void forceUpdateVariable();
/// change flag of updateIntVar to false
void forceNotUpdateVariable();
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type) override;
protected:
void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u, Real & epot,
Tensor3<Real> & sigma_v,
Tensor3<Real> & epsilon_v);
/// update the dissipated energy, is called after the stress have been
/// computed
void updateDissipatedEnergy(ElementType el_type);
void updateDissipatedEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
const Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Real & dis_energy, Real & mech_work,
const Real & pot_energy);
/// compute stresses on a quadrature point
void computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma, Tensor3<Real> & sigma_v,
const Real & sigma_th);
/// compute tangent moduli on a quadrature point
void computeTangentModuliOnQuad(Matrix<Real> & tangent);
bool hasStiffnessMatrixChanged() override {
Real dt = this->model.getTimeStep();
return ((this->previous_dt == dt)
? (!(this->previous_dt == dt)) * (this->was_stiffness_assembled)
: (!(this->previous_dt == dt)));
// return (!(this->previous_dt == dt));
}
MatrixType getTangentType() override {
return _symmetric;
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the potential energy
Real getPotentialEnergy() const;
Real getPotentialEnergy(ElementType type, UInt index) const;
/// get the potential energy
Real getMechanicalWork() const;
Real getMechanicalWork(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
Real getEnergy(const std::string & type) override;
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
using voigt_h = VoigtHelper<spatial_dimension>;
/// Vectors of viscosity, viscous elastic modulus, one spring element elastic
/// modulus
Vector<Real> Eta;
Vector<Real> Ev;
Real Einf;
/// time step from previous solveStep
Real previous_dt;
/// Stiffness matrix template
Matrix<Real> C;
/// Compliance matrix template
Matrix<Real> D;
/// Internal variable: viscous_stress
InternalField<Real> sigma_v;
/// Internal variable: spring strain in Maxwell element
InternalField<Real> epsilon_v;
/// Dissipated energy
InternalField<Real> dissipated_energy;
/// Mechanical work
InternalField<Real> mechanical_work;
/// Update internal variable after solve step or not
bool update_variable_flag;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_VISCOELASTIC_MAXWELL_HH_ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
index 27001f495..dc68fdc80 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
@@ -1,103 +1,105 @@
/**
* @file plane_stress_toolbox.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 16 2014
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Tools to implement the plane stress behavior in a material
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PLANE_STRESS_TOOLBOX_HH_
#define AKANTU_PLANE_STRESS_TOOLBOX_HH_
namespace akantu {
class SolidMechanicsModel;
class FEEngine;
} // namespace akantu
namespace akantu {
/**
* Empty class in dimensions different from 2
* This class is only specialized for 2D in the tmpl file
*/
template <UInt dim, class ParentMaterial = Material>
class PlaneStressToolbox : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "")
: ParentMaterial(model, id) {}
PlaneStressToolbox(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "")
: ParentMaterial(model, spatial_dimension, mesh, fe_engine, id) {}
~PlaneStressToolbox() override = default;
protected:
void initialize();
public:
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
ParentMaterial::computeAllCauchyStresses(ghost_type);
}
virtual void computeCauchyStressPlaneStress(ElementType /*el_type*/,
GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
AKANTU_ERROR("The function \"computeCauchyStressPlaneStress\" can "
"only be used in 2D Plane stress problems, which means "
"that you made a mistake somewhere!! ");
AKANTU_DEBUG_OUT();
}
virtual void computeThirdAxisDeformation(ElementType /*unused*/,
GhostType /*unused*/) {}
protected:
bool initialize_third_axis_deformation{false};
};
#define AKANTU_PLANE_STRESS_TOOL_SPEC(dim) \
template <> \
inline PlaneStressToolbox<dim, Material>::PlaneStressToolbox( \
SolidMechanicsModel & model, const ID & id) \
: Material(model, id) {}
AKANTU_PLANE_STRESS_TOOL_SPEC(1)
AKANTU_PLANE_STRESS_TOOL_SPEC(3)
} // namespace akantu
#include "plane_stress_toolbox_tmpl.hh"
#endif /* AKANTU_PLANE_STRESS_TOOLBOX_HH_ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
index 6c6d3a7f4..baf843086 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
@@ -1,165 +1,167 @@
/**
* @file plane_stress_toolbox_tmpl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Sep 16 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief 2D specialization of the akantu::PlaneStressToolbox class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_
#define AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class ParentMaterial>
class PlaneStressToolbox<2, ParentMaterial> : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "");
PlaneStressToolbox(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
~PlaneStressToolbox() override = default;
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ThirdAxisDeformation,
third_axis_deformation, Real);
protected:
void initialize() {
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
void initMaterial() override {
ParentMaterial::initMaterial();
if (this->plane_stress && this->initialize_third_axis_deformation) {
this->third_axis_deformation.initialize(1);
this->third_axis_deformation.resize();
}
}
/* ------------------------------------------------------------------------ */
void computeStress(ElementType el_type, GhostType ghost_type) override {
ParentMaterial::computeStress(el_type, ghost_type);
if (this->plane_stress) {
computeThirdAxisDeformation(el_type, ghost_type);
}
}
/* ------------------------------------------------------------------------ */
virtual void computeThirdAxisDeformation(ElementType /*unused*/,
GhostType /*unused*/) {}
/// Computation of Cauchy stress tensor in the case of finite deformation
void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
AKANTU_DEBUG_ASSERT(this->finite_deformation,
"The Cauchy stress can only be computed if you are "
"working in finite deformation.");
for (auto & type : this->fem.getMesh().elementTypes(2, ghost_type)) {
this->computeCauchyStressPlaneStress(type, ghost_type);
}
} else {
ParentMaterial::computeAllCauchyStresses(ghost_type);
}
AKANTU_DEBUG_OUT();
}
virtual void
computeCauchyStressPlaneStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// third axis strain measure value
InternalField<Real> third_axis_deformation;
/// Plane stress or plane strain
bool plane_stress;
/// For non linear materials, the \f[\epsilon_{zz}\f] might be required
bool initialize_third_axis_deformation;
};
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: ParentMaterial(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->initialize();
}
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: ParentMaterial(model, dim, mesh, fe_engine, id),
third_axis_deformation("third_axis_deformation", *this, dim, fe_engine,
this->element_filter),
plane_stress(false), initialize_third_axis_deformation(false) {
this->initialize();
}
template <>
inline PlaneStressToolbox<2, Material>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: Material(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
} // namespace akantu
#endif /* AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field.hh b/src/model/solid_mechanics/materials/random_internal_field.hh
index e615356ac..2696aa03d 100644
--- a/src/model/solid_mechanics/materials/random_internal_field.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field.hh
@@ -1,103 +1,105 @@
/**
* @file random_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Mar 26 2021
*
* @brief Random internal material parameter
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_RANDOM_INTERNAL_FIELD_HH_
#define AKANTU_RANDOM_INTERNAL_FIELD_HH_
namespace akantu {
/**
* class for the internal fields of materials with a random
* distribution
*/
template <typename T, template <typename> class BaseField = InternalField,
template <typename> class Generator = RandomGenerator>
class RandomInternalField : public BaseField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
RandomInternalField(const ID & id, Material & material);
~RandomInternalField() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
RandomInternalField operator=(const RandomInternalField &) = delete;
public:
AKANTU_GET_MACRO(RandomParameter, random_parameter, const RandomParameter<T>&);
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
/// set the field to a given value
void setDefaultValue(const T & value) override;
/// set the specified random distribution to a given parameter
void setRandomDistribution(const RandomParameter<T> & param);
/// print the content
void printself(std::ostream & stream, int indent = 0) const override;
protected:
void setArrayValues(T * begin, T * end) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline operator Real() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// random parameter containing the distribution and base value
RandomParameter<T> random_parameter;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const RandomInternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_RANDOM_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
index 2ecbe586b..73487ded8 100644
--- a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
@@ -1,124 +1,126 @@
/**
* @file random_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Feb 08 2018
+ * @date last modification: Fri Mar 26 2021
*
* @brief Random internal material parameter implementation
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_
#define AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::RandomInternalField(
const ID & id, Material & material)
: BaseField<T>(id, material), random_parameter(T()) {}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::~RandomInternalField() = default;
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::initialize(
UInt nb_component) {
this->internalInitialize(nb_component);
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setDefaultValue(
const T & value) {
random_parameter.setBaseValue(value);
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setRandomDistribution(
const RandomParameter<T> & param) {
random_parameter = param;
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::printself(
std::ostream & stream, int indent [[gnu::unused]]) const {
stream << "RandomInternalField [ ";
random_parameter.printself(stream);
stream << " ]";
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
InternalField<T>::printself(stream, indent);
}
#endif
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setArrayValues(T * begin,
T * end) {
random_parameter.template setValues<Generator>(begin, end);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
inline RandomInternalField<T, BaseField, Generator>::operator Real() const {
return random_parameter.getBaseValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<RandomInternalField<Real>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
index a7fe4da1b..e20b1fd12 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
@@ -1,79 +1,81 @@
/**
* @file damaged_weight_function.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Damaged weight function for non local materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_
#define AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
class DamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
DamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "damaged"), damage(nullptr) {
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
/// set the pointers of internals to the right flattend version
void init() override;
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "damaged_weight_function_inline_impl.hh"
#endif /* AKANTU_DAMAGED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.hh
index 367c8403f..1ac2b9850 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function_inline_impl.hh
@@ -1,80 +1,84 @@
/**
* @file damaged_weight_function_inline_impl.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Fri Jan 15 2016
*
* @brief Implementation of inline function of damaged weight function
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "damaged_weight_function.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real DamagedWeightFunction::operator()(Real r,
const __attribute__((unused))
IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
Array<Real> & dam_array = (*this->damage)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real Radius_t = 0;
Real Radius_init = this->R2;
// if(D <= 0.5)
// {
// Radius_t = 2*D*Radius_init;
// }
// else
// {
// Radius_t = 2*Radius_init*(1-D);
// }
//
Radius_t = Radius_init * (1 - D);
Radius_init *= Radius_init;
Radius_t *= Radius_t;
if (Radius_t < Math::getTolerance()) {
Radius_t = 0.001 * Radius_init;
}
Real expb =
(2 * std::log(0.51)) / (std::log(1.0 - 0.49 * Radius_t / Radius_init));
Int expb_floor = std::floor(expb);
Real b = expb_floor + expb_floor % 2;
Real alpha = std::max(0., 1. - r * r / Radius_init);
Real w = std::pow(alpha, b);
return w;
}
/* -------------------------------------------------------------------------- */
inline void DamagedWeightFunction::init() {
this->damage = &(this->manager.registerWeightFunctionInternal("damage"));
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
index f388bd420..136fa6a97 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
@@ -1,95 +1,98 @@
/**
* @file remove_damaged_weight_function.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Removed damaged weight function for non local materials
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_
#define AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damaged"), damage(nullptr) {
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable,
"Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline void init() override;
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// limit at which a point is considered as complitely broken
Real damage_limit;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "remove_damaged_weight_function_inline_impl.hh"
#endif /* AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
index f76ef07f1..681fb9e47 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function_inline_impl.hh
@@ -1,105 +1,108 @@
/**
* @file remove_damaged_weight_function_inline_impl.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Thu Jul 06 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of inline function of remove damaged weight function
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "remove_damaged_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_
#define AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWeightFunction::
operator()(Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
if (q1 == q2) {
return 1.;
}
Array<Real> & dam_array = (*this->damage)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
if (D < damage_limit * (1 - Math::getTolerance())) {
Real alpha = std::max(0., 1. - r * r / this->R2);
w = alpha * alpha;
}
return w;
}
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWeightFunction::init() {
this->damage = &(this->manager.registerWeightFunctionInternal("damage"));
}
/* -------------------------------------------------------------------------- */
inline UInt
RemoveDamagedWeightFunction::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_mnl_weight) {
return this->manager.getModel().getNbIntegrationPoints(elements) *
sizeof(Real);
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == SynchronizationTag::_mnl_weight) {
DataAccessor<Element>::packElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
inline void
RemoveDamagedWeightFunction::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == SynchronizationTag::_mnl_weight) {
DataAccessor<Element>::unpackElementalDataHelper<Real>(
*damage, buffer, elements, true,
this->manager.getModel().getFEEngine());
}
}
} // namespace akantu
#endif /* AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
index 401660b6d..dfe8d7808 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
@@ -1,82 +1,85 @@
/**
* @file remove_damaged_with_damage_rate_weight_function.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Removed damaged weight function for non local materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH_
#define AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged with damage rate weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWithDamageRateWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWithDamageRateWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "remove_damage_with_damage_rate"),
damage_with_damage_rate(nullptr) {
this->registerParam<Real>("damage_limit",
this->damage_limit_with_damage_rate, 1,
_pat_parsable, "Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
inline void init() override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// limit at which a point is considered as complitely broken
Real damage_limit_with_damage_rate;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage_with_damage_rate;
};
} // namespace akantu
#include "remove_damaged_with_damage_rate_weight_function_inline_impl.hh"
#endif /* AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
index 4ff028a57..8e282516b 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function_inline_impl.hh
@@ -1,67 +1,71 @@
/**
* @file remove_damaged_with_damage_rate_weight_function_inline_impl.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Fri Jan 15 2016
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "remove_damaged_with_damage_rate_weight_function.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void RemoveDamagedWithDamageRateWeightFunction::init() {
this->damage_with_damage_rate =
&(this->manager.registerWeightFunctionInternal("damage-rate"));
}
/* -------------------------------------------------------------------------- */
inline Real RemoveDamagedWithDamageRateWeightFunction::operator()(
Real r, const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2) {
/// compute the weight
UInt quad = q2.global_num;
if (q1.global_num == quad) {
return 1.;
}
Array<Real> & dam_array =
(*this->damage_with_damage_rate)(q2.type, q2.ghost_type);
Real D = dam_array(quad);
Real w = 0.;
Real alphaexp = 1.;
Real betaexp = 2.;
if (D < damage_limit_with_damage_rate) {
Real alpha = std::max(0., 1. - pow((r * r / this->R2), alphaexp));
w = pow(alpha, betaexp);
}
return w;
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
index 72b092275..536ee7095 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
@@ -1,122 +1,125 @@
/**
* @file stress_based_weight_function.cc
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 24 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief implementation of the stres based weight function classes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "stress_based_weight_function.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
StressBasedWeightFunction::StressBasedWeightFunction(NonLocalManager & manager)
: BaseWeightFunction(manager, "stress_based")
// stress_diag("stress_diag", material), selected_stress_diag(NULL),
// stress_base("stress_base", material), selected_stress_base(NULL),
// characteristic_size("lc", material), selected_characteristic_size(NULL)
{
// this->registerParam("ft", this->ft, 0., _pat_parsable, "Tensile strength");
// stress_diag.initialize(spatial_dimension);
// stress_base.initialize(spatial_dimension * spatial_dimension);
// characteristic_size.initialize(1);
}
/* -------------------------------------------------------------------------- */
/// During intialization the characteristic sizes for all quadrature
/// points are computed
void StressBasedWeightFunction::init() {
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// for (UInt g = _not_ghost; g <= _ghost; ++g) {
// GhostType gt = GhostType(g);
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, gt);
// for(; it != last_type; ++it) {
// UInt nb_quadrature_points =
// this->material.getModel().getFEEngine().getNbQuadraturePoints(*it, gt);
// const Array<UInt> & element_filter =
// this->material.getElementFilter(*it, gt);
// UInt nb_element = element_filter.size();
// Array<Real> ones(nb_element*nb_quadrature_points, 1, 1.);
// Array<Real> & lc = characteristic_size(*it, gt);
// this->material.getModel().getFEEngine().integrateOnQuadraturePoints(ones,
// lc,
// 1,
// *it,
// gt,
// element_filter);
// for (UInt q = 0; q < nb_quadrature_points * nb_element; q++) {
// lc(q) = pow(lc(q), 1./ Real(spatial_dimension));
// }
// }
// }
}
/* -------------------------------------------------------------------------- */
/// computation of principals stresses and principal directions
void StressBasedWeightFunction::updatePrincipalStress(__attribute__((unused))
GhostType ghost_type) {
// AKANTU_DEBUG_IN();
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension,
// ghost_type);
// for(; it != last_type; ++it) {
// Array<Real>::const_matrix_iterator sigma =
// this->material.getStress(*it, ghost_type).begin(spatial_dimension,
// spatial_dimension);
// auto eigenvalues =
// stress_diag(*it, ghost_type).begin(spatial_dimension);
// auto eigenvalues_end =
// stress_diag(*it, ghost_type).end(spatial_dimension);
// Array<Real>::matrix_iterator eigenvector =
// stress_base(*it, ghost_type).begin(spatial_dimension,
// spatial_dimension);
// #ifndef __trick__
// auto cl = characteristic_size(*it, ghost_type).begin();
// #endif
// UInt q = 0;
// for(;eigenvalues != eigenvalues_end; ++sigma, ++eigenvalues,
// ++eigenvector, ++cl, ++q) {
// sigma->eig(*eigenvalues, *eigenvector);
// *eigenvalues /= ft;
// #ifndef __trick__
// // specify a lower bound for principal stress based on the size of
// the element
// for (UInt i = 0; i < spatial_dimension; ++i) {
// (*eigenvalues)(i) = std::max(*cl / this->R, (*eigenvalues)(i));
// }
// #endif
// }
// }
// AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
index 9af580897..628bf311c 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
@@ -1,98 +1,101 @@
/**
* @file stress_based_weight_function.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Wed Nov 08 2017
*
* @brief Removed damaged weight function for non local materials
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_
#define AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Stress Based Weight */
/* -------------------------------------------------------------------------- */
/// based on based on Giry et al.: Stress-based nonlocal damage model,
/// IJSS, 48, 2011
class StressBasedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
StressBasedWeightFunction(NonLocalManager & manager);
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
void init() override;
inline void updateInternals() override;
void updatePrincipalStress(GhostType ghost_type);
inline void updateQuadraturePointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates);
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// computation of ellipsoid
inline Real computeRhoSquare(Real r, Vector<Real> & eigs,
Matrix<Real> & eigenvects, Vector<Real> & x_s);
protected:
inline void setInternal();
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// tensile strength
Real ft;
/// prinicipal stresses
ElementTypeMapReal * stress_diag;
/// for preselection of types (optimization)
ElementTypeMapReal * selected_stress_diag;
/// principal directions
ElementTypeMapReal * stress_base;
/// lenght intrinisic to the material
ElementTypeMapReal * characteristic_size;
};
} // namespace akantu
#include "stress_based_weight_function_inline_impl.hh"
#endif /* AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH_ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
index 248b9826e..8fe5492c2 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function_inline_impl.hh
@@ -1,194 +1,198 @@
/**
* @file stress_based_weight_function_inline_impl.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Apr 13 2012
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Tue Dec 04 2018
*
* @brief Implementation of inline function of remove damaged with
* damage rate weight function
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "stress_based_weight_function.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void StressBasedWeightFunction::updateInternals() {
// updatePrincipalStress(_not_ghost);
// updatePrincipalStress(_ghost);
}
/* -------------------------------------------------------------------------- */
// inline void StressBasedWeightFunction::selectType(ElementType type1,
// GhostType ghost_type1,
// ElementType type2,
// GhostType ghost_type2) {
// selected_stress_diag = &stress_diag(type2, ghost_type2);
// selected_stress_base = &stress_base(type2, ghost_type2);
// selected_characteristic_size = &characteristic_size(type1, ghost_type1);
// }
/* -------------------------------------------------------------------------- */
inline Real StressBasedWeightFunction::
computeRhoSquare( // NOLINT(readability-convert-member-functions-to-static)
Real /*r*/, Vector<Real> & /*eigs*/, Matrix<Real> & /*eigenvects*/,
Vector<Real> & /*x_s*/) {
// if (spatial_dimension == 1)
// return eigs[0];
// else if (spatial_dimension == 2) {
// Vector<Real> u1(eigenvects.storage(), 2);
// Real cos_t = x_s.dot(u1) / (x_s.norm() * u1.norm());
// Real cos_t_2;
// Real sin_t_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// #ifdef __trick__
// Real zero = std::numeric_limits<Real>::epsilon();
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// Real rhop1 = std::max(0., cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_t_2 / sigma2_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// Real rhop1 = cos_t_2 / sigma1_2;
// Real rhop2 = sin_t_2 / sigma2_2;
// #endif
// return 1./ (rhop1 + rhop2);
// } else if (spatial_dimension == 3) {
// Vector<Real> u1(eigenvects.storage() + 0*3, 3);
// //Vector<Real> u2(eigenvects.storage() + 1*3, 3);
// Vector<Real> u3(eigenvects.storage() + 2*3, 3);
// Real zero = std::numeric_limits<Real>::epsilon();
// Vector<Real> tmp(3);
// tmp.crossProduct(x_s, u3);
// Vector<Real> u3_C_x_s_C_u3(3);
// u3_C_x_s_C_u3.crossProduct(u3, tmp);
// Real norm_u3_C_x_s_C_u3 = u3_C_x_s_C_u3.norm();
// Real cos_t = 0.;
// if(std::abs(norm_u3_C_x_s_C_u3) > zero) {
// Real inv_norm_u3_C_x_s_C_u3 = 1. / norm_u3_C_x_s_C_u3;
// cos_t = u1.dot(u3_C_x_s_C_u3) * inv_norm_u3_C_x_s_C_u3;
// }
// Real cos_p = u3.dot(x_s) / r;
// Real cos_t_2;
// Real sin_t_2;
// Real cos_p_2;
// Real sin_p_2;
// Real sigma1_2 = eigs[0]*eigs[0];
// Real sigma2_2 = eigs[1]*eigs[1];
// Real sigma3_2 = eigs[2]*eigs[2];
// #ifdef __trick__
// if(std::abs(cos_t) < zero) {
// cos_t_2 = 0;
// sin_t_2 = 1;
// } else {
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// }
// if(std::abs(cos_p) < zero) {
// cos_p_2 = 0;
// sin_p_2 = 1;
// } else {
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// }
// Real rhop1 = std::max(0., sin_p_2 * cos_t_2 / sigma1_2);
// Real rhop2 = std::max(0., sin_p_2 * sin_t_2 / sigma2_2);
// Real rhop3 = std::max(0., cos_p_2 / sigma3_2);
// #else
// cos_t_2 = cos_t * cos_t;
// sin_t_2 = (1 - cos_t_2);
// cos_p_2 = cos_p * cos_p;
// sin_p_2 = (1 - cos_p_2);
// Real rhop1 = sin_p_2 * cos_t_2 / sigma1_2;
// Real rhop2 = sin_p_2 * sin_t_2 / sigma2_2;
// Real rhop3 = cos_p_2 / sigma3_2;
// #endif
// return 1./ (rhop1 + rhop2 + rhop3);
// }
return 0.;
}
/* -------------------------------------------------------------------------- */
inline Real
StressBasedWeightFunction::operator()(Real /*r*/,
const IntegrationPoint & /*q1*/,
const IntegrationPoint & /*q2*/) {
// Real zero = std::numeric_limits<Real>::epsilon();
// if(r < zero) return 1.; // means x and s are the same points
// const Vector<Real> & x = q1.getPosition();
// const Vector<Real> & s = q2.getPosition();
// Vector<Real> eigs =
// selected_stress_diag->begin(spatial_dimension)[q2.global_num];
// Matrix<Real> eigenvects =
// selected_stress_base->begin(spatial_dimension,
// spatial_dimension)[q2.global_num];
// Real min_rho_lc = selected_characteristic_size->begin()[q1.global_num];
// Vector<Real> x_s(spatial_dimension);
// x_s = x;
// x_s -= s;
// Real rho_2 = computeRhoSquare(r, eigs, eigenvects, x_s);
// Real rho_lc_2 = std::max(this->R2 * rho_2, min_rho_lc*min_rho_lc);
// // Real w = std::max(0., 1. - r*r / rho_lc_2);
// // w = w*w;
// Real w = exp(- 2*2*r*r / rho_lc_2);
// return w;
return 0.;
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index f311597f6..a2777134a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1253 +1,1256 @@
/**
* @file solid_mechanics_model.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Implementation of the SolidMechanicsModel class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model_tmpl.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "sparse_matrix.hh"
#include "synchronizer_registry.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A solid mechanics model need a mesh and a dimension to be created. the model
* by it self can not do a lot, the good init functions should be called in
* order to configure the model depending on what we want to do.
*
* @param mesh mesh representing the model we want to simulate
* @param dim spatial dimension of the problem, if dim = 0 (default value) the
* dimension of the problem is assumed to be the on of the mesh
* @param id an id to identify the model
* @param model_type this is an internal parameter for inheritance purposes
*/
SolidMechanicsModel::SolidMechanicsModel(
Mesh & mesh, UInt dim, const ID & id,
std::shared_ptr<DOFManager> dof_manager, const ModelType model_type)
: Model(mesh, model_type, std::move(dof_manager), dim, id),
material_index("material index", id),
material_local_numbering("material local numbering", id) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh,
Model::spatial_dimension);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("solid_mechanics_model", id, true);
this->mesh.addDumpMesh(mesh, Model::spatial_dimension, _not_ghost,
_ek_regular);
#endif
material_selector = std::make_shared<DefaultMaterialSelector>(material_index);
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, SynchronizationTag::_material_id);
this->registerSynchronizer(synchronizer, SynchronizationTag::_smm_mass);
this->registerSynchronizer(synchronizer, SynchronizationTag::_smm_stress);
this->registerSynchronizer(synchronizer, SynchronizationTag::_for_dump);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialization */
/* -------------------------------------------------------------------------- */
/**
* This function groups many of the initialization in on function. For most of
* basics case the function should be enough. The functions initialize the
* model, the internal vectors, set them to 0, and depending on the parameters
* it also initialize the explicit or implicit solver.
*
* @param options
* \parblock
* contains the different options to initialize the model
* \li \c analysis_method specify the type of solver to use
* \endparblock
*/
void SolidMechanicsModel::initFullImpl(const ModelOptions & options) {
material_index.initialize(mesh, _element_kind = _ek_not_defined,
_default_value = UInt(-1), _with_nb_element = true);
material_local_numbering.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true);
Model::initFullImpl(options);
// initialize the materials
if (not this->parser.getLastParsedFile().empty()) {
this->instantiateMaterials();
this->initMaterials();
}
this->initBC(*this, *displacement, *displacement_increment, *external_force);
}
/* -------------------------------------------------------------------------- */
TimeStepSolverType SolidMechanicsModel::getDefaultSolverType() const {
return TimeStepSolverType::_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions SolidMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_dynamic_lumped: {
options.non_linear_solver_type = NonLinearSolverType::_lumped;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case TimeStepSolverType::_static: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
} else {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_trapezoidal_rule_2;
options.solution_type["displacement"] = IntegrationScheme::_displacement;
}
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
std::tuple<ID, TimeStepSolverType>
SolidMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _explicit_lumped_mass: {
return std::make_tuple("explicit_lumped",
TimeStepSolverType::_dynamic_lumped);
}
case _explicit_consistent_mass: {
return std::make_tuple("explicit", TimeStepSolverType::_dynamic);
}
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType /*unused*/) {
auto & dof_manager = this->getDOFManager();
/* ------------------------------------------------------------------------ */
// for alloc type of solvers
this->allocNodalField(this->displacement, spatial_dimension, "displacement");
this->allocNodalField(this->previous_displacement, spatial_dimension,
"previous_displacement");
this->allocNodalField(this->displacement_increment, spatial_dimension,
"displacement_increment");
this->allocNodalField(this->internal_force, spatial_dimension,
"internal_force");
this->allocNodalField(this->external_force, spatial_dimension,
"external_force");
this->allocNodalField(this->blocked_dofs, spatial_dimension, "blocked_dofs");
this->allocNodalField(this->current_position, spatial_dimension,
"current_position");
// initialize the current positions
this->current_position->copy(this->mesh.getNodes());
/* ------------------------------------------------------------------------ */
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *this->displacement, _dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
dof_manager.registerDOFsIncrement("displacement",
*this->displacement_increment);
dof_manager.registerDOFsPrevious("displacement",
*this->previous_displacement);
}
/* ------------------------------------------------------------------------ */
// for dynamic
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(this->velocity, spatial_dimension, "velocity");
this->allocNodalField(this->acceleration, spatial_dimension,
"acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModel::initModel() {
/// \todo add the current position as a parameter to initShapeFunctions for
/// large deformation
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
// computes the internal forces
this->assembleInternalForces();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->assembleInternalForces();
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MatrixType SolidMechanicsModel::getMatrixType(const ID & matrix_id) {
// \TODO check the materials to know what is the correct answer
if (matrix_id == "C") {
return _mt_not_defined;
}
if (matrix_id == "K") {
auto matrix_type = _unsymmetric;
for (auto & material : materials) {
matrix_type = std::max(matrix_type, material->getMatrixType(matrix_id));
}
}
return _symmetric;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
this->assembleStiffnessMatrix();
} else if (matrix_id == "M") {
this->assembleMass();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
this->assembleMassLumped();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::beforeSolveStep() {
for (auto & material : materials) {
material->beforeSolveStep();
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::afterSolveStep(bool converged) {
for (auto & material : materials) {
material->afterSolveStep(converged);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::predictor() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::corrector() { ++displacement_release; }
/* -------------------------------------------------------------------------- */
/**
* This function computes the internal forces as \f$F_{int} = \int_{\Omega} N
* \sigma d\Omega@\f$
*/
void SolidMechanicsModel::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
this->internal_force->zero();
// compute the stresses of local elements
AKANTU_DEBUG_INFO("Compute local stresses");
for (auto & material : materials) {
material->computeAllStresses(_not_ghost);
}
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
if (this->non_local_manager) {
this->non_local_manager->computeAllNonLocalStresses();
}
// communicate the stresses
AKANTU_DEBUG_INFO("Send data for residual assembly");
this->asynchronousSynchronize(SynchronizationTag::_smm_stress);
// assemble the forces due to local stresses
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for (auto & material : materials) {
material->assembleInternalForces(_not_ghost);
}
// finalize communications
AKANTU_DEBUG_INFO("Wait distant stresses");
this->waitEndSynchronize(SynchronizationTag::_smm_stress);
// assemble the stresses due to ghost elements
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for (auto & material : materials) {
material->assembleInternalForces(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix(bool need_to_reassemble) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
// Check if materials need to recompute the matrix
for (auto & material : materials) {
need_to_reassemble |= material->hasMatrixChanged("K");
}
if (need_to_reassemble) {
this->getDOFManager().getMatrix("K").zero();
// call compute stiffness matrix on each local elements
for (auto & material : materials) {
material->assembleStiffnessMatrix(_not_ghost);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
if (this->current_position_release == this->displacement_release) {
return;
}
this->current_position->copy(this->mesh.getNodes());
auto cpos_it = this->current_position->begin(Model::spatial_dimension);
auto cpos_end = this->current_position->end(Model::spatial_dimension);
auto disp_it = this->displacement->begin(Model::spatial_dimension);
for (; cpos_it != cpos_end; ++cpos_it, ++disp_it) {
*cpos_it += *disp_it;
}
this->current_position_release = this->displacement_release;
}
/* -------------------------------------------------------------------------- */
const Array<Real> & SolidMechanicsModel::getCurrentPosition() {
this->updateCurrentPosition();
return *this->current_position;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateDataForNonLocalCriterion(
ElementTypeMapReal & criterion) {
const ID field_name = criterion.getName();
for (auto & material : materials) {
if (!material->isInternal<Real>(field_name, _ek_regular)) {
continue;
}
for (auto ghost_type : ghost_types) {
material->flattenInternal(field_name, criterion, ghost_type, _ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
mesh.getCommunicator().allReduce(min_dt, SynchronizerOperation::_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real min_dt = std::numeric_limits<Real>::max();
this->updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
elem.type = type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
auto mat_indexes = material_index(type, ghost_type).begin();
auto mat_loc_num = material_local_numbering(type, ghost_type).begin();
Array<Real> X(0, nb_nodes_per_element * Model::spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position, X, type,
_not_ghost);
auto X_el = X.begin(Model::spatial_dimension, nb_nodes_per_element);
for (UInt el = 0; el < nb_element;
++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
elem.element = *mat_loc_num;
Real el_h = getFEEngine().getElementInradius(*X_el, type);
Real el_c = this->materials[*mat_indexes]->getCelerity(elem);
Real el_dt = el_h / el_c;
min_dt = std::min(min_dt, el_dt);
}
}
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
if (this->getDOFManager().hasLumpedMatrix("M")) {
auto m_it = this->mass->begin(Model::spatial_dimension);
auto m_end = this->mass->end(Model::spatial_dimension);
auto v_it = this->velocity->begin(Model::spatial_dimension);
for (UInt n = 0; m_it != m_end; ++n, ++m_it, ++v_it) {
const auto & v = *v_it;
const auto & m = *m_it;
Real mv2 = 0.;
auto is_local_node = mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
auto count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
if (m(i) > std::numeric_limits<Real>::epsilon()) {
mv2 += v(i) * v(i) * m(i);
}
}
}
ekin += mv2;
}
} else if (this->getDOFManager().hasMatrix("M")) {
Array<Real> Mv(nb_nodes, Model::spatial_dimension);
this->getDOFManager().assembleMatMulVectToArray("displacement", "M",
*this->velocity, Mv);
for (auto && data : zip(arange(nb_nodes), make_view(Mv, spatial_dimension),
make_view(*this->velocity, spatial_dimension))) {
ekin += std::get<2>(data).dot(std::get<1>(data)) *
static_cast<Real>(mesh.isLocalOrMasterNode(std::get<0>(data)));
}
} else {
AKANTU_ERROR("No function called to assemble the mass matrix.");
}
mesh.getCommunicator().allReduce(ekin, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy(ElementType type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, Model::spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
Model::spatial_dimension, type,
_not_ghost, filter_element);
auto vit = vel_on_quad.begin(Model::spatial_dimension);
auto vend = vel_on_quad.end(Model::spatial_dimension);
Vector<Real> rho_v2(nb_quadrature_points);
Real rho = materials[material_index(type)(index)]->getRho();
for (UInt q = 0; vit != vend; ++vit, ++q) {
rho_v2(q) = rho * vit->dot(*vit);
}
AKANTU_DEBUG_OUT();
return .5 * getFEEngine().integrate(rho_v2, type, index);
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getExternalWork() {
AKANTU_DEBUG_IN();
auto ext_force_it = external_force->begin(Model::spatial_dimension);
auto int_force_it = internal_force->begin(Model::spatial_dimension);
auto boun_it = blocked_dofs->begin(Model::spatial_dimension);
decltype(ext_force_it) incr_or_velo_it;
if (this->method == _static) {
incr_or_velo_it =
this->displacement_increment->begin(Model::spatial_dimension);
} else {
incr_or_velo_it = this->velocity->begin(Model::spatial_dimension);
}
Real work = 0.;
UInt nb_nodes = this->mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes;
++n, ++ext_force_it, ++int_force_it, ++boun_it, ++incr_or_velo_it) {
const auto & int_force = *int_force_it;
const auto & ext_force = *ext_force_it;
const auto & boun = *boun_it;
const auto & incr_or_velo = *incr_or_velo_it;
bool is_local_node = this->mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
bool count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < Model::spatial_dimension; ++i) {
if (boun(i)) {
work -= int_force(i) * incr_or_velo(i);
} else {
work += ext_force(i) * incr_or_velo(i);
}
}
}
}
mesh.getCommunicator().allReduce(work, SynchronizerOperation::_sum);
if (this->method != _static) {
work *= this->getTimeStep();
}
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
}
if (energy_id == "external work") {
return getExternalWork();
}
Real energy = 0.;
for (auto & material : materials) {
energy += material->getEnergy(energy_id);
}
/// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
ElementType type, UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
UInt mat_index = this->material_index(type, _not_ghost)(index);
UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
Real energy =
this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const ID & energy_id,
const ID & group_id) {
auto && group = mesh.getElementGroup(group_id);
auto energy = 0.;
for(auto && type : group.elementTypes()) {
for(auto el : group.getElementsIterable(type)) {
energy += getEnergy(energy_id, el);
}
}
/// reduction sum over all processors
mesh.getCommunicator().allReduce(energy, SynchronizerOperation::_sum);
return energy;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
this->material_index.initialize(mesh, _element_kind = _ek_not_defined,
_with_nb_element = true,
_default_value = UInt(-1));
this->material_local_numbering.initialize(
mesh, _element_kind = _ek_not_defined, _with_nb_element = true,
_default_value = UInt(-1));
ElementTypeMapArray<UInt> filter("new_element_filter", this->getID());
for (const auto & elem : element_list) {
if (mesh.getSpatialDimension(elem.type) != spatial_dimension) {
continue;
}
if (!filter.exists(elem.type, elem.ghost_type)) {
filter.alloc(0, 1, elem.type, elem.ghost_type);
}
filter(elem.type, elem.ghost_type).push_back(elem.element);
}
// this fails in parallel if the event is sent on facet between constructor
// and initFull \todo: to debug...
this->assignMaterialToElements(&filter);
for (auto & material : materials) {
material->onElementsAdded(element_list, event);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
for (auto & material : materials) {
material->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if (displacement) {
displacement->resize(nb_nodes, 0.);
++displacement_release;
}
if (mass) {
mass->resize(nb_nodes, 0.);
}
if (velocity) {
velocity->resize(nb_nodes, 0.);
}
if (acceleration) {
acceleration->resize(nb_nodes, 0.);
}
if (external_force) {
external_force->resize(nb_nodes, 0.);
}
if (internal_force) {
internal_force->resize(nb_nodes, 0.);
}
if (blocked_dofs) {
blocked_dofs->resize(nb_nodes, false);
}
if (current_position) {
current_position->resize(nb_nodes, 0.);
}
if (previous_displacement) {
previous_displacement->resize(nb_nodes, 0.);
}
if (displacement_increment) {
displacement_increment->resize(nb_nodes, 0.);
}
for (auto & material : materials) {
material->onNodesAdded(nodes_list, event);
}
need_to_reassemble_lumped_mass = true;
need_to_reassemble_mass = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(const Array<UInt> & /*element_list*/,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & /*event*/) {
if (displacement) {
mesh.removeNodesFromArray(*displacement, new_numbering);
++displacement_release;
}
if (mass) {
mesh.removeNodesFromArray(*mass, new_numbering);
}
if (velocity) {
mesh.removeNodesFromArray(*velocity, new_numbering);
}
if (acceleration) {
mesh.removeNodesFromArray(*acceleration, new_numbering);
}
if (internal_force) {
mesh.removeNodesFromArray(*internal_force, new_numbering);
}
if (external_force) {
mesh.removeNodesFromArray(*external_force, new_numbering);
}
if (blocked_dofs) {
mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
}
// if (increment_acceleration)
// mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
if (displacement_increment) {
mesh.removeNodesFromArray(*displacement_increment, new_numbering);
}
if (previous_displacement) {
mesh.removeNodesFromArray(*previous_displacement, new_numbering);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "Solid Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << Model::spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + nodals information [" << std::endl;
displacement->printself(stream, indent + 2);
if (velocity) {
velocity->printself(stream, indent + 2);
}
if (acceleration) {
acceleration->printself(stream, indent + 2);
}
if (mass) {
mass->printself(stream, indent + 2);
}
external_force->printself(stream, indent + 2);
internal_force->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + material information [" << std::endl;
material_index.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
stream << space << " + materials [" << std::endl;
for (const auto & material : materials) {
material->printself(stream, indent + 2);
}
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initializeNonLocal() {
this->non_local_manager->synchronize(*this, SynchronizationTag::_material_id);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::insertIntegrationPointsInNeighborhoods(
GhostType ghost_type) {
for (auto & mat : materials) {
MaterialNonLocalInterface * mat_non_local;
if ((mat_non_local =
dynamic_cast<MaterialNonLocalInterface *>(mat.get())) == nullptr) {
continue;
}
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
for (const auto & type : quadrature_points_coordinates.elementTypes(
Model::spatial_dimension, ghost_type)) {
this->getFEEngine().computeIntegrationPointsCoordinates(
quadrature_points_coordinates(type, ghost_type), type, ghost_type);
}
mat_non_local->initMaterialNonLocal();
mat_non_local->insertIntegrationPointsInNeighborhoods(
ghost_type, quadrature_points_coordinates);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeNonLocalStresses(GhostType ghost_type) {
for (auto & mat : materials) {
if (not aka::is_of_type<MaterialNonLocalInterface>(*mat)) {
continue;
}
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.computeNonLocalStresses(ghost_type);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateLocalInternal(
ElementTypeMapReal & internal_flat, GhostType ghost_type,
ElementKind kind) {
const ID field_name = internal_flat.getName();
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, kind)) {
material->flattenInternal(field_name, internal_flat, ghost_type, kind);
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateNonLocalInternal(
ElementTypeMapReal & internal_flat, GhostType ghost_type,
ElementKind kind) {
const ID field_name = internal_flat.getName();
for (auto & mat : materials) {
if (not aka::is_of_type<MaterialNonLocalInterface>(*mat)) {
continue;
}
auto & mat_non_local = dynamic_cast<MaterialNonLocalInterface &>(*mat);
mat_non_local.updateNonLocalInternals(internal_flat, field_name, ghost_type,
kind);
}
}
/* -------------------------------------------------------------------------- */
FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
return getFEEngineClassBoundary<MyFEEngineType>(name);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::splitElementByMaterial(
const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const {
for (const auto & el : elements) {
Element mat_el = el;
mat_el.element = this->material_local_numbering(el);
elements_per_mat[this->material_index(el)].push_back(mat_el);
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
UInt nb_nodes_per_element = 0;
for (const Element & el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
switch (tag) {
case SynchronizationTag::_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case SynchronizationTag::_smm_mass: {
size += nb_nodes_per_element * sizeof(Real) *
Model::spatial_dimension; // mass vector
break;
}
case SynchronizationTag::_smm_for_gradu: {
size += nb_nodes_per_element * Model::spatial_dimension *
sizeof(Real); // displacement
break;
}
case SynchronizationTag::_smm_boundary: {
// force, displacement, boundary
size += nb_nodes_per_element * Model::spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
case SynchronizationTag::_for_dump: {
// displacement, velocity, acceleration, residual, force
size += nb_nodes_per_element * Model::spatial_dimension * sizeof(Real) * 5;
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_material_id: {
packElementalDataHelper(
material_index, buffer, elements, false, getFEEngine());
break;
}
case SynchronizationTag::_smm_mass: {
packNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_for_gradu: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case SynchronizationTag::_for_dump: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*acceleration, buffer, elements, mesh);
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_boundary: {
packNodalDataHelper(*external_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
if (mat_index != UInt(-1)) {
continue;
}
// add ghosts element to the correct material
mat_index = recv_mat_index;
UInt index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
}
break;
}
case SynchronizationTag::_smm_mass: {
unpackNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_for_gradu: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case SynchronizationTag::_for_dump: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*acceleration, buffer, elements, mesh);
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
break;
}
case SynchronizationTag::_smm_boundary: {
unpackNodalDataHelper(*external_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModel::getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch (tag) {
case SynchronizationTag::_smm_uv: {
size += sizeof(Real) * Model::spatial_dimension * 2;
break;
}
case SynchronizationTag::_smm_res: /* FALLTHRU */
case SynchronizationTag::_smm_mass: {
size += sizeof(Real) * Model::spatial_dimension;
break;
}
case SynchronizationTag::_for_dump: {
size += sizeof(Real) * Model::spatial_dimension * 5;
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size * dofs.size();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_smm_uv: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
break;
}
case SynchronizationTag::_smm_res: {
packDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case SynchronizationTag::_smm_mass: {
packDOFDataHelper(*mass, buffer, dofs);
break;
}
case SynchronizationTag::_for_dump: {
packDOFDataHelper(*displacement, buffer, dofs);
packDOFDataHelper(*velocity, buffer, dofs);
packDOFDataHelper(*acceleration, buffer, dofs);
packDOFDataHelper(*internal_force, buffer, dofs);
packDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
switch (tag) {
case SynchronizationTag::_smm_uv: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
break;
}
case SynchronizationTag::_smm_res: {
unpackDOFDataHelper(*internal_force, buffer, dofs);
break;
}
case SynchronizationTag::_smm_mass: {
unpackDOFDataHelper(*mass, buffer, dofs);
break;
}
case SynchronizationTag::_for_dump: {
unpackDOFDataHelper(*displacement, buffer, dofs);
unpackDOFDataHelper(*velocity, buffer, dofs);
unpackDOFDataHelper(*acceleration, buffer, dofs);
unpackDOFDataHelper(*internal_force, buffer, dofs);
unpackDOFDataHelper(*external_force, buffer, dofs);
break;
}
default: {
AKANTU_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index 30cb1d620..7aa62cbed 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,592 +1,594 @@
/**
* @file solid_mechanics_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 27 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Model of Solid Mechanics
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
#include "non_local_manager_callback.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_HH_
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class SolidMechanicsModel
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<SolidMechanicsModel>,
public NonLocalManagerCallback,
public EventHandlerManager<SolidMechanicsModelEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewMaterialElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array<UInt> &);
AKANTU_GET_MACRO(MaterialList, material, const Array<UInt> &);
protected:
Array<UInt> material;
};
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
protected:
using EventManager = EventHandlerManager<SolidMechanicsModelEventHandler>;
public:
SolidMechanicsModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "solid_mechanics_model",
std::shared_ptr<DOFManager> dof_manager = nullptr,
ModelType model_type = ModelType::_solid_mechanics_model);
~SolidMechanicsModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize completely the model
void initFullImpl(
const ModelOptions & options = SolidMechanicsModelOptions()) override;
public:
/// initialize all internal arrays for materials
virtual void initMaterials();
protected:
/// initialize the model
void initModel() override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the stiffness matrix,
virtual void assembleStiffnessMatrix(bool need_to_reassemble = false);
/// assembles the internal forces in the array internal_forces
virtual void assembleInternalForces();
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// callback for the solver, this adds f_{ext} or f_{int} to the residual
void assembleResidual(const ID & residual_part) override;
bool canSplitResidual() override { return true; }
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep(bool converged = true) override;
/// Callback for the model to instantiate the matricees when needed
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
protected:
/* ------------------------------------------------------------------------ */
TimeStepSolverType getDefaultSolverType() const override;
/* ------------------------------------------------------------------------ */
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() {
return method == _explicit_lumped_mass ||
method == _explicit_consistent_mass;
}
protected:
/// update the current position vector
void updateCurrentPosition();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// register an empty material of a given type
Material & registerNewMaterial(const ID & mat_name, const ID & mat_type,
const ID & opt_param);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
/// apply a constant eigen_grad_u on all quadrature points of a given material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & material_name,
GhostType ghost_type = _not_ghost);
protected:
/// register a material in the dynamic database
Material & registerNewMaterial(const ParserSection & mat_section);
/// read the material files to instantiate all the materials
void instantiateMaterials();
/// set the element_id_by_material and add the elements to the good materials
virtual void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = nullptr);
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
public:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
protected:
/// fill a vector of rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// compute the kinetic energy
Real getKineticEnergy();
Real getKineticEnergy(ElementType type, UInt index);
/// compute the external work (for impose displacement, the velocity should be
/// given too)
Real getExternalWork();
/* ------------------------------------------------------------------------ */
/* NonLocalManager inherited members */
/* ------------------------------------------------------------------------ */
protected:
void initializeNonLocal() override;
void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;
void computeNonLocalStresses(GhostType ghost_type) override;
void insertIntegrationPointsInNeighborhoods(GhostType ghost_type) override;
/// update the values of the non local internal
void updateLocalInternal(ElementTypeMapReal & internal_flat,
GhostType ghost_type, ElementKind kind) override;
/// copy the results of the averaging in the materials
void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
GhostType ghost_type, ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
void
splitElementByMaterial(const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const;
template <typename Operation>
void splitByMaterial(const Array<Element> & elements, Operation && op) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
void onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsChanged(const Array<Element> & /*unused*/,
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) override{};
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
//! decide wether a field is a material internal or not
bool isInternal(const std::string & field_name, ElementKind element_kind);
//! give the amount of data per element
virtual ElementTypeMap<UInt>
getInternalDataPerElem(const std::string & field_name, ElementKind kind);
//! flatten a given material internal field
ElementTypeMapArray<Real> &
flattenInternal(const std::string & field_name, ElementKind kind,
GhostType ghost_type = _not_ghost);
//! flatten all the registered material internals
void flattenAllRegisteredInternals(ElementKind kind);
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension, ElementKind kind) override;
void dump(const std::string & dumper_name) override;
void dump(const std::string & dumper_name, UInt step) override;
void dump(const std::string & dumper_name, Real time, UInt step) override;
void dump() override;
void dump(UInt step) override;
void dump(Real time, UInt step) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// get the value of the conversion from forces/ mass to acceleration
AKANTU_GET_MACRO(F_M2A, f_m2a, Real);
/// set the value of the conversion from forces/ mass to acceleration
AKANTU_SET_MACRO(F_M2A, f_m2a, Real);
/// get the SolidMechanicsModel::displacement array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Displacement, displacement);
/// get the SolidMechanicsModel::displacement array
AKANTU_GET_MACRO_DEREF_PTR(Displacement, displacement);
/// get the SolidMechanicsModel::previous_displacement array
AKANTU_GET_MACRO_DEREF_PTR(PreviousDisplacement, previous_displacement);
/// get the SolidMechanicsModel::current_position array
const Array<Real> & getCurrentPosition();
/// get the SolidMechanicsModel::displacement_increment array
AKANTU_GET_MACRO_DEREF_PTR(Increment, displacement_increment);
/// get the SolidMechanicsModel::displacement_increment array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Increment, displacement_increment);
/// get the lumped SolidMechanicsModel::mass array
AKANTU_GET_MACRO_DEREF_PTR(Mass, mass);
/// get the SolidMechanicsModel::velocity array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Velocity, velocity);
/// get the SolidMechanicsModel::velocity array
AKANTU_GET_MACRO_DEREF_PTR(Velocity, velocity);
/// get the SolidMechanicsModel::acceleration array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(Acceleration, acceleration);
/// get the SolidMechanicsModel::acceleration array
AKANTU_GET_MACRO_DEREF_PTR(Acceleration, acceleration);
/// get the SolidMechanicsModel::external_force array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(ExternalForce, external_force);
/// get the SolidMechanicsModel::external_force array
AKANTU_GET_MACRO_DEREF_PTR(ExternalForce, external_force);
/// get the SolidMechanicsModel::force array (external forces)
[[deprecated("Use getExternalForce instead of this function")]] Array<Real> &
getForce() {
return getExternalForce();
}
/// get the SolidMechanicsModel::internal_force array (internal forces)
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(InternalForce, internal_force);
/// get the SolidMechanicsModel::internal_force array (internal forces)
AKANTU_GET_MACRO_DEREF_PTR(InternalForce, internal_force);
/// get the SolidMechanicsModel::blocked_dofs array
AKANTU_GET_MACRO_DEREF_PTR_NOT_CONST(BlockedDOFs, blocked_dofs);
/// get the SolidMechanicsModel::blocked_dofs array
AKANTU_GET_MACRO_DEREF_PTR(BlockedDOFs, blocked_dofs);
/// get an iterable on the materials
inline decltype(auto) getMaterials();
/// get an iterable on the materials
inline decltype(auto) getMaterials() const;
/// get a particular material (by numerical material index)
inline Material & getMaterial(UInt mat_index);
/// get a particular material (by numerical material index)
inline const Material & getMaterial(UInt mat_index) const;
/// get a particular material (by material name)
inline Material & getMaterial(const std::string & name);
/// get a particular material (by material name)
inline const Material & getMaterial(const std::string & name) const;
/// get a particular material id from is name
inline UInt getMaterialIndex(const std::string & name) const;
/// give the number of materials
inline UInt getNbMaterials() const { return materials.size(); }
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/**
* @brief Returns the total energy for a given energy type
*
* Energy types of SolidMechanicsModel expected as argument are:
* - `kinetic`
* - `external work`
*
* Other energy types are passed on to the materials. All materials should
* define a `potential` energy type. For additional energy types, see material
* documentation.
*/
Real getEnergy(const std::string & energy_id);
/// Compute energy for an element type and material index
Real getEnergy(const std::string & energy_id, ElementType type, UInt index);
/// Compute energy for an individual element
Real getEnergy(const std::string & energy_id, const Element & element) {
return getEnergy(energy_id, element.type, element.element);
}
/// Compute energy for an element group
Real getEnergy(const ID & energy_id, const ID & group_id);
AKANTU_GET_MACRO(MaterialByElement, material_index,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(MaterialLocalNumbering, material_local_numbering,
const ElementTypeMapArray<UInt> &);
/// vectors containing local material element index for each global element
/// index
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialByElement, material_index,
UInt);
// AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialByElement, material_index, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialLocalNumbering,
material_local_numbering, UInt);
// AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialLocalNumbering,
// material_local_numbering, UInt);
AKANTU_GET_MACRO_NOT_CONST(MaterialSelector, material_selector,
std::shared_ptr<MaterialSelector>);
void
setMaterialSelector(std::shared_ptr<MaterialSelector> material_selector) {
this->material_selector = std::move(material_selector);
}
/// Access the non_local_manager interface
AKANTU_GET_MACRO(NonLocalManager, *non_local_manager, NonLocalManager &);
/// get the FEEngine object to integrate or interpolate on the boundary
FEEngine & getFEEngineBoundary(const ID & name = "") override;
protected:
/// compute the stable time step
Real getStableTimeStep(GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// release version of the displacement array
UInt displacement_release{0};
/// release version of the current_position array
UInt current_position_release{0};
/// Check if materials need to recompute the mass array
bool need_to_reassemble_lumped_mass{true};
/// Check if materials need to recompute the mass matrix
bool need_to_reassemble_mass{true};
/// mapping between material name and material internal id
std::map<std::string, UInt> materials_names_to_id;
protected:
/// conversion coefficient form force/mass to acceleration
Real f_m2a{1.0};
/// displacements array
std::unique_ptr<Array<Real>> displacement;
/// displacements array at the previous time step (used in finite deformation)
std::unique_ptr<Array<Real>> previous_displacement;
/// increment of displacement
std::unique_ptr<Array<Real>> displacement_increment;
/// lumped mass array
std::unique_ptr<Array<Real>> mass;
/// velocities array
std::unique_ptr<Array<Real>> velocity;
/// accelerations array
std::unique_ptr<Array<Real>> acceleration;
/// external forces array
std::unique_ptr<Array<Real>> external_force;
/// internal forces array
std::unique_ptr<Array<Real>> internal_force;
/// array specifing if a degree of freedom is blocked or not
std::unique_ptr<Array<bool>> blocked_dofs;
/// array of current position used during update residual
std::unique_ptr<Array<Real>> current_position;
/// Arrays containing the material index for each element
ElementTypeMapArray<UInt> material_index;
/// Arrays containing the position in the element filter of the material
/// (material's local numbering)
ElementTypeMapArray<UInt> material_local_numbering;
/// list of used materials
std::vector<std::unique_ptr<Material>> materials;
/// class defining of to choose a material
std::shared_ptr<MaterialSelector> material_selector;
using flatten_internal_map =
std::map<std::pair<std::string, ElementKind>,
std::unique_ptr<ElementTypeMapArray<Real>>>;
/// tells if the material are instantiated
flatten_internal_map registered_internals;
/// non local manager
std::unique_ptr<NonLocalManager> non_local_manager;
/// tells if the material are instantiated
bool are_materials_instantiated{false};
friend class Material;
template <class Model_> friend class CouplerSolidContactTemplate;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
using FromStress = FromHigherDim;
using FromTraction = FromSameDim;
} // namespace Neumann
} // namespace BC
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "parser.hh"
#include "solid_mechanics_model_inline_impl.hh"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_SOLID_MECHANICS_MODEL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
index ebc197151..7fcc980c6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
@@ -1,545 +1,547 @@
/**
* @file fragment_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Mon Mar 29 2021
*
* @brief Group manager to handle fragments
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "aka_iterators.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "material_cohesive.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <functional>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FragmentManager::FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data, const ID & id)
: GroupManager(model.getMesh(), id), model(model),
mass_center(0, model.getSpatialDimension(), "mass_center"),
mass(0, model.getSpatialDimension(), "mass"),
velocity(0, model.getSpatialDimension(), "velocity"),
inertia_moments(0, model.getSpatialDimension(), "inertia_moments"),
principal_directions(
0, model.getSpatialDimension() * model.getSpatialDimension(),
"principal_directions"),
quad_coordinates("quad_coordinates", id),
mass_density("mass_density", id),
nb_elements_per_fragment(0, 1, "nb_elements_per_fragment"),
dump_data(dump_data) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
/// compute quadrature points' coordinates
quad_coordinates.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(quad_coordinates, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
mass_density.initialize(mesh, _spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(mass_density, 1, spatial_dimension,
// _not_ghost);
storeMassDensityPerIntegrationPoint();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class CohesiveElementFilter : public GroupManager::ClusteringFilter {
public:
CohesiveElementFilter(const SolidMechanicsModelCohesive & model,
const Real max_damage = 1.)
: model(model), is_unbroken(max_damage) {}
bool operator()(const Element & el) const override {
if (Mesh::getKind(el.type) == _ek_regular) {
return true;
}
const Array<UInt> & mat_indexes =
model.getMaterialByElement(el.type, el.ghost_type);
const Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(el.type, el.ghost_type);
const auto & mat = static_cast<const MaterialCohesive &>(
model.getMaterial(mat_indexes(el.element)));
UInt el_index = mat_loc_num(el.element);
UInt nb_quad_per_element =
model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(el.type, el.ghost_type);
const Array<Real> & damage_array = mat.getDamage(el.type, el.ghost_type);
AKANTU_DEBUG_ASSERT(nb_quad_per_element * el_index < damage_array.size(),
"This quadrature point is out of range");
const Real * element_damage =
damage_array.storage() + nb_quad_per_element * el_index;
UInt unbroken_quads = std::count_if(
element_damage, element_damage + nb_quad_per_element, is_unbroken);
return (unbroken_quads > 0);
}
private:
struct IsUnbrokenFunctor {
IsUnbrokenFunctor(const Real & max_damage) : max_damage(max_damage) {}
bool operator()(const Real & x) const { return x < max_damage; }
const Real max_damage;
};
const SolidMechanicsModelCohesive & model;
const IsUnbrokenFunctor is_unbroken;
};
/* -------------------------------------------------------------------------- */
void FragmentManager::buildFragments(Real damage_limit) {
AKANTU_DEBUG_IN();
if (mesh.isDistributed()) {
auto & cohesive_synchronizer = model.getCohesiveSynchronizer();
cohesive_synchronizer.synchronize(model, SynchronizationTag::_smmc_damage);
}
auto & mesh_facets = mesh.getMeshFacets();
UInt spatial_dimension = model.getSpatialDimension();
std::string fragment_prefix("fragment");
/// generate fragments
global_nb_fragment =
createClusters(spatial_dimension, mesh_facets, fragment_prefix,
CohesiveElementFilter(model, damage_limit));
nb_fragment = getNbElementGroups(spatial_dimension);
fragment_index.resize(nb_fragment);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
auto name = std::get<0>(data).getName();
/// get fragment index
std::string fragment_index_string = name.substr(fragment_prefix.size() + 1);
std::get<1>(data) = std::stoul(fragment_index_string);
}
/// compute fragments' mass
computeMass();
if (dump_data) {
createDumpDataArray(fragment_index, "fragments", true);
createDumpDataArray(mass, "fragments mass");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeMass() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// create a unit field per quadrature point, since to compute mass
/// it's neccessary to integrate only density
ElementTypeMapArray<Real> unit_field("unit_field", id);
unit_field.initialize(model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
integrateFieldOnFragments(unit_field, mass);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeCenterOfMass() {
AKANTU_DEBUG_IN();
/// integrate position multiplied by density
integrateFieldOnFragments(quad_coordinates, mass_center);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * mass_center_storage = mass_center.storage();
UInt total_components = mass_center.size() * mass_center.getNbComponent();
for (UInt i = 0; i < total_components; ++i) {
mass_center_storage[i] /= mass_storage[i];
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeVelocity() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// compute velocity per quadrature point
ElementTypeMapArray<Real> velocity_field("velocity_field", id);
velocity_field.initialize(
model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension, _ghost_type = _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getVelocity(),
velocity_field);
/// integrate on fragments
integrateFieldOnFragments(velocity_field, velocity);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * velocity_storage = velocity.storage();
UInt total_components = velocity.size() * velocity.getNbComponent();
for (UInt i = 0; i < total_components; ++i) {
velocity_storage[i] /= mass_storage[i];
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Given the distance @f$ \mathbf{r} @f$ between a quadrature point
* and its center of mass, the moment of inertia is computed as \f[
* I_\mathrm{CM} = \mathrm{tr}(\mathbf{r}\mathbf{r}^\mathrm{T})
* \mathbf{I} - \mathbf{r}\mathbf{r}^\mathrm{T} \f] for more
* information check Wikipedia
* (http://en.wikipedia.org/wiki/Moment_of_inertia#Identities_for_a_skew-symmetric_matrix)
*
*/
void FragmentManager::computeInertiaMoments() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
computeCenterOfMass();
/// compute local coordinates products with respect to the center of match
ElementTypeMapArray<Real> moments_coords("moments_coords", id);
moments_coords.initialize(model.getFEEngine(),
_nb_component =
spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
/// loop over fragments
for (auto && data :
zip(iterateElementGroups(), make_view(mass_center, spatial_dimension))) {
const auto & el_list = std::get<0>(data).getElements();
auto & mass_center = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
auto nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
auto & moments_coords_array = moments_coords(type);
const auto & quad_coordinates_array = quad_coordinates(type);
const auto & el_list_array = el_list(type);
auto moments_begin =
moments_coords_array.begin(spatial_dimension, spatial_dimension);
auto quad_coordinates_begin =
quad_coordinates_array.begin(spatial_dimension);
Vector<Real> relative_coords(spatial_dimension);
for (UInt el = 0; el < el_list_array.size(); ++el) {
UInt global_el = el_list_array(el);
/// loop over quadrature points
for (UInt q = 0; q < nb_quad_per_element; ++q) {
UInt global_q = global_el * nb_quad_per_element + q;
Matrix<Real> moments_matrix = moments_begin[global_q];
const Vector<Real> & quad_coord_vector =
quad_coordinates_begin[global_q];
/// to understand this read the documentation written just
/// before this function
relative_coords = quad_coord_vector;
relative_coords -= mass_center;
moments_matrix.outerProduct(relative_coords, relative_coords);
Real trace = moments_matrix.trace();
moments_matrix *= -1.;
moments_matrix += Matrix<Real>::eye(spatial_dimension, trace);
}
}
}
}
/// integrate moments
Array<Real> integrated_moments(global_nb_fragment,
spatial_dimension * spatial_dimension);
integrateFieldOnFragments(moments_coords, integrated_moments);
/// compute and store principal moments
inertia_moments.resize(global_nb_fragment);
principal_directions.resize(global_nb_fragment);
auto integrated_moments_it =
integrated_moments.begin(spatial_dimension, spatial_dimension);
auto inertia_moments_it = inertia_moments.begin(spatial_dimension);
auto principal_directions_it =
principal_directions.begin(spatial_dimension, spatial_dimension);
for (UInt frag = 0; frag < global_nb_fragment; ++frag,
++integrated_moments_it, ++inertia_moments_it,
++principal_directions_it) {
integrated_moments_it->eig(*inertia_moments_it, *principal_directions_it);
}
if (dump_data) {
createDumpDataArray(inertia_moments, "moments of inertia");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeAllData(Real damage_limit) {
AKANTU_DEBUG_IN();
buildFragments(damage_limit);
computeVelocity();
computeInertiaMoments();
computeNbElementsPerFragment();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::storeMassDensityPerIntegrationPoint() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : mesh.elementTypes(_spatial_dimension = spatial_dimension,
_element_kind = _ek_regular)) {
Array<Real> & mass_density_array = mass_density(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
mass_density_array.resize(nb_element * nb_quad_per_element);
const Array<UInt> & mat_indexes = model.getMaterialByElement(type);
Real * mass_density_it = mass_density_array.storage();
/// store mass_density for each element and quadrature point
for (UInt el = 0; el < nb_element; ++el) {
Material & mat = model.getMaterial(mat_indexes(el));
for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it) {
*mass_density_it = mat.getRho();
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::integrateFieldOnFragments(
ElementTypeMapArray<Real> & field, Array<Real> & output) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
UInt nb_component = output.getNbComponent();
/// integration part
output.resize(global_nb_fragment);
output.zero();
auto output_begin = output.begin(nb_component);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & el_list = std::get<0>(data).getElements();
auto fragment_index = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
const Array<Real> & density_array = mass_density(type);
Array<Real> & field_array = field(type);
const Array<UInt> & elements = el_list(type);
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.size() * nb_quad_per_element,
nb_component);
auto field_array_begin = field_array.begin_reinterpret(
nb_quad_per_element, nb_component,
field_array.size() / nb_quad_per_element);
auto density_array_begin = density_array.begin_reinterpret(
nb_quad_per_element, density_array.size() / nb_quad_per_element);
for (auto && data : enumerate(make_view(
integration_array, nb_quad_per_element, nb_component))) {
UInt global_el = elements(std::get<0>(data));
auto & int_array = std::get<1>(data);
int_array = field_array_begin[global_el];
/// multiply field by density
const Vector<Real> & density_vector = density_array_begin[global_el];
for (UInt i = 0; i < nb_quad_per_element; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
int_array(i, j) *= density_vector(i);
}
}
}
/// integrate the field over the fragment
Array<Real> integrated_array(elements.size(), nb_component);
model.getFEEngine().integrate(integration_array, integrated_array,
nb_component, type, _not_ghost, elements);
/// sum over all elements and store the result
Vector<Real> output_tmp(output_begin[fragment_index]);
output_tmp += std::accumulate(integrated_array.begin(nb_component),
integrated_array.end(nb_component),
Vector<Real>(nb_component));
}
}
/// sum output over all processors
const Communicator & comm = mesh.getCommunicator();
comm.allReduce(output, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeNbElementsPerFragment() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
nb_elements_per_fragment.resize(global_nb_fragment);
nb_elements_per_fragment.zero();
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & el_list = std::get<0>(data).getElements();
auto fragment_index = std::get<1>(data);
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_element = el_list(type).size();
nb_elements_per_fragment(fragment_index) += nb_element;
}
}
/// sum values over all processors
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_elements_per_fragment, SynchronizerOperation::_sum);
if (dump_data) {
createDumpDataArray(nb_elements_per_fragment, "elements per fragment");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FragmentManager::createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output) {
AKANTU_DEBUG_IN();
if (data.empty()) {
return;
}
auto & mesh_not_const = const_cast<Mesh &>(mesh);
auto && spatial_dimension = mesh.getSpatialDimension();
auto && nb_component = data.getNbComponent();
auto && data_begin = data.begin(nb_component);
/// loop over fragments
for (auto && data : zip(iterateElementGroups(), fragment_index)) {
const auto & fragment = std::get<0>(data);
auto fragment_idx = std::get<1>(data);
/// loop over cluster types
for (auto && type : fragment.elementTypes(spatial_dimension)) {
/// init mesh data
auto & mesh_data = mesh_not_const.getDataPointer<T>(
name, type, _not_ghost, nb_component);
auto mesh_data_begin = mesh_data.begin(nb_component);
/// fill mesh data
for (const auto & elem : fragment.getElements(type)) {
Vector<T> md_tmp = mesh_data_begin[elem];
if (fragment_index_output) {
md_tmp(0) = fragment_idx;
} else {
md_tmp = data_begin[fragment_idx];
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
index 3ef723a11..c702c9522 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
@@ -1,167 +1,169 @@
/**
* @file fragment_manager.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
- * @date last modification: Thu Jul 06 2017
+ * @date last modification: Mon Mar 29 2021
*
* @brief Group manager to handle fragments
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "group_manager.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FRAGMENT_MANAGER_HH_
#define AKANTU_FRAGMENT_MANAGER_HH_
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
class FragmentManager : public GroupManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FragmentManager(SolidMechanicsModelCohesive & model, bool dump_data = true,
const ID & id = "fragment_manager");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// store mass density per integration point
void storeMassDensityPerIntegrationPoint();
/// integrate an elemental field multiplied by density on global
/// fragments
void integrateFieldOnFragments(ElementTypeMapArray<Real> & field,
Array<Real> & output);
/// compute fragments' mass
void computeMass();
/// create dump data for a single array
template <typename T>
void createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output = false);
public:
/// build fragment list (cohesive elements are considered broken if
/// damage >= damage_limit)
void buildFragments(Real damage_limit = 1.);
/// compute fragments' center of mass
void computeCenterOfMass();
/// compute fragments' velocity
void computeVelocity();
/// computes principal moments of inertia with respect to the center
/// of mass of each fragment
void computeInertiaMoments();
/// compute all fragments' data
void computeAllData(Real damage_limit = 1.);
/// compute number of elements per fragment
void computeNbElementsPerFragment();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get number of fragments
AKANTU_GET_MACRO(NbFragment, global_nb_fragment, UInt);
/// get fragments' mass
AKANTU_GET_MACRO(Mass, mass, const Array<Real> &);
/// get fragments' center of mass
AKANTU_GET_MACRO(CenterOfMass, mass_center, const Array<Real> &);
/// get fragments' velocity
AKANTU_GET_MACRO(Velocity, velocity, const Array<Real> &);
/// get fragments' principal moments of inertia
AKANTU_GET_MACRO(MomentsOfInertia, inertia_moments, const Array<Real> &);
/// get fragments' principal directions
AKANTU_GET_MACRO(PrincipalDirections, principal_directions,
const Array<Real> &);
/// get number of elements per fragment
AKANTU_GET_MACRO(NbElementsPerFragment, nb_elements_per_fragment,
const Array<UInt> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// local_fragment index
Array<UInt> fragment_index;
/// global number of fragments (parallel simulations)
UInt global_nb_fragment;
/// number of fragments
UInt nb_fragment;
/// cohesive solid mechanics model associated
SolidMechanicsModelCohesive & model;
/// fragments' center of mass
Array<Real> mass_center;
/// fragments' mass
Array<Real> mass;
/// fragments' velocity
Array<Real> velocity;
/// fragments' principal moments of inertia with respect to the
/// center of mass
Array<Real> inertia_moments;
/// fragments' principal directions
Array<Real> principal_directions;
/// quadrature points' coordinates
ElementTypeMapArray<Real> quad_coordinates;
/// mass density per quadrature point
ElementTypeMapArray<Real> mass_density;
/// fragment filter
Array<UInt> nb_elements_per_fragment;
/// dump data
bool dump_data;
};
} // namespace akantu
#endif /* AKANTU_FRAGMENT_MANAGER_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
index 6d700f04f..9da4bd348 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
@@ -1,167 +1,169 @@
/**
* @file material_selector_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material selector for cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DefaultMaterialCohesiveSelector::DefaultMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: facet_material(model.getFacetMaterial()), mesh(model.getMesh()) {
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<DefaultMaterialSelector>(model.getMaterialByElement());
}
/* -------------------------------------------------------------------------- */
UInt DefaultMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive) {
try {
const Array<Element> & cohesive_el_to_facet =
mesh.getMeshFacets().getSubelementToElement(element.type,
element.ghost_type);
bool third_dimension = (mesh.getSpatialDimension() == 3);
const Element & facet =
cohesive_el_to_facet(element.element, UInt(third_dimension));
if (facet_material.exists(facet.type, facet.ghost_type)) {
return facet_material(facet.type, facet.ghost_type)(facet.element);
}
return fallback_value;
} catch (...) {
return fallback_value;
}
} else if (Mesh::getSpatialDimension(element.type) ==
mesh.getSpatialDimension() - 1) {
return facet_material(element.type, element.ghost_type)(element.element);
} else {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
MeshDataMaterialCohesiveSelector::MeshDataMaterialCohesiveSelector(
const SolidMechanicsModelCohesive & model)
: model(model), mesh_facets(model.getMeshFacets()),
material_index(mesh_facets.getData<std::string>("physical_names")) {
third_dimension = (model.getSpatialDimension() == 3);
// backward compatibility v3: to get the former behavior back when the user
// creates its own selector
this->fallback_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
}
/* -------------------------------------------------------------------------- */
UInt MeshDataMaterialCohesiveSelector::operator()(const Element & element) {
if (Mesh::getKind(element.type) == _ek_cohesive or
Mesh::getSpatialDimension(element.type) ==
mesh_facets.getSpatialDimension() - 1) {
Element facet;
if (Mesh::getKind(element.type) == _ek_cohesive) {
facet =
mesh_facets.getSubelementToElement(element.type, element.ghost_type)(
element.element, UInt(third_dimension));
} else {
facet = element;
}
try {
std::string material_name = this->material_index(facet);
return this->model.getMaterialIndex(material_name);
} catch (...) {
return fallback_value;
}
}
return MaterialSelector::operator()(element);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MaterialCohesiveRulesSelector::MaterialCohesiveRulesSelector(
const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id) // what we have here is the name of model and also
// the name of different materials
: model(model), mesh_data_id(std::move(mesh_data_id)),
mesh(model.getMesh()), mesh_facets(model.getMeshFacets()),
spatial_dimension(model.getSpatialDimension()), rules(rules) {
// cohesive fallback
this->fallback_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(model);
// non cohesive fallback
this->fallback_selector->setFallback(
std::make_shared<MeshDataMaterialSelector<std::string>>(mesh_data_id,
model));
}
/* -------------------------------------------------------------------------- */
UInt MaterialCohesiveRulesSelector::operator()(const Element & element) {
if (mesh_facets.getSpatialDimension(element.type) ==
(spatial_dimension - 1)) {
const std::vector<Element> & element_to_subelement =
mesh_facets.getElementToSubelement(element.type,
element.ghost_type)(element.element);
// Array<bool> & facets_check = model.getFacetsCheck();
const Element & el1 = element_to_subelement[0];
const Element & el2 = element_to_subelement[1];
ID id1 = mesh.getData<std::string>(mesh_data_id, el1.type,
el1.ghost_type)(el1.element);
ID id2 = id1;
if (el2 != ElementNull) {
id2 = mesh.getData<std::string>(mesh_data_id, el2.type,
el2.ghost_type)(el2.element);
}
auto rit = rules.find(std::make_pair(id1, id2));
if (rit == rules.end()) {
rit = rules.find(std::make_pair(id2, id1));
}
if (rit != rules.end()) {
return model.getMaterialIndex(rit->second);
}
}
return MaterialSelector::operator()(element);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
index ecb618f63..e4108e199 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
@@ -1,98 +1,100 @@
/**
* @file material_selector_cohesive.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Material selectors for cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_selector.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
#ifndef AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_
#define AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first cohesive material by default to the
* cohesive elements
*/
class DefaultMaterialCohesiveSelector : public MaterialSelector {
public:
DefaultMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
private:
const ElementTypeMapArray<UInt> & facet_material;
const Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/// To be used with intrinsic elements inserted along mesh physical surfaces
class MeshDataMaterialCohesiveSelector : public MaterialSelector {
public:
MeshDataMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
UInt operator()(const Element & element) override;
protected:
const SolidMechanicsModelCohesive & model;
const Mesh & mesh_facets;
const ElementTypeMapArray<std::string> & material_index;
bool third_dimension;
};
/// bulk1, bulk2 -> cohesive
using MaterialCohesiveRules = std::map<std::pair<ID, ID>, ID>;
/* -------------------------------------------------------------------------- */
class MaterialCohesiveRulesSelector : public MaterialSelector {
public:
MaterialCohesiveRulesSelector(const SolidMechanicsModelCohesive & model,
const MaterialCohesiveRules & rules,
ID mesh_data_id = "physical_names");
UInt operator()(const Element & element) override;
private:
const SolidMechanicsModelCohesive & model;
ID mesh_data_id;
const Mesh & mesh;
const Mesh & mesh_facets;
UInt spatial_dimension;
MaterialCohesiveRules rules;
};
#endif /* AKANTU_MATERIAL_SELECTOR_COHESIVE_HH_ */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
index c78ded4b1..333afb0e7 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
@@ -1,66 +1,68 @@
/**
* @file cohesive_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Internal field for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#ifndef AKANTU_COHESIVE_INTERNAL_FIELD_HH_
#define AKANTU_COHESIVE_INTERNAL_FIELD_HH_
namespace akantu {
/// internal field class for cohesive materials
template <typename T> class CohesiveInternalField : public InternalField<T> {
public:
CohesiveInternalField(const ID & id, Material & material);
~CohesiveInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
private:
CohesiveInternalField operator=(__attribute__((unused))
const CohesiveInternalField & other){};
};
/* -------------------------------------------------------------------------- */
/* Facet Internal Field */
/* -------------------------------------------------------------------------- */
template <typename T> class FacetInternalField : public InternalField<T> {
public:
FacetInternalField(const ID & id, Material & material);
~FacetInternalField() override;
/// initialize the field to a given number of component
void initialize(UInt nb_component) override;
};
} // namespace akantu
#endif /* AKANTU_COHESIVE_INTERNAL_FIELD_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
index 5a677f252..0104a5d99 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field_tmpl.hh
@@ -1,94 +1,96 @@
/**
* @file cohesive_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief implementation of the cohesive internal field
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_
#define AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_
namespace akantu {
template <typename T>
CohesiveInternalField<T>::CohesiveInternalField(const ID & id,
Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("CohesiveFEEngine"),
aka::as_type<MaterialCohesive>(material).getElementFilter()) {
this->element_kind = _ek_cohesive;
}
template <typename T>
CohesiveInternalField<T>::~CohesiveInternalField() = default;
template <typename T>
void CohesiveInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
FacetInternalField<T>::FacetInternalField(const ID & id, Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("FacetsFEEngine"),
aka::as_type<MaterialCohesive>(material).getFacetFilter()) {
this->spatial_dimension -= 1;
this->element_kind = _ek_regular;
}
template <typename T> FacetInternalField<T>::~FacetInternalField() = default;
template <typename T>
void FacetInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, FacetInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<RandomInternalField<Real, CohesiveInternalField>>::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
} // namespace akantu
#endif /* AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
index 50a7782fa..13f78e652 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.cc
@@ -1,213 +1,215 @@
/**
* @file material_cohesive_bilinear.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Sat Dec 19 2020
*
* @brief Bilinear cohesive constitutive law
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_bilinear.hh"
//#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveBilinear<spatial_dimension>::MaterialCohesiveBilinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("delta_0", delta_0, Real(0.),
_pat_parsable | _pat_readable,
"Elastic limit displacement");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->sigma_c_eff.setRandomDistribution(this->sigma_c.getRandomParameter());
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
this->delta_max.setDefaultValue(delta_0);
this->insertion_stress.setDefaultValue(0);
this->delta_max.reset();
this->insertion_stress.reset();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::onElementsAdded(element_list,
event);
bool scale_traction = false;
// don't scale sigma_c if volume_s hasn't been specified by the user
if (!Math::are_float_equal(this->volume_s, 0.)) {
scale_traction = true;
}
Array<Element>::const_scalar_iterator el_it = element_list.begin();
Array<Element>::const_scalar_iterator el_end = element_list.end();
for (; el_it != el_end; ++el_it) {
// filter not ghost cohesive elements
if ((el_it->ghost_type != _not_ghost) or
(Mesh::getKind(el_it->type) != _ek_cohesive)) {
continue;
}
UInt index = el_it->element;
ElementType type = el_it->type;
UInt nb_element = this->model->getMesh().getNbElement(type);
UInt nb_quad_per_element = this->fem_cohesive.getNbIntegrationPoints(type);
auto sigma_c_begin = this->sigma_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> sigma_c_vec = sigma_c_begin[index];
auto delta_c_begin = this->delta_c_eff(type).begin_reinterpret(
nb_quad_per_element, nb_element);
Vector<Real> delta_c_vec = delta_c_begin[index];
if (scale_traction) {
scaleTraction(*el_it, sigma_c_vec);
}
/**
* Recompute sigma_c as
* @f$ {\sigma_c}_\textup{new} =
* \frac{{\sigma_c}_\textup{old} \delta_c} {\delta_c - \delta_0} @f$
*/
for (UInt q = 0; q < nb_quad_per_element; ++q) {
delta_c_vec(q) = 2 * this->G_c / sigma_c_vec(q);
if (delta_c_vec(q) - delta_0 < Math::getTolerance()) {
AKANTU_ERROR("delta_0 = " << delta_0 << " must be lower than delta_c = "
<< delta_c_vec(q)
<< ", modify your material file");
}
sigma_c_vec(q) *= delta_c_vec(q) / (delta_c_vec(q) - delta_0);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::scaleTraction(
const Element & el, Vector<Real> & sigma_c_vec) {
AKANTU_DEBUG_IN();
Real base_sigma_c = this->sigma_c_eff;
const Mesh & mesh_facets = this->model->getMeshFacets();
const FEEngine & fe_engine = this->model->getFEEngine();
auto coh_element_to_facet_begin =
mesh_facets.getSubelementToElement(el.type).begin(2);
const Vector<Element> & coh_element_to_facet =
coh_element_to_facet_begin[el.element];
// compute bounding volume
Real volume = 0;
// loop over facets
for (UInt f = 0; f < 2; ++f) {
const Element & facet = coh_element_to_facet(f);
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(facet.type, facet.ghost_type);
const std::vector<Element> & element_list = facet_to_element(facet.element);
auto elem = element_list.begin();
auto elem_end = element_list.end();
// loop over elements connected to each facet
for (; elem != elem_end; ++elem) {
// skip cohesive elements and dummy elements
if (*elem == ElementNull || Mesh::getKind(elem->type) == _ek_cohesive) {
continue;
}
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
}
// scale sigma_c
sigma_c_vec -= base_sigma_c;
sigma_c_vec *= std::pow(this->volume_s / volume, 1. / this->m_s);
sigma_c_vec += base_sigma_c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::computeTraction(normal, el_type,
ghost_type);
// adjust damage
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto delta_max_it = this->delta_max(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto damage_end = this->damage(el_type, ghost_type).end();
for (; damage_it != damage_end; ++damage_it, ++delta_max_it, ++delta_c_it) {
*damage_it =
std::max((*delta_max_it - delta_0) / (*delta_c_it - delta_0), Real(0.));
*damage_it = std::min(*damage_it, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_bilinear, MaterialCohesiveBilinear);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
index b55fe0911..dd21d5211 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_bilinear.hh
@@ -1,104 +1,106 @@
/**
* @file material_cohesive_bilinear.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Bilinear cohesive constitutive law
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#ifndef AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_
#define AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material bilinear
*
* parameters in the material files :
* - delta_0 : elastic limit displacement (default: 0)
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveBilinear
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveBilinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// set material parameters for new elements
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/**
* Scale traction sigma_c according to the volume of the
* two elements surrounding an element
*/
void scaleTraction(const Element & el, Vector<Real> & sigma_c_vec);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// elastic limit displacement
Real delta_0;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_cohesive_elastic_inline_impl.hh"
} // namespace akantu
#endif /* AKANTU_MATERIAL_COHESIVE_BILINEAR_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
index 9732044eb..c8dd09cbf 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.cc
@@ -1,343 +1,345 @@
/**
* @file material_cohesive_exponential.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Mon Jul 09 2012
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_exponential.hh"
#include "dof_synchronizer.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveExponential<spatial_dimension>::MaterialCohesiveExponential(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable, "Beta parameter");
this->registerParam("exponential_penalty", exp_penalty, true, _pat_parsable,
"Is contact penalty following the exponential law?");
this->registerParam(
"contact_tangent", contact_tangent, Real(1.0), _pat_parsable,
"Ratio of contact tangent over the initial exponential tangent");
// this->initInternalArray(delta_max, 1, _ek_cohesive);
use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
if ((exp_penalty) && (contact_tangent != 1)) {
contact_tangent = 1;
AKANTU_DEBUG_WARNING("The parsed paramter <contact_tangent> is forced to "
"1.0 when the contact penalty follows the exponential "
"law");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it = delta_max.previous(el_type, ghost_type).begin();
/// compute scalars
Real beta2 = beta * beta;
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++opening_it, ++normal_it,
++delta_max_it, ++delta_max_prev_it) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \beta^2 \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTraction(*traction_it, *normal_it, delta, delta_s,
*delta_max_it, *delta_max_prev_it);
computeCompressiveTraction(*traction_it, *normal_it, normal_opening_norm,
*opening_it);
} else {
computeCoupledTraction(*traction_it, *normal_it, delta, *opening_it,
*delta_max_it, *delta_max_prev_it);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real & delta_max_new, Real delta_max) {
AKANTU_DEBUG_IN();
/// full damage case
if (std::abs(delta) < Math::getTolerance()) {
/// set traction to zero
tract.zero();
} else { /// element not fully damaged
/**
* Compute traction loading @f$ \mathbf{T} =
* e \sigma_c \frac{\delta}{\delta_c} e^{-\delta/ \delta_c}@f$
*/
/**
* Compute traction unloading @f$ \mathbf{T} =
* \frac{t_{max}}{\delta_{max}} \delta @f$
*/
Real beta2 = beta * beta;
Real normal_open_norm = opening.dot(normal);
Vector<Real> op_n_n(spatial_dimension);
op_n_n = normal;
op_n_n *= (1 - beta2);
op_n_n *= normal_open_norm;
tract = beta2 * opening;
tract += op_n_n;
delta_max_new = std::max(delta_max, delta);
tract *=
std::exp(1.) * sigma_c * std::exp(-delta_max_new / delta_c) / delta_c;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressiveTraction(
Vector<Real> & tract, const Vector<Real> & normal, Real delta_n,
__attribute__((unused)) const Vector<Real> & opening) {
Vector<Real> temp_tract(normal);
if (exp_penalty) {
temp_tract *= delta_n * std::exp(1) * sigma_c *
std::exp(-delta_n / delta_c) / delta_c;
} else {
Real initial_tg =
contact_tangent * std::exp(1.) * sigma_c * delta_n / delta_c;
temp_tract *= initial_tg;
}
tract += temp_tract;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTangentTraction(
ElementType el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
Real beta2 = beta * beta;
/**
* compute tangent matrix @f$ \frac{\partial \mathbf{t}}
* {\partial \delta} = \hat{\mathbf{t}} \otimes
* \frac{\partial (t/\delta)}{\partial \delta}
* \frac{\hat{\mathbf{t}}}{\delta}+ \frac{t}{\delta} [ \beta^2 \mathbf{I} +
* (1-\beta^2) (\mathbf{n} \otimes \mathbf{n})] @f$
**/
/**
* In which @f$
* \frac{\partial(t/ \delta)}{\partial \delta} =
* \left\{\begin{array} {l l}
* -e \frac{\sigma_c}{\delta_c^2 }e^{-\delta / \delta_c} & \quad if
* \delta \geq \delta_{max} \\
* 0 & \quad if \delta < \delta_{max}, \delta_n > 0
* \end{array}\right. @f$
**/
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++delta_max_it) {
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) &&
(std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTangent(*tangent_it, *normal_it, delta, delta_s,
*delta_max_it);
computeCompressivePenalty(*tangent_it, *normal_it, normal_opening_norm);
} else {
computeCoupledTangent(*tangent_it, *normal_it, delta, *opening_it,
*delta_max_it);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTangent(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real /*unused*/) {
AKANTU_DEBUG_IN();
Real beta2 = beta * beta;
Matrix<Real> J(spatial_dimension, spatial_dimension);
J.eye(beta2);
if (std::abs(delta) < Math::getTolerance()) {
delta = Math::getTolerance();
}
Real opening_normal;
opening_normal = opening.dot(normal);
Vector<Real> delta_e(normal);
delta_e *= opening_normal;
delta_e *= (1. - beta2);
delta_e += (beta2 * opening);
Real exponent = std::exp(1. - delta / delta_c) * sigma_c / delta_c;
Matrix<Real> first_term(spatial_dimension, spatial_dimension);
first_term.outerProduct(normal, normal);
first_term *= (1. - beta2);
first_term += J;
Matrix<Real> second_term(spatial_dimension, spatial_dimension);
second_term.outerProduct(delta_e, delta_e);
second_term /= delta;
second_term /= delta_c;
Matrix<Real> diff(first_term);
diff -= second_term;
tangent = diff;
tangent *= exponent;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressivePenalty(
Matrix<Real> & tangent, const Vector<Real> & normal, Real delta_n) {
if (!exp_penalty) {
delta_n = 0.;
}
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
Real normal_tg = contact_tangent * std::exp(1.) * sigma_c *
std::exp(-delta_n / delta_c) * (1. - delta_n / delta_c) /
delta_c;
n_outer_n *= normal_tg;
tangent += n_outer_n;
}
INSTANTIATE_MATERIAL(cohesive_exponential, MaterialCohesiveExponential);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
index 24495057c..eead5b55e 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_exponential.hh
@@ -1,121 +1,123 @@
/**
* @file material_cohesive_exponential.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_
#define AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material Exponential damage
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - delta_c : critical opening (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveExponential : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveExponential(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Initialization
void initMaterial() override;
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type = _not_ghost) override;
private:
void computeCoupledTraction(Vector<Real> & tract, const Vector<Real> & normal,
Real delta, const Vector<Real> & opening,
Real & delta_max_new, Real delta_max);
void computeCompressiveTraction(Vector<Real> & tract,
const Vector<Real> & normal, Real delta_n,
const Vector<Real> & opening);
void computeCoupledTangent(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real delta_max_new);
void computeCompressivePenalty(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta_n);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// contact penalty = initial slope ?
bool exp_penalty;
/// Ratio of contact tangent over the initial exponential tangent
Real contact_tangent;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
// #include "material_cohesive_exponential_inline_impl.hh"
} // namespace akantu
#endif /* AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
index d3aadeb8c..2c73ea05a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.cc
@@ -1,431 +1,433 @@
/**
* @file material_cohesive_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Jan 14 2021
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "dof_synchronizer.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinear<spatial_dimension>::MaterialCohesiveLinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id), sigma_c_eff("sigma_c_eff", *this),
delta_c_eff("delta_c_eff", *this),
insertion_stress("insertion_stress", *this) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable | _pat_readable,
"Beta parameter");
this->registerParam("G_c", G_c, Real(0.), _pat_parsable | _pat_readable,
"Mode I fracture energy");
this->registerParam("penalty", penalty, Real(0.),
_pat_parsable | _pat_readable, "Penalty coefficient");
this->registerParam("volume_s", volume_s, Real(0.),
_pat_parsable | _pat_readable,
"Reference volume for sigma_c scaling");
this->registerParam("m_s", m_s, Real(1.), _pat_parsable | _pat_readable,
"Weibull exponent for sigma_c scaling");
this->registerParam("kappa", kappa, Real(1.), _pat_parsable | _pat_readable,
"Kappa parameter");
this->registerParam(
"contact_after_breaking", contact_after_breaking, false,
_pat_parsable | _pat_readable,
"Activation of contact when the elements are fully damaged");
this->registerParam("max_quad_stress_insertion", max_quad_stress_insertion,
false, _pat_parsable | _pat_readable,
"Insertion of cohesive element when stress is high "
"enough just on one quadrature point");
this->registerParam("recompute", recompute, false,
_pat_parsable | _pat_modifiable, "recompute solution");
this->use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
sigma_c_eff.initialize(1);
delta_c_eff.initialize(1);
insertion_stress.initialize(spatial_dimension);
if (not Math::are_float_equal(delta_c, 0.)) {
delta_c_eff.setDefaultValue(delta_c);
} else {
delta_c_eff.setDefaultValue(2 * G_c / sigma_c);
}
if (model->getIsExtrinsic()) {
scaleInsertionTraction();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::updateInternalParameters() {
/// compute scalars
beta2_kappa2 = beta * beta / kappa / kappa;
beta2_kappa = beta * beta / kappa;
if (Math::are_float_equal(beta, 0)) {
beta2_inv = 0;
} else {
beta2_inv = 1. / beta / beta;
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::scaleInsertionTraction() {
AKANTU_DEBUG_IN();
// do nothing if volume_s hasn't been specified by the user
if (Math::are_float_equal(volume_s, 0.)) {
return;
}
const Mesh & mesh_facets = model->getMeshFacets();
const auto & fe_engine = model->getFEEngine();
const auto & fe_engine_facet = model->getFEEngine("FacetsFEEngine");
Real base_sigma_c = sigma_c;
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
const Array<std::vector<Element>> & facet_to_element =
mesh_facets.getElementToSubelement(type_facet);
UInt nb_facet = facet_to_element.size();
UInt nb_quad_per_facet = fe_engine_facet.getNbIntegrationPoints(type_facet);
// iterator to modify sigma_c for all the quadrature points of a facet
auto sigma_c_iterator =
sigma_c(type_facet).begin_reinterpret(nb_quad_per_facet, nb_facet);
for (UInt f = 0; f < nb_facet; ++f, ++sigma_c_iterator) {
const std::vector<Element> & element_list = facet_to_element(f);
// compute bounding volume
Real volume = 0;
auto elem = element_list.begin();
auto elem_end = element_list.end();
for (; elem != elem_end; ++elem) {
if (*elem == ElementNull) {
continue;
}
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
// scale sigma_c
*sigma_c_iterator -= base_sigma_c;
*sigma_c_iterator *= std::pow(volume_s / volume, 1. / m_s);
*sigma_c_iterator += base_sigma_c;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkInsertion(
bool check_only) {
AKANTU_DEBUG_IN();
const Mesh & mesh_facets = model->getMeshFacets();
CohesiveElementInserter & inserter = model->getElementInserter();
for (auto && type_facet : mesh_facets.elementTypes(spatial_dimension - 1)) {
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const auto & facets_check = inserter.getCheckFacets(type_facet);
auto & f_insertion = inserter.getInsertionFacets(type_facet);
auto & f_filter = facet_filter(type_facet);
auto & sig_c_eff = sigma_c_eff(type_cohesive);
auto & del_c = delta_c_eff(type_cohesive);
auto & ins_stress = insertion_stress(type_cohesive);
auto & trac_old = tractions.previous(type_cohesive);
const auto & f_stress = model->getStressOnFacets(type_facet);
const auto & sigma_lim = sigma_c(type_facet);
UInt nb_quad_facet =
model->getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
#ifndef AKANTU_NDEBUG
UInt nb_quad_cohesive = model->getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive);
AKANTU_DEBUG_ASSERT(nb_quad_cohesive == nb_quad_facet,
"The cohesive element and the corresponding facet do "
"not have the same numbers of integration points");
#endif
UInt nb_facet = f_filter.size();
// if (nb_facet == 0) continue;
auto sigma_lim_it = sigma_lim.begin();
Matrix<Real> stress_tmp(spatial_dimension, spatial_dimension);
Matrix<Real> normal_traction(spatial_dimension, nb_quad_facet);
Vector<Real> stress_check(nb_quad_facet);
UInt sp2 = spatial_dimension * spatial_dimension;
const auto & tangents = model->getTangents(type_facet);
const auto & normals = model->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
auto normal_begin = normals.begin(spatial_dimension);
auto tangent_begin = tangents.begin(tangents.getNbComponent());
auto facet_stress_begin =
f_stress.begin(spatial_dimension, spatial_dimension * 2);
std::vector<Real> new_sigmas;
std::vector<Vector<Real>> new_normal_traction;
std::vector<Real> new_delta_c;
// loop over each facet belonging to this material
for (UInt f = 0; f < nb_facet; ++f, ++sigma_lim_it) {
UInt facet = f_filter(f);
// skip facets where check shouldn't be realized
if (!facets_check(facet)) {
continue;
}
// compute the effective norm on each quadrature point of the facet
for (UInt q = 0; q < nb_quad_facet; ++q) {
UInt current_quad = facet * nb_quad_facet + q;
const Vector<Real> & normal = normal_begin[current_quad];
const Vector<Real> & tangent = tangent_begin[current_quad];
const Matrix<Real> & facet_stress_it = facet_stress_begin[current_quad];
// compute average stress on the current quadrature point
Matrix<Real> stress_1(facet_stress_it.storage(), spatial_dimension,
spatial_dimension);
Matrix<Real> stress_2(facet_stress_it.storage() + sp2,
spatial_dimension, spatial_dimension);
stress_tmp.copy(stress_1);
stress_tmp += stress_2;
stress_tmp /= 2.;
Vector<Real> normal_traction_vec(normal_traction(q));
// compute normal and effective stress
stress_check(q) = computeEffectiveNorm(stress_tmp, normal, tangent,
normal_traction_vec);
}
// verify if the effective stress overcomes the threshold
Real final_stress = stress_check.mean();
if (max_quad_stress_insertion) {
final_stress = *std::max_element(
stress_check.storage(), stress_check.storage() + nb_quad_facet);
}
if (final_stress > *sigma_lim_it) {
f_insertion(facet) = true;
if (check_only) {
continue;
}
// store the new cohesive material parameters for each quadrature
// point
for (UInt q = 0; q < nb_quad_facet; ++q) {
Real new_sigma = stress_check(q);
Vector<Real> normal_traction_vec(normal_traction(q));
if (spatial_dimension != 3) {
normal_traction_vec *= -1.;
}
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(normal_traction_vec);
Real new_delta;
// set delta_c in function of G_c or a given delta_c value
if (Math::are_float_equal(delta_c, 0.)) {
new_delta = 2 * G_c / new_sigma;
} else {
new_delta = (*sigma_lim_it) / new_sigma * delta_c;
}
new_delta_c.push_back(new_delta);
}
}
}
// update material data for the new elements
UInt old_nb_quad_points = sig_c_eff.size();
UInt new_nb_quad_points = new_sigmas.size();
sig_c_eff.resize(old_nb_quad_points + new_nb_quad_points);
ins_stress.resize(old_nb_quad_points + new_nb_quad_points);
trac_old.resize(old_nb_quad_points + new_nb_quad_points);
del_c.resize(old_nb_quad_points + new_nb_quad_points);
for (UInt q = 0; q < new_nb_quad_points; ++q) {
sig_c_eff(old_nb_quad_points + q) = new_sigmas[q];
del_c(old_nb_quad_points + q) = new_delta_c[q];
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
ins_stress(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
trac_old(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it = tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end = tractions(el_type, ghost_type).end(spatial_dimension);
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = delta_max(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto insertion_stress_it =
insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it) {
Real normal_opening_norm{0};
Real tangential_opening_norm{0};
bool penetration{false};
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTangentTraction(
ElementType el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto opening_it = opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_max_it = delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = delta_c_eff(el_type, ghost_type).begin();
auto damage_it = damage(el_type, ghost_type).begin();
auto contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it,
++damage_it, ++contact_opening_it) {
Real normal_opening_norm{0};
Real tangential_opening_norm{0};
bool penetration{false};
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear, MaterialCohesiveLinear);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
index 686b164ea..a91c5a986 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear.hh
@@ -1,187 +1,189 @@
/**
* @file material_cohesive_linear.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Mon Sep 14 2020
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_HH_
#define AKANTU_MATERIAL_COHESIVE_LINEAR_HH_
namespace akantu {
/**
* Cohesive material linear damage for extrinsic case
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default:
* 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinear : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
void updateInternalParameters() override;
/// check stress for cohesive elements' insertion
void checkInsertion(bool check_only = false) override;
/// compute effective stress norm for insertion check
Real computeEffectiveNorm(const Matrix<Real> & stress,
const Vector<Real> & normal,
const Vector<Real> & tangent,
Vector<Real> & normal_traction) const;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/**
* Scale insertion traction sigma_c according to the volume of the
* two elements surrounding a facet
*
* see the article: F. Zhou and J. F. Molinari "Dynamic crack
* propagation with cohesive elements: a methodology to address mesh
* dependency" International Journal for Numerical Methods in
* Engineering (2004)
*/
void scaleInsertionTraction();
/// compute the traction for a given quadrature point
inline void computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening);
inline void computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get sigma_c_eff
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(InsertionTraction, sigma_c_eff, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// beta square inverse to compute effective norm
Real beta2_inv;
/// mode I fracture energy
Real G_c;
/// kappa parameter
Real kappa;
/// constitutive law scalar to compute delta
Real beta2_kappa2;
/// constitutive law scalar to compute traction
Real beta2_kappa;
/// penalty coefficient
Real penalty;
/// reference volume used to scale sigma_c
Real volume_s;
/// weibull exponent used to scale sigma_c
Real m_s;
/// variable defining if we are recomputing the last loading step
/// after load_reduction
bool recompute;
/// critical effective stress
RandomInternalField<Real, CohesiveInternalField> sigma_c_eff;
/// effective critical displacement (each element can have a
/// different value)
CohesiveInternalField<Real> delta_c_eff;
/// stress at insertion
CohesiveInternalField<Real> insertion_stress;
/// variable saying if there should be penalty contact also after
/// breaking the cohesive elements
bool contact_after_breaking;
/// insertion of cohesive element when stress is high enough just on
/// one quadrature point
bool max_quad_stress_insertion;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "material_cohesive_linear_inline_impl.hh"
#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
index 60831c62c..df3b83375 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.cc
@@ -1,304 +1,306 @@
/**
* @file material_cohesive_linear_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief See material_cohesive_linear_fatigue.hh for information
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_fatigue.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFatigue<spatial_dimension>::MaterialCohesiveLinearFatigue(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_prec("delta_prec", *this), K_plus("K_plus", *this),
K_minus("K_minus", *this), T_1d("T_1d", *this),
switches("switches", *this), delta_dot_prec("delta_dot_prec", *this),
normal_regime("normal_regime", *this) {
this->registerParam("delta_f", delta_f, Real(-1.),
_pat_parsable | _pat_readable, "delta_f");
this->registerParam("progressive_delta_f", progressive_delta_f, false,
_pat_parsable | _pat_readable,
"Whether or not delta_f is equal to delta_max");
this->registerParam("count_switches", count_switches, false,
_pat_parsable | _pat_readable,
"Count the opening/closing switches per element");
this->registerParam(
"fatigue_ratio", fatigue_ratio, Real(1.), _pat_parsable | _pat_readable,
"What portion of the cohesive law is subjected to fatigue");
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::initMaterial() {
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
// check that delta_f has a proper value or assign a defaul value
if (delta_f < 0) {
delta_f = this->delta_c_eff;
} else if (delta_f < this->delta_c_eff) {
AKANTU_ERROR("Delta_f must be greater or equal to delta_c");
}
delta_prec.initialize(1);
K_plus.initialize(1);
K_minus.initialize(1);
T_1d.initialize(1);
normal_regime.initialize(1);
if (count_switches) {
switches.initialize(1);
delta_dot_prec.initialize(1);
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = normal.begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
const Array<Real> & sigma_c_array = this->sigma_c_eff(el_type, ghost_type);
Array<Real> & delta_max_array = this->delta_max(el_type, ghost_type);
const Array<Real> & delta_c_array = this->delta_c_eff(el_type, ghost_type);
Array<Real> & damage_array = this->damage(el_type, ghost_type);
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<Real> & delta_prec_array = delta_prec(el_type, ghost_type);
Array<Real> & K_plus_array = K_plus(el_type, ghost_type);
Array<Real> & K_minus_array = K_minus(el_type, ghost_type);
Array<Real> & T_1d_array = T_1d(el_type, ghost_type);
Array<bool> & normal_regime_array = normal_regime(el_type, ghost_type);
Array<UInt> * switches_array = nullptr;
Array<Real> * delta_dot_prec_array = nullptr;
if (count_switches) {
switches_array = &switches(el_type, ghost_type);
delta_dot_prec_array = &delta_dot_prec(el_type, ghost_type);
}
auto * memory_space = new Real[2 * spatial_dimension];
Vector<Real> normal_opening(memory_space, spatial_dimension);
Vector<Real> tangential_opening(memory_space + spatial_dimension,
spatial_dimension);
Real tolerance = Math::getTolerance();
/// loop on each quadrature point
for (UInt q = 0; traction_it != traction_end; ++traction_it, ++opening_it,
++normal_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++q) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
bool penetration = normal_opening_norm < -tolerance;
if (not this->contact_after_breaking and
Math::are_float_equal(damage_array(q), 1.)) {
penetration = false;
}
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
normal_opening.zero();
} else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction_it->zero();
contact_opening_it->zero();
}
delta = std::sqrt(delta);
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
// update maximum displacement and damage
delta_max_array(q) = std::max(delta, delta_max_array(q));
damage_array(q) = std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
Real delta_dot = delta - delta_prec_array(q);
// count switches if asked
if (count_switches) {
if ((delta_dot > 0. && (*delta_dot_prec_array)(q) <= 0.) ||
(delta_dot < 0. && (*delta_dot_prec_array)(q) >= 0.)) {
++((*switches_array)(q));
}
(*delta_dot_prec_array)(q) = delta_dot;
}
// set delta_f equal to delta_max if desired
if (progressive_delta_f) {
delta_f = delta_max_array(q);
}
// broken element case
if (Math::are_float_equal(damage_array(q), 1.)) {
traction_it->zero();
// just inserted element case
} else if (Math::are_float_equal(damage_array(q), 0.)) {
if (penetration) {
traction_it->zero();
} else {
*traction_it = *insertion_stress_it;
}
// initialize the 1d traction to sigma_c
T_1d_array(q) = sigma_c_array(q);
}
// normal case
else {
// if element is closed then there are zero tractions
if (delta <= tolerance) {
traction_it->zero();
// otherwise compute new tractions if the new delta is different
// than the previous one
} else if (std::abs(delta_dot) > tolerance) {
// loading case
if (delta_dot > 0.) {
if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) *= 1. - delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) += K_plus_array(q) * delta_dot;
// in case of reloading, traction must not exceed that of the
// envelop of the cohesive law
Real max_traction =
sigma_c_array(q) * (1 - delta / delta_c_array(q));
bool max_traction_exceeded = T_1d_array(q) > max_traction;
if (max_traction_exceeded) {
T_1d_array(q) = max_traction;
}
// switch to standard linear cohesive law
if (delta_max_array(q) > fatigue_ratio * delta_c_array(q)) {
// reset delta_max to avoid big jumps in the traction
delta_max_array(q) =
sigma_c_array(q) /
(T_1d_array(q) / delta + sigma_c_array(q) / delta_c_array(q));
damage_array(q) =
std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
K_minus_array(q) = sigma_c_array(q) / delta_max_array(q) *
(1. - damage_array(q));
normal_regime_array(q) = true;
} else {
// equation (3) of the article
K_minus_array(q) = T_1d_array(q) / delta;
// if the traction is following the cohesive envelop, then
// K_plus has to be reset
if (max_traction_exceeded) {
K_plus_array(q) = K_minus_array(q);
}
}
} else {
// compute stiffness according to the standard law
K_minus_array(q) =
sigma_c_array(q) / delta_max_array(q) * (1. - damage_array(q));
}
}
// unloading case
else if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) +=
(K_plus_array(q) - K_minus_array(q)) * delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) = K_minus_array(q) * delta;
}
// applying the actual stiffness
*traction_it = tangential_opening;
*traction_it *= this->beta2_kappa;
*traction_it += normal_opening;
*traction_it *= K_minus_array(q);
}
}
// update precendent delta
delta_prec_array(q) = delta;
}
delete[] memory_space;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_fatigue, MaterialCohesiveLinearFatigue);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
index 07044e052..da9255785 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_fatigue.hh
@@ -1,131 +1,133 @@
/**
* @file material_cohesive_linear_fatigue.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Thu Feb 20 2020
*
* @brief Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_
#define AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* This law uses two different stiffnesses during unloading and
* reloading. The implementation is based on the article entitled "A
* cohesive model for fatigue crack growth" by Nguyen, Repetto, Ortiz
* and Radovitzky (2001). This law is identical to the
* MaterialCohesiveLinear one except for the unloading-reloading
* phase.
*
* input parameter:
*
* - delta_f : it must be greater than delta_c and it is inversely
* proportional to the dissipation in the unloading-reloading
* cycles (default: delta_c)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFatigue
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinearFatigue(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the switches
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Switches, switches, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// delta_f parameter
Real delta_f;
/// variable saying if delta_f is equal to delta_max for each
/// element when the traction is computed
bool progressive_delta_f;
/// count the opening/closing switches per element
bool count_switches;
/// delta of the previous step
CohesiveInternalField<Real> delta_prec;
/// stiffness for reloading
CohesiveInternalField<Real> K_plus;
/// stiffness for unloading
CohesiveInternalField<Real> K_minus;
/// 1D traction in the cohesive law
CohesiveInternalField<Real> T_1d;
/// Number of opening/closing switches
CohesiveInternalField<UInt> switches;
/// delta increment of the previous time step
CohesiveInternalField<Real> delta_dot_prec;
/// has the element passed to normal regime (not in fatigue anymore)
CohesiveInternalField<bool> normal_regime;
/// ratio indicating until what point fatigue is applied in the cohesive law
Real fatigue_ratio;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
index ed20e1034..857bcddbc 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.cc
@@ -1,276 +1,283 @@
/**
* @file material_cohesive_linear_friction.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue Jan 12 2016
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Dec 11 2020
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_friction.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFriction<spatial_dimension>::
MaterialCohesiveLinearFriction(SolidMechanicsModel & model, const ID & id)
: MaterialParent(model, id), residual_sliding("residual_sliding", *this),
friction_force("friction_force", *this) {
AKANTU_DEBUG_IN();
this->registerParam("mu", mu_max, Real(0.), _pat_parsable | _pat_readable,
"Maximum value of the friction coefficient");
this->registerParam("penalty_for_friction", friction_penalty, Real(0.),
_pat_parsable | _pat_readable,
"Penalty parameter for the friction behavior");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialParent::initMaterial();
friction_force.initialize(spatial_dimension);
residual_sliding.initialize(1);
residual_sliding.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTraction(
__attribute__((unused)) const Array<Real> & normal, ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
residual_sliding.resize();
friction_force.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_max_it = this->delta_max(el_type, ghost_type).begin();
auto delta_max_prev_it =
this->delta_max.previous(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_it = this->residual_sliding(el_type, ghost_type).begin();
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
auto friction_force_it =
this->friction_force(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
if (not this->model->isDefaultSolverExplicit()) {
this->delta_max(el_type, ghost_type)
.copy(this->delta_max.previous(el_type, ghost_type));
}
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++sigma_c_it, ++delta_max_it,
++delta_c_it, ++damage_it, ++contact_traction_it, ++insertion_stress_it,
++contact_opening_it, ++delta_max_prev_it, ++res_sliding_it,
++res_sliding_prev_it, ++friction_force_it, ++previous_opening_it) {
Real normal_opening_norm;
Real tangential_opening_norm;
bool penetration;
this->computeTractionOnQuad(
*traction_it, *opening_it, *normal_it, *delta_max_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, normal_opening, tangential_opening,
normal_opening_norm, tangential_opening_norm, *damage_it, penetration,
*contact_traction_it, *contact_opening_it);
if (penetration) {
/// the friction coefficient mu increases with the damage. It
/// equals the maximum value when damage = 1.
// Real damage = std::min(*delta_max_prev_it / *delta_c_it,
// Real(1.));
Real mu = mu_max; // * damage;
/// the definition of tau_max refers to the opening
/// (penetration) of the previous incremental step
Real tau_max = mu * this->penalty * (std::abs(normal_opening_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
/// tau is the norm of the friction force, acting tangentially to the
/// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if ((tangential_opening_norm - *res_sliding_prev_it) < 0.0) {
tau = -tau;
}
/// from tau get the x and y components of friction, to be added in the
/// force vector
Vector<Real> tangent_unit_vector(spatial_dimension);
tangent_unit_vector = tangential_opening / tangential_opening_norm;
*friction_force_it = tau * tangent_unit_vector;
/// update residual_sliding
- *res_sliding_it =
- tangential_opening_norm - (std::abs(tau) / friction_penalty);
+ if (friction_penalty == 0.) {
+ *res_sliding_it =
+ tangential_opening_norm;
+ } else {
+ *res_sliding_it =
+ tangential_opening_norm - (std::abs(tau) / friction_penalty);
+ }
} else {
friction_force_it->zero();
}
*traction_it += *friction_force_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTangentTraction(
ElementType el_type, Array<Real> & tangent_matrix,
__attribute__((unused)) const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto previous_opening_it =
this->opening.previous(el_type, ghost_type).begin(spatial_dimension);
/**
* NB: delta_max_it points on delta_max_previous, i.e. the
* delta_max related to the solution of the previous incremental
* step
*/
auto delta_max_it = this->delta_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_it = this->damage(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++previous_opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it, ++damage_it,
++contact_opening_it, ++res_sliding_prev_it) {
Real normal_opening_norm;
Real tangential_opening_norm;
bool penetration;
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *contact_opening_it);
if (penetration) {
// Real damage = std::min(*delta_max_it / *delta_c_it, Real(1.));
Real mu = mu_max; // * damage;
Real normal_opening_prev_norm =
std::min(previous_opening_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * this->penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm =
std::abs(tangential_opening_norm - *res_sliding_prev_it);
// tau is the norm of the friction force, acting tangentially to the
// surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if (tau < tau_max && tau_max > Math::getTolerance()) {
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(1.);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
Matrix<Real> nn(n_outer_n);
I -= nn;
*tangent_it += I * friction_penalty;
}
}
// check if the tangential stiffness matrix is symmetric
// for (UInt h = 0; h < spatial_dimension; ++h){
// for (UInt l = h; l < spatial_dimension; ++l){
// if (l > h){
// Real k_ls = (*tangent_it)[spatial_dimension*h+l];
// Real k_us = (*tangent_it)[spatial_dimension*l+h];
// // std::cout << "k_ls = " << k_ls << std::endl;
// // std::cout << "k_us = " << k_us << std::endl;
// if (std::abs(k_ls) > 1e-13 && std::abs(k_us) > 1e-13){
// Real error = std::abs((k_ls - k_us) / k_us);
// if (error > 1e-10){
// std::cout << "non symmetric cohesive matrix" << std::endl;
// // std::cout << "error " << error << std::endl;
// }
// }
// }
// }
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_friction, MaterialCohesiveLinearFriction);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
index 55c463118..fa6de4a8f 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_friction.hh
@@ -1,104 +1,106 @@
/**
* @file material_cohesive_linear_friction.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Apr 28 2020
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_
#define AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with friction force
*
* parameters in the material files :
* - mu : friction coefficient
* - penalty_for_friction : Penalty parameter for the friction behavior
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFriction
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
using MaterialParent = MaterialCohesiveLinear<spatial_dimension>;
public:
MaterialCohesiveLinearFriction(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// maximum value of the friction coefficient
Real mu_max;
/// penalty parameter for the friction law
Real friction_penalty;
/// history parameter for the friction law
CohesiveInternalField<Real> residual_sliding;
/// friction force
CohesiveInternalField<Real> friction_force;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
index 9d9ac04bc..9d56e90f7 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_inline_impl.hh
@@ -1,269 +1,271 @@
/**
* @file material_cohesive_linear_inline_impl.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 22 2015
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Jan 14 2021
*
* @brief Inline functions of the MaterialCohesiveLinear
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
#define AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline Real MaterialCohesiveLinear<dim>::computeEffectiveNorm(
const Matrix<Real> & stress, const Vector<Real> & normal,
const Vector<Real> & tangent, Vector<Real> & normal_traction) const {
normal_traction.mul<false>(stress, normal);
Real normal_contrib = normal_traction.dot(normal);
/// in 3D tangential components must be summed
Real tangent_contrib = 0;
if (dim == 2) {
Real tangent_contrib_tmp = normal_traction.dot(tangent);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
} else if (dim == 3) {
for (UInt s = 0; s < dim - 1; ++s) {
const Vector<Real> tangent_v(tangent.storage() + s * dim, dim);
Real tangent_contrib_tmp = normal_traction.dot(tangent_v);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
}
}
tangent_contrib = std::sqrt(tangent_contrib);
normal_contrib = std::max(Real(0.), normal_contrib);
return std::sqrt(normal_contrib * normal_contrib +
tangent_contrib * tangent_contrib * beta2_inv);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTractionOnQuad(
Vector<Real> & traction, Vector<Real> & opening,
const Vector<Real> & normal, Real & delta_max, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_traction,
Vector<Real> & contact_opening) {
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm / delta_c < -Math::getTolerance();
// penetration = normal_opening_norm < 0.;
if (not this->contact_after_breaking and
Math::are_float_equal(damage, 1.)) {
penetration = false;
}
if (penetration) {
/// use penalty coefficient in case of penetration
contact_traction = normal_opening;
contact_traction *= this->penalty;
contact_opening = normal_opening;
/// don't consider penetration contribution for delta
opening = tangential_opening;
normal_opening.zero();
} else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction.zero();
contact_opening.zero();
}
delta = std::sqrt(delta);
/// update maximum displacement and damage
delta_max = std::max(delta_max, delta);
damage = std::min(delta_max / delta_c, Real(1.));
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
if (Math::are_float_equal(damage, 1.)) {
traction.zero();
} else if (Math::are_float_equal(damage, 0.)) {
if (penetration) {
traction.zero();
} else {
traction = insertion_stress;
}
} else {
traction = tangential_opening;
traction *= this->beta2_kappa;
traction += normal_opening;
AKANTU_DEBUG_ASSERT(delta_max != 0.,
"Division by zero, tolerance might be too low");
traction *= sigma_c / delta_max * (1. - damage);
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTangentTractionOnQuad(
Matrix<Real> & tangent, Real & delta_max, const Real & delta_c,
const Real & sigma_c, Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, Vector<Real> & contact_opening) {
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
opening += contact_opening;
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (not this->contact_after_breaking and
Math::are_float_equal(damage, 1.)) {
penetration = false;
}
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real t = 0;
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
if (penetration) {
/// stiffness in compression given by the penalty parameter
tangent += n_outer_n;
tangent *= penalty;
opening = tangential_opening;
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
} else {
delta += normal_opening_norm * normal_opening_norm;
}
delta = std::sqrt(delta);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta < Math::getTolerance()) {
delta = delta_c / 1000.;
}
if (delta >= delta_max) {
if (delta <= delta_c) {
derivative = -sigma_c / (delta * delta);
t = sigma_c * (1 - delta / delta_c);
} else {
derivative = 0.;
t = 0.;
}
} else if (delta < delta_max) {
Real tmax = sigma_c * (1 - delta_max / delta_c);
t = tmax / delta_max * delta;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(this->beta2_kappa);
Matrix<Real> nn(n_outer_n);
nn *= (1. - this->beta2_kappa);
nn += I;
nn *= t / delta;
Vector<Real> t_tilde(normal_opening);
t_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(opening);
mm *= this->beta2_kappa2;
t_tilde += mm;
Vector<Real> t_hat(normal_opening);
t_hat += this->beta2_kappa * tangential_opening;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(t_hat, t_tilde);
prov *= derivative / delta;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
tangent += prov_t;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
#endif //AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
index 0da10cc32..36346d8ea 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.cc
@@ -1,418 +1,420 @@
/**
* @file material_cohesive_linear_uncoupled.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Mon Jul 25 2016
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_uncoupled.hh"
#include "solid_mechanics_model_cohesive.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearUncoupled<spatial_dimension>::
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model, const ID & id)
: MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_n_max("delta_n_max", *this), delta_t_max("delta_t_max", *this),
damage_n("damage_n", *this), damage_t("damage_t", *this) {
AKANTU_DEBUG_IN();
this->registerParam(
"roughness", R, Real(1.), _pat_parsable | _pat_readable,
"Roughness to define coupling between mode II and mode I");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
delta_n_max.initialize(1);
delta_t_max.initialize(1);
damage_n.initialize(1);
damage_t.initialize(1);
delta_n_max.initializeHistory();
delta_t_max.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTraction(
const Array<Real> & /*unused*/, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
delta_n_max.resize();
delta_t_max.resize();
damage_n.resize();
damage_t.resize();
/// define iterators
auto traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
auto traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
auto contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_n_max_it = delta_n_max(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto damage_t_it = damage_t(el_type, ghost_type).begin();
auto insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++contact_traction_it, ++contact_opening_it,
++normal_it, ++sigma_c_it, ++delta_n_max_it, ++delta_t_max_it,
++delta_c_it, ++damage_n_it, ++damage_t_it, ++insertion_stress_it) {
Real normal_opening_norm;
Real tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
// std::cout<< "normal_opening_norm = " << normal_opening_norm
// <<std::endl;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/// compute effective opening displacement
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (not this->contact_after_breaking and
Math::are_float_equal(*damage_n_it, 1.)) {
penetration = false;
}
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
//*opening_it = tangential_opening;
normal_opening.zero();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
contact_traction_it->zero();
contact_opening_it->zero();
}
delta_n = std::sqrt(delta_n);
delta_t = std::sqrt(delta_t);
/// update maximum displacement and damage
*delta_n_max_it = std::max(*delta_n_max_it, delta_n);
*damage_n_it = std::min(*delta_n_max_it / *delta_c_it, Real(1.));
*delta_t_max_it = std::max(*delta_t_max_it, delta_t);
*damage_t_it = std::min(*delta_t_max_it / *delta_c_it, Real(1.));
Vector<Real> normal_traction(spatial_dimension);
Vector<Real> shear_traction(spatial_dimension);
/// NORMAL TRACTIONS
if (Math::are_float_equal(*damage_n_it, 1.)) {
normal_traction.zero();
} else if (Math::are_float_equal(*damage_n_it, 0.)) {
if (penetration) {
normal_traction.zero();
} else {
normal_traction = *insertion_stress_it;
}
} else {
// the following formulation holds both in loading and in
// unloading-reloading
normal_traction = normal_opening;
AKANTU_DEBUG_ASSERT(*delta_n_max_it != 0.,
"Division by zero, tolerance might be too low");
normal_traction *= *sigma_c_it / (*delta_n_max_it) * (1. - *damage_n_it);
}
/// SHEAR TRACTIONS
if (Math::are_float_equal(*damage_t_it, 1.) or
Math::are_float_equal(*damage_t_it, 0.)) {
shear_traction.zero();
} else {
shear_traction = tangential_opening;
AKANTU_DEBUG_ASSERT(*delta_t_max_it != 0.,
"Division by zero, tolerance might be too low");
shear_traction *= this->beta2_kappa;
shear_traction *= *sigma_c_it / (*delta_t_max_it) * (1. - *damage_t_it);
}
*traction_it = normal_traction;
*traction_it += shear_traction;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTangentTraction(
ElementType el_type, Array<Real> & tangent_matrix,
const Array<Real> & /*unused*/, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
auto tangent_it = tangent_matrix.begin(spatial_dimension, spatial_dimension);
auto tangent_end = tangent_matrix.end(spatial_dimension, spatial_dimension);
auto normal_it = this->normal.begin(spatial_dimension);
auto opening_it = this->opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
auto delta_n_max_it = delta_n_max.previous(el_type, ghost_type).begin();
auto delta_t_max_it = delta_t_max.previous(el_type, ghost_type).begin();
auto sigma_c_it = this->sigma_c_eff(el_type, ghost_type).begin();
auto delta_c_it = this->delta_c_eff(el_type, ghost_type).begin();
auto damage_n_it = damage_n(el_type, ghost_type).begin();
auto contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++sigma_c_it, ++delta_c_it,
++delta_n_max_it, ++delta_t_max_it,
++damage_n_it, ++contact_opening_it) {
Real normal_opening_norm;
Real tangential_opening_norm;
bool penetration;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
*opening_it += *contact_opening_it;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta_n =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t =
tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (not this->contact_after_breaking and
Math::are_float_equal(*damage_n_it, 1.)) {
penetration = false;
}
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real T = 0;
/// TANGENT STIFFNESS FOR NORMAL TRACTIONS
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
if (penetration) {
/// stiffness in compression given by the penalty parameter
*tangent_it = n_outer_n;
*tangent_it *= this->penalty;
//*opening_it = tangential_opening;
normal_opening.zero();
} else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_n = std::sqrt(delta_n);
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_n < Math::getTolerance()) {
delta_n = *delta_c_it / 1000.;
}
// loading
if (delta_n >= *delta_n_max_it) {
if (delta_n <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_n * delta_n);
T = *sigma_c_it * (1 - delta_n / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_n < *delta_n_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_n_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_n_max_it * delta_n;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> nn(n_outer_n);
nn *= T / delta_n;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
const Vector<Real> & Delta_hat(normal_opening);
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_n;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
*tangent_it = prov_t;
}
derivative = 0.;
T = 0.;
/// TANGENT STIFFNESS FOR SHEAR TRACTIONS
delta_t = std::sqrt(delta_t);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_t < Math::getTolerance()) {
delta_t = *delta_c_it / 1000.;
}
// loading
if (delta_t >= *delta_t_max_it) {
if (delta_t <= *delta_c_it) {
derivative = -(*sigma_c_it) / (delta_t * delta_t);
T = *sigma_c_it * (1 - delta_t / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_t < *delta_t_max_it) {
Real T_max = *sigma_c_it * (1 - *delta_t_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_t_max_it * delta_t;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye();
Matrix<Real> nn(n_outer_n);
I -= nn;
I *= T / delta_t;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (delta_c2_R2 - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
Vector<Real> Delta_hat(tangential_opening);
Delta_hat *= this->beta2_kappa;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_t;
prov += I;
Matrix<Real> prov_t = prov.transpose();
*tangent_it += prov_t;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(cohesive_linear_uncoupled,
MaterialCohesiveLinearUncoupled);
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
index a931b7feb..c7d19a437 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/constitutive_laws/material_cohesive_linear_uncoupled.hh
@@ -1,101 +1,103 @@
/**
* @file material_cohesive_linear_uncoupled.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Feb 20 2020
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_
#define AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* Cohesive material linear with two different laws for mode I and
* mode II, for extrinsic case
*
* parameters in the material files :
* - roughness : define the interaction between mode I and mode II (default: 0)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearUncoupled
: public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// typedef MaterialCohesiveLinear<spatial_dimension> MaterialParent;
public:
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
void initMaterial() override;
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute tangent stiffness matrix
void computeTangentTraction(ElementType el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// parameter to tune the interaction between mode II and mode I
Real R;
/// maximum normal displacement
CohesiveInternalField<Real> delta_n_max;
/// maximum tangential displacement
CohesiveInternalField<Real> delta_t_max;
/// damage associated to normal tractions
CohesiveInternalField<Real> damage_n;
/// damage associated to shear tractions
CohesiveInternalField<Real> damage_t;
};
} // namespace akantu
#endif /* AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
index 3ceebd44d..8c14d14b0 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.cc
@@ -1,568 +1,570 @@
/**
* @file material_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Thu Jan 14 2021
*
* @brief Specialization of the material class for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
#include "aka_random_generator.hh"
#include "dof_synchronizer.hh"
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialCohesive::MaterialCohesive(SolidMechanicsModel & model, const ID & id)
: Material(model, id),
facet_filter("facet_filter", id),
fem_cohesive(
model.getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine")),
reversible_energy("reversible_energy", *this),
total_energy("total_energy", *this), opening("opening", *this),
tractions("tractions", *this),
contact_tractions("contact_tractions", *this),
contact_opening("contact_opening", *this), delta_max("delta max", *this),
use_previous_delta_max(false), use_previous_opening(false),
damage("damage", *this), sigma_c("sigma_c", *this),
normal(0, spatial_dimension, "normal") {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<SolidMechanicsModelCohesive *>(&model);
this->registerParam("sigma_c", sigma_c, _pat_parsable | _pat_readable,
"Critical stress");
this->registerParam("delta_c", delta_c, Real(0.),
_pat_parsable | _pat_readable, "Critical displacement");
this->element_filter.initialize(this->model->getMesh(),
_spatial_dimension = spatial_dimension,
_element_kind = _ek_cohesive);
// this->model->getMesh().initElementTypeMapArray(
// this->element_filter, 1, spatial_dimension, false, _ek_cohesive);
if (this->model->getIsExtrinsic()) {
this->facet_filter.initialize(this->model->getMeshFacets(),
_spatial_dimension = spatial_dimension - 1,
_element_kind = _ek_regular);
}
// this->model->getMeshFacets().initElementTypeMapArray(facet_filter, 1,
// spatial_dimension -
// 1);
this->reversible_energy.initialize(1);
this->total_energy.initialize(1);
this->tractions.initialize(spatial_dimension);
this->tractions.initializeHistory();
this->contact_tractions.initialize(spatial_dimension);
this->contact_opening.initialize(spatial_dimension);
this->opening.initialize(spatial_dimension);
this->opening.initializeHistory();
this->delta_max.initialize(1);
this->damage.initialize(1);
if (this->model->getIsExtrinsic()) {
this->sigma_c.initialize(1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MaterialCohesive::~MaterialCohesive() = default;
/* -------------------------------------------------------------------------- */
void MaterialCohesive::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
if (this->use_previous_delta_max) {
this->delta_max.initializeHistory();
}
if (this->use_previous_opening) {
this->opening.initializeHistory();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Tractions", tractions);
#endif
auto & internal_force = const_cast<Array<Real> &>(model->getInternalForce());
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
auto & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0) {
continue;
}
const auto & shapes = fem_cohesive.getShapes(type, ghost_type);
auto & traction = tractions(type, ghost_type);
auto & contact_traction = contact_tractions(type, ghost_type);
UInt size_of_shapes = shapes.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
/// compute @f$t_i N_a@f$
auto * traction_cpy = new Array<Real>(nb_element * nb_quadrature_points,
spatial_dimension * size_of_shapes);
auto traction_it = traction.begin(spatial_dimension, 1);
auto contact_traction_it = contact_traction.begin(spatial_dimension, 1);
auto shapes_filtered_begin = shapes.begin(1, size_of_shapes);
auto traction_cpy_it =
traction_cpy->begin(spatial_dimension, size_of_shapes);
Matrix<Real> traction_tmp(spatial_dimension, 1);
for (UInt el = 0; el < nb_element; ++el) {
UInt current_quad = elem_filter(el) * nb_quadrature_points;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++traction_it,
++contact_traction_it, ++current_quad, ++traction_cpy_it) {
const Matrix<Real> & shapes_filtered =
shapes_filtered_begin[current_quad];
traction_tmp.copy(*traction_it);
traction_tmp += *contact_traction_it;
traction_cpy_it->mul<false, false>(traction_tmp, shapes_filtered);
}
}
/**
* compute @f$\int t \cdot N\, dS@f$ by @f$ \sum_q \mathbf{N}^t
* \mathbf{t}_q \overline w_q J_q@f$
*/
auto * partial_int_t_N = new Array<Real>(
nb_element, spatial_dimension * size_of_shapes, "int_t_N");
fem_cohesive.integrate(*traction_cpy, *partial_int_t_N,
spatial_dimension * size_of_shapes, type, ghost_type,
elem_filter);
delete traction_cpy;
auto * int_t_N = new Array<Real>(
nb_element, 2 * spatial_dimension * size_of_shapes, "int_t_N");
Real * int_t_N_val = int_t_N->storage();
Real * partial_int_t_N_val = partial_int_t_N->storage();
for (UInt el = 0; el < nb_element; ++el) {
std::copy_n(partial_int_t_N_val, size_of_shapes * spatial_dimension,
int_t_N_val);
std::copy_n(partial_int_t_N_val, size_of_shapes * spatial_dimension,
int_t_N_val + size_of_shapes * spatial_dimension);
for (UInt n = 0; n < size_of_shapes * spatial_dimension; ++n) {
int_t_N_val[n] *= -1.;
}
int_t_N_val += nb_nodes_per_element * spatial_dimension;
partial_int_t_N_val += size_of_shapes * spatial_dimension;
}
delete partial_int_t_N;
/// assemble
model->getDOFManager().assembleElementalArrayLocalArray(
*int_t_N, internal_force, type, ghost_type, 1, elem_filter);
delete int_t_N;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type,
_ek_cohesive)) {
UInt nb_quadrature_points =
fem_cohesive.getNbIntegrationPoints(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<Real> & shapes = fem_cohesive.getShapes(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0U) {
continue;
}
UInt size_of_shapes = shapes.getNbComponent();
auto * shapes_filtered = new Array<Real>(nb_element * nb_quadrature_points,
size_of_shapes, "filtered shapes");
Real * shapes_filtered_val = shapes_filtered->storage();
UInt * elem_filter_val = elem_filter.storage();
for (UInt el = 0; el < nb_element; ++el) {
auto * shapes_val = shapes.storage() + elem_filter_val[el] *
size_of_shapes *
nb_quadrature_points;
memcpy(shapes_filtered_val, shapes_val,
size_of_shapes * nb_quadrature_points * sizeof(Real));
shapes_filtered_val += size_of_shapes * nb_quadrature_points;
}
Matrix<Real> A(spatial_dimension * size_of_shapes,
spatial_dimension * nb_nodes_per_element);
for (UInt i = 0; i < spatial_dimension * size_of_shapes; ++i) {
A(i, i) = 1;
A(i, i + spatial_dimension * size_of_shapes) = -1;
}
/// get the tangent matrix @f$\frac{\partial{(t/\delta)}}{\partial{\delta}}
/// @f$
auto * tangent_stiffness_matrix = new Array<Real>(
nb_element * nb_quadrature_points,
spatial_dimension * spatial_dimension, "tangent_stiffness_matrix");
// Array<Real> * normal = new Array<Real>(nb_element *
// nb_quadrature_points, spatial_dimension, "normal");
normal.resize(nb_quadrature_points);
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
// computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
// ghost_type);
tangent_stiffness_matrix->zero();
computeTangentTraction(type, *tangent_stiffness_matrix, normal, ghost_type);
// delete normal;
UInt size_at_nt_d_n_a = spatial_dimension * nb_nodes_per_element *
spatial_dimension * nb_nodes_per_element;
auto * at_nt_d_n_a = new Array<Real>(nb_element * nb_quadrature_points,
size_at_nt_d_n_a, "A^t*N^t*D*N*A");
Array<Real>::iterator<Vector<Real>> shapes_filt_it =
shapes_filtered->begin(size_of_shapes);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator At_Nt_D_N_A_it =
at_nt_d_n_a->begin(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Array<Real>::matrix_iterator At_Nt_D_N_A_end =
at_nt_d_n_a->end(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> N(spatial_dimension, spatial_dimension * size_of_shapes);
Matrix<Real> N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> D_N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
for (; At_Nt_D_N_A_it != At_Nt_D_N_A_end;
++At_Nt_D_N_A_it, ++D_it, ++shapes_filt_it) {
N.zero();
/**
* store the shapes in voigt notations matrix @f$\mathbf{N} =
* \begin{array}{cccccc} N_0(\xi) & 0 & N_1(\xi) &0 & N_2(\xi) & 0 \\
* 0 & * N_0(\xi)& 0 &N_1(\xi)& 0 & N_2(\xi) \end{array} @f$
**/
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt n = 0; n < size_of_shapes; ++n) {
N(i, i + spatial_dimension * n) = (*shapes_filt_it)(n);
}
}
/**
* compute stiffness matrix @f$ \mathbf{K} = \delta \mathbf{U}^T
* \int_{\Gamma_c} {\mathbf{P}^t \frac{\partial{\mathbf{t}}}
*{\partial{\delta}}
* \mathbf{P} d\Gamma \Delta \mathbf{U}} @f$
**/
N_A.mul<false, false>(N, A);
D_N_A.mul<false, false>(*D_it, N_A);
(*At_Nt_D_N_A_it).mul<true, false>(D_N_A, N_A);
}
delete tangent_stiffness_matrix;
delete shapes_filtered;
auto * K_e = new Array<Real>(nb_element, size_at_nt_d_n_a, "K_e");
fem_cohesive.integrate(*at_nt_d_n_a, *K_e, size_at_nt_d_n_a, type,
ghost_type, elem_filter);
delete at_nt_d_n_a;
model->getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _unsymmetric, elem_filter);
delete K_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- *
* Compute traction from displacements
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void MaterialCohesive::computeTraction(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Openings", opening);
#endif
for (const auto & type : element_filter.elementTypes(
spatial_dimension, ghost_type, _ek_cohesive)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element == 0) {
continue;
}
UInt nb_quadrature_points =
nb_element * fem_cohesive.getNbIntegrationPoints(type, ghost_type);
normal.resize(nb_quadrature_points);
/// compute normals @f$\mathbf{n}@f$
computeNormal(model->getCurrentPosition(), normal, type, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
computeOpening(model->getDisplacement(), opening(type, ghost_type), type,
ghost_type);
/// compute traction @f$\mathbf{t}@f$
computeTraction(normal, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeNormal(const Array<Real> & position,
Array<Real> & normal, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
normal.zero();
#define COMPUTE_NORMAL(type) \
fem_cohesive.getShapeFunctions() \
.computeNormalsOnIntegrationPoints<type, CohesiveReduceFunctionMean>( \
position, normal, ghost_type, element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_NORMAL);
#undef COMPUTE_NORMAL
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeOpening(const Array<Real> & displacement,
Array<Real> & opening, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem_cohesive =
this->model->getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine");
#define COMPUTE_OPENING(type) \
fem_cohesive.getShapeFunctions() \
.interpolateOnIntegrationPoints<type, CohesiveReduceFunctionOpening>( \
displacement, opening, spatial_dimension, ghost_type, \
element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_OPENING);
#undef COMPUTE_OPENING
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::updateEnergies(ElementType type) {
AKANTU_DEBUG_IN();
if (Mesh::getKind(type) != _ek_cohesive) {
return;
}
Vector<Real> b(spatial_dimension);
Vector<Real> h(spatial_dimension);
auto erev = reversible_energy(type).begin();
auto etot = total_energy(type).begin();
auto traction_it = tractions(type).begin(spatial_dimension);
auto traction_old_it = tractions.previous(type).begin(spatial_dimension);
auto opening_it = opening(type).begin(spatial_dimension);
auto opening_old_it = opening.previous(type).begin(spatial_dimension);
auto traction_end = tractions(type).end(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++traction_old_it,
++opening_it, ++opening_old_it, ++erev,
++etot) {
/// trapezoidal integration
b = *opening_it;
b -= *opening_old_it;
h = *traction_old_it;
h += *traction_it;
*etot += .5 * b.dot(h);
*erev = .5 * traction_it->dot(*opening_it);
}
/// update old values
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getReversibleEnergy() {
AKANTU_DEBUG_IN();
Real erev = 0.;
/// integrate reversible energy for each type of elements
for (const auto & type : element_filter.elementTypes(
spatial_dimension, _not_ghost, _ek_cohesive)) {
erev +=
fem_cohesive.integrate(reversible_energy(type, _not_ghost), type,
_not_ghost, element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return erev;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getDissipatedEnergy() {
AKANTU_DEBUG_IN();
Real edis = 0.;
/// integrate dissipated energy for each type of elements
for (const auto & type : element_filter.elementTypes(
spatial_dimension, _not_ghost, _ek_cohesive)) {
Array<Real> dissipated_energy(total_energy(type, _not_ghost));
dissipated_energy -= reversible_energy(type, _not_ghost);
edis += fem_cohesive.integrate(dissipated_energy, type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return edis;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getContactEnergy() {
AKANTU_DEBUG_IN();
Real econ = 0.;
/// integrate contact energy for each type of elements
for (const auto & type : element_filter.elementTypes(
spatial_dimension, _not_ghost, _ek_cohesive)) {
auto & el_filter = element_filter(type, _not_ghost);
UInt nb_quad_per_el = fem_cohesive.getNbIntegrationPoints(type, _not_ghost);
UInt nb_quad_points = el_filter.size() * nb_quad_per_el;
Array<Real> contact_energy(nb_quad_points);
auto contact_traction_it =
contact_tractions(type, _not_ghost).begin(spatial_dimension);
auto contact_opening_it =
contact_opening(type, _not_ghost).begin(spatial_dimension);
/// loop on each quadrature point
for (UInt q = 0; q < nb_quad_points;
++contact_traction_it, ++contact_opening_it, ++q) {
contact_energy(q) = .5 * contact_traction_it->dot(*contact_opening_it);
}
econ += fem_cohesive.integrate(contact_energy, type, _not_ghost, el_filter);
}
AKANTU_DEBUG_OUT();
return econ;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getEnergy(const std::string & type) {
if (type == "reversible") {
return getReversibleEnergy();
}
if (type == "dissipated") {
return getDissipatedEnergy();
}
if (type == "cohesive contact") {
return getContactEnergy();
}
return 0.;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
index 9bc05fb2e..b584246f2 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
@@ -1,234 +1,236 @@
/**
* @file material_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Thu Jan 14 2021
*
* @brief Specialization of the material class for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
/* -------------------------------------------------------------------------- */
#include "cohesive_internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MATERIAL_COHESIVE_HH_
#define AKANTU_MATERIAL_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
class MaterialCohesive : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
public:
MaterialCohesive(SolidMechanicsModel & model, const ID & id = "");
~MaterialCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial() override;
/// compute tractions (including normals and openings)
void computeTraction(GhostType ghost_type = _not_ghost);
/// assemble residual
void assembleInternalForces(GhostType ghost_type = _not_ghost) override;
/// check stress for cohesive elements' insertion, by default it
/// also updates the cohesive elements' data
virtual void checkInsertion(bool /*check_only*/ = false) {
AKANTU_TO_IMPLEMENT();
}
/// interpolate stress on given positions for each element (empty
/// implemantation to avoid the generic call to be done on cohesive elements)
virtual void interpolateStress(const ElementType /*type*/,
Array<Real> & /*result*/) {}
/// compute the stresses
void computeAllStresses(GhostType /*ghost_type*/ = _not_ghost) override{};
// add the facet to be handled by the material
UInt addFacet(const Element & element);
protected:
virtual void computeTangentTraction(ElementType /*el_type*/,
Array<Real> & /*tangent_matrix*/,
const Array<Real> & /*normal*/,
GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_TO_IMPLEMENT();
}
/// compute the normal
void computeNormal(const Array<Real> & position, Array<Real> & normal,
ElementType type, GhostType ghost_type);
/// compute the opening
void computeOpening(const Array<Real> & displacement, Array<Real> & opening,
ElementType type, GhostType ghost_type);
template <ElementType type>
void computeNormal(const Array<Real> & position, Array<Real> & normal,
GhostType ghost_type);
/// assemble stiffness
void assembleStiffnessMatrix(GhostType ghost_type) override;
/// constitutive law
virtual void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) = 0;
/// parallelism functions
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
protected:
void updateEnergies(ElementType el_type) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the opening
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Opening, opening, Real);
/// get the traction
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Traction, tractions, Real);
/// get damage
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
/// get facet filter
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO(FacetFilter, facet_filter,
const ElementTypeMapArray<UInt> &);
// AKANTU_GET_MACRO(ElementFilter, element_filter, const
// ElementTypeMapArray<UInt> &);
/// compute reversible energy
Real getReversibleEnergy();
/// compute dissipated energy
Real getDissipatedEnergy();
/// compute contact energy
Real getContactEnergy();
/// get energy
Real getEnergy(const std::string & type) override;
/// return the energy (identified by id) for the provided element
Real getEnergy(const std::string & energy_id, ElementType type,
UInt index) override {
return Material::getEnergy(energy_id, type, index);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of facets assigned to this material
ElementTypeMapArray<UInt> facet_filter;
/// Link to the cohesive fem object in the model
FEEngine & fem_cohesive;
private:
/// reversible energy by quadrature point
CohesiveInternalField<Real> reversible_energy;
/// total energy by quadrature point
CohesiveInternalField<Real> total_energy;
protected:
/// opening in all elements and quadrature points
CohesiveInternalField<Real> opening;
/// traction in all elements and quadrature points
CohesiveInternalField<Real> tractions;
/// traction due to contact
CohesiveInternalField<Real> contact_tractions;
/// normal openings for contact tractions
CohesiveInternalField<Real> contact_opening;
/// maximum displacement
CohesiveInternalField<Real> delta_max;
/// tell if the previous delta_max state is needed (in iterative schemes)
bool use_previous_delta_max;
/// tell if the previous opening state is needed (in iterative schemes)
bool use_previous_opening;
/// damage
CohesiveInternalField<Real> damage;
/// pointer to the solid mechanics model for cohesive elements
SolidMechanicsModelCohesive * model;
/// critical stress
RandomInternalField<Real, FacetInternalField> sigma_c;
/// critical displacement
Real delta_c;
/// array to temporarily store the normals
Array<Real> normal;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_cohesive_inline_impl.hh"
#include "cohesive_internal_field_tmpl.hh"
#endif /* AKANTU_MATERIAL_COHESIVE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
index 821c4545d..95b80ad2a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_includes.hh
@@ -1,48 +1,50 @@
/**
* @file material_cohesive_includes.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
- * @date last modification: Fri Oct 13 2017
+ * @date last modification: Fri Apr 02 2021
*
* @brief List of includes for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
// /* --------------------------------------------------------------------------
// */
// #ifndef AKANTU_CMAKE_LIST_MATERIALS
// #include "material_cohesive.hh"
// #include "material_cohesive_bilinear.hh"
// #include "material_cohesive_exponential.hh"
// #include "material_cohesive_linear.hh"
// #include "material_cohesive_linear_fatigue.hh"
// #include "material_cohesive_linear_friction.hh"
// #include "material_cohesive_linear_uncoupled.hh"
// #endif
#define AKANTU_COHESIVE_MATERIAL_LIST \
((2, (cohesive_linear, MaterialCohesiveLinear)))( \
(2, (cohesive_linear_fatigue, MaterialCohesiveLinearFatigue)))( \
(2, (cohesive_linear_friction, MaterialCohesiveLinearFriction)))( \
(2, (cohesive_linear_uncoupled, MaterialCohesiveLinearUncoupled)))( \
(2, (cohesive_bilinear, MaterialCohesiveBilinear)))( \
(2, (cohesive_exponential, MaterialCohesiveExponential)))
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.hh
index 41779217c..9234567ca 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive_inline_impl.hh
@@ -1,107 +1,110 @@
/**
* @file material_cohesive_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief MaterialCohesive inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt MaterialCohesive::addFacet(const Element & element) {
Array<UInt> & f_filter = facet_filter(element.type, element.ghost_type);
f_filter.push_back(element.element);
return f_filter.size() - 1;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void MaterialCohesive::computeNormal(const Array<Real> & /*position*/,
Array<Real> & /*normal*/,
GhostType /*ghost_type*/) {}
/* -------------------------------------------------------------------------- */
inline UInt MaterialCohesive::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
switch (tag) {
case SynchronizationTag::_smm_stress: {
return 2 * spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements,
"CohesiveFEEngine");
}
case SynchronizationTag::_smmc_damage: {
return sizeof(Real) * this->getModel().getNbIntegrationPoints(
elements, "CohesiveFEEngine");
}
default: {
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void MaterialCohesive::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
switch (tag) {
case SynchronizationTag::_smm_stress: {
packElementDataHelper(tractions, buffer, elements, "CohesiveFEEngine");
packElementDataHelper(contact_tractions, buffer, elements,
"CohesiveFEEngine");
break;
}
case SynchronizationTag::_smmc_damage:
packElementDataHelper(damage, buffer, elements, "CohesiveFEEngine");
break;
default: {
}
}
}
/* -------------------------------------------------------------------------- */
inline void MaterialCohesive::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
switch (tag) {
case SynchronizationTag::_smm_stress: {
unpackElementDataHelper(tractions, buffer, elements, "CohesiveFEEngine");
unpackElementDataHelper(contact_tractions, buffer, elements,
"CohesiveFEEngine");
break;
}
case SynchronizationTag::_smmc_damage:
unpackElementDataHelper(damage, buffer, elements, "CohesiveFEEngine");
break;
default: {
}
}
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
index 03a95d527..bb08d0bf6 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
@@ -1,723 +1,696 @@
/**
* @file solid_mechanics_model_cohesive.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Solid mechanics model for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "aka_iterators.hh"
#include "cohesive_element_inserter.hh"
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "fe_engine_template.hh"
#include "global_ids_updater.hh"
#include "integrator_gauss.hh"
#include "material_cohesive.hh"
#include "mesh_accessor.hh"
#include "mesh_global_data_updater.hh"
#include "parser.hh"
#include "shape_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
class CohesiveMeshGlobalDataUpdater : public MeshGlobalDataUpdater {
public:
CohesiveMeshGlobalDataUpdater(SolidMechanicsModelCohesive & model)
: model(model), mesh(model.getMesh()),
global_ids_updater(model.getMesh(), *model.cohesive_synchronizer) {}
/* ------------------------------------------------------------------------ */
std::tuple<UInt, UInt>
updateData(NewNodesEvent & nodes_event,
NewElementsEvent & elements_event) override {
auto *cohesive_nodes_event =
dynamic_cast<CohesiveNewNodesEvent *>(&nodes_event);
if (cohesive_nodes_event == nullptr) {
return std::make_tuple(nodes_event.getList().size(),
elements_event.getList().size());
}
/// update nodes type
auto & new_nodes = cohesive_nodes_event->getList();
auto & old_nodes = cohesive_nodes_event->getOldNodesList();
auto local_nb_new_nodes = new_nodes.size();
auto nb_new_nodes = local_nb_new_nodes;
if (mesh.isDistributed()) {
MeshAccessor mesh_accessor(mesh);
auto & nodes_flags = mesh_accessor.getNodesFlags();
auto nb_old_nodes = nodes_flags.size();
nodes_flags.resize(nb_old_nodes + local_nb_new_nodes);
for (auto && data : zip(old_nodes, new_nodes)) {
UInt old_node;
UInt new_node;
std::tie(old_node, new_node) = data;
nodes_flags(new_node) = nodes_flags(old_node);
}
model.updateCohesiveSynchronizers(elements_event);
nb_new_nodes = global_ids_updater.updateGlobalIDs(new_nodes.size());
}
- Vector<UInt> nb_new_stuff = {nb_new_nodes, elements_event.getList().size()};
+ auto nb_new_elements = elements_event.getList().size();
const auto & comm = mesh.getCommunicator();
- comm.allReduce(nb_new_stuff, SynchronizerOperation::_sum);
+ comm.allReduce(nb_new_elements, SynchronizerOperation::_sum);
- if (nb_new_stuff(1) > 0) {
+ if (nb_new_elements > 0) {
mesh.sendEvent(elements_event);
}
- if (nb_new_stuff(0) > 0) {
+ if (nb_new_nodes > 0) {
mesh.sendEvent(nodes_event);
- // mesh.sendEvent(global_ids_updater.getChangedNodeEvent());
}
- return std::make_tuple(nb_new_stuff(0), nb_new_stuff(1));
+ return std::make_tuple(nb_new_nodes, nb_new_elements);
}
private:
SolidMechanicsModelCohesive & model;
Mesh & mesh;
GlobalIdsUpdater global_ids_updater;
};
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(
Mesh & mesh, UInt dim, const ID & id, std::shared_ptr<DOFManager> dof_manager)
: SolidMechanicsModel(mesh, dim, id, dof_manager,
ModelType::_solid_mechanics_model_cohesive),
tangents("tangents", id), facet_stress("facet_stress", id),
facet_material("facet_material", id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh,
Model::spatial_dimension);
auto && tmp_material_selector =
std::make_shared<DefaultMaterialCohesiveSelector>(*this);
tmp_material_selector->setFallback(this->material_selector);
this->material_selector = tmp_material_selector;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
this->mesh.addDumpMeshToDumper("cohesive elements", mesh,
Model::spatial_dimension, _not_ghost,
_ek_cohesive);
#endif
if (this->mesh.isDistributed()) {
/// create the distributed synchronizer for cohesive elements
this->cohesive_synchronizer = std::make_unique<ElementSynchronizer>(
mesh, "cohesive_distributed_synchronizer");
auto & synchronizer = mesh.getElementSynchronizer();
this->cohesive_synchronizer->split(synchronizer, [](auto && el) {
return Mesh::getKind(el.type) == _ek_cohesive;
});
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_material_id);
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_smm_stress);
this->registerSynchronizer(*cohesive_synchronizer,
SynchronizationTag::_smm_boundary);
}
this->inserter = std::make_unique<CohesiveElementInserter>(
this->mesh, id + ":cohesive_element_inserter");
registerFEEngineObject<MyFEEngineFacetType>(
"FacetsFEEngine", mesh.getMeshFacets(), Model::spatial_dimension - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() = default;
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::setTimeStep(Real time_step,
const ID & solver_id) {
SolidMechanicsModel::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("cohesive elements").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initFullImpl(const ModelOptions & options) {
AKANTU_DEBUG_IN();
const auto & smmc_options =
aka::as_type<SolidMechanicsModelCohesiveOptions>(options);
this->is_extrinsic = smmc_options.is_extrinsic;
inserter->setIsExtrinsic(is_extrinsic);
if (mesh.isDistributed()) {
auto & mesh_facets = inserter->getMeshFacets();
auto & synchronizer =
aka::as_type<FacetSynchronizer>(mesh_facets.getElementSynchronizer());
// synchronizeGhostFacetsConnectivity();
/// create the facet synchronizer for extrinsic simulations
if (is_extrinsic) {
facet_stress_synchronizer = std::make_unique<ElementSynchronizer>(
synchronizer, id + ":facet_stress_synchronizer");
facet_stress_synchronizer->swapSendRecv();
this->registerSynchronizer(*facet_stress_synchronizer,
SynchronizationTag::_smmc_facets_stress);
}
}
MeshAccessor mesh_accessor(mesh);
mesh_accessor.registerGlobalDataUpdater(
std::make_unique<CohesiveMeshGlobalDataUpdater>(*this));
ParserSection section;
bool is_empty;
std::tie(section, is_empty) = this->getParserSection();
if (not is_empty) {
auto inserter_section =
section.getSubSections(ParserType::_cohesive_inserter);
if (inserter_section.begin() != inserter_section.end()) {
inserter->parseSection(*inserter_section.begin());
}
}
SolidMechanicsModel::initFullImpl(options);
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if (not are_materials_instantiated) {
instantiateMaterials();
}
/// find the first cohesive material
UInt cohesive_index = UInt(-1);
for (auto && material : enumerate(materials)) {
if (dynamic_cast<MaterialCohesive *>(std::get<1>(material).get()) !=
nullptr) {
cohesive_index = std::get<0>(material);
break;
}
}
if (cohesive_index == UInt(-1)) {
AKANTU_EXCEPTION("No cohesive materials in the material input file");
}
material_selector->setFallback(cohesive_index);
// set the facet information in the material in case of dynamic insertion
// to know what material to call for stress checks
const Mesh & mesh_facets = inserter->getMeshFacets();
facet_material.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true,
_default_value = material_selector->getFallbackValue());
for_each_element(
mesh_facets,
[&](auto && element) {
auto mat_index = (*material_selector)(element);
auto & mat = aka::as_type<MaterialCohesive>(*materials[mat_index]);
facet_material(element) = mat_index;
if (is_extrinsic) {
mat.addFacet(element);
}
},
_spatial_dimension = spatial_dimension - 1, _ghost_type = _not_ghost);
SolidMechanicsModel::initMaterials();
if (is_extrinsic) {
this->initAutomaticInsertion();
} else {
this->insertIntrinsicElements();
}
AKANTU_DEBUG_OUT();
} // namespace akantu
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*/
void SolidMechanicsModelCohesive::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
/// add cohesive type connectivity
ElementType type = _not_defined;
for (auto && type_ghost : ghost_types) {
for (const auto & tmp_type :
mesh.elementTypes(spatial_dimension, type_ghost)) {
const auto & connectivity = mesh.getConnectivity(tmp_type, type_ghost);
if (connectivity.empty()) {
continue;
}
type = tmp_type;
auto type_facet = Mesh::getFacetType(type);
auto type_cohesive = FEEngine::getCohesiveElementType(type_facet);
mesh.addConnectivityType(type_cohesive, type_ghost);
}
}
AKANTU_DEBUG_ASSERT(type != _not_defined, "No elements in the mesh");
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
if (is_extrinsic) {
getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
inserter->insertIntrinsicElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
this->resizeFacetStress();
/// compute normals on facets
this->computeNormals();
this->initStressInterpolation();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
AKANTU_DEBUG_IN();
this->inserter->limitCheckFacets();
this->updateFacetStressSynchronizer();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initStressInterpolation() {
Mesh & mesh_facets = inserter->getMeshFacets();
/// compute quadrature points coordinates on facets
Array<Real> & position = mesh.getNodes();
ElementTypeMapArray<Real> quad_facets("quad_facets", id);
quad_facets.initialize(mesh_facets, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(quad_facets, Model::spatial_dimension,
// Model::spatial_dimension - 1);
getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets);
/// compute elements quadrature point positions and build
/// element-facet quadrature points data structure
ElementTypeMapArray<Real> elements_quad_facets("elements_quad_facets", id);
elements_quad_facets.initialize(
mesh, _nb_component = Model::spatial_dimension,
_spatial_dimension = Model::spatial_dimension);
// mesh.initElementTypeMapArray(elements_quad_facets,
// Model::spatial_dimension,
// Model::spatial_dimension);
for (auto elem_gt : ghost_types) {
for (const auto & type : mesh.elementTypes(Model::spatial_dimension, elem_gt)) {
UInt nb_element = mesh.getNbElement(type, elem_gt);
if (nb_element == 0) {
continue;
}
/// compute elements' quadrature points and list of facet
/// quadrature points positions by element
const auto & facet_to_element =
mesh_facets.getSubelementToElement(type, elem_gt);
auto & el_q_facet = elements_quad_facets(type, elem_gt);
auto facet_type = Mesh::getFacetType(type);
auto nb_quad_per_facet =
getFEEngine("FacetsFEEngine").getNbIntegrationPoints(facet_type);
auto nb_facet_per_elem = facet_to_element.getNbComponent();
// small hack in the loop to skip boundary elements, they are silently
// initialized to NaN to see if this causes problems
el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet,
std::numeric_limits<Real>::quiet_NaN());
for (auto && data :
zip(make_view(facet_to_element),
make_view(el_q_facet, spatial_dimension, nb_quad_per_facet))) {
const auto & global_facet = std::get<0>(data);
auto & el_q = std::get<1>(data);
if (global_facet == ElementNull) {
continue;
}
Matrix<Real> quad_f =
make_view(quad_facets(global_facet.type, global_facet.ghost_type),
spatial_dimension, nb_quad_per_facet)
.begin()[global_facet.element];
el_q = quad_f;
-
- // for (UInt q = 0; q < nb_quad_per_facet; ++q) {
- // for (UInt s = 0; s < Model::spatial_dimension; ++s) {
- // el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
- // f * nb_quad_per_facet + q,
- // s) = quad_f(global_facet * nb_quad_per_facet + q,
- // s);
- // }
- // }
- //}
}
}
}
/// loop over non cohesive materials
for (auto && material : materials) {
if (aka::is_of_type<MaterialCohesive>(material)) {
continue;
}
/// initialize the interpolation function
material->initElementalFieldInterpolation(elements_quad_facets);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::assembleInternalForces() {
AKANTU_DEBUG_IN();
// f_int += f_int_cohe
for (auto & material : this->materials) {
try {
auto & mat = aka::as_type<MaterialCohesive>(*material);
mat.computeTraction(_not_ghost);
} catch (std::bad_cast & bce) {
}
}
SolidMechanicsModel::assembleInternalForces();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::computeNormals() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = this->inserter->getMeshFacets();
this->getFEEngine("FacetsFEEngine")
.computeNormalsOnIntegrationPoints(_not_ghost);
/**
* @todo store tangents while computing normals instead of
* recomputing them as follows:
*/
/* ------------------------------------------------------------------------ */
UInt tangent_components =
Model::spatial_dimension * (Model::spatial_dimension - 1);
tangents.initialize(mesh_facets, _nb_component = tangent_components,
_spatial_dimension = Model::spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(tangents, tangent_components,
// Model::spatial_dimension - 1);
for (auto facet_type :
mesh_facets.elementTypes(Model::spatial_dimension - 1)) {
const Array<Real> & normals =
this->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(facet_type);
Array<Real> & tangents = this->tangents(facet_type);
Math::compute_tangents(normals, tangents);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::interpolateStress() {
ElementTypeMapArray<Real> by_elem_result("temporary_stress_by_facets", id);
for (auto & material : materials) {
if (not aka::is_of_type<MaterialCohesive>(material)) {
/// interpolate stress on facet quadrature points positions
material->interpolateStressOnFacets(facet_stress, by_elem_result);
}
}
this->synchronize(SynchronizationTag::_smmc_facets_stress);
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
AKANTU_DEBUG_IN();
if (not is_extrinsic) {
AKANTU_EXCEPTION(
"This function can only be used for extrinsic cohesive elements");
}
interpolateStress();
for (auto & mat : materials) {
if (aka::is_of_type<MaterialCohesive>(mat)) {
/// check which not ghost cohesive elements are to be created
auto * mat_cohesive = aka::as_type<MaterialCohesive>(mat.get());
mat_cohesive->checkInsertion();
}
}
/// communicate data among processors
// this->synchronize(SynchronizationTag::_smmc_facets);
/// insert cohesive elements
UInt nb_new_elements = inserter->insertElements();
// if (nb_new_elements > 0) {
// this->reinitializeSolver();
// }
AKANTU_DEBUG_OUT();
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
SolidMechanicsModel::onElementsAdded(element_list, event);
if (is_extrinsic) {
resizeFacetStress();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onNodesAdded(const Array<UInt> & new_nodes,
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
SolidMechanicsModel::onNodesAdded(new_nodes, event);
const CohesiveNewNodesEvent * cohesive_event;
if ((cohesive_event = dynamic_cast<const CohesiveNewNodesEvent *>(&event)) ==
nullptr) {
return;
}
const auto & old_nodes = cohesive_event->getOldNodesList();
auto copy = [this, &new_nodes, &old_nodes](auto & arr) {
UInt new_node;
UInt old_node;
auto view = make_view(arr, spatial_dimension);
auto begin = view.begin();
for (auto && pair : zip(new_nodes, old_nodes)) {
std::tie(new_node, old_node) = pair;
auto old_ = begin + old_node;
auto new_ = begin + new_node;
*new_ = *old_;
}
};
copy(*displacement);
copy(*blocked_dofs);
if (velocity) {
copy(*velocity);
}
if (acceleration) {
copy(*acceleration);
}
if (current_position) {
copy(*current_position);
}
if (previous_displacement) {
copy(*previous_displacement);
}
- // if (external_force)
- // copy(*external_force);
- // if (internal_force)
- // copy(*internal_force);
-
if (displacement_increment) {
copy(*displacement_increment);
}
copy(getDOFManager().getSolution("displacement"));
// this->assembleMassLumped();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::afterSolveStep(bool converged) {
AKANTU_DEBUG_IN();
/*
* This is required because the Cauchy stress is the stress measure that
* is used to check the insertion of cohesive elements
*/
if (converged) {
for (auto & mat : materials) {
if (mat->isFiniteDeformation()) {
mat->computeAllCauchyStresses(_not_ghost);
}
}
}
SolidMechanicsModel::afterSolveStep(converged);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolidMechanicsModelCohesive ["
<< "\n";
SolidMechanicsModel::printself(stream, indent + 2);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::resizeFacetStress() {
AKANTU_DEBUG_IN();
this->facet_stress.initialize(getFEEngine("FacetsFEEngine"),
_nb_component =
2 * spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension - 1);
- // for (auto && ghost_type : ghost_types) {
- // for (const const auto & type :
- // mesh_facets.elementTypes(spatial_dimension - 1, ghost_type)) {
- // UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
-
- // UInt nb_quadrature_points = getFEEngine("FacetsFEEngine")
- // .getNbIntegrationPoints(type,
- // ghost_type);
-
- // UInt new_size = nb_facet * nb_quadrature_points;
-
- // facet_stress(type, ghost_type).resize(new_size);
- // }
- // }
-
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
const std::string & group_name, ElementKind element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = Model::spatial_dimension;
ElementKind _element_kind = element_kind;
if (dumper_name == "cohesive elements") {
_element_kind = _ek_cohesive;
} else if (dumper_name == "facets") {
spatial_dimension = Model::spatial_dimension - 1;
}
+
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id,
group_name, spatial_dimension,
_element_kind, padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onDump() {
this->flattenAllRegisteredInternals(_ek_cohesive);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
index c8a0081b2..85ce58462 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
@@ -1,308 +1,310 @@
/**
* @file solid_mechanics_model_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
- * @date last modification: Mon Feb 05 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Solid mechanics model for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
#include "material_selector_cohesive.hh"
#include "random_internal_field.hh" // included to have the specialization of
// ParameterTyped::operator Real()
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class FacetSynchronizer;
class FacetStressSynchronizer;
class ElementSynchronizer;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
struct FacetsCohesiveIntegrationOrderFunctor {
template <ElementType type, ElementType cohesive_type =
CohesiveFacetProperty<type>::cohesive_type>
struct _helper {
static constexpr int get() {
return ElementClassProperty<cohesive_type>::polynomial_degree;
}
};
template <ElementType type> struct _helper<type, _not_defined> {
static constexpr int get() {
return ElementClassProperty<type>::polynomial_degree;
}
};
template <ElementType type> static inline constexpr int getOrder() {
return _helper<type>::get();
}
};
/* -------------------------------------------------------------------------- */
/* Solid Mechanics Model for Cohesive elements */
/* -------------------------------------------------------------------------- */
class SolidMechanicsModelCohesive : public SolidMechanicsModel,
public SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewCohesiveNodesEvent : public NewNodesEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
protected:
Array<UInt> old_nodes;
};
using MyFEEngineCohesiveType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>;
using MyFEEngineFacetType =
FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
FacetsCohesiveIntegrationOrderFunctor>;
SolidMechanicsModelCohesive(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "solid_mechanics_model_cohesive",
std::shared_ptr<DOFManager> dof_manager = nullptr);
~SolidMechanicsModelCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// initialize the cohesive model
void initFullImpl(const ModelOptions & options) override;
public:
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// assemble the residual for the explicit scheme
void assembleInternalForces() override;
/// function to perform a stress check on each facet and insert
/// cohesive elements if needed (returns the number of new cohesive
/// elements)
UInt checkCohesiveStress();
/// interpolate stress on facets
void interpolateStress();
/// update automatic insertion after a change in the element inserter
void updateAutomaticInsertion();
/// insert intrinsic cohesive elements
void insertIntrinsicElements();
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria
// criteria> bool solveStepCohesive(Real tolerance, Real & error, UInt
// max_iteration = 100,
// bool load_reduction = false,
// Real tol_increase_factor = 1.0,
// bool do_not_factorize = false);
protected:
/// initialize stress interpolation
void initStressInterpolation();
/// initialize the model
void initModel() override;
/// initialize cohesive material
void initMaterials() override;
/// init facet filters for cohesive materials
void initFacetFilter();
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
private:
/// insert cohesive elements along a given physical surface of the mesh
void insertElementsFromMeshData(const std::string & physical_name);
/// initialize completely the model for extrinsic elements
void initAutomaticInsertion();
/// compute facets' normals
void computeNormals();
/// resize facet stress
void resizeFacetStress();
/// init facets_check array
void initFacetsCheck();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & new_nodes,
const NewNodesEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void afterSolveStep(bool converged = true) override;
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
void onDump() override;
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
ElementKind element_kind,
bool padding_flag) override;
public:
/// register the tags associated with the parallel synchronizer for
/// cohesive elements
// void initParallel(MeshPartition * partition,
// DataAccessor * data_accessor = NULL,
// bool extrinsic = false);
protected:
//void synchronizeGhostFacetsConnectivity();
void updateCohesiveSynchronizers(NewElementsEvent & elements_event);
void updateFacetStressSynchronizer();
friend class CohesiveElementInserter;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
protected:
UInt getNbQuadsForFacetCheck(const Array<Element> & elements) const;
template <typename T>
void packFacetStressDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T>
void unpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <typename T, bool pack_helper>
void packUnpackFacetStressDataHelper(ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & element) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get facet mesh
AKANTU_GET_MACRO(MeshFacets, mesh.getMeshFacets(), const Mesh &);
/// get stress on facets vector
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(StressOnFacets, facet_stress, Real);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO(FacetMaterial, facet_material,
const ElementTypeMapArray<UInt> &);
/// @todo THIS HAS TO BE CHANGED
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Tangents, tangents, Real);
/// get element inserter
AKANTU_GET_MACRO_NOT_CONST(ElementInserter, *inserter,
CohesiveElementInserter &);
/// get is_extrinsic boolean
AKANTU_GET_MACRO(IsExtrinsic, is_extrinsic, bool);
/// get cohesive elements synchronizer
AKANTU_GET_MACRO_NOT_CONST(CohesiveSynchronizer, *cohesive_synchronizer,
ElementSynchronizer &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
friend class CohesiveMeshGlobalDataUpdater;
/// @todo store tangents when normals are computed:
ElementTypeMapArray<Real> tangents;
/// stress on facets on the two sides by quadrature point
ElementTypeMapArray<Real> facet_stress;
/// material to use if a cohesive element is created on a facet
ElementTypeMapArray<UInt> facet_material;
bool is_extrinsic{false};
/// cohesive element inserter
std::unique_ptr<CohesiveElementInserter> inserter;
/// facet stress synchronizer
std::unique_ptr<ElementSynchronizer> facet_stress_synchronizer;
/// cohesive elements synchronizer
std::unique_ptr<ElementSynchronizer> cohesive_synchronizer;
};
} // namespace akantu
#include "solid_mechanics_model_cohesive_inline_impl.hh"
#endif /* AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
index ada180a26..c4dfdbf5a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.hh
@@ -1,305 +1,307 @@
/**
* @file solid_mechanics_model_cohesive_inline_impl.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 18 2013
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief Implementation of inline functions for the Cohesive element model
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModelCohesive::solveStepCohesive(
// Real tolerance, Real & error, UInt max_iteration, bool load_reduction,
// Real tol_increase_factor, bool do_not_factorize) {
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
// // this->implicitPred();
// // bool insertion_new_element = true;
// // bool converged = false;
// // Array<Real> * displacement_tmp = NULL;
// // Array<Real> * velocity_tmp = NULL;
// // Array<Real> * acceleration_tmp = NULL;
// // StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// // Int prank = comm.whoAmI();
// // /// Loop for the insertion of new cohesive elements
// // while (insertion_new_element) {
// // if (is_extrinsic) {
// // /**
// // * If in extrinsic the solution of the previous incremental step
// // * is saved in temporary arrays created for displacements,
// // * velocities and accelerations. Such arrays are used to find
// // * the solution with the Newton-Raphson scheme (this is done by
// // * pointing the pointer "displacement" to displacement_tmp). In
// // * this way, inside the array "displacement" is kept the
// // * solution of the previous incremental step, and in
// // * "displacement_tmp" is saved the current solution.
// // */
// // if (!displacement_tmp)
// // displacement_tmp = new Array<Real>(0, spatial_dimension);
// // displacement_tmp->copy(*(this->displacement));
// // if (!velocity_tmp)
// // velocity_tmp = new Array<Real>(0, spatial_dimension);
// // velocity_tmp->copy(*(this->velocity));
// // if (!acceleration_tmp) {
// // acceleration_tmp = new Array<Real>(0, spatial_dimension);
// // }
// // acceleration_tmp->copy(*(this->acceleration));
// // std::swap(displacement, displacement_tmp);
// // std::swap(velocity, velocity_tmp);
// // std::swap(acceleration, acceleration_tmp);
// // }
// // this->updateResidual();
// // AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
// // "You should first initialize the implicit solver and
// "
// // "assemble the stiffness matrix");
// // bool need_factorize = !do_not_factorize;
// // if (method == _implicit_dynamic) {
// // AKANTU_DEBUG_ASSERT(mass_matrix != NULL, "You should first initialize
// "
// // "the implicit solver and "
// // "assemble the mass matrix");
// // }
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // case _scm_newton_raphson_tangent_not_computed:
// // break;
// // case _scm_newton_raphson_tangent_modified:
// // this->assembleStiffnessMatrix();
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // UInt iter = 0;
// // converged = false;
// // error = 0.;
// // if (criteria == SolveConvergenceCriteria::_residual) {
// // converged = this->testConvergence<criteria>(tolerance, error);
// // if (converged)
// // return converged;
// // }
// // /// Loop to solve the nonlinear system
// // do {
// // if (cmethod == _scm_newton_raphson_tangent)
// // this->assembleStiffnessMatrix();
// // solve<NewmarkBeta::_displacement_corrector>(*increment, 1.,
// // need_factorize);
// // this->implicitCorr();
// // this->updateResidual();
// // converged = this->testConvergence<criteria>(tolerance, error);
// // iter++;
// // AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
// // << std::setw(std::log10(max_iteration)) << iter
// // << ": error " << error
// // << (converged ? " < " : " > ") << tolerance);
// // switch (cmethod) {
// // case _scm_newton_raphson_tangent:
// // need_factorize = true;
// // break;
// // case _scm_newton_raphson_tangent_not_computed:
// // case _scm_newton_raphson_tangent_modified:
// // need_factorize = false;
// // break;
// // default:
// // AKANTU_ERROR("The resolution method "
// // << cmethod << " has not been implemented!");
// // }
// // } while (!converged && iter < max_iteration);
// // /**
// // * This is to save the obtained result and proceed with the
// // * simulation even if the error is higher than the pre-fixed
// // * tolerance. This is done only after loading reduction
// // * (load_reduction = true).
// // */
// // // if (load_reduction && (error < tolerance * tol_increase_factor))
// // // converged = true;
// // if ((error < tolerance * tol_increase_factor))
// // converged = true;
// // if (converged) {
// // } else if (iter == max_iteration) {
// // if (prank == 0) {
// // AKANTU_DEBUG_WARNING(
// // "[" << criteria << "] Convergence not reached after "
// // << std::setw(std::log10(max_iteration)) << iter << "
// iteration"
// // << (iter == 1 ? "" : "s") << "!" << std::endl);
// // }
// // }
// // if (is_extrinsic) {
// // /**
// // * If is extrinsic the pointer "displacement" is moved back to
// // * the array displacement. In this way, the array displacement is
// // * correctly resized during the checkCohesiveStress function (in
// // * case new cohesive elements are added). This is possible
// // * because the procedure called by checkCohesiveStress does not
// // * use the displacement field (the correct one is now stored in
// // * displacement_tmp), but directly the stress field that is
// // * already computed.
// // */
// // Array<Real> * tmp_swap;
// // tmp_swap = displacement_tmp;
// // displacement_tmp = this->displacement;
// // this->displacement = tmp_swap;
// // tmp_swap = velocity_tmp;
// // velocity_tmp = this->velocity;
// // this->velocity = tmp_swap;
// // tmp_swap = acceleration_tmp;
// // acceleration_tmp = this->acceleration;
// // this->acceleration = tmp_swap;
// // /// If convergence is reached, call checkCohesiveStress in order
// // /// to check if cohesive elements have to be introduced
// // if (converged) {
// // UInt new_cohesive_elements = checkCohesiveStress();
// // if (new_cohesive_elements == 0) {
// // insertion_new_element = false;
// // } else {
// // insertion_new_element = true;
// // }
// // }
// // }
// // if (!converged && load_reduction)
// // insertion_new_element = false;
// // /**
// // * If convergence is not reached, there is the possibility to
// // * return back to the main file and reduce the load. Before doing
// // * this, a pre-fixed value as to be defined for the parameter
// // * delta_max of the cohesive elements introduced in the current
// // * incremental step. This is done by calling the function
// // * checkDeltaMax.
// // */
// // if (!converged) {
// // insertion_new_element = false;
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.checkDeltaMax(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // }
// // } // end loop for the insertion of new cohesive elements
// // /**
// // * When the solution to the current incremental step is computed (no
// // * more cohesive elements have to be introduced), call the function
// // * to compute the energies.
// // */
// // if ((is_extrinsic && converged)) {
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.computeEnergies();
// // } catch (std::bad_cast & bce) {
// // }
// // }
// // EventManager::sendEvent(
// // SolidMechanicsModelEvent::AfterSolveStepEvent(method));
// // /**
// // * The function resetVariables is necessary to correctly set a
// // * variable that permit to decrease locally the penalty parameter
// // * for compression.
// // */
// // for (UInt m = 0; m < materials.size(); ++m) {
// // try {
// // MaterialCohesive & mat =
// // aka::as_type<MaterialCohesive>(*materials[m]);
// // mat.resetVariables(_not_ghost);
// // } catch (std::bad_cast &) {
// // }
// // }
// // /// The correct solution is saved
// // this->displacement->copy(*displacement_tmp);
// // this->velocity->copy(*velocity_tmp);
// // this->acceleration->copy(*acceleration_tmp);
// // }
// // delete displacement_tmp;
// // delete velocity_tmp;
// // delete acceleration_tmp;
// // return insertion_new_element;
//}
} // namespace akantu
#endif /* AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
index 1a4ae385e..bfd5e2ed8 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
@@ -1,522 +1,524 @@
/**
* @file solid_mechanics_model_cohesive_parallel.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Functions for parallel cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_synchronizer.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModelCohesive::synchronizeGhostFacetsConnectivity() {
// AKANTU_DEBUG_IN();
// const Communicator & comm = mesh.getCommunicator();
// Int psize = comm.getNbProc();
// if (psize == 1) {
// AKANTU_DEBUG_OUT();
// return;
// }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateCohesiveSynchronizers(
NewElementsEvent & elements_event) {
/// update synchronizers if needed
if (not mesh.isDistributed()) {
return;
}
ElementTypeMap<Int> nb_new_cohesive_elements;
for (auto ghost_type : ghost_types) {
for(auto cohesive_type : mesh.elementTypes(spatial_dimension, ghost_type, _ek_cohesive)){
nb_new_cohesive_elements(cohesive_type, ghost_type) = 0;
}
}
for(auto & el : elements_event.getList()) {
if(el.kind() != _ek_cohesive) continue;
++nb_new_cohesive_elements(el.type, el.ghost_type);
}
auto & mesh_facets = inserter->getMeshFacets();
auto & facet_synchronizer = mesh_facets.getElementSynchronizer();
const auto & cfacet_synchronizer = facet_synchronizer;
// update the cohesive element synchronizer
cohesive_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && direction) {
auto & facet_scheme =
cfacet_synchronizer.getCommunications().getScheme(proc, direction);
for (auto && facet : facet_scheme) {
const auto & cohesive_element = const_cast<const Mesh &>(mesh_facets)
.getElementToSubelement(facet)[1];
if (cohesive_element == ElementNull or
cohesive_element.kind() != _ek_cohesive) {
continue;
}
auto && cohesive_type = FEEngine::getCohesiveElementType(facet.type);
auto old_nb_cohesive_elements =
mesh.getNbElement(cohesive_type, facet.ghost_type);
old_nb_cohesive_elements -=
nb_new_cohesive_elements(cohesive_type, facet.ghost_type);
if (cohesive_element.element >= old_nb_cohesive_elements) {
scheme.push_back(cohesive_element);
}
}
});
if (not facet_stress_synchronizer) {
return;
}
const auto & element_synchronizer = mesh.getElementSynchronizer();
const auto & comm = mesh.getCommunicator();
auto && my_rank = comm.whoAmI();
// update the facet stress synchronizer
facet_stress_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && /*direction*/) {
auto it_element = scheme.begin();
for (auto && element : scheme) {
auto && facet_check = inserter->getCheckFacets(
element.type, element.ghost_type)(element.element); // slow access
// here
if (facet_check) {
auto && connected_elements = mesh_facets.getElementToSubelement(
element.type, element.ghost_type)(element.element); // slow access
// here
auto && rank_left = element_synchronizer.getRank(connected_elements[0]);
auto && rank_right =
element_synchronizer.getRank(connected_elements[1]);
// keep element if the element is still a boundary element between two
// processors
if ((rank_left == Int(proc) and rank_right == my_rank) or
(rank_left == my_rank and rank_right == Int(proc))) {
*it_element = element;
++it_element;
}
}
}
scheme.resize(it_element - scheme.begin());
});
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateFacetStressSynchronizer() {
if (facet_stress_synchronizer != nullptr) {
const auto & rank_to_element =
mesh.getElementSynchronizer().getElementToRank();
const auto & facet_checks = inserter->getCheckFacets();
const auto & mesh_facets = inserter->getMeshFacets();
const auto & element_to_facet = mesh_facets.getElementToSubelement();
UInt rank = mesh.getCommunicator().whoAmI();
facet_stress_synchronizer->updateSchemes(
[&](auto & scheme, auto & proc, auto & /*direction*/) {
UInt el = 0;
for (auto && element : scheme) {
if (not facet_checks(element)) {
continue;
}
const auto & next_el = element_to_facet(element);
UInt rank_left = rank_to_element(next_el[0]);
UInt rank_right = rank_to_element(next_el[1]);
if ((rank_left == rank and rank_right == proc) or
(rank_left == proc and rank_right == rank)) {
scheme[el] = element;
++el;
}
}
scheme.resize(el);
});
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::packFacetStressDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::unpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, false>(data_to_unpack, buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void SolidMechanicsModelCohesive::packUnpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt sp2 = spatial_dimension * spatial_dimension;
UInt nb_component = sp2 * 2;
bool element_rank = false;
Mesh & mesh_facets = inserter->getMeshFacets();
Array<T> * vect = nullptr;
const Array<std::vector<Element>> * element_to_facet = nullptr;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (auto && el : elements) {
if (el.type == _not_defined) {
AKANTU_EXCEPTION(
"packUnpackFacetStressDataHelper called with wrong inputs");
}
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
element_to_facet =
&(mesh_facets.getElementToSubelement(el.type, el.ghost_type));
nb_quad_per_elem =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
if (pack_helper) {
element_rank =
(*element_to_facet)(el.element)[0].ghost_type != _not_ghost;
} else {
element_rank =
(*element_to_facet)(el.element)[0].ghost_type == _not_ghost;
}
for (UInt q = 0; q < nb_quad_per_elem; ++q) {
Vector<T> data(vect->storage() +
(el.element * nb_quad_per_elem + q) * nb_component +
element_rank * sp2,
sp2);
if (pack_helper) {
buffer << data;
} else {
buffer >> data;
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbQuadsForFacetCheck(
const Array<Element> & elements) const {
UInt nb_quads = 0;
UInt nb_quad_per_facet = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
nb_quad_per_facet =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
nb_quads += nb_quad_per_facet;
}
return nb_quads;
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (elements.empty()) {
return 0;
}
/// regular element case
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// size += elements.size() * sizeof(bool);
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
UInt nb_quads = getNbQuadsForFacetCheck(elements);
size += nb_quads * spatial_dimension * spatial_dimension * sizeof(Real);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) ==
(spatial_dimension - 1)) {
size += sizeof(UInt);
}
}
size += SolidMechanicsModel::getNbData(elements, tag);
break;
}
default: {
size += SolidMechanicsModel::getNbData(elements, tag);
}
}
}
/// cohesive element case
else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case SynchronizationTag::_smm_boundary: {
UInt nb_nodes_per_element = 0;
for (auto && el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
default:
break;
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (elements.empty()) {
return;
}
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// packElementalDataHelper(inserter->getInsertionFacetsByElement(),
// buffer,
// elements, false, getFEEngine());
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
packFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) !=
(spatial_dimension - 1)) {
continue;
}
buffer << material_index(element);
}
SolidMechanicsModel::packData(buffer, elements, tag);
break;
}
default: {
SolidMechanicsModel::packData(buffer, elements, tag);
}
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
packElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case SynchronizationTag::_smm_boundary: {
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (elements.empty()) {
return;
}
if (elements(0).kind() == _ek_regular) {
switch (tag) {
// case SynchronizationTag::_smmc_facets: {
// unpackElementalDataHelper(inserter->getInsertionFacetsByElement(),
// buffer,
// elements, false, getFEEngine());
// break;
// }
case SynchronizationTag::_smmc_facets_stress: {
unpackFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
if (Mesh::getSpatialDimension(element.type) !=
(spatial_dimension - 1)) {
continue;
}
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
if (mat_index != UInt(-1)) {
continue;
}
// add ghosts element to the correct material
mat_index = recv_mat_index;
auto & mat = aka::as_type<MaterialCohesive>(*materials[mat_index]);
if (is_extrinsic) {
mat.addFacet(element);
}
facet_material(element) = recv_mat_index;
}
SolidMechanicsModel::unpackData(buffer, elements, tag);
break;
}
default: {
SolidMechanicsModel::unpackData(buffer, elements, tag);
}
}
AKANTU_DEBUG_OUT();
return;
}
if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case SynchronizationTag::_material_id: {
for (auto && element : elements) {
UInt recv_mat_index;
buffer >> recv_mat_index;
UInt & mat_index = material_index(element);
if (mat_index != UInt(-1)) {
continue;
}
// add ghosts element to the correct material
mat_index = recv_mat_index;
UInt index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
}
break;
}
case SynchronizationTag::_smm_boundary: {
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if (tag != SynchronizationTag::_material_id &&
tag != SynchronizationTag::_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
index a10b96a4b..a43eeb1a1 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
@@ -1,170 +1,172 @@
/**
* @file embedded_interface_intersector.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue May 21 2019
*
* @brief Class that loads the interface from mesh and computes intersections
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_intersector.hh"
#include "mesh_segment_intersector.hh"
/// Helper macro for types in the mesh. Creates an intersector and computes
/// intersection queries
#define INTERFACE_INTERSECTOR_CASE(dim, type) \
do { \
MeshSegmentIntersector<dim, type> intersector(this->mesh, interface_mesh); \
name_to_primitives_it = name_to_primitives_map.begin(); \
for (; name_to_primitives_it != name_to_primitives_end; \
++name_to_primitives_it) { \
intersector.setPhysicalName(name_to_primitives_it->first); \
intersector.buildResultFromQueryList(name_to_primitives_it->second); \
} \
} while (0)
#define INTERFACE_INTERSECTOR_CASE_2D(type) INTERFACE_INTERSECTOR_CASE(2, type)
#define INTERFACE_INTERSECTOR_CASE_3D(type) INTERFACE_INTERSECTOR_CASE(3, type)
namespace akantu {
EmbeddedInterfaceIntersector::EmbeddedInterfaceIntersector(
Mesh & mesh, const Mesh & primitive_mesh)
: MeshGeomAbstract(mesh),
interface_mesh(mesh.getSpatialDimension(), "interface_mesh"),
primitive_mesh(primitive_mesh) {
// Initiating mesh connectivity and data
interface_mesh.addConnectivityType(_segment_2, _not_ghost);
interface_mesh.addConnectivityType(_segment_2, _ghost);
interface_mesh.getElementalData<Element>("associated_element")
.alloc(0, 1, _segment_2);
interface_mesh.getElementalData<std::string>("physical_names")
.alloc(0, 1, _segment_2);
}
void EmbeddedInterfaceIntersector::constructData(GhostType /*ghost_type*/) {
AKANTU_DEBUG_IN();
const UInt dim = this->mesh.getSpatialDimension();
if (dim == 1) {
AKANTU_ERROR(
"No embedded model in 1D. Deactivate intersection initialization");
}
Array<std::string> * physical_names = nullptr;
try {
physical_names = &const_cast<Array<std::string> &>(
this->primitive_mesh.getData<std::string>("physical_names",
_segment_2));
} catch (debug::Exception & e) {
AKANTU_ERROR("You must define physical names to reinforcements in "
"order to use the embedded model");
throw e;
}
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_segment_2);
auto connectivity =
primitive_mesh.getConnectivity(_segment_2).begin(nb_nodes_per_element);
auto names_it = physical_names->begin();
auto names_end = physical_names->end();
std::map<std::string, std::list<K::Segment_3>> name_to_primitives_map;
// Loop over the physical names and register segment lists in
// name_to_primitives_map
for (; names_it != names_end; ++names_it) {
UInt element_id = names_it - physical_names->begin();
const Vector<UInt> el_connectivity = connectivity[element_id];
K::Segment_3 segment = this->createSegment(el_connectivity);
name_to_primitives_map[*names_it].push_back(segment);
}
// Loop over the background types of the mesh
auto name_to_primitives_end = name_to_primitives_map.end();
decltype(name_to_primitives_end) name_to_primitives_it;
for (auto type : this->mesh.elementTypes(dim, _not_ghost)) {
// Used in AKANTU_BOOST_ELEMENT_SWITCH
AKANTU_DEBUG_INFO("Computing intersections with background element type "
<< type);
switch (dim) {
case 1:
break;
case 2:
// Compute intersections for supported 2D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_2D,
(_triangle_3)(_triangle_6));
break;
case 3:
// Compute intersections for supported 3D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_3D,
(_tetrahedron_4));
break;
}
}
AKANTU_DEBUG_OUT();
}
K::Segment_3
EmbeddedInterfaceIntersector::createSegment(const Vector<UInt> & connectivity) {
AKANTU_DEBUG_IN();
std::unique_ptr<K::Point_3> source;
std::unique_ptr<K::Point_3> target;
const Array<Real> & nodes = this->primitive_mesh.getNodes();
if (this->mesh.getSpatialDimension() == 2) {
source = std::make_unique<K::Point_3>(nodes(connectivity(0), 0),
nodes(connectivity(0), 1), 0.);
target = std::make_unique<K::Point_3>(nodes(connectivity(1), 0),
nodes(connectivity(1), 1), 0.);
} else if (this->mesh.getSpatialDimension() == 3) {
source = std::make_unique<K::Point_3>(nodes(connectivity(0), 0),
nodes(connectivity(0), 1),
nodes(connectivity(0), 2));
target = std::make_unique<K::Point_3>(nodes(connectivity(1), 0),
nodes(connectivity(1), 1),
nodes(connectivity(1), 2));
}
K::Segment_3 segment(*source, *target);
AKANTU_DEBUG_OUT();
return segment;
}
} // namespace akantu
#undef INTERFACE_INTERSECTOR_CASE
#undef INTERFACE_INTERSECTOR_CASE_2D
#undef INTERFACE_INTERSECTOR_CASE_3D
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
index 54520ec8a..5f9daae8e 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
@@ -1,97 +1,99 @@
/**
* @file embedded_interface_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
* @date last modification: Wed Jan 31 2018
*
* @brief Class that loads the interface from mesh and computes intersections
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
#define AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
#include "mesh_geom_common.hh"
#include "mesh_segment_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
using K = cgal::Cartesian;
}
/**
* @brief Computes the intersections of the reinforcements defined in the
* primitive mesh
*
* The purpose of this class is to look for reinforcements in the primitive
* mesh, which
* should be defined by physical groups with the same names as the reinforcement
* materials
* in the model.
*
* It then constructs the CGAL primitives from the elements of those
* reinforcements
* and computes the intersections with the background mesh, to create an
* `interface_mesh`,
* which is in turn used by the EmbeddedInterfaceModel.
*
* @see MeshSegmentIntersector, MeshGeomAbstract
* @see EmbeddedInterfaceModel
*/
class EmbeddedInterfaceIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh and a reinforcement mesh
explicit EmbeddedInterfaceIntersector(Mesh & mesh,
const Mesh & primitive_mesh);
/// Destructor
~EmbeddedInterfaceIntersector() override = default;
public:
/// Generate the interface mesh
void constructData(GhostType ghost_type = _not_ghost) override;
/// Create a segment with an element connectivity
K::Segment_3 createSegment(const Vector<UInt> & connectivity);
/// Getter for interface mesh
AKANTU_GET_MACRO_NOT_CONST(InterfaceMesh, interface_mesh, Mesh &);
protected:
/// Resulting mesh of intersection
Mesh interface_mesh;
/// Mesh used for primitive construction
const Mesh & primitive_mesh;
};
} // namespace akantu
#endif // AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
index 0b5a8b4d3..58a5d0fba 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
@@ -1,172 +1,174 @@
/**
* @file embedded_interface_model.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Wed Feb 14 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_model.hh"
#include "integrator_gauss.hh"
#include "material_elastic.hh"
#include "material_reinforcement.hh"
#include "mesh_iterators.hh"
#include "shape_lagrange.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_iohelper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::EmbeddedInterfaceModel(Mesh & mesh,
Mesh & primitive_mesh,
UInt spatial_dimension,
const ID & id)
: SolidMechanicsModel(mesh, spatial_dimension, id),
intersector(mesh, primitive_mesh), interface_mesh(nullptr),
primitive_mesh(primitive_mesh), interface_material_selector(nullptr) {
this->model_type = ModelType::_embedded_model;
// This pointer should be deleted by ~SolidMechanicsModel()
auto mat_sel_pointer =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
*this);
this->setMaterialSelector(mat_sel_pointer);
interface_mesh = &(intersector.getInterfaceMesh());
// Create 1D FEEngine on the interface mesh
registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine",
*interface_mesh, 1);
// Registering allocator for material reinforcement
MaterialFactory::getInstance().registerAllocator(
"reinforcement",
[&](UInt dim, const ID & constitutive, SolidMechanicsModel & /*unused*/,
const ID & id) -> std::unique_ptr<Material> {
if (constitutive == "elastic") {
using mat = MaterialElastic<1>;
switch (dim) {
case 2:
return std::make_unique<MaterialReinforcement<mat, 2>>(*this, id);
case 3:
return std::make_unique<MaterialReinforcement<mat, 3>>(*this, id);
default:
AKANTU_EXCEPTION("Dimension 1 is invalid for reinforcements");
}
} else {
AKANTU_EXCEPTION("Reinforcement type" << constitutive
<< " is not recognized");
}
});
}
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::~EmbeddedInterfaceModel() {
delete interface_material_selector;
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::initFullImpl(const ModelOptions & options) {
const auto & eim_options =
aka::as_type<EmbeddedInterfaceModelOptions>(options);
// Do no initialize interface_mesh if told so
if (eim_options.has_intersections) {
intersector.constructData();
}
SolidMechanicsModel::initFullImpl(options);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("reinforcement", id);
this->mesh.addDumpMeshToDumper("reinforcement", *interface_mesh, 1,
_not_ghost, _ek_regular);
#endif
}
void EmbeddedInterfaceModel::initModel() {
// Initialize interface FEEngine
SolidMechanicsModel::initModel();
FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
engine.initShapeFunctions(_not_ghost);
engine.initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
delete interface_material_selector;
interface_material_selector =
new InterfaceMeshDataMaterialSelector<std::string>("physical_names",
*this);
for_each_element(getInterfaceMesh(),
[&](auto && element) {
auto mat_index = (*interface_material_selector)(element);
// material_index(element) = mat_index;
materials[mat_index]->addElement(element);
// this->material_local_numbering(element) = index;
},
_element_filter = filter, _spatial_dimension = 1);
SolidMechanicsModel::assignMaterialToElements(filter);
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
const std::string & group_name, ElementKind element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> field;
// If dumper is reinforcement, create a 1D elemental field
if (dumper_name == "reinforcement") {
field = this->createElementalField(field_id, group_name, padding_flag, 1,
element_kind);
} else {
try {
SolidMechanicsModel::addDumpGroupFieldToDumper(
dumper_name, field_id, group_name, element_kind, padding_flag);
} catch (...) {
}
}
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
Model::addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
index eb9922ce2..4dc5c4084 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
@@ -1,153 +1,155 @@
/**
* @file embedded_interface_model.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 31 2018
*
* @brief Model of Solid Mechanics with embedded interfaces
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
#define AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
#include "aka_common.hh"
#include "mesh.hh"
#include "solid_mechanics_model.hh"
#include "embedded_interface_intersector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* @brief Solid mechanics model using the embedded model.
*
* This SolidMechanicsModel subclass implements the embedded model,
* a method used to represent 1D elements in a finite elements model
* (eg. reinforcements in concrete).
*
* In addition to the SolidMechanicsModel properties, this model has
* a mesh of the 1D elements embedded in the model, and an instance of the
* EmbeddedInterfaceIntersector class for the computation of the intersections
* of the
* 1D elements with the background (bulk) mesh.
*
* @see MaterialReinforcement
*/
class EmbeddedInterfaceModel : public SolidMechanicsModel {
using MyFEEngineType = SolidMechanicsModel::MyFEEngineType;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief Constructor
*
* @param mesh main mesh (concrete)
* @param primitive_mesh mesh of the embedded reinforcement
* @param spatial_dimension the spatial dimension to be considered by this model
* @param id the id of the model
*/
EmbeddedInterfaceModel(Mesh & mesh, Mesh & primitive_mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "embedded_interface_model");
/// Destructor
~EmbeddedInterfaceModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialise the model
void initFullImpl(
const ModelOptions & options = EmbeddedInterfaceModelOptions()) override;
/// Initialise the materials
void
assignMaterialToElements(const ElementTypeMapArray<UInt> * filter) override;
/// Initialize the embedded shape functions
void initModel() override;
/// Allows filtering of dump fields which need to be dumpes on interface mesh
void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
ElementKind element_kind,
bool padding_flag) override;
// virtual ElementTypeMap<UInt> getInternalDataPerElem(const std::string &
// field_name,
// ElementKind
// kind);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get interface mesh
AKANTU_GET_MACRO(InterfaceMesh, *interface_mesh, Mesh &);
/// Get associated elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(
InterfaceAssociatedElements,
interface_mesh->getData<Element>("associated_element"), Element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Intersector object to build the interface mesh
EmbeddedInterfaceIntersector intersector;
/// Interface mesh (weak reference)
Mesh * interface_mesh;
/// Mesh used to create the CGAL primitives for intersections
Mesh & primitive_mesh;
/// Material selector for interface
MaterialSelector * interface_material_selector;
};
/// Material selector based on mesh data for interface elements
template <typename T>
class InterfaceMeshDataMaterialSelector
: public ElementDataMaterialSelector<T> {
public:
InterfaceMeshDataMaterialSelector(const std::string & name,
const EmbeddedInterfaceModel & model,
UInt first_index = 1)
: ElementDataMaterialSelector<T>(
model.getInterfaceMesh().getData<T>(name), model, first_index) {}
};
} // namespace akantu
#endif // AKANTU_EMBEDDED_INTERFACE_MODEL_HH_
diff --git a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
index 986b46735..eba37f94b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
@@ -1,125 +1,127 @@
/**
* @file solid_mechanics_model_event_handler.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief EventHandler implementation for SolidMechanicsEvents
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_
namespace akantu {
/// akantu::SolidMechanicsModelEvent is the base event for model
namespace SolidMechanicsModelEvent {
struct BeforeSolveStepEvent {
BeforeSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct AfterSolveStepEvent {
AfterSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct BeforeDumpEvent {
BeforeDumpEvent() = default;
};
struct BeginningOfDamageIterationEvent {
BeginningOfDamageIterationEvent() = default;
};
struct AfterDamageEvent {
AfterDamageEvent() = default;
};
} // namespace SolidMechanicsModelEvent
/// akantu::SolidMechanicsModelEvent
class SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~SolidMechanicsModelEventHandler() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Send what is before the solve step to the beginning of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::BeforeSolveStepEvent & event) {
onBeginningSolveStep(event.method);
}
/// Send what is after the solve step to the end of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::AfterSolveStepEvent & event) {
onEndSolveStep(event.method);
}
/// Send what is before dump to current dump through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::BeforeDumpEvent & event) {
onDump();
}
/// Send what is at the beginning of damage iteration to Damage iteration
/// through EventManager
inline void sendEvent(
__attribute__((unused))
const SolidMechanicsModelEvent::BeginningOfDamageIterationEvent & event) {
onDamageIteration();
}
/// Send what is after damage for the damage update through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::AfterDamageEvent & event) {
onDamageUpdate();
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::BeforeSolveStepEvent
virtual void onBeginningSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::AfterSolveStepEvent
virtual void onEndSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::BeforeDumpEvent
virtual void onDump() {}
/// function to implement to react on akantu::BeginningOfDamageIterationEvent
virtual void onDamageIteration() {}
/// function to implement to react on akantu::AfterDamageEvent
virtual void onDamageUpdate() {}
};
} // namespace akantu
#endif /* AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
index c6319a5c3..5a62684d9 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.hh
@@ -1,106 +1,108 @@
/**
* @file solid_mechanics_model_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 04 2010
- * @date last modification: Tue Dec 05 2017
+ * @date last modification: Fri Mar 26 2021
*
* @brief Implementation of the inline functions of the SolidMechanicsModel
* class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "material_selector.hh"
#include "material_selector_tmpl.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline decltype(auto) SolidMechanicsModel::getMaterials() {
return make_dereference_adaptor(materials);
}
/* -------------------------------------------------------------------------- */
inline decltype(auto) SolidMechanicsModel::getMaterials() const {
return make_dereference_adaptor(materials);
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(UInt mat_index) {
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "
<< mat_index);
return *materials.at(mat_index);
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(UInt mat_index) const {
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "
<< mat_index);
return *materials.at(mat_index);
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(const std::string & name) {
std::map<std::string, UInt>::const_iterator it =
materials_names_to_id.find(name);
if(it == materials_names_to_id.end()) {
AKANTU_SILENT_EXCEPTION("The model " << id << " has no material named " << name);
}
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline UInt
SolidMechanicsModel::getMaterialIndex(const std::string & name) const {
auto it = materials_names_to_id.find(name);
if (it == materials_names_to_id.end()) {
AKANTU_SILENT_EXCEPTION("The model " << id << " has no material named " << name);
}
return it->second;
}
/* -------------------------------------------------------------------------- */
inline const Material &
SolidMechanicsModel::getMaterial(const std::string & name) const {
auto it = materials_names_to_id.find(name);
if(it == materials_names_to_id.end()) {
AKANTU_SILENT_EXCEPTION("The model " << id << " has no material named " << name);
}
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_SOLID_MECHANICS_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_io.cc b/src/model/solid_mechanics/solid_mechanics_model_io.cc
index 43f56ed73..d4797c909 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_io.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_io.cc
@@ -1,333 +1,335 @@
/**
* @file solid_mechanics_model_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 09 2017
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri Apr 09 2021
*
* @brief Dumpable part of the SolidMechnicsModel
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "group_manager_inline_impl.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_material_padders.hh"
#include "dumper_paraview.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
ElementKind element_kind) {
/// check if at least one material contains field_id as an internal
for (auto & material : materials) {
bool is_internal = material->isInternal<Real>(field_name, element_kind);
if (is_internal) {
return true;
}
}
return false;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt>
SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
ElementKind element_kind) {
if (!(this->isInternal(field_name, element_kind))) {
AKANTU_EXCEPTION("unknown internal " << field_name);
}
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, element_kind)) {
return material->getInternalDataPerElem<Real>(field_name, element_kind);
}
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> &
SolidMechanicsModel::flattenInternal(const std::string & field_name,
ElementKind kind,
const GhostType ghost_type) {
auto key = std::make_pair(field_name, kind);
ElementTypeMapArray<Real> * internal_flat;
auto it = this->registered_internals.find(key);
if (it == this->registered_internals.end()) {
auto internal =
std::make_unique<ElementTypeMapArray<Real>>(field_name, this->id);
internal_flat = internal.get();
this->registered_internals[key] = std::move(internal);
} else {
internal_flat = it->second.get();
}
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, kind)) {
if (internal_flat->exists(type, ghost_type)) {
auto & internal = (*internal_flat)(type, ghost_type);
internal.resize(0);
}
}
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, kind)) {
material->flattenInternal(field_name, *internal_flat, ghost_type, kind);
}
}
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(ElementKind kind) {
ElementKind _kind;
ID _id;
for (auto & internal : this->registered_internals) {
std::tie(_id, _kind) = internal.first;
if (kind == _kind) {
this->flattenInternal(_id, kind);
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump() {
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
std::shared_ptr<dumpers::Field> SolidMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, UInt spatial_dimension, ElementKind kind) {
std::shared_ptr<dumpers::Field> field;
if (field_name == "partitions") {
field = mesh.createElementalField<UInt, dumpers::ElementPartitionField>(
mesh.getConnectivities(), group_name, spatial_dimension, kind);
} else if (field_name == "material_index") {
field = mesh.createElementalField<UInt, Vector, dumpers::ElementalField>(
material_index, group_name, spatial_dimension, kind);
} else {
// this copy of field_name is used to compute derivated data such as
// strain and von mises stress that are based on grad_u and stress
std::string field_name_copy(field_name);
if (field_name == "strain" || field_name == "Green strain" ||
field_name == "principal strain" ||
field_name == "principal Green strain") {
field_name_copy = "grad_u";
} else if (field_name == "Von Mises stress") {
field_name_copy = "stress";
}
bool is_internal = this->isInternal(field_name_copy, kind);
if (is_internal) {
auto nb_data_per_elem =
this->getInternalDataPerElem(field_name_copy, kind);
auto & internal_flat = this->flattenInternal(field_name_copy, kind);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
internal_flat, group_name, spatial_dimension, kind, nb_data_per_elem);
std::unique_ptr<dumpers::ComputeFunctorInterface> func;
if (field_name == "strain") {
func = std::make_unique<dumpers::ComputeStrain<false>>(*this);
} else if (field_name == "Von Mises stress") {
func = std::make_unique<dumpers::ComputeVonMisesStress>(*this);
} else if (field_name == "Green strain") {
func = std::make_unique<dumpers::ComputeStrain<true>>(*this);
} else if (field_name == "principal strain") {
func = std::make_unique<dumpers::ComputePrincipalStrain<false>>(*this);
} else if (field_name == "principal Green strain") {
func = std::make_unique<dumpers::ComputePrincipalStrain<true>>(*this);
}
if (func) {
field = dumpers::FieldComputeProxy::createFieldCompute(field,
std::move(func));
}
// treat the paddings
if (padding_flag) {
if (field_name == "stress") {
if (spatial_dimension == 2) {
auto foo = std::make_unique<dumpers::StressPadder<2>>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(
field, std::move(foo));
}
} else if (field_name == "strain" || field_name == "Green strain") {
if (spatial_dimension == 2) {
auto foo = std::make_unique<dumpers::StrainPadder<2>>(*this);
field = dumpers::FieldComputeProxy::createFieldCompute(
field, std::move(foo));
}
}
}
// homogenize the field
auto foo = dumpers::HomogenizerProxy::createHomogenizer(*field);
field =
dumpers::FieldComputeProxy::createFieldCompute(field, std::move(foo));
}
}
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["displacement"] = this->displacement.get();
real_nodal_fields["mass"] = this->mass.get();
real_nodal_fields["velocity"] = this->velocity.get();
real_nodal_fields["acceleration"] = this->acceleration.get();
real_nodal_fields["external_force"] = this->external_force.get();
real_nodal_fields["internal_force"] = this->internal_force.get();
real_nodal_fields["increment"] = this->displacement_increment.get();
if (field_name == "force") {
AKANTU_EXCEPTION("The 'force' field has been renamed in 'external_force'");
} else if (field_name == "residual") {
AKANTU_EXCEPTION(
"The 'residual' field has been replaced by 'internal_force'");
}
std::shared_ptr<dumpers::Field> field;
if (padding_flag) {
field = this->mesh.createNodalField(real_nodal_fields[field_name],
group_name, 3);
} else {
field =
this->mesh.createNodalField(real_nodal_fields[field_name], group_name);
}
return field;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> SolidMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs.get();
std::shared_ptr<dumpers::Field> field;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> SolidMechanicsModel::createElementalField(
const std::string &, const std::string &, bool, const UInt &, ElementKind) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
std::shaed_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldReal(const std::string &,
const std::string &, bool) {
return nullptr;
}
/* --------------------------------------------------------------------------
*/
std::shared_ptr<dumpers::Field>
SolidMechanicsModel::createNodalFieldBool(const std::string &,
const std::string &, bool) {
return nullptr;
}
#endif
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time,
UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, time, step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump() {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(step);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(time, step);
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_mass.cc b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
index 89ab7708d..23ad3716b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_mass.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
@@ -1,154 +1,156 @@
/**
* @file solid_mechanics_model_mass.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief function handling mass computation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "model_solver.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctor {
public:
explicit ComputeRhoFunctor(const SolidMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) {
const Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Real mat_rho =
model.getMaterial(mat_indexes(element.element)).getParam("rho");
rho.set(mat_rho);
}
private:
const SolidMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_lumped_mass) {
return;
}
this->allocNodalField(this->mass, spatial_dimension, "mass");
mass->zero();
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
this->getDOFManager().zeroLumpedMatrix("M");
assembleMassLumped(_not_ghost);
assembleMassLumped(_ghost);
this->getDOFManager().getLumpedMatrixPerDOFs("displacement", "M",
*(this->mass));
/// for not connected nodes put mass to one in order to avoid
#if !defined(AKANTU_NDEBUG)
bool has_unconnected_nodes = false;
auto mass_it = mass->begin_reinterpret(mass->size() * mass->getNbComponent());
auto mass_end = mass->end_reinterpret(mass->size() * mass->getNbComponent());
for (; mass_it != mass_end; ++mass_it) {
if (std::abs(*mass_it) < std::numeric_limits<Real>::epsilon() ||
Math::isnan(*mass_it)) {
has_unconnected_nodes = true;
break;
}
}
if (has_unconnected_nodes) {
AKANTU_DEBUG_WARNING("There are nodes that seem to not be connected to any "
"elements, beware that they have lumped mass of 0.");
}
#endif
this->synchronize(SynchronizationTag::_smm_mass);
need_to_reassemble_lumped_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_mass) {
return;
}
this->getDOFManager().zeroMatrix("M");
assembleMass(_not_ghost);
need_to_reassemble_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldLumped(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type :
mesh.elementTypes(Model::spatial_dimension, ghost_type, _ek_regular)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_material.cc b/src/model/solid_mechanics/solid_mechanics_model_material.cc
index 6992dd52e..0e3ee0422 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_material.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_material.cc
@@ -1,243 +1,246 @@
/**
* @file solid_mechanics_model_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 26 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Mar 26 2021
*
* @brief instatiation of materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_math.hh"
#include "material_non_local.hh"
#include "mesh_iterators.hh"
#include "non_local_manager.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material &
SolidMechanicsModel::registerNewMaterial(const ParserSection & section) {
std::string mat_name;
std::string mat_type = section.getName();
std::string opt_param = section.getOption();
try {
std::string tmp = section.getParameter("name");
mat_name = tmp; /** this can seam weird, but there is an ambiguous operator
* overload that i couldn't solve. @todo remove the
* weirdness of this code
*/
} catch (debug::Exception &) {
AKANTU_ERROR("A material of type \'"
<< mat_type
<< "\' in the input file has been defined without a name!");
}
Material & mat = this->registerNewMaterial(mat_name, mat_type, opt_param);
mat.parseSection(section);
return mat;
}
/* -------------------------------------------------------------------------- */
Material & SolidMechanicsModel::registerNewMaterial(const ID & mat_name,
const ID & mat_type,
const ID & opt_param) {
AKANTU_DEBUG_ASSERT(materials_names_to_id.find(mat_name) ==
materials_names_to_id.end(),
"A material with this name '"
<< mat_name << "' has already been registered. "
<< "Please use unique names for materials");
UInt mat_count = materials.size();
materials_names_to_id[mat_name] = mat_count;
std::stringstream sstr_mat;
sstr_mat << this->id << ":" << mat_count << ":" << mat_type;
ID mat_id = sstr_mat.str();
std::unique_ptr<Material> material = MaterialFactory::getInstance().allocate(
mat_type, spatial_dimension, opt_param, *this, mat_id);
materials.push_back(std::move(material));
return *(materials.back());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::instantiateMaterials() {
ParserSection model_section;
bool is_empty;
std::tie(model_section, is_empty) = this->getParserSection();
if (not is_empty) {
auto model_materials = model_section.getSubSections(ParserType::_material);
for (const auto & section : model_materials) {
this->registerNewMaterial(section);
}
}
auto sub_sections = this->parser.getSubSections(ParserType::_material);
for (const auto & section : sub_sections) {
this->registerNewMaterial(section);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
for (auto & material : materials) {
if (dynamic_cast<MaterialNonLocalInterface *>(material.get()) == nullptr) {
continue;
}
this->non_local_manager = std::make_unique<NonLocalManager>(
*this, *this, id + ":non_local_manager");
break;
}
#endif
if (materials.empty()) {
AKANTU_EXCEPTION("No materials where instantiated for the model"
<< getID());
}
are_materials_instantiated = true;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
for_each_element(
mesh,
[&](auto && element) {
UInt mat_index = (*material_selector)(element);
AKANTU_DEBUG_ASSERT(
mat_index < materials.size(),
"The material selector returned an index that does not exists");
material_index(element) = mat_index;
},
_element_filter = filter, _ghost_type = _not_ghost);
if (non_local_manager) {
non_local_manager->synchronize(*this, SynchronizationTag::_material_id);
}
for_each_element(
mesh,
[&](auto && element) {
auto mat_index = material_index(element);
auto index = materials[mat_index]->addElement(element);
material_local_numbering(element) = index;
},
_element_filter = filter, _ghost_type = _not_ghost);
// synchronize the element material arrays
this->synchronize(SynchronizationTag::_material_id);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initMaterials() {
AKANTU_DEBUG_ASSERT(not materials.empty(), "No material to initialize !");
// if (!are_materials_instantiated)
// instantiateMaterials();
this->assignMaterialToElements();
for (auto & material : materials) {
/// init internals properties
material->initMaterial();
}
this->synchronize(SynchronizationTag::_smm_init_mat);
if (this->non_local_manager) {
this->non_local_manager->initialize();
}
}
/* -------------------------------------------------------------------------- */
Int SolidMechanicsModel::getInternalIndexFromID(const ID & id) const {
AKANTU_DEBUG_IN();
auto it = materials.begin();
auto end = materials.end();
for (; it != end; ++it) {
if ((*it)->getID() == id) {
AKANTU_DEBUG_OUT();
return (it - materials.begin());
}
}
AKANTU_DEBUG_OUT();
return -1;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::reassignMaterial() {
AKANTU_DEBUG_IN();
std::vector<Array<Element>> element_to_add(materials.size());
std::vector<Array<Element>> element_to_remove(materials.size());
for_each_element(mesh, [&](auto && element) {
auto old_material = material_index(element);
auto new_material = (*material_selector)(element);
if (old_material != new_material) {
element_to_add[new_material].push_back(element);
element_to_remove[old_material].push_back(element);
}
});
for (auto && data : enumerate(materials)) {
auto mat_index = std::get<0>(data);
auto & mat = *std::get<1>(data);
mat.removeElements(element_to_remove[mat_index]);
mat.addElements(element_to_add[mat_index]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
const GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
spatial_dimension * spatial_dimension,
"The prescribed grad_u is not of the good size");
for (auto & material : materials) {
if (material->getName() == material_name) {
material->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
index b5294877c..5d1a3a50d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_tmpl.hh
@@ -1,61 +1,63 @@
/**
* @file solid_mechanics_model_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Mar 26 2021
*
* @brief template part of solid mechanics model
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_
#define AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_
namespace akantu {
#define FWD(...) ::std::forward<decltype(__VA_ARGS__)>(__VA_ARGS__)
/* -------------------------------------------------------------------------- */
template <typename Operation>
void SolidMechanicsModel::splitByMaterial(const Array<Element> & elements,
Operation && op) const {
std::vector<Array<Element>> elements_per_mat(materials.size());
this->splitElementByMaterial(elements, elements_per_mat);
for (auto && mat : zip(materials, elements_per_mat)) {
FWD(op)(FWD(*std::get<0>(mat)), FWD(std::get<1>(mat)));
}
}
#undef FWD
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_SOLID_MECHANICS_MODEL_TMPL_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
index 84ca974d4..637619027 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_2.hh
@@ -1,70 +1,72 @@
/**
* @file structural_element_bernoulli_beam_2.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 11 2017
- * @date last modification: Wed Jan 10 2018
+ * @date last modification: Fri Feb 05 2021
*
* @brief Specific functions for bernoulli beam 2d
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_
#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_2>(
Array<Real> & tangent_moduli) {
// auto nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
auto nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_2);
auto tangent_size = 2;
tangent_moduli.zero();
auto D_it = tangent_moduli.begin(tangent_size, tangent_size);
auto el_mat = element_material(_bernoulli_beam_2, _not_ghost).begin();
for (auto & mat : element_material(_bernoulli_beam_2, _not_ghost)) {
auto E = materials[mat].E;
auto A = materials[mat].A;
auto I = materials[mat].I;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
auto & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * I;
}
}
}
} // namespace akantu
#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_2_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
index 7a5a0f668..70f543ad5 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_bernoulli_beam_3.hh
@@ -1,74 +1,76 @@
/**
* @file structural_element_bernoulli_beam_3.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Wed Oct 11 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Feb 05 2021
*
* @brief Specific functions for bernoulli beam 3d
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_
#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_3>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_3);
UInt tangent_size = 4;
tangent_moduli.zero();
Array<Real>::matrix_iterator D_it =
tangent_moduli.begin(tangent_size, tangent_size);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = element_material(_bernoulli_beam_3, _not_ghost)(e);
Real E = materials[mat].E;
Real A = materials[mat].A;
Real Iz = materials[mat].Iz;
Real Iy = materials[mat].Iy;
Real GJ = materials[mat].GJ;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * Iz;
D(2, 2) = E * Iy;
D(3, 3) = GJ;
}
}
}
} // namespace akantu
#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_BEAM_3_HH_ */
diff --git a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
index a574fe15f..8e9f2ffef 100644
--- a/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
+++ b/src/model/structural_mechanics/structural_elements/structural_element_kirchhoff_shell.hh
@@ -1,72 +1,74 @@
/**
* @file structural_element_kirchhoff_shell.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Wed Oct 11 2017
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Feb 05 2021
*
* @brief Specific functions for bernoulli kirchhoff shell
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH_
#define AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_KIRCHHOFF_SHELL_HH_
#include "structural_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<
_discrete_kirchhoff_triangle_18>(Array<Real> & tangent_moduli) {
auto tangent_size =
ElementClass<_discrete_kirchhoff_triangle_18>::getNbStressComponents();
auto nb_quad =
getFEEngine().getNbIntegrationPoints(_discrete_kirchhoff_triangle_18);
auto H_it = tangent_moduli.begin(tangent_size, tangent_size);
for (UInt mat :
element_material(_discrete_kirchhoff_triangle_18, _not_ghost)) {
auto & m = materials[mat];
for (UInt q = 0; q < nb_quad; ++q, ++H_it) {
auto & H = *H_it;
H.zero();
Matrix<Real> D = {{1, m.nu, 0}, {m.nu, 1, 0}, {0, 0, (1 - m.nu) / 2}};
D *= m.E * m.t / (1 - m.nu * m.nu);
H.block(D, 0, 0); // in plane membrane behavior
H.block(D * Math::pow<3>(m.t) / 12., 3, 3); // bending behavior
}
}
}
} // namespace akantu
#endif /* AKANTU_STRUCTURAL_ELEMENT_BERNOULLI_DISCRETE_KIRCHHOFF_TRIANGLE_18_HH_ \
*/
diff --git a/src/model/structural_mechanics/structural_mechanics_model.cc b/src/model/structural_mechanics/structural_mechanics_model.cc
index 4ffa28fcf..57c7b6e89 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model.cc
@@ -1,620 +1,627 @@
/**
* @file structural_mechanics_model.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Mon Mar 15 2021
*
* @brief Model implementation for Structural Mechanics elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
#include "dof_manager.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "shape_structural.hh"
#include "sparse_matrix.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumpable_inline_impl.hh"
#include "dumper_elemental_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper_paraview.hh"
#include "group_manager_inline_impl.hh"
#endif
/* -------------------------------------------------------------------------- */
#include "structural_element_bernoulli_beam_2.hh"
#include "structural_element_bernoulli_beam_3.hh"
#include "structural_element_kirchhoff_shell.hh"
/* -------------------------------------------------------------------------- */
//#include "structural_mechanics_model_inline_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt StructuralMechanicsModel::getNbDegreeOfFreedom(ElementType type) {
UInt ndof = 0;
#define GET_(type) ndof = ElementClass<type>::getNbDegreeOfFreedom()
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_, _ek_structural);
#undef GET_
return ndof;
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::StructuralMechanicsModel(Mesh & mesh, UInt dim,
const ID & id)
: Model(mesh, ModelType::_structural_mechanics_model, dim, id), f_m2a(1.0),
stress("stress", id), element_material("element_material", id),
set_ID("beam sets", id) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineType>("StructuralMechanicsFEEngine", mesh,
spatial_dimension);
if (spatial_dimension == 2) {
nb_degree_of_freedom = 3;
} else if (spatial_dimension == 3) {
nb_degree_of_freedom = 6;
} else {
AKANTU_TO_IMPLEMENT();
}
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("structural_mechanics_model", id,
true);
#endif
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_structural);
this->initDOFManager();
this->dumper_default_element_kind = _ek_structural;
mesh.getElementalData<Real>("extra_normal")
.initialize(mesh, _element_kind = _ek_structural,
_nb_component = spatial_dimension, _with_nb_element = true,
_default_value = 0.);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::~StructuralMechanicsModel() = default;
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFullImpl(const ModelOptions & options) {
Model::initFullImpl(options);
// Initializing stresses
ElementTypeMap<UInt> stress_components;
/// TODO this is ugly af, maybe add a function to FEEngine
for (auto && type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_structural)) {
UInt nb_components = 0;
// Getting number of components for each element type
#define GET_(type) nb_components = ElementClass<type>::getNbStressComponents()
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_);
#undef GET_
stress_components(nb_components, type);
}
stress.initialize(
getFEEngine(), _spatial_dimension = _all_dimensions,
_element_kind = _ek_structural,
_nb_component = [&stress_components](ElementType type,
GhostType /*unused*/) -> UInt {
return stress_components(type);
});
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFEEngineBoundary() {
/// TODO: this function should not be reimplemented
/// we're just avoiding a call to Model::initFEEngineBoundary()
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::setTimeStep(Real time_step,
const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initSolver(
TimeStepSolverType time_step_solver_type, NonLinearSolverType /*unused*/) {
AKANTU_DEBUG_IN();
this->allocNodalField(displacement_rotation, nb_degree_of_freedom,
"displacement");
this->allocNodalField(external_force, nb_degree_of_freedom, "external_force");
this->allocNodalField(internal_force, nb_degree_of_freedom, "internal_force");
this->allocNodalField(blocked_dofs, nb_degree_of_freedom, "blocked_dofs");
auto & dof_manager = this->getDOFManager();
if (not dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *displacement_rotation,
_dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
}
if (time_step_solver_type == TimeStepSolverType::_dynamic ||
time_step_solver_type == TimeStepSolverType::_dynamic_lumped) {
this->allocNodalField(velocity, nb_degree_of_freedom, "velocity");
this->allocNodalField(acceleration, nb_degree_of_freedom, "acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initModel() {
element_material.initialize(mesh, _element_kind = _ek_structural,
_default_value = 0, _with_nb_element = true);
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_stiffness) {
return;
}
if (not getDOFManager().hasMatrix("K")) {
getDOFManager().getNewMatrix("K", getMatrixType("K"));
}
this->getDOFManager().zeroMatrix("K");
for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define ASSEMBLE_STIFFNESS_MATRIX(type) assembleStiffnessMatrix<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_STIFFNESS_MATRIX);
#undef ASSEMBLE_STIFFNESS_MATRIX
}
need_to_reassemble_stiffness = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeStresses() {
AKANTU_DEBUG_IN();
for (const auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_structural)) {
#define COMPUTE_STRESS_ON_QUAD(type) computeStressOnQuad<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_STRESS_ON_QUAD);
#undef COMPUTE_STRESS_ON_QUAD
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> StructuralMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs.get();
return mesh.createNodalField(uint_nodal_fields[field_name], group_name);
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field>
StructuralMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
UInt n;
if (spatial_dimension == 2) {
n = 2;
} else {
n = 3;
}
UInt padding_size = 0;
if (padding_flag) {
padding_size = 3;
}
if (field_name == "displacement") {
return mesh.createStridedNodalField(displacement_rotation.get(), group_name,
n, 0, padding_size);
}
if (field_name == "velocity") {
return mesh.createStridedNodalField(velocity.get(), group_name, n, 0,
padding_size);
}
if (field_name == "acceleration") {
return mesh.createStridedNodalField(acceleration.get(), group_name, n, 0,
padding_size);
}
if (field_name == "rotation") {
return mesh.createStridedNodalField(displacement_rotation.get(), group_name,
nb_degree_of_freedom - n, n,
padding_size);
}
if (field_name == "force") {
return mesh.createStridedNodalField(external_force.get(), group_name, n, 0,
padding_size);
}
if (field_name == "external_force") {
return mesh.createStridedNodalField(external_force.get(), group_name, n, 0,
padding_size);
}
if (field_name == "momentum") {
return mesh.createStridedNodalField(external_force.get(), group_name,
nb_degree_of_freedom - n, n,
padding_size);
}
if (field_name == "internal_force") {
return mesh.createStridedNodalField(internal_force.get(), group_name, n, 0,
padding_size);
}
if (field_name == "internal_momentum") {
return mesh.createStridedNodalField(internal_force.get(), group_name,
nb_degree_of_freedom - n, n,
padding_size);
}
return nullptr;
}
/* -------------------------------------------------------------------------- */
std::shared_ptr<dumpers::Field> StructuralMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
bool /*unused*/, UInt spatial_dimension, ElementKind kind) {
std::shared_ptr<dumpers::Field> field;
if (field_name == "element_index_by_material") {
field = mesh.createElementalField<UInt, Vector, dumpers::ElementalField>(
field_name, group_name, spatial_dimension, kind);
}
if (field_name == "stress") {
ElementTypeMap<UInt> nb_data_per_elem = this->mesh.getNbDataPerElem(stress);
field = mesh.createElementalField<Real, dumpers::InternalMaterialField>(
stress, group_name, this->spatial_dimension, kind, nb_data_per_elem);
}
return field;
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from SolverCallback */
/* -------------------------------------------------------------------------- */
/// get the type of matrix needed
MatrixType StructuralMechanicsModel::getMatrixType(const ID & /*id*/) {
return _symmetric;
}
/// callback to assemble a Matrix
void StructuralMechanicsModel::assembleMatrix(const ID & id) {
if (id == "K") {
assembleStiffnessMatrix();
} else if (id == "M") {
assembleMassMatrix();
}
}
/// callback to assemble a lumped Matrix
void StructuralMechanicsModel::assembleLumpedMatrix(const ID & /*id*/) {}
/// callback to assemble the residual StructuralMechanicsModel::(rhs)
void StructuralMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
auto & dof_manager = getDOFManager();
assembleInternalForce();
dof_manager.assembleToResidual("displacement", *external_force, 1);
dof_manager.assembleToResidual("displacement", *internal_force, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleResidual(const ID & residual_part) {
AKANTU_DEBUG_IN();
if ("external" == residual_part) {
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
AKANTU_DEBUG_OUT();
return;
}
if ("internal" == residual_part) {
this->assembleInternalForce();
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, 1);
AKANTU_DEBUG_OUT();
return;
}
AKANTU_CUSTOM_EXCEPTION(
debug::SolverCallbackResidualPartUnknown(residual_part));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Virtual methods from Model */
/* -------------------------------------------------------------------------- */
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
StructuralMechanicsModel::getDefaultSolverID(const AnalysisMethod & method) {
switch (method) {
case _static: {
return std::make_tuple("static", TimeStepSolverType::_static);
}
case _implicit_dynamic: {
return std::make_tuple("implicit", TimeStepSolverType::_dynamic);
}
default:
return std::make_tuple("unknown", TimeStepSolverType::_not_defined);
}
}
/* ------------------------------------------------------------------------ */
ModelSolverOptions StructuralMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case TimeStepSolverType::_static: {
- options.non_linear_solver_type = NonLinearSolverType::_linear;
+ options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
case TimeStepSolverType::_dynamic: {
options.non_linear_solver_type = NonLinearSolverType::_newton_raphson;
options.integration_scheme_type["displacement"] =
IntegrationSchemeType::_trapezoidal_rule_2;
options.solution_type["displacement"] = IntegrationScheme::_displacement;
break;
}
default:
AKANTU_EXCEPTION(type << " is not a valid time step solver type");
}
return options;
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleInternalForce() {
-
internal_force->zero();
computeStresses();
for (auto type : mesh.elementTypes(_spatial_dimension = _all_dimensions,
_element_kind = _ek_structural)) {
assembleInternalForce(type, _not_ghost);
// assembleInternalForce(type, _ghost);
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleInternalForce(ElementType type,
GhostType gt) {
auto & fem = getFEEngine();
auto & sigma = stress(type, gt);
auto ndof = getNbDegreeOfFreedom(type);
auto nb_nodes = mesh.getNbNodesPerElement(type);
auto ndof_per_elem = ndof * nb_nodes;
Array<Real> BtSigma(fem.getNbIntegrationPoints(type) *
mesh.getNbElement(type),
ndof_per_elem, "BtSigma");
fem.computeBtD(sigma, BtSigma, type, gt);
Array<Real> intBtSigma(0, ndof_per_elem, "intBtSigma");
fem.integrate(BtSigma, intBtSigma, ndof_per_elem, type, gt);
getDOFManager().assembleElementalArrayLocalArray(intBtSigma, *internal_force,
type, gt, -1.);
}
/* -------------------------------------------------------------------------- */
Real StructuralMechanicsModel::getKineticEnergy() {
-
if (not this->getDOFManager().hasMatrix("M")) {
return 0.;
}
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
Array<Real> Mv(nb_nodes, nb_degree_of_freedom);
this->getDOFManager().assembleMatMulVectToArray("displacement", "M",
*this->velocity, Mv);
for (auto && data : zip(arange(nb_nodes), make_view(Mv, nb_degree_of_freedom),
make_view(*this->velocity, nb_degree_of_freedom))) {
ekin += std::get<2>(data).dot(std::get<1>(data)) *
static_cast<Real>(mesh.isLocalOrMasterNode(std::get<0>(data)));
}
mesh.getCommunicator().allReduce(ekin, SynchronizerOperation::_sum);
return ekin / 2.;
}
/* -------------------------------------------------------------------------- */
Real StructuralMechanicsModel::getPotentialEnergy() {
Real epot = 0.;
UInt nb_nodes = mesh.getNbNodes();
Array<Real> Ku(nb_nodes, nb_degree_of_freedom);
this->getDOFManager().assembleMatMulVectToArray(
"displacement", "K", *this->displacement_rotation, Ku);
for (auto && data :
zip(arange(nb_nodes), make_view(Ku, nb_degree_of_freedom),
make_view(*this->displacement_rotation, nb_degree_of_freedom))) {
epot += std::get<2>(data).dot(std::get<1>(data)) *
static_cast<Real>(mesh.isLocalOrMasterNode(std::get<0>(data)));
}
mesh.getCommunicator().allReduce(epot, SynchronizerOperation::_sum);
return epot / 2.;
}
/* -------------------------------------------------------------------------- */
Real StructuralMechanicsModel::getEnergy(const ID & energy) {
if (energy == "kinetic") {
return getKineticEnergy();
}
if (energy == "potential") {
return getPotentialEnergy();
}
return 0;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeForcesByLocalTractionArray(
const Array<Real> & tractions, ElementType type) {
AKANTU_DEBUG_IN();
auto nb_element = getFEEngine().getMesh().getNbElement(type);
auto nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(type);
auto nb_quad = getFEEngine().getNbIntegrationPoints(type);
// check dimension match
AKANTU_DEBUG_ASSERT(
Mesh::getSpatialDimension(type) == getFEEngine().getElementDimension(),
"element type dimension does not match the dimension of boundaries : "
<< getFEEngine().getElementDimension()
<< " != " << Mesh::getSpatialDimension(type));
// check size of the vector
AKANTU_DEBUG_ASSERT(
tractions.size() == nb_quad * nb_element,
"the size of the vector should be the total number of quadrature points");
// check number of components
AKANTU_DEBUG_ASSERT(tractions.getNbComponent() == nb_degree_of_freedom,
"the number of components should be the spatial "
"dimension of the problem");
Array<Real> Ntbs(nb_element * nb_quad,
nb_degree_of_freedom * nb_nodes_per_element);
auto & fem = getFEEngine();
fem.computeNtb(tractions, Ntbs, type);
// allocate the vector that will contain the integrated values
auto name = id + std::to_string(type) + ":integral_boundary";
Array<Real> int_funct(nb_element, nb_degree_of_freedom * nb_nodes_per_element,
name);
// do the integration
getFEEngine().integrate(Ntbs, int_funct,
nb_degree_of_freedom * nb_nodes_per_element, type);
// assemble the result into force vector
getDOFManager().assembleElementalArrayLocalArray(int_funct, *external_force,
type, _not_ghost, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeForcesByGlobalTractionArray(
const Array<Real> & traction_global, ElementType type) {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
Array<Real> traction_local(nb_element * nb_quad, nb_degree_of_freedom,
id + ":structuralmechanics:imposed_linear_load");
auto R_it = getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.getRotations(type)
.begin(nb_degree_of_freedom, nb_degree_of_freedom);
auto Te_it = traction_global.begin(nb_degree_of_freedom);
auto te_it = traction_local.begin(nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++R_it) {
for (UInt q = 0; q < nb_quad; ++q, ++Te_it, ++te_it) {
// turn the traction in the local referential
te_it->template mul<false>(*R_it, *Te_it);
}
}
computeForcesByLocalTractionArray(traction_local, type);
AKANTU_DEBUG_OUT();
}
+/* -------------------------------------------------------------------------- */
+void StructuralMechanicsModel::afterSolveStep(bool converged) {
+ if (converged) {
+ assembleInternalForce();
+ }
+}
+
} // namespace akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model.hh b/src/model/structural_mechanics/structural_mechanics_model.hh
index 17863d2a8..770ebb5a0 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model.hh
@@ -1,335 +1,335 @@
/**
* @file structural_mechanics_model.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Philip Mueller <philip.paul.mueller@bluemail.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Apr 01 2021
*
* @brief Particular implementation of the structural elements in the
* StructuralMechanicsModel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
- * You should have received a copy of the GNU Lesser General Public License
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_named_argument.hh"
#include "boundary_condition.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_
#define AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeStructural;
} // namespace akantu
namespace akantu {
struct StructuralMaterial {
Real E{0};
Real A{1};
Real I{0};
Real Iz{0};
Real Iy{0};
Real GJ{0};
Real rho{0};
Real t{0};
Real nu{0};
};
class StructuralMechanicsModel : public Model {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using MyFEEngineType =
FEEngineTemplate<IntegratorGauss, ShapeStructural, _ek_structural>;
StructuralMechanicsModel(Mesh & mesh, UInt dim = _all_dimensions,
const ID & id = "structural_mechanics_model");
~StructuralMechanicsModel() override;
/// Init full model
void initFullImpl(const ModelOptions & options) override;
/// Init boundary FEEngine
void initFEEngineBoundary() override;
/* ------------------------------------------------------------------------ */
/* Virtual methods from SolverCallback */
/* ------------------------------------------------------------------------ */
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback to assemble a Matrix
void assembleMatrix(const ID & matrix_id) override;
/// callback to assemble a lumped Matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback to assemble the residual (rhs)
void assembleResidual() override;
void assembleResidual(const ID & residual_part) override;
- bool canSplitResidual() override { return false; }
+ bool canSplitResidual() override { return true; }
+
+ void afterSolveStep(bool converged) override;
/// compute kinetic energy
Real getKineticEnergy();
/// compute potential energy
Real getPotentialEnergy();
/// compute the specified energy
Real getEnergy(const ID & energy);
/* ------------------------------------------------------------------------ */
/* Virtual methods from Model */
/* ------------------------------------------------------------------------ */
protected:
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
static UInt getNbDegreeOfFreedom(ElementType type);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
/// initialize the model
void initModel() override;
/// compute the stresses per elements
void computeStresses();
/// compute the nodal forces
void assembleInternalForce();
/// compute the nodal forces for an element type
void assembleInternalForce(ElementType type, GhostType gt);
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
/// assemble the mass matrix for consistent mass resolutions
void assembleMassMatrix();
protected:
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMassMatrix(GhostType ghost_type);
/// computes rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// finish the computation of residual to solve in increment
void updateResidualInternal();
/* ------------------------------------------------------------------------ */
private:
template <ElementType type> void assembleStiffnessMatrix();
template <ElementType type> void computeStressOnQuad();
template <ElementType type>
void computeTangentModuli(Array<Real> & tangent_moduli);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
std::shared_ptr<dumpers::Field>
createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
std::shared_ptr<dumpers::Field>
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
UInt spatial_dimension, ElementKind kind) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// get the StructuralMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement_rotation, Array<Real> &);
/// get the StructuralMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array<Real> &);
/// get the StructuralMechanicsModel::acceleration vector, updated
/// by
/// StructuralMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array<Real> &);
/// get the StructuralMechanicsModel::external_force vector
AKANTU_GET_MACRO(ExternalForce, *external_force, Array<Real> &);
/// get the StructuralMechanicsModel::internal_force vector (boundary forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the StructuralMechanicsModel::boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(RotationMatrix, rotation_matrix, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementMaterial, element_material, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Set_ID, set_ID, UInt);
/**
- * \brief This function adds the `StructuralMaterial` material to the list of
+ * \brief This function adds the `StructuralMaterial` material to the list of
* materials managed by *this.
*
* It is important that this function might invalidate all references to
* structural materials, that were previously optained by `getMaterial()`.
*
* \param material The new material.
*
* \return The ID of the material that was added.
*
* \note The return type is is new.
*/
UInt addMaterial(StructuralMaterial & material, const ID & name = "");
const StructuralMaterial &
getMaterialByElement(const Element & element) const;
/**
- * \brief Returns the ith material of *this.
- * \param i The ith material
+ * \brief Returns the ith material of *this.
+ * \param i The ith material
*/
const StructuralMaterial & getMaterial(UInt material_index) const;
const StructuralMaterial & getMaterial(const ID & name) const;
/**
- * \brief Returns the number of the different materials inside *this.
+ * \brief Returns the number of the different materials inside *this.
*/
UInt getNbMaterials() const { return materials.size(); }
/* ------------------------------------------------------------------------ */
/* Boundaries (structural_mechanics_model_boundary.cc) */
/* ------------------------------------------------------------------------ */
public:
/// Compute Linear load function set in global axis
void computeForcesByGlobalTractionArray(const Array<Real> & traction_global,
ElementType type);
/// Compute Linear load function set in local axis
void computeForcesByLocalTractionArray(const Array<Real> & tractions,
ElementType type);
- /// compute force vector from a function(x,y,momentum) that describe stresses
- // template <ElementType type>
- // void computeForcesFromFunction(BoundaryFunction in_function,
- // BoundaryFunctionType function_type);
-
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
std::unique_ptr<Array<Real>> displacement_rotation;
/// velocities array
std::unique_ptr<Array<Real>> velocity;
/// accelerations array
std::unique_ptr<Array<Real>> acceleration;
/// forces array
std::unique_ptr<Array<Real>> internal_force;
/// forces array
std::unique_ptr<Array<Real>> external_force;
/// lumped mass array
std::unique_ptr<Array<Real>> mass;
/// boundaries array
std::unique_ptr<Array<bool>> blocked_dofs;
/// stress array
ElementTypeMapArray<Real> stress;
ElementTypeMapArray<UInt> element_material;
// Define sets of beams
ElementTypeMapArray<UInt> set_ID;
/// number of degre of freedom
UInt nb_degree_of_freedom;
// Rotation matrix
ElementTypeMapArray<Real> rotation_matrix;
// /// analysis method check the list in akantu::AnalysisMethod
// AnalysisMethod method;
/// flag defining if the increment must be computed or not
bool increment_flag;
bool need_to_reassemble_mass{true};
bool need_to_reassemble_stiffness{true};
/* ------------------------------------------------------------------------ */
std::vector<StructuralMaterial> materials;
std::map<std::string, UInt> materials_names_to_id;
};
} // namespace akantu
#include "structural_mechanics_model_inline_impl.hh"
#endif /* AKANTU_STRUCTURAL_MECHANICS_MODEL_HH_ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
index 1eecd570e..6a7e7c1fa 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
@@ -1,45 +1,47 @@
/**
* @file structural_mechanics_model_boundary.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Fri Oct 13 2017
*
* @brief Implementation of the boundary conditions for
* StructuralMechanicsModel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "model.hh"
#include "shape_structural.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
index 3428080f6..fd638f708 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model_inline_impl.hh
@@ -1,280 +1,282 @@
/**
* @file structural_mechanics_model_inline_impl.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Mon Mar 15 2021
*
* @brief Implementation of inline functions of StructuralMechanicsModel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_
#define AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt StructuralMechanicsModel::addMaterial(StructuralMaterial & material,
const ID & name) {
const auto material_index = materials.size();
auto material_name = name;
if (name.empty()) {
material_name = "material_" + std::to_string(material_index);
}
if (materials_names_to_id.find(material_name) !=
materials_names_to_id.end()) {
AKANTU_EXCEPTION("The material " << material_name
<< " already exists in the model " << id);
}
AKANTU_DEBUG_ASSERT(material_index <=
(::std::size_t)::std::numeric_limits<UInt>::max(),
"Can not represent the material ID");
materials_names_to_id[material_name] = material_index;
materials.push_back(material); // add the material, might cause
// reallocation.
return UInt(material_index);
}
/* -------------------------------------------------------------------------- */
inline const StructuralMaterial &
StructuralMechanicsModel::getMaterialByElement(const Element & element) const {
return materials[element_material(element)];
}
/* -------------------------------------------------------------------------- */
inline const StructuralMaterial &
StructuralMechanicsModel::getMaterial(UInt material_index) const {
return materials.at(material_index);
}
/* -------------------------------------------------------------------------- */
inline const StructuralMaterial &
StructuralMechanicsModel::getMaterial(const ID & name) const {
auto it = materials_names_to_id.find(name);
if (it == materials_names_to_id.end()) {
AKANTU_EXCEPTION("The material " << name << " was not found in the model "
<< id);
}
return materials.at(it->second);
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeTangentModuli(
Array<Real> & /*tangent_moduli*/) {
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
auto nb_element = getFEEngine().getMesh().getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto bt_d_b = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, bt_d_b_size * bt_d_b_size, "B^t*D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
Matrix<Real> BtD(bt_d_b_size, tangent_size);
for (auto && tuple :
zip(make_view(b, tangent_size, bt_d_b_size),
make_view(*tangent_moduli, tangent_size, tangent_size),
make_view(*bt_d_b, bt_d_b_size, bt_d_b_size))) {
auto & B = std::get<0>(tuple);
auto & D = std::get<1>(tuple);
auto & BtDB = std::get<2>(tuple);
BtD.mul<true, false>(B, D);
BtDB.template mul<false, false>(BtD, B);
}
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
auto int_bt_d_b = std::make_unique<Array<Real>>(
nb_element, bt_d_b_size * bt_d_b_size, "int_B^t*D*B");
getFEEngine().integrate(*bt_d_b, *int_bt_d_b, bt_d_b_size * bt_d_b_size,
type);
getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *int_bt_d_b, type, _not_ghost, _symmetric);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void StructuralMechanicsModel::computeStressOnQuad() {
AKANTU_DEBUG_IN();
auto & sigma = stress(type, _not_ghost);
auto nb_element = mesh.getNbElement(type);
auto nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
auto nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
auto tangent_size = ElementClass<type>::getNbStressComponents();
auto tangent_moduli = std::make_unique<Array<Real>>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
computeTangentModuli<type>(*tangent_moduli);
/// compute DB
auto d_b_size = nb_degree_of_freedom * nb_nodes_per_element;
auto d_b = std::make_unique<Array<Real>>(nb_element * nb_quadrature_points,
d_b_size * tangent_size, "D*B");
const auto & b = getFEEngine().getShapesDerivatives(type);
auto B = b.begin(tangent_size, d_b_size);
auto D = tangent_moduli->begin(tangent_size, tangent_size);
auto D_B = d_b->begin(tangent_size, d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++B, ++D, ++D_B) {
D_B->template mul<false, false>(*D, *B);
}
}
/// compute DBu
D_B = d_b->begin(tangent_size, d_b_size);
auto DBu = sigma.begin(tangent_size);
Array<Real> u_el(0, d_b_size);
FEEngine::extractNodalToElementField(mesh, *displacement_rotation, u_el,
type);
auto ug = u_el.begin(d_b_size);
// No need to rotate because B is post-multiplied
for (UInt e = 0; e < nb_element; ++e, ++ug) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_B, ++DBu) {
DBu->template mul<false>(*D_B, *ug);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @param myf pointer to a function that fills a vector/tensor with respect to
* passed coordinates
*/
#if 0
template <ElementType type>
inline void StructuralMechanicsModel::computeForcesFromFunction(
BoundaryFunction myf, BoundaryFunctionType function_type) {
/** function type is
** _bft_forces : linear load is given
** _bft_stress : stress function is given -> Not already done for this kind
*of model
*/
std::stringstream name;
name << id << ":structuralmechanics:imposed_linear_load";
Array<Real> lin_load(0, nb_degree_of_freedom, name.str());
name.zero();
UInt offset = nb_degree_of_freedom;
// prepare the loop over element types
UInt nb_quad = getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
name.zero();
name << id << ":structuralmechanics:quad_coords";
Array<Real> quad_coords(nb_element * nb_quad, spatial_dimension,
"quad_coords");
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(getFEEngine().getMesh().getNodes(),
quad_coords, spatial_dimension);
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 1, 1);
if (spatial_dimension == 3)
getFEEngineClass<MyFEEngineType>()
.getShapeFunctions()
.interpolateOnIntegrationPoints<type>(
getFEEngine().getMesh().getNodes(), quad_coords, spatial_dimension,
_not_ghost, empty_filter, true, 0, 2, 2);
lin_load.resize(nb_element * nb_quad);
Real * imposed_val = lin_load.storage();
/// sigma/load on each quadrature points
Real * qcoord = quad_coords.storage();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt q = 0; q < nb_quad; ++q) {
myf(qcoord, imposed_val, NULL, 0);
imposed_val += offset;
qcoord += spatial_dimension;
}
}
switch (function_type) {
case _bft_traction_local:
computeForcesByLocalTractionArray<type>(lin_load);
break;
case _bft_traction:
computeForcesByGlobalTractionArray<type>(lin_load);
break;
default:
break;
}
}
#endif
} // namespace akantu
#endif /* AKANTU_STRUCTURAL_MECHANICS_MODEL_INLINE_IMPL_HH_ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_mass.cc b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
index c168e2877..768322ab0 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_mass.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
@@ -1,89 +1,91 @@
/**
* @file structural_mechanics_model_mass.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
- * @date last modification: Fri Dec 15 2017
+ * @date last modification: Thu Mar 04 2021
*
* @brief function handling mass computation
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "material.hh"
#include "shape_structural.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctorStruct {
public:
explicit ComputeRhoFunctorStruct(const StructuralMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) const {
Real mat_rho = model.getMaterialByElement(element).rho;
rho.set(mat_rho);
}
private:
const StructuralMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMassMatrix() {
AKANTU_DEBUG_IN();
if (not need_to_reassemble_mass) {
return;
}
if (not getDOFManager().hasMatrix("M")) {
getDOFManager().getNewMatrix("M", getMatrixType("M"));
}
this->getDOFManager().zeroMatrix("M");
assembleMassMatrix(_not_ghost);
need_to_reassemble_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMassMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctorStruct compute_rho(*this);
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_structural)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/solver/petsc_wrapper.hh b/src/solver/petsc_wrapper.hh
index d9379a7b3..247032eb5 100644
--- a/src/solver/petsc_wrapper.hh
+++ b/src/solver/petsc_wrapper.hh
@@ -1,79 +1,80 @@
/**
-
* @file petsc_wrapper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
- * @date last modification: Sat Feb 03 2018
+ * @date last modification: Sat May 23 2020
*
* @brief Wrapper of PETSc structures
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PETSC_WRAPPER_HH_
#define AKANTU_PETSC_WRAPPER_HH_
/* -------------------------------------------------------------------------- */
#include <mpi.h>
#include <petscao.h>
#include <petscis.h>
#include <petscksp.h>
#include <petscmat.h>
#include <petscvec.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
struct PETScMatrixWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// MPI communicator for PETSc commands
MPI_Comm communicator;
};
/* -------------------------------------------------------------------------- */
struct PETScSolverWrapper {
KSP ksp;
Vec solution;
Vec rhs;
// MPI communicator for PETSc commands
MPI_Comm communicator;
};
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { \
AKANTU_EXCEPTION("Error in PETSC"); \
} \
} while (0)
#endif
} // namespace akantu
#endif /* AKANTU_PETSC_WRAPPER_HH_ */
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index 28629e923..72352ebb7 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,91 +1,93 @@
/**
* @file solver_petsc.cc
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Tue May 26 2020
*
* @brief Solver class implementation for the petsc solver
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_vector_petsc.hh"
#include "sparse_matrix_petsc.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
//#include <petscsys.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverPETSc::SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id)
: SparseSolver(dof_manager, matrix_id, id),
dof_manager(dof_manager), matrix(dof_manager.getMatrix(matrix_id)) {
auto && mpi_comm = dof_manager.getMPIComm();
/// create a solver context
PETSc_call(KSPCreate, mpi_comm, &this->ksp);
}
/* -------------------------------------------------------------------------- */
SolverPETSc::~SolverPETSc() {
if (ksp != nullptr) {
PETSc_call(KSPDestroy, &ksp);
}
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::setOperators() {
// set the matrix that defines the linear system and the matrix for
// preconditioning (here they are the same)
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
PETSc_call(KSPSetOperators, ksp, this->matrix.getMat(),
this->matrix.getMat());
#else
PETSc_call(KSPSetOperators, ksp, this->matrix.getMat(), this->matrix.getMat(),
SAME_NONZERO_PATTERN);
#endif
// If this is not called the solution vector is zeroed in the call to
// KSPSolve().
PETSc_call(KSPSetInitialGuessNonzero, ksp, PETSC_TRUE);
PETSc_call(KSPSetFromOptions, ksp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve() {
Vec & rhs(this->dof_manager.getResidual());
Vec & solution(this->dof_manager.getSolution());
PETSc_call(KSPSolve, ksp, rhs, solution);
}
} // namespace akantu
diff --git a/src/solver/solver_petsc.hh b/src/solver/solver_petsc.hh
index d61abe941..8bf5d32b4 100644
--- a/src/solver/solver_petsc.hh
+++ b/src/solver/solver_petsc.hh
@@ -1,81 +1,83 @@
/**
* @file solver_petsc.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Tue May 26 2020
*
* @brief Solver class interface for the petsc solver
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_PETSC_HH_
#define AKANTU_SOLVER_PETSC_HH_
namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc;
} // namespace akantu
namespace akantu {
class SolverPETSc : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id = "solver_petsc");
~SolverPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create the solver context and set the matrices
virtual void setOperators();
void solve() override;
private:
/// DOFManager correctly typed
DOFManagerPETSc & dof_manager;
/// PETSc linear solver
KSP ksp;
/// Matrix defining the system of equations
SparseMatrixPETSc & matrix;
};
} // namespace akantu
#endif /* AKANTU_SOLVER_PETSC_HH_ */
diff --git a/src/solver/solver_vector.hh b/src/solver/solver_vector.hh
index d413cd56a..c3a02d5fe 100644
--- a/src/solver/solver_vector.hh
+++ b/src/solver/solver_vector.hh
@@ -1,87 +1,91 @@
/**
* @file solver_vector.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Tue May 26 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface base class
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_VECTOR_HH_
#define AKANTU_SOLVER_VECTOR_HH_
namespace akantu {
class DOFManager;
}
namespace akantu {
class SolverVector {
public:
SolverVector(DOFManager & dof_manager, const ID & id = "solver_vector")
: id(id), _dof_manager(dof_manager) {}
SolverVector(const SolverVector & vector, const ID & id = "solver_vector")
: id(id), _dof_manager(vector._dof_manager) {}
virtual ~SolverVector() = default;
// resize the vector to the size of the problem
virtual void resize() = 0;
// clear the vector
virtual void set(Real val) = 0;
void zero() { this->set({}); }
virtual operator const Array<Real> &() const = 0;
virtual Int size() const = 0;
virtual Int localSize() const = 0;
virtual SolverVector & operator+(const SolverVector & y) = 0;
virtual SolverVector & operator=(const SolverVector & y) = 0;
UInt & release() { return release_; }
UInt release() const { return release_; }
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
protected:
ID id;
/// Underlying dof manager
DOFManager & _dof_manager;
UInt release_{0};
};
inline std::ostream & operator<<(std::ostream & stream, SolverVector & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* AKANTU_SOLVER_VECTOR_HH_ */
diff --git a/src/solver/solver_vector_default.cc b/src/solver/solver_vector_default.cc
deleted file mode 100644
index 8b209a517..000000000
--- a/src/solver/solver_vector_default.cc
+++ /dev/null
@@ -1,33 +0,0 @@
-/**
- * @file solver_vector_default.cc
- *
- * @author Nicolas Richart
- *
- * @date creation Tue Jan 01 2019
- *
- * @brief A Documented file.
- *
- *
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
- * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
- *
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
- * details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-/* -------------------------------------------------------------------------- */
-#include "solver_vector_default.hh"
-#include "dof_manager_default.hh"
-/* -------------------------------------------------------------------------- */
-
-namespace akantu {} // namespace akantu
diff --git a/src/solver/solver_vector_default.hh b/src/solver/solver_vector_default.hh
index 915d5a4d3..19b167d76 100644
--- a/src/solver/solver_vector_default.hh
+++ b/src/solver/solver_vector_default.hh
@@ -1,140 +1,144 @@
/**
* @file solver_vector_default.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Tue Jan 01 2019
+ * @date last modification: Sat May 23 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface to Array
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solver_vector.hh"
/* -------------------------------------------------------------------------- */
#include <utility>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_VECTOR_DEFAULT_HH_
#define AKANTU_SOLVER_VECTOR_DEFAULT_HH_
namespace akantu {
class DOFManagerDefault;
} // namespace akantu
namespace akantu {
class SolverVectorArray : public SolverVector {
public:
SolverVectorArray(DOFManagerDefault & dof_manager, const ID & id);
SolverVectorArray(const SolverVectorArray & vector, const ID & id);
~SolverVectorArray() override = default;
virtual Array<Real> & getVector() = 0;
virtual const Array<Real> & getVector() const = 0;
void printself(std::ostream & stream, int indent = 0) const override {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolverVectorArray [" << std::endl;
stream << space << " + id: " << id << std::endl;
this->getVector().printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
};
/* -------------------------------------------------------------------------- */
template <class Array_> class SolverVectorArrayTmpl : public SolverVectorArray {
public:
SolverVectorArrayTmpl(DOFManagerDefault & dof_manager, Array_ & vector,
const ID & id = "solver_vector_default")
: SolverVectorArray(dof_manager, id), dof_manager(dof_manager),
vector(vector) {}
template <class A = Array_,
std::enable_if_t<not std::is_reference<A>::value> * = nullptr>
SolverVectorArrayTmpl(DOFManagerDefault & dof_manager,
const ID & id = "solver_vector_default")
: SolverVectorArray(dof_manager, id), dof_manager(dof_manager),
vector(0, 1, id + ":vector") {}
SolverVectorArrayTmpl(const SolverVectorArrayTmpl & vector,
const ID & id = "solver_vector_default")
: SolverVectorArray(vector, id), dof_manager(vector.dof_manager),
vector(vector.vector) {}
operator const Array<Real> &() const override { return getVector(); };
virtual operator Array<Real> &() { return getVector(); };
SolverVector & operator+(const SolverVector & y) override;
SolverVector & operator=(const SolverVector & y) override;
void resize() override {
static_assert(not std::is_const<std::remove_reference_t<Array_>>::value,
"Cannot resize a const Array");
this->vector.resize(this->localSize(), 0.);
++this->release_;
}
void set(Real val) override {
static_assert(not std::is_const<std::remove_reference_t<Array_>>::value,
"Cannot clear a const Array");
this->vector.set(val);
++this->release_;
}
public:
Array<Real> & getVector() override { return vector; }
const Array<Real> & getVector() const override { return vector; }
Int size() const override;
Int localSize() const override;
virtual Array<Real> & getGlobalVector() { return this->vector; }
virtual void setGlobalVector(const Array<Real> & solution) {
this->vector.copy(solution);
}
protected:
DOFManagerDefault & dof_manager;
Array_ vector;
template <class A> friend class SolverVectorArrayTmpl;
};
/* -------------------------------------------------------------------------- */
using SolverVectorDefault = SolverVectorArrayTmpl<Array<Real>>;
/* -------------------------------------------------------------------------- */
template <class Array>
using SolverVectorDefaultWrap = SolverVectorArrayTmpl<Array &>;
template <class Array>
decltype(auto) make_solver_vector_default_wrap(DOFManagerDefault & dof_manager,
Array & vector) {
return SolverVectorDefaultWrap<Array>(dof_manager, vector);
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "solver_vector_default_tmpl.hh"
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_SOLVER_VECTOR_DEFAULT_HH_ */
diff --git a/src/solver/solver_vector_default_tmpl.hh b/src/solver/solver_vector_default_tmpl.hh
index 6e2cdb9cb..9e0683669 100644
--- a/src/solver/solver_vector_default_tmpl.hh
+++ b/src/solver/solver_vector_default_tmpl.hh
@@ -1,83 +1,87 @@
/**
* @file solver_vector_default_tmpl.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Tue Jan 01 2019
+ * @date last modification: Sat May 23 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface to Array
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_
#define AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline SolverVectorArray::SolverVectorArray(DOFManagerDefault & dof_manager,
const ID & id)
: SolverVector(dof_manager, id) {}
/* -------------------------------------------------------------------------- */
inline SolverVectorArray::SolverVectorArray(const SolverVectorArray & vector,
const ID & id)
: SolverVector(vector, id) {}
/* -------------------------------------------------------------------------- */
template <class Array_>
SolverVector & SolverVectorArrayTmpl<Array_>::
operator+(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorArray>(y);
this->vector += y_.getVector();
++this->release_;
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Array_>
SolverVector & SolverVectorArrayTmpl<Array_>::
operator=(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorArray>(y);
this->vector.copy(y_.getVector());
this->release_ = y.release();
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Array_> inline Int SolverVectorArrayTmpl<Array_>::size() const {
return this->dof_manager.getSystemSize();
}
/* -------------------------------------------------------------------------- */
template <class Array_>
inline Int SolverVectorArrayTmpl<Array_>::localSize() const {
return dof_manager.getLocalSystemSize();
}
} // namespace akantu
#endif /* AKANTU_SOLVER_VECTOR_DEFAULT_TMPL_HH_ */
diff --git a/src/solver/solver_vector_distributed.cc b/src/solver/solver_vector_distributed.cc
index b2b5c1e83..90e1aa108 100644
--- a/src/solver/solver_vector_distributed.cc
+++ b/src/solver/solver_vector_distributed.cc
@@ -1,77 +1,81 @@
/**
* @file solver_vector_distributed.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Tue Jan 01 2019
+ * @date last modification: Sat May 23 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface for distributed arrays
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solver_vector_distributed.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverVectorDistributed::SolverVectorDistributed(
DOFManagerDefault & dof_manager, const ID & id)
: SolverVectorDefault(dof_manager, id) {}
/* -------------------------------------------------------------------------- */
SolverVectorDistributed::SolverVectorDistributed(
const SolverVectorDefault & vector, const ID & id)
: SolverVectorDefault(vector, id) {}
/* -------------------------------------------------------------------------- */
Array<Real> & SolverVectorDistributed::getGlobalVector() {
auto & synchronizer = dof_manager.getSynchronizer();
if (not this->global_vector) {
this->global_vector =
std::make_unique<Array<Real>>(0, 1, "global_residual");
}
if (synchronizer.getCommunicator().whoAmI() == 0) {
this->global_vector->resize(dof_manager.getSystemSize());
synchronizer.gather(this->vector, *this->global_vector);
} else {
synchronizer.gather(this->vector);
}
return *this->global_vector;
}
/* -------------------------------------------------------------------------- */
void SolverVectorDistributed::setGlobalVector(const Array<Real> & solution) {
auto & synchronizer = dof_manager.getSynchronizer();
if (synchronizer.getCommunicator().whoAmI() == 0) {
synchronizer.scatter(this->vector, solution);
} else {
synchronizer.scatter(this->vector);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/solver_vector_distributed.hh b/src/solver/solver_vector_distributed.hh
index d2c2d3c05..65e8127ec 100644
--- a/src/solver/solver_vector_distributed.hh
+++ b/src/solver/solver_vector_distributed.hh
@@ -1,55 +1,59 @@
/**
* @file solver_vector_distributed.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Tue Jan 01 2019
*
- * @brief A Documented file.
+ * @brief Solver vector interface for distributed arrays
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solver_vector_default.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_
#define AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_
namespace akantu {
class SolverVectorDistributed : public SolverVectorDefault {
public:
SolverVectorDistributed(DOFManagerDefault & dof_manager,
const ID & id = "solver_vector_mumps");
SolverVectorDistributed(const SolverVectorDefault & vector,
const ID & id = "solver_vector_mumps");
Array<Real> & getGlobalVector() override;
void setGlobalVector(const Array<Real> & solution) override;
protected:
// full vector in case it needs to be centralized on master
std::unique_ptr<Array<Real>> global_vector;
};
} // namespace akantu
#endif /* AKANTU_SOLVER_VECTOR_DISTRIBUTED_HH_ */
diff --git a/src/solver/solver_vector_petsc.cc b/src/solver/solver_vector_petsc.cc
index ec791614e..ac9f76af4 100644
--- a/src/solver/solver_vector_petsc.cc
+++ b/src/solver/solver_vector_petsc.cc
@@ -1,289 +1,293 @@
/**
* @file solver_vector_petsc.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Tue Jan 01 2019
+ * @date last modification: Fri Jul 24 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface for PETSc
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "solver_vector_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(VecCreate, mpi_comm, &x);
detail::PETScSetName(x, id);
PETSc_call(VecSetFromOptions, x);
auto local_system_size = dof_manager.getLocalSystemSize();
auto nb_local_dofs = dof_manager.getPureLocalSystemSize();
PETSc_call(VecSetSizes, x, nb_local_dofs, PETSC_DECIDE);
VecType vec_type;
PETSc_call(VecGetType, x, &vec_type);
if (std::string(vec_type) == std::string(VECMPI)) {
PetscInt lowest_gidx;
PetscInt highest_gidx;
PETSc_call(VecGetOwnershipRange, x, &lowest_gidx, &highest_gidx);
std::vector<PetscInt> ghost_idx;
for (auto && d : arange(local_system_size)) {
int gidx = dof_manager.localToGlobalEquationNumber(d);
if (gidx != -1) {
if ((gidx < lowest_gidx) or (gidx >= highest_gidx)) {
ghost_idx.push_back(gidx);
}
}
}
PETSc_call(VecMPISetGhost, x, ghost_idx.size(), ghost_idx.data());
} else {
std::vector<int> idx(nb_local_dofs);
std::iota(idx.begin(), idx.end(), 0);
ISLocalToGlobalMapping is;
PETSc_call(ISLocalToGlobalMappingCreate, PETSC_COMM_SELF, 1, idx.size(),
idx.data(), PETSC_COPY_VALUES, &is);
PETSc_call(VecSetLocalToGlobalMapping, x, is);
PETSc_call(ISLocalToGlobalMappingDestroy, &is);
}
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc( // NOLINT(bugprone-copy-constructor-init)
const SolverVectorPETSc & vector, const ID & id)
: SolverVector(vector, id), dof_manager(vector.dof_manager) {
if (vector.x != nullptr) {
PETSc_call(VecDuplicate, vector.x, &x);
PETSc_call(VecCopy, vector.x, x);
detail::PETScSetName(x, id);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::printself(std::ostream & stream, int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "SolverVectorPETSc [" << std::endl;
stream << space << " + id: " << id << std::endl;
PETSc_call(PetscViewerPushFormat, PETSC_VIEWER_STDOUT_WORLD,
PETSC_VIEWER_ASCII_INDEX);
PETSc_call(VecView, x, PETSC_VIEWER_STDOUT_WORLD);
PETSc_call(PetscViewerPopFormat, PETSC_VIEWER_STDOUT_WORLD);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::SolverVectorPETSc(Vec x, DOFManagerPETSc & dof_manager,
const ID & id)
: SolverVector(dof_manager, id), dof_manager(dof_manager) {
PETSc_call(VecDuplicate, x, &this->x);
PETSc_call(VecCopy, x, this->x);
detail::PETScSetName(x, id);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::~SolverVectorPETSc() {
if (x != nullptr) {
PETSc_call(VecDestroy, &x);
}
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::resize() {
// the arrays are destroyed and recreated in the dof manager
// resize is so not implemented
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::set(Real val) {
PETSc_call(VecSet, x, val);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::applyModifications() {
PETSc_call(VecAssemblyBegin, x);
PETSc_call(VecAssemblyEnd, x);
updateGhost();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::updateGhost() {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
if (x_ghosted != nullptr) {
PETSc_call(VecGhostUpdateBegin, x, INSERT_VALUES, SCATTER_FORWARD);
PETSc_call(VecGhostUpdateEnd, x, INSERT_VALUES, SCATTER_FORWARD);
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValues(const Array<Int> & idx,
Array<Real> & values) const {
if (idx.empty()) {
return;
}
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
PetscInt n;
Array<PetscInt> lidx(idx.size());
PETSc_call(ISGlobalToLocalMappingApply, is_ltog_map, IS_GTOLM_MASK,
idx.size(), idx.storage(), &n, lidx.storage());
getValuesLocal(lidx, values);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::getValuesLocal(const Array<Int> & idx,
Array<Real> & values) const {
if (idx.empty()) {
return;
}
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
// VecScatterBegin(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
// VecScatterEnd(scatter, x, x_local, INSERT_VALUES, SCATTER_FORWARD);
if (x_ghosted == nullptr) {
const PetscScalar * array;
PETSc_call(VecGetArrayRead, x, &array);
for (auto && data : zip(idx, make_view(values))) {
auto i = std::get<0>(data);
if (i != -1) {
std::get<1>(data) = array[i];
}
}
PETSc_call(VecRestoreArrayRead, x, &array);
return;
}
PETSc_call(VecSetOption, x_ghosted, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecGetValues, x_ghosted, idx.size(), idx.storage(),
values.storage());
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValues(const Array<Int> & gidx,
const Array<Real> & values,
Real scale_factor) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValues, x, gidx.size(), gidx.storage(), to_add, ADD_VALUES);
applyModifications();
}
/* -------------------------------------------------------------------------- */
void SolverVectorPETSc::addValuesLocal(const Array<Int> & lidx,
const Array<Real> & values,
Real scale_factor) {
Vec x_ghosted{nullptr};
PETSc_call(VecGhostGetLocalForm, x, &x_ghosted);
if (x_ghosted == nullptr) {
Real * to_add = values.storage();
Array<Real> scaled_array;
if (scale_factor != 1.) {
scaled_array.copy(values, false);
scaled_array *= scale_factor;
to_add = scaled_array.storage();
}
PETSc_call(VecSetOption, x, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE);
PETSc_call(VecSetValuesLocal, x, lidx.size(), lidx.storage(), to_add,
ADD_VALUES);
return;
}
PETSc_call(VecGhostRestoreLocalForm, x, &x_ghosted);
ISLocalToGlobalMapping is_ltog_map;
PETSc_call(VecGetLocalToGlobalMapping, x, &is_ltog_map);
Array<Int> gidx(lidx.size());
PETSc_call(ISLocalToGlobalMappingApply, is_ltog_map, lidx.size(),
lidx.storage(), gidx.storage());
addValues(gidx, values, scale_factor);
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc::operator const Array<Real> &() const {
const_cast<Array<Real> &>(cache).resize(local_size());
auto xl = internal::make_petsc_local_vector(x);
auto cachep = internal::make_petsc_wraped_vector(this->cache);
PETSc_call(VecCopy, cachep, xl);
return cache;
}
/* -------------------------------------------------------------------------- */
SolverVectorPETSc & SolverVectorPETSc::operator=(const SolverVectorPETSc & y) {
if (size() != y.size()) {
PETSc_call(VecDuplicate, y, &x);
}
PETSc_call(VecCopy, y.x, x);
release_ = y.release_;
return *this;
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator=(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorPETSc>(y);
return operator=(y_);
}
/* -------------------------------------------------------------------------- */
SolverVector & SolverVectorPETSc::operator+(const SolverVector & y) {
const auto & y_ = aka::as_type<SolverVectorPETSc>(y);
PETSc_call(VecAXPY, x, 1., y_.x);
release_ = y_.release_;
return *this;
}
} // namespace akantu
diff --git a/src/solver/solver_vector_petsc.hh b/src/solver/solver_vector_petsc.hh
index d34999f04..0155667c2 100644
--- a/src/solver/solver_vector_petsc.hh
+++ b/src/solver/solver_vector_petsc.hh
@@ -1,204 +1,208 @@
/**
* @file solver_vector_petsc.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue Jan 01 2019
+ * @date creation: Tue Jan 01 2019
+ * @date last modification: Fri Jul 24 2020
*
- * @brief A Documented file.
+ * @brief Solver vector interface for PETSc
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "dof_manager_petsc.hh"
#include "solver_vector.hh"
/* -------------------------------------------------------------------------- */
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_VECTOR_PETSC_HH_
#define AKANTU_SOLVER_VECTOR_PETSC_HH_
namespace akantu {
class DOFManagerPETSc;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace internal {
/* ------------------------------------------------------------------------ */
class PETScVector {
public:
virtual ~PETScVector() = default;
operator Vec &() { return x; }
operator const Vec &() const { return x; }
Int size() const {
PetscInt n;
PETSc_call(VecGetSize, x, &n);
return n;
}
Int local_size() const {
PetscInt n;
PETSc_call(VecGetLocalSize, x, &n);
return n;
}
AKANTU_GET_MACRO_NOT_CONST(Vec, x, auto &);
AKANTU_GET_MACRO(Vec, x, const auto &);
protected:
Vec x{nullptr};
};
} // namespace internal
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class SolverVectorPETSc : public SolverVector, public internal::PETScVector {
public:
SolverVectorPETSc(DOFManagerPETSc & dof_manager,
const ID & id = "solver_vector_petsc");
SolverVectorPETSc(const SolverVectorPETSc & vector,
const ID & id = "solver_vector_petsc");
SolverVectorPETSc(Vec x, DOFManagerPETSc & dof_manager,
const ID & id = "solver_vector_petsc");
~SolverVectorPETSc() override;
// resize the vector to the size of the problem
void resize() override;
void set(Real val) override;
operator const Array<Real> &() const override;
SolverVector & operator+(const SolverVector & y) override;
SolverVector & operator=(const SolverVector & y) override;
SolverVectorPETSc & operator=(const SolverVectorPETSc & y);
/// get values using processors global indexes
void getValues(const Array<Int> & idx, Array<Real> & values) const;
/// get values using processors local indexes
void getValuesLocal(const Array<Int> & idx, Array<Real> & values) const;
/// adding values to the vector using the global indices
void addValues(const Array<Int> & gidx, const Array<Real> & values,
Real scale_factor = 1.);
/// adding values to the vector using the local indices
void addValuesLocal(const Array<Int> & lidx, const Array<Real> & values,
Real scale_factor = 1.);
Int size() const override { return internal::PETScVector::size(); }
Int localSize() const override { return internal::PETScVector::local_size(); }
void printself(std::ostream & stream, int indent = 0) const override;
protected:
void applyModifications();
void updateGhost();
protected:
DOFManagerPETSc & dof_manager;
// used for the conversion operator
Array<Real> cache;
};
/* -------------------------------------------------------------------------- */
namespace internal {
/* ------------------------------------------------------------------------ */
template <class Array> class PETScWrapedVector : public PETScVector {
public:
PETScWrapedVector(Array && array) : array(array) {
PETSc_call(VecCreateSeqWithArray, PETSC_COMM_SELF, 1, array.size(),
array.storage(), &x);
}
~PETScWrapedVector() override { PETSc_call(VecDestroy, &x); }
private:
Array array;
};
/* ------------------------------------------------------------------------ */
template <bool read_only> class PETScLocalVector : public PETScVector {
public:
PETScLocalVector(const Vec & g) : g(g) {
PETSc_call(VecGetLocalVectorRead, g, x);
}
PETScLocalVector(const SolverVectorPETSc & g)
: PETScLocalVector(g.getVec()) {}
~PETScLocalVector() override {
PETSc_call(VecRestoreLocalVectorRead, g, x);
PETSc_call(VecDestroy, &x);
}
private:
const Vec & g;
};
template <> class PETScLocalVector<false> : public PETScVector {
public:
PETScLocalVector(Vec & g) : g(g) {
PETSc_call(VecGetLocalVectorRead, g, x);
}
PETScLocalVector(SolverVectorPETSc & g) : PETScLocalVector(g.getVec()) {}
~PETScLocalVector() override {
PETSc_call(VecRestoreLocalVectorRead, g, x);
PETSc_call(VecDestroy, &x);
}
private:
Vec & g;
};
/* ------------------------------------------------------------------------ */
template <class Array>
decltype(auto) make_petsc_wraped_vector(Array && array) {
return PETScWrapedVector<Array>(std::forward<Array>(array));
}
template <
typename V,
std::enable_if_t<std::is_same<Vec, std::decay_t<V>>::value> * = nullptr>
decltype(auto) make_petsc_local_vector(V && vec) {
constexpr auto read_only = std::is_const<std::remove_reference_t<V>>::value;
return PETScLocalVector<read_only>(vec);
}
template <typename V, std::enable_if_t<std::is_base_of<
SolverVector, std::decay_t<V>>::value> * = nullptr>
decltype(auto) make_petsc_local_vector(V && vec) {
constexpr auto read_only = std::is_const<std::remove_reference_t<V>>::value;
return PETScLocalVector<read_only>(
dynamic_cast<std::conditional_t<read_only, const SolverVectorPETSc,
SolverVectorPETSc> &>(vec));
}
} // namespace internal
} // namespace akantu
#endif /* AKANTU_SOLVER_VECTOR_PETSC_HH_ */
diff --git a/src/solver/sparse_matrix.cc b/src/solver/sparse_matrix.cc
index 4d366d552..2706faedd 100644
--- a/src/solver/sparse_matrix.cc
+++ b/src/solver/sparse_matrix.cc
@@ -1,78 +1,82 @@
/**
* @file sparse_matrix.cc
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue May 26 2020
*
* @brief implementation of the SparseMatrix class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(DOFManager & dof_manager,
const MatrixType & matrix_type, const ID & id)
: id(id), _dof_manager(dof_manager), matrix_type(matrix_type),
size_(dof_manager.getSystemSize()), nb_non_zero(0) {
AKANTU_DEBUG_IN();
const auto & comm = _dof_manager.getCommunicator();
this->nb_proc = comm.getNbProc();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(const SparseMatrix & matrix, const ID & id)
: SparseMatrix(matrix._dof_manager, matrix.matrix_type, id) {
nb_non_zero = matrix.nb_non_zero;
}
/* -------------------------------------------------------------------------- */
SparseMatrix::~SparseMatrix() = default;
// /* --------------------------------------------------------------------------
// */ Array<Real> & operator*=(SolverVector & vect, const SparseMatrix & mat) {
// Array<Real> tmp(vect.size(), vect.getNbComponent(), 0.);
// mat.matVecMul(vect, tmp);
// vect.copy(tmp);
// return vect;
// }
/* -------------------------------------------------------------------------- */
void SparseMatrix::add(const SparseMatrix & B, Real alpha) {
B.addMeTo(*this, alpha);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/sparse_matrix.hh b/src/solver/sparse_matrix.hh
index d3d062928..4720a2ac8 100644
--- a/src/solver/sparse_matrix.hh
+++ b/src/solver/sparse_matrix.hh
@@ -1,168 +1,170 @@
/**
* @file sparse_matrix.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Sep 16 2020
*
* @brief sparse matrix storage class (distributed assembled matrix)
* This is a COO format (Coordinate List)
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SPARSE_MATRIX_HH_
#define AKANTU_SPARSE_MATRIX_HH_
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
class TermsToAssemble;
class SolverVector;
} // namespace akantu
namespace akantu {
class SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrix(DOFManager & dof_manager, const MatrixType & matrix_type,
const ID & id = "sparse_matrix");
SparseMatrix(const SparseMatrix & matrix, const ID & id = "sparse_matrix");
virtual ~SparseMatrix();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
virtual void clearProfile();
/// set the matrix to 0
virtual void set(Real val) = 0;
virtual void zero() { this->set(0); }
/// add a non-zero element to the profile
virtual UInt add(UInt i, UInt j) = 0;
/// assemble a local matrix in the sparse one
virtual void add(UInt i, UInt j, Real value) = 0;
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
}
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(const std::string & /* filename */) const {
AKANTU_TO_IMPLEMENT();
};
/// multiply the matrix by a coefficient
virtual void mul(Real alpha) = 0;
/// add matrices
virtual void add(const SparseMatrix & B, Real alpha = 1.);
/// Equivalent of *gemv in blas
virtual void matVecMul(const SolverVector & x, SolverVector & y,
Real alpha = 1., Real beta = 0.) const = 0;
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(Real block_val = 1.) = 0;
/// copy the profile of another matrix
virtual void copyProfile(const SparseMatrix & other) = 0;
/// operator *=
SparseMatrix & operator*=(Real alpha) {
this->mul(alpha);
return *this;
}
protected:
/// This is the revert of add \f[B += \alpha * *this\f];
virtual void addMeTo(SparseMatrix & B, Real alpha) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
virtual inline Real operator()(UInt /*i*/, UInt /*j*/) const {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
virtual inline Real & operator()(UInt /*i*/, UInt /*j*/) {
AKANTU_TO_IMPLEMENT();
}
/// return the minimum value
virtual inline Real min() {
AKANTU_TO_IMPLEMENT();
}
AKANTU_GET_MACRO(NbNonZero, nb_non_zero, UInt);
UInt size() const { return size_; }
AKANTU_GET_MACRO(MatrixType, matrix_type, const MatrixType &);
virtual UInt getRelease() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
ID id;
/// Underlying dof manager
DOFManager & _dof_manager;
/// sparce matrix type
MatrixType matrix_type;
/// Size of the matrix
UInt size_;
/// number of processors
UInt nb_proc;
/// number of non zero element
UInt nb_non_zero;
};
// Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat);
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_inline_impl.hh"
#endif /* AKANTU_SPARSE_MATRIX_HH_ */
diff --git a/src/solver/sparse_matrix_aij.cc b/src/solver/sparse_matrix_aij.cc
index c6551625a..317045647 100644
--- a/src/solver/sparse_matrix_aij.cc
+++ b/src/solver/sparse_matrix_aij.cc
@@ -1,300 +1,302 @@
/**
* @file sparse_matrix_aij.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 21 2015
- * @date last modification: Mon Dec 04 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of the AIJ sparse matrix
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "solver_vector_default.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type, const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager),
irn(0, 1, id + ":irn"), jcn(0, 1, id + ":jcn"), a(0, 1, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(const SparseMatrixAIJ & matrix, const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager),
irn(matrix.irn, id + ":irn"), jcn(matrix.jcn, id + ":jcn"),
a(matrix.a, id + ":a") {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::~SparseMatrixAIJ() = default;
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
auto begin = blocked_dofs.begin();
auto end = blocked_dofs.end();
auto is_blocked = [&](auto && i) -> bool {
auto il = this->dof_manager.globalToLocalEquationNumber(i);
return std::binary_search(begin, end, il);
};
for (auto && ij_a : zip(irn, jcn, a)) {
UInt ni = std::get<0>(ij_a) - 1;
UInt nj = std::get<1>(ij_a) - 1;
if (is_blocked(ni) or is_blocked(nj)) {
std::get<2>(ij_a) =
std::get<0>(ij_a) != std::get<1>(ij_a)
? 0.
: this->dof_manager.isLocalOrMasterDOF(
this->dof_manager.globalToLocalEquationNumber(ni))
? block_val
: 0.;
}
}
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveProfile(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.open(filename.c_str());
UInt m = this->size_;
auto & comm = dof_manager.getCommunicator();
// write header
if (comm.whoAmI() == 0) {
outfile << "%%MatrixMarket matrix coordinate pattern";
if (this->matrix_type == _symmetric) {
outfile << " symmetric";
} else {
outfile << " general";
}
outfile << std::endl;
outfile << m << " " << m << " " << this->nb_non_zero << std::endl;
}
for (auto p : arange(comm.getNbProc())) {
// write content
if (comm.whoAmI() == p) {
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn.storage()[i] << " " << this->jcn.storage()[i]
<< " 1" << std::endl;
}
}
comm.barrier();
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
auto & comm = dof_manager.getCommunicator();
// open and set the properties of the stream
std::ofstream outfile;
if (0 == comm.whoAmI()) {
outfile.open(filename.c_str());
} else {
outfile.open(filename.c_str(), std::ios_base::app);
}
outfile.precision(std::numeric_limits<Real>::digits10);
// write header
decltype(nb_non_zero) nnz = this->nb_non_zero;
comm.allReduce(nnz);
if (comm.whoAmI() == 0) {
outfile << "%%MatrixMarket matrix coordinate real";
if (this->matrix_type == _symmetric) {
outfile << " symmetric";
} else {
outfile << " general";
}
outfile << std::endl;
outfile << this->size_ << " " << this->size_ << " " << nnz << std::endl;
}
for (auto p : arange(comm.getNbProc())) {
// write content
if (comm.whoAmI() == p) {
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn(i) << " " << this->jcn(i) << " " << this->a(i)
<< std::endl;
}
}
comm.barrier();
}
// time to end
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
y *= beta;
auto i_it = this->irn.begin();
auto j_it = this->jcn.begin();
auto a_it = this->a.begin();
auto a_end = this->a.end();
auto x_it = x.begin_reinterpret(x.size() * x.getNbComponent());
auto y_it = y.begin_reinterpret(x.size() * x.getNbComponent());
for (; a_it != a_end; ++i_it, ++j_it, ++a_it) {
Int i = this->dof_manager.globalToLocalEquationNumber(*i_it - 1);
Int j = this->dof_manager.globalToLocalEquationNumber(*j_it - 1);
const Real & A = *a_it;
y_it[i] += alpha * A * x_it[j];
if ((this->matrix_type == _symmetric) && (i != j)) {
y_it[j] += alpha * A * x_it[i];
}
}
if (this->dof_manager.hasSynchronizer()) {
this->dof_manager.getSynchronizer().reduceSynchronizeArray<AddOperation>(y);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const SolverVector & _x, SolverVector & _y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
auto && x = aka::as_type<SolverVectorArray>(_x).getVector();
auto && y = aka::as_type<SolverVectorArray>(_y).getVector();
this->matVecMul(x, y, alpha, beta);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyContent(const SparseMatrix & matrix) {
AKANTU_DEBUG_IN();
const auto & mat = aka::as_type<SparseMatrixAIJ>(matrix);
AKANTU_DEBUG_ASSERT(nb_non_zero == mat.getNbNonZero(),
"The to matrix don't have the same profiles");
memcpy(a.storage(), mat.getA().storage(), nb_non_zero * sizeof(Real));
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyProfile(const SparseMatrix & other) {
const auto & A = aka::as_type<SparseMatrixAIJ>(other);
SparseMatrix::clearProfile();
this->irn.copy(A.irn);
this->jcn.copy(A.jcn);
this->irn_jcn_k.clear();
UInt i;
UInt j;
UInt k;
for (auto && data : enumerate(irn, jcn)) {
std::tie(k, i, j) = data;
this->irn_jcn_k[this->key(i - 1, j - 1)] = k;
}
this->nb_non_zero = this->irn.size();
this->a.resize(this->nb_non_zero);
this->a.set(0.);
this->size_ = A.size_;
this->profile_release = A.profile_release;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
template <class MatrixType>
void SparseMatrixAIJ::addMeToTemplated(MatrixType & B, Real alpha) const {
UInt i;
UInt j;
Real A_ij;
for (auto && tuple : zip(irn, jcn, a)) {
std::tie(i, j, A_ij) = tuple;
B.add(i - 1, j - 1, alpha * A_ij);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::addMeTo(SparseMatrix & B, Real alpha) const {
if (aka::is_of_type<SparseMatrixAIJ>(B)) {
this->addMeToTemplated<SparseMatrixAIJ>(aka::as_type<SparseMatrixAIJ>(B),
alpha);
} else {
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::mul(Real alpha) {
this->a *= alpha;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::set(Real val) {
a.set(val);
this->value_release++;
}
} // namespace akantu
diff --git a/src/solver/sparse_matrix_aij.hh b/src/solver/sparse_matrix_aij.hh
index 8ff16e8a6..3a7e143ff 100644
--- a/src/solver/sparse_matrix_aij.hh
+++ b/src/solver/sparse_matrix_aij.hh
@@ -1,202 +1,204 @@
/**
* @file sparse_matrix_aij.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Sep 16 2020
*
* @brief AIJ implementation of the SparseMatrix (this the format used by
* Mumps)
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SPARSE_MATRIX_AIJ_HH_
#define AKANTU_SPARSE_MATRIX_AIJ_HH_
namespace akantu {
class DOFManagerDefault;
class TermsToAssemble;
} // namespace akantu
namespace akantu {
class SparseMatrixAIJ : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_aij");
SparseMatrixAIJ(const SparseMatrixAIJ & matrix,
const ID & id = "sparse_matrix_aij");
~SparseMatrixAIJ() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile() override;
/// add a non-zero element
inline UInt add(UInt i, UInt j) override;
/// set the matrix to 0
void set(Real val) override;
/// assemble a local matrix in the sparse one
inline void add(UInt i, UInt j, Real value) override;
/// add a block of values
inline void addValues(const Vector<Int> & is, const Vector<Int> & js,
const Matrix<Real> & values, MatrixType values_type);
/// set the size of the matrix
void resize(UInt size) { this->size_ = size; }
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// save the profil in a file using the MatrixMarket file format
void saveProfile(const std::string & filename) const override;
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// multiply the matrix by a scalar
void mul(Real alpha) override;
/// Equivalent of *gemv in blas
void matVecMul(const SolverVector & x, SolverVector & y, Real alpha = 1.,
Real beta = 0.) const override;
void matVecMul(const Array<Real> & x, Array<Real> & y, Real alpha = 1.,
Real beta = 0.) const;
/// copy the profile of another matrix
void copyProfile(const SparseMatrix & other) override;
/* ------------------------------------------------------------------------ */
/// accessor to A_{ij} - if (i, j) not present it returns 0
inline Real operator()(UInt i, UInt j) const override;
/// accessor to A_{ij} - if (i, j) not present it fails, (i, j) should be
/// first added to the profile
inline Real & operator()(UInt i, UInt j) override;
/// accessor to get the minimum value of A_{ij}
inline Real min() override;
protected:
void addMeTo(SparseMatrix & B, Real alpha) const override;
inline void addSymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
inline void addUnsymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
inline void addValuesToUnsymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values);
private:
/// This is just to inline the addToMatrix function
template <class MatrixType>
void addMeToTemplated(MatrixType & B, Real alpha) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(IRN, irn, const Array<Int> &);
AKANTU_GET_MACRO(JCN, jcn, const Array<Int> &);
AKANTU_GET_MACRO(A, a, const Array<Real> &);
/// The release changes at each call of a function that changes the profile,
/// it in increasing but could overflow so it should be checked as
/// (my_release != release) and not as (my_release < release)
AKANTU_GET_MACRO(ProfileRelease, profile_release, UInt);
AKANTU_GET_MACRO(ValueRelease, value_release, UInt);
UInt getRelease() const override { return value_release; }
protected:
using KeyCOO = std::pair<UInt, UInt>;
using coordinate_list_map = std::unordered_map<KeyCOO, UInt>;
/// get the pair corresponding to (i, j)
inline KeyCOO key(UInt i, UInt j) const {
if (this->matrix_type == _symmetric && (i > j)) {
return std::make_pair(j, i);
}
return std::make_pair(i, j);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// row indexes
Array<Int> irn;
/// column indexes
Array<Int> jcn;
/// values : A[k] = Matrix[irn[k]][jcn[k]]
Array<Real> a;
/// Profile release
UInt profile_release{1};
/// Value release
UInt value_release{1};
/// map for (i, j) -> k correspondence
coordinate_list_map irn_jcn_k;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij_inline_impl.hh"
#endif /* AKANTU_SPARSE_MATRIX_AIJ_HH_ */
diff --git a/src/solver/sparse_matrix_aij_inline_impl.hh b/src/solver/sparse_matrix_aij_inline_impl.hh
index 5a1f1a35f..e381871fb 100644
--- a/src/solver/sparse_matrix_aij_inline_impl.hh
+++ b/src/solver/sparse_matrix_aij_inline_impl.hh
@@ -1,201 +1,203 @@
/**
* @file sparse_matrix_aij_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 21 2015
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Mar 31 2020
*
* @brief Implementation of inline functions of SparseMatrixAIJ
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_
#define AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_
namespace akantu {
inline UInt SparseMatrixAIJ::add(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto it = this->irn_jcn_k.find(jcn_irn);
if (!(it == this->irn_jcn_k.end())) {
return it->second;
}
if (i + 1 > this->size_) {
this->size_ = i + 1;
}
if (j + 1 > this->size_) {
this->size_ = j + 1;
}
this->irn.push_back(i + 1);
this->jcn.push_back(j + 1);
this->a.push_back(0.);
this->irn_jcn_k[jcn_irn] = this->nb_non_zero;
(this->nb_non_zero)++;
this->profile_release++;
this->value_release++;
return (this->nb_non_zero - 1);
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::clearProfile() {
SparseMatrix::clearProfile();
this->irn_jcn_k.clear();
this->irn.clear();
this->jcn.clear();
this->a.clear();
this->size_ = 0;
this->nb_non_zero = 0;
this->profile_release++;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::add(UInt i, UInt j, Real value) {
UInt idx = this->add(i, j);
this->a(idx) += value;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline Real SparseMatrixAIJ::operator()(UInt i, UInt j) const {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
if (irn_jcn_k_it == this->irn_jcn_k.end()) {
return 0.;
}
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline Real & SparseMatrixAIJ::operator()(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
auto irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
AKANTU_DEBUG_ASSERT(irn_jcn_k_it != this->irn_jcn_k.end(),
"Couple (i,j) = (" << i << "," << j
<< ") does not exist in the profile");
// it may change the profile so it is considered as a change
this->value_release++;
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addSymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = i; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addUnsymmetricValuesToSymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = 0; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
if (c_jcn >= c_irn) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void
SparseMatrixAIJ::addValuesToUnsymmetric(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values) {
for (UInt i = 0; i < values.rows(); ++i) {
UInt c_irn = is(i);
if (c_irn < size_) {
for (UInt j = 0; j < values.cols(); ++j) {
UInt c_jcn = js(j);
if (c_jcn < size_) {
operator()(c_irn, c_jcn) += values(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::addValues(const Vector<Int> & is,
const Vector<Int> & js,
const Matrix<Real> & values,
MatrixType values_type) {
if (getMatrixType() == _symmetric) {
if (values_type == _symmetric) {
this->addSymmetricValuesToSymmetric(is, js, values);
} else {
this->addUnsymmetricValuesToSymmetric(is, js, values);
}
} else {
this->addValuesToUnsymmetric(is, js, values);
}
}
/* -------------------------------------------------------------------------- */
inline Real SparseMatrixAIJ::min() {
return *std::min(this->a.begin(), this->a.end());
}
} // namespace akantu
#endif /* AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_HH_ */
diff --git a/src/solver/sparse_matrix_inline_impl.hh b/src/solver/sparse_matrix_inline_impl.hh
index c5dd3c811..fbdc8fc75 100644
--- a/src/solver/sparse_matrix_inline_impl.hh
+++ b/src/solver/sparse_matrix_inline_impl.hh
@@ -1,34 +1,37 @@
/**
* @file sparse_matrix_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Mon Jun 19 2017
+ * @date last modification: Fri Jan 15 2016
*
* @brief implementation of inline methods of the SparseMatrix class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
namespace akantu {
inline void SparseMatrix::clearProfile() { this->nb_non_zero = 0; }
} // namespace akantu
diff --git a/src/solver/sparse_matrix_petsc.cc b/src/solver/sparse_matrix_petsc.cc
index 9f857b14d..4170d01c4 100644
--- a/src/solver/sparse_matrix_petsc.cc
+++ b/src/solver/sparse_matrix_petsc.cc
@@ -1,286 +1,289 @@
/**
* @file sparse_matrix_petsc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Sat Feb 03 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of PETSc matrix class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_petsc.hh"
#include "dof_manager_petsc.hh"
#include "mpi_communicator_data.hh"
#include "solver_vector_petsc.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager) {
AKANTU_DEBUG_IN();
auto && mpi_comm = dof_manager.getMPIComm();
PETSc_call(MatCreate, mpi_comm, &mat);
detail::PETScSetName(mat, id);
resize();
PETSc_call(MatSetFromOptions, mat);
PETSc_call(MatSetUp, mat);
PETSc_call(MatSetOption, mat, MAT_ROW_ORIENTED, PETSC_TRUE);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
if (matrix_type == _symmetric) {
PETSc_call(MatSetOption, mat, MAT_SYMMETRIC, PETSC_TRUE);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager) {
PETSc_call(MatDuplicate, matrix.mat, MAT_COPY_VALUES, &mat);
detail::PETScSetName(mat, id);
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
if (mat != nullptr) {
PETSc_call(MatDestroy, &mat);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::resize() {
auto local_size = dof_manager.getPureLocalSystemSize();
PETSc_call(MatSetSizes, mat, local_size, local_size, size_, size_);
auto & is_ltog_mapping = dof_manager.getISLocalToGlobalMapping();
PETSc_call(MatSetLocalToGlobalMapping, mat, is_ltog_mapping, is_ltog_mapping);
}
/* -------------------------------------------------------------------------- */
/**
* Method to save the nonzero pattern and the values stored at each position
* @param filename name of the file in which the information will be stored
*/
void SparseMatrixPETSc::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
auto && mpi_comm = dof_manager.getMPIComm();
/// create Petsc viewer
PetscViewer viewer;
PETSc_call(PetscViewerASCIIOpen, mpi_comm, filename.c_str(), &viewer);
PETSc_call(PetscViewerPushFormat, viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
PETSc_call(MatView, mat, viewer);
PETSc_call(PetscViewerPopFormat, viewer);
PETSc_call(PetscViewerDestroy, &viewer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// Equivalent of *gemv in blas
void SparseMatrixPETSc::matVecMul(const SolverVector & _x, SolverVector & _y,
Real alpha, Real beta) const {
const auto & x = aka::as_type<SolverVectorPETSc>(_x);
auto & y = aka::as_type<SolverVectorPETSc>(_y);
// y = alpha A x + beta y
SolverVectorPETSc w(x, this->id + ":tmp");
// w = A x
if (release == 0) {
PETSc_call(VecZeroEntries, w);
} else {
PETSc_call(MatMult, mat, x, w);
}
if (alpha != 1.) {
// w = alpha w
PETSc_call(VecScale, w, alpha);
}
// y = w + beta y
PETSc_call(VecAYPX, y, beta, w);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeToImpl(SparseMatrixPETSc & B, Real alpha) const {
PETSc_call(MatAXPY, B.mat, alpha, mat, SAME_NONZERO_PATTERN);
B.release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addMeTo(SparseMatrix & B, Real alpha) const {
if (aka::is_of_type<SparseMatrixPETSc>(B)) {
auto & B_petsc = aka::as_type<SparseMatrixPETSc>(B);
this->addMeToImpl(B_petsc, alpha);
} else {
AKANTU_TO_IMPLEMENT();
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
/**
* MatSetValues() generally caches the values. The matrix is ready to
* use only after MatAssemblyBegin() and MatAssemblyEnd() have been
* called. (http://www.mcs.anl.gov/petsc/)
*/
void SparseMatrixPETSc::applyModifications() {
this->beginAssembly();
this->endAssembly();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
PETSc_call(MatAssemblyBegin, mat, MAT_FINAL_ASSEMBLY);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
PETSc_call(MatAssemblyEnd, mat, MAT_FINAL_ASSEMBLY);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::copyProfile(const SparseMatrix & other) {
const auto & A = aka::as_type<SparseMatrixPETSc>(other);
MatDestroy(&mat);
MatDuplicate(A.mat, MAT_DO_NOT_COPY_VALUES, &mat);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
// std::vector<PetscInt> rows;
// for (auto && data : enumerate(blocked)) {
// if (std::get<1>(data)) {
// rows.push_back(std::get<0>(data));
// }
// }
// applyModifications();
static int c = 0;
saveMatrix("before_blocked_" + std::to_string(c) + ".mtx");
PETSc_call(MatZeroRowsColumnsLocal, mat, blocked_dofs.size(),
blocked_dofs.storage(), block_val, nullptr, nullptr);
saveMatrix("after_blocked_" + std::to_string(c) + ".mtx");
++c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::mul(Real alpha) {
PETSc_call(MatScale, mat, alpha);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::zero() {
PETSc_call(MatZeroEntries, mat);
this->release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::clearProfile() {
SparseMatrix::clearProfile();
PETSc_call(MatResetPreallocation, mat);
PETSc_call(MatSetOption, mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_KEEP_NONZERO_PATTERN, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATIONS, PETSC_TRUE);
// PETSc_call(MatSetOption, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
this->zero();
}
/* -------------------------------------------------------------------------- */
UInt SparseMatrixPETSc::add(UInt i, UInt j) {
PETSc_call(MatSetValue, mat, i, j, 0, ADD_VALUES);
return 0;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::add(UInt i, UInt j, Real val) {
PETSc_call(MatSetValue, mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j) {
PETSc_call(MatSetValueLocal, mat, i, j, 0, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(UInt i, UInt j, Real val) {
PETSc_call(MatSetValueLocal, mat, i, j, val, ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addLocal(const Vector<Int> & rows,
const Vector<Int> & cols,
const Matrix<Real> & values) {
PETSc_call(MatSetValuesLocal, mat, rows.size(), rows.storage(), cols.size(),
cols.storage(), values.storage(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::addValues(const Vector<Int> & rows,
const Vector<Int> & cols,
const Matrix<Real> & values, MatrixType values_type) {
if (values_type == _unsymmetric and matrix_type == _symmetric) {
PETSc_call(MatSetOption, mat, MAT_SYMMETRIC, PETSC_FALSE);
PETSc_call(MatSetOption, mat, MAT_STRUCTURALLY_SYMMETRIC, PETSC_FALSE);
}
PETSc_call(MatSetValues, mat, rows.size(), rows.storage(), cols.size(),
cols.storage(), values.storage(), ADD_VALUES);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/solver/sparse_matrix_petsc.hh b/src/solver/sparse_matrix_petsc.hh
index a52c4f5e3..e7ff7b21d 100644
--- a/src/solver/sparse_matrix_petsc.hh
+++ b/src/solver/sparse_matrix_petsc.hh
@@ -1,159 +1,162 @@
/**
* @file sparse_matrix_petsc.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 06 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief Interface for PETSc matrices
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PETSC_MATRIX_HH_
#define AKANTU_PETSC_MATRIX_HH_
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerPETSc;
}
namespace akantu {
class SparseMatrixPETSc : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_petsc");
SparseMatrixPETSc(const SparseMatrixPETSc & matrix,
const ID & id = "sparse_matrix_petsc");
~SparseMatrixPETSc() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the matrix to 0
void zero() override;
void set(Real /*val*/) override {
AKANTU_TO_IMPLEMENT();
}
void clearProfile() override;
/// add a non-zero element to the profile
UInt add(UInt i, UInt j) override;
/// assemble a local matrix in the sparse one
void add(UInt i, UInt j, Real value) override;
void addLocal(UInt i, UInt j);
void addLocal(UInt i, UInt j, Real val);
void addLocal(const Vector<Int> & rows, const Vector<Int> & cols,
const Matrix<Real> & values);
/// add a block of values
void addValues(const Vector<Int> & rows, const Vector<Int> & cols,
const Matrix<Real> & values, MatrixType values_type);
/// save the profil in a file using the MatrixMarket file format
// void saveProfile(__attribute__((unused)) const std::string &) const
// override {
// AKANTU_DEBUG_TO_IMPLEMENT();
// }
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// multiply the matrix by a coefficient
void mul(Real alpha) override;
/// Equivalent of *gemv in blas
void matVecMul(const SolverVector & x, SolverVector & y, Real alpha = 1.,
Real beta = 0.) const override;
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// copy the profile of a matrix
void copyProfile(const SparseMatrix & other) override;
void applyModifications();
void resize();
protected:
void addMeTo(SparseMatrix & B, Real alpha) const override;
/// This is the specific implementation
void addMeToImpl(SparseMatrixPETSc & B, Real alpha) const;
void beginAssembly();
void endAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the values at potition i, j
inline Real operator()(UInt /*i*/, UInt /*j*/) const override {
AKANTU_TO_IMPLEMENT();
}
/// return the values at potition i, j
inline Real & operator()(UInt /*i*/, UInt /*j*/) override {
AKANTU_TO_IMPLEMENT();
}
UInt getRelease() const override { return release; };
operator Mat &() { return mat; }
operator const Mat &() const { return mat; }
AKANTU_GET_MACRO(Mat, mat, const Mat &);
AKANTU_GET_MACRO_NOT_CONST(Mat, mat, Mat &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// DOFManagerPETSc that contains the numbering for petsc
DOFManagerPETSc & dof_manager;
/// store the PETSc matrix
Mat mat;
/// matrix release
UInt release{0};
};
} // namespace akantu
#endif /* AKANTU_PETSC_MATRIX_HH_ */
diff --git a/src/solver/sparse_solver.cc b/src/solver/sparse_solver.cc
index 930f0384d..fb3de0afb 100644
--- a/src/solver/sparse_solver.cc
+++ b/src/solver/sparse_solver.cc
@@ -1,83 +1,85 @@
/**
* @file sparse_solver.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Fri Dec 08 2017
+ * @date last modification: Tue Feb 02 2016
*
* @brief Solver interface class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
#include "communicator.hh"
#include "dof_manager.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolver::SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id)
: Parsable(ParserType::_solver, id),
_dof_manager(dof_manager), matrix_id(matrix_id),
communicator(dof_manager.getCommunicator()) {
AKANTU_DEBUG_IN();
// OK this is fishy...
this->communicator.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolver::~SparseSolver() {
AKANTU_DEBUG_IN();
// this->destroyInternalData();
this->communicator.unregisterEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try {
this->destroyInternalData();
} catch (...) {
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::createSynchronizerRegistry() {
// this->synch_registry = new SynchronizerRegistry(this);
}
void SparseSolver::onCommunicatorFinalize() { this->destroyInternalData(); }
} // namespace akantu
diff --git a/src/solver/sparse_solver.hh b/src/solver/sparse_solver.hh
index dd8936d53..7e43ef63a 100644
--- a/src/solver/sparse_solver.hh
+++ b/src/solver/sparse_solver.hh
@@ -1,126 +1,128 @@
/**
* @file sparse_solver.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 24 2018
*
* @brief interface for solvers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator_event_handler.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_HH_
#define AKANTU_SOLVER_HH_
namespace akantu {
enum SolverParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
class DOFManager;
} // namespace akantu
namespace akantu {
class SparseSolver : public Parsable, public CommunicatorEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id = "solver");
~SparseSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver
virtual void initialize() = 0;
virtual void analysis(){};
virtual void factorize(){};
virtual void solve(){};
protected:
virtual void destroyInternalData(){};
public:
virtual void beforeStaticSolverDestroy();
void createSynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
void onCommunicatorFinalize() override;
// inline virtual UInt getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// manager handling the dofs for this SparseMatrix solver
DOFManager & _dof_manager;
/// The id of the associated matrix
ID matrix_id;
/// How to parallelize the solve
SolverParallelMethod parallel_method;
/// Communicator used by the solver
Communicator & communicator;
};
namespace debug {
class SingularMatrixException : public Exception {
public:
SingularMatrixException(const SparseMatrix & matrix)
: Exception("Solver encountered singular matrix"), matrix(matrix) {}
const SparseMatrix & matrix;
};
} // namespace debug
} // namespace akantu
#endif /* AKANTU_SOLVER_HH_ */
diff --git a/src/solver/sparse_solver_inline_impl.hh b/src/solver/sparse_solver_inline_impl.hh
index 99a7dc9d9..6ee1343ca 100644
--- a/src/solver/sparse_solver_inline_impl.hh
+++ b/src/solver/sparse_solver_inline_impl.hh
@@ -1,86 +1,88 @@
/**
* @file sparse_solver_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Sun Aug 13 2017
+ * @date last modification: Sun Dec 30 2018
*
* @brief implementation of solver inline functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
// inline UInt Solver::getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const {
// AKANTU_DEBUG_IN();
// UInt size = 0;
// switch(tag) {
// case SynchronizationTag::_solver_solution: {
// size += dofs.size() * sizeof(Real);
// break;
// }
// default: { }
// }
// AKANTU_DEBUG_OUT();
// return size;
// }
// /* --------------------------------------------------------------------------
// */
// inline void Solver::packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const {
// AKANTU_DEBUG_IN();
// switch(tag) {
// case SynchronizationTag::_solver_solution: {
// packDOFDataHelper(*solution, buffer, dofs);
// break;
// }
// default: {
// }
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */
// inline void Solver::unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) {
// AKANTU_DEBUG_IN();
// switch(tag) {
// case SynchronizationTag::_solver_solution: {
// unpackDOFDataHelper(*solution, buffer, dofs);
// break;
// }
// default: {
// }
// }
// AKANTU_DEBUG_OUT();
// }
diff --git a/src/solver/sparse_solver_mumps.cc b/src/solver/sparse_solver_mumps.cc
index b1500f1fd..2e38531bd 100644
--- a/src/solver/sparse_solver_mumps.cc
+++ b/src/solver/sparse_solver_mumps.cc
@@ -1,454 +1,398 @@
/**
* @file sparse_solver_mumps.cc
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Sep 02 2020
*
* @brief implem of SparseSolverMumps class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
- *
- * @subsection Ctrl_param Control parameters
- *
- * ICNTL(1),
- * ICNTL(2),
- * ICNTL(3) : output streams for error, diagnostics, and global messages
- *
- * ICNTL(4) : verbose level : 0 no message - 4 all messages
- *
- * ICNTL(5) : type of matrix, 0 assembled, 1 elementary
- *
- * ICNTL(6) : control the permutation and scaling(default 7) see mumps doc for
- * more information
- *
- * ICNTL(7) : determine the pivot order (default 7) see mumps doc for more
- * information
- *
- * ICNTL(8) : describe the scaling method used
- *
- * ICNTL(9) : 1 solve A x = b, 0 solve At x = b
- *
- * ICNTL(10) : number of iterative refinement when NRHS = 1
- *
- * ICNTL(11) : > 0 return statistics
- *
- * ICNTL(12) : only used for SYM = 2, ordering strategy
- *
- * ICNTL(13) :
- *
- * ICNTL(14) : percentage of increase of the estimated working space
- *
- * ICNTL(15-17) : not used
- *
- * ICNTL(18) : only used if ICNTL(5) = 0, 0 matrix centralized, 1 structure on
- * host and mumps give the mapping, 2 structure on host and distributed matrix
- * for facto, 3 distributed matrix
- *
- * ICNTL(19) : > 0, Shur complement returned
- *
- * ICNTL(20) : 0 rhs dense, 1 rhs sparse
- *
- * ICNTL(21) : 0 solution in rhs, 1 solution distributed in ISOL_loc and SOL_loc
- * allocated by user
- *
- * ICNTL(22) : 0 in-core, 1 out-of-core
- *
- * ICNTL(23) : maximum memory allocatable by mumps pre proc
- *
- * ICNTL(24) : controls the detection of "null pivot rows"
- *
- * ICNTL(25) :
- *
- * ICNTL(26) :
- *
- * ICNTL(27) :
- *
- * ICNTL(28) : 0 automatic choice, 1 sequential analysis, 2 parallel analysis
- *
- * ICNTL(29) : 0 automatic choice, 1 PT-Scotch, 2 ParMetis
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "solver_vector_default.hh"
#include "sparse_matrix_aij.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// static std::ostream & operator <<(std::ostream & stream, const DMUMPS_STRUC_C
// & _this) {
// stream << "DMUMPS Data [" << std::endl;
// stream << " + job : " << _this.job << std::endl;
// stream << " + par : " << _this.par << std::endl;
// stream << " + sym : " << _this.sym << std::endl;
// stream << " + comm_fortran : " << _this.comm_fortran << std::endl;
// stream << " + nz : " << _this.nz << std::endl;
// stream << " + irn : " << _this.irn << std::endl;
// stream << " + jcn : " << _this.jcn << std::endl;
// stream << " + nz_loc : " << _this.nz_loc << std::endl;
// stream << " + irn_loc : " << _this.irn_loc << std::endl;
// stream << " + jcn_loc : " << _this.jcn_loc << std::endl;
// stream << "]";
// return stream;
// }
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolverMumps::SparseSolverMumps(DOFManagerDefault & dof_manager,
const ID & matrix_id, const ID & id)
: SparseSolver(dof_manager, matrix_id, id),
dof_manager(dof_manager), master_rhs_solution(0, 1) {
AKANTU_DEBUG_IN();
this->prank = communicator.whoAmI();
#ifdef AKANTU_USE_MPI
this->parallel_method = _fully_distributed;
#else // AKANTU_USE_MPI
this->parallel_method = _not_parallel;
#endif // AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolverMumps::~SparseSolverMumps() {
AKANTU_DEBUG_IN();
mumpsDataDestroy();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::mumpsDataDestroy() {
#ifdef AKANTU_USE_MPI
int finalized = 0;
MPI_Finalized(&finalized);
if (finalized != 0) { // Da fuck !?
return;
}
#endif
if (this->is_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_initialized = false;
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::destroyInternalData() { mumpsDataDestroy(); }
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::checkInitialized() {
if (this->is_initialized) {
return;
}
this->initialize();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::setOutputLevel() {
// Output setup
icntl(1) = 0; // error output
icntl(2) = 0; // diagnostics output
icntl(3) = 0; // information
icntl(4) = 0;
#if !defined(AKANTU_NDEBUG)
DebugLevel dbg_lvl = debug::debugger.getDebugLevel();
if (AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
// clang-format off
icntl(1) = (dbg_lvl >= dblWarning) ? 6 : 0;
icntl(3) = (dbg_lvl >= dblInfo) ? 6 : 0;
icntl(2) = (dbg_lvl >= dblTrace) ? 6 : 0;
icntl(4) =
dbg_lvl >= dblDump ? 4 :
dbg_lvl >= dblTrace ? 3 :
dbg_lvl >= dblInfo ? 2 :
dbg_lvl >= dblWarning ? 1 :
0;
// clang-format on
#endif
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initMumpsData() {
auto & A = dof_manager.getMatrix(matrix_id);
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
// automatic choice for analysis
icntl(28) = 0;
UInt size = A.size();
if (prank == 0) {
this->master_rhs_solution.resize(size);
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
switch (this->parallel_method) {
case _fully_distributed:
icntl(18) = 3; // fully distributed
this->mumps_data.nz_loc = A.getNbNonZero();
this->mumps_data.irn_loc = A.getIRN().storage();
this->mumps_data.jcn_loc = A.getJCN().storage();
break;
case _not_parallel:
case _master_slave_distributed:
icntl(18) = 0; // centralized
if (prank == 0) {
this->mumps_data.nz = A.getNbNonZero();
this->mumps_data.irn = A.getIRN().storage();
this->mumps_data.jcn = A.getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = nullptr;
this->mumps_data.jcn = nullptr;
}
break;
default:
AKANTU_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initialize() {
AKANTU_DEBUG_IN();
this->mumps_data.par = 1; // The host is part of computations
switch (this->parallel_method) {
case _not_parallel:
break;
case _master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
/* FALLTHRU */
/* [[fallthrough]]; un-comment when compiler will get it */
case _fully_distributed:
#ifdef AKANTU_USE_MPI
const auto & mpi_data =
aka::as_type<MPICommunicatorData>(communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_comm);
#else
AKANTU_ERROR(
"You cannot use parallel method to solve without activating MPI");
#endif
break;
}
const auto & A = dof_manager.getMatrix(matrix_id);
this->mumps_data.sym = 2 * static_cast<int>(A.getMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->setOutputLevel();
this->mumps_data.job = _smj_initialize; // initialize
dmumps_c(&this->mumps_data);
this->setOutputLevel();
this->is_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; // analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::factorize() {
AKANTU_DEBUG_IN();
auto & A = dof_manager.getMatrix(matrix_id);
if (parallel_method == _fully_distributed) {
this->mumps_data.a_loc = A.getA().storage();
} else {
if (prank == 0) {
this->mumps_data.a = A.getA().storage();
}
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve(Array<Real> & x, const Array<Real> & b) {
auto & synch = this->dof_manager.getSynchronizer();
if (this->prank == 0) {
this->master_rhs_solution.resize(this->dof_manager.getSystemSize());
synch.gather(b, this->master_rhs_solution);
} else {
synch.gather(b);
}
this->solveInternal();
if (this->prank == 0) {
synch.scatter(x, this->master_rhs_solution);
} else {
synch.scatter(x);
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve() {
this->master_rhs_solution.copy(
aka::as_type<SolverVectorDefault>(this->dof_manager.getResidual())
.getGlobalVector());
this->solveInternal();
aka::as_type<SolverVectorDefault>(this->dof_manager.getSolution())
.setGlobalVector(this->master_rhs_solution);
this->dof_manager.splitSolutionPerDOFs();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solveInternal() {
AKANTU_DEBUG_IN();
this->checkInitialized();
const auto & A = dof_manager.getMatrix(matrix_id);
this->setOutputLevel();
if (this->last_profile_release != A.getProfileRelease()) {
this->analysis();
this->last_profile_release = A.getProfileRelease();
}
if (AKANTU_DEBUG_TEST(dblDump)) {
A.saveMatrix("solver_mumps" + std::to_string(prank) + ".mtx");
}
if (this->last_value_release != A.getValueRelease()) {
this->factorize();
this->last_value_release = A.getValueRelease();
}
if (prank == 0) {
this->mumps_data.rhs = this->master_rhs_solution.storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::printError() {
Vector<Int> _info_v(2);
_info_v[0] = info(1); // to get errors
_info_v[1] = -info(1); // to get warnings
dof_manager.getCommunicator().allReduce(_info_v, SynchronizerOperation::_min);
_info_v[1] = -_info_v[1];
if (_info_v[0] < 0) { // < 0 is an error
switch (_info_v[0]) {
case -10: {
AKANTU_CUSTOM_EXCEPTION(
debug::SingularMatrixException(dof_manager.getMatrix(matrix_id)));
break;
}
case -9: {
icntl(14) += 10;
if (icntl(14) != 90) {
// std::cout << "Dynamic memory increase of 10%" << std::endl;
AKANTU_DEBUG_WARNING("MUMPS dynamic memory is insufficient it will be "
"increased allowed to use 10% more");
// change releases to force a recompute
this->last_value_release--;
this->last_profile_release--;
this->solve();
} else {
AKANTU_ERROR("The MUMPS workarray is too small INFO(2)="
<< info(2) << "No further increase possible");
}
break;
}
default:
AKANTU_ERROR("Error in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
} else if (_info_v[1] > 0) {
AKANTU_DEBUG_WARNING("Warning in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
}
} // namespace akantu
diff --git a/src/solver/sparse_solver_mumps.hh b/src/solver/sparse_solver_mumps.hh
index 430ac3eed..63e78b8e3 100644
--- a/src/solver/sparse_solver_mumps.hh
+++ b/src/solver/sparse_solver_mumps.hh
@@ -1,155 +1,158 @@
/**
* @file sparse_solver_mumps.hh
*
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Fri May 19 2017
*
* @brief Solver class implementation for the mumps solver
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <dmumps_c.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SOLVER_MUMPS_HH_
#define AKANTU_SOLVER_MUMPS_HH_
namespace akantu {
class DOFManagerDefault;
class SparseMatrixAIJ;
} // namespace akantu
namespace akantu {
class SparseSolverMumps : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolverMumps(DOFManagerDefault & dof_manager, const ID & matrix_id,
const ID & id = "sparse_solver_mumps");
~SparseSolverMumps() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
void initialize() override;
/// analysis (symbolic facto + permutations)
void analysis() override;
/// factorize the matrix
void factorize() override;
/// solve the system
virtual void solve(Array<Real> & x, const Array<Real> & b);
/// solve using residual and solution from the dof_manager
void solve() override;
private:
/// print the error if any happened in mumps
void printError();
/// solve the system with master_rhs_solution as b and x
void solveInternal();
/// set internal values;
void initMumpsData();
/// set the level of verbosity of mumps based on the debug level of akantu
void setOutputLevel();
protected:
/// de-initialize the internal data
void destroyInternalData() override;
/// check if initialized and except if it is not the case
void checkInitialized();
private:
void mumpsDataDestroy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
/// access the control variable
inline Int & icntl(UInt i) { return mumps_data.icntl[i - 1]; }
/// access the results info
inline Int & info(UInt i) { return mumps_data.info[i - 1]; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// DOFManager used by the Mumps implementation of the SparseSolver
DOFManagerDefault & dof_manager;
/// Full right hand side on the master processors and solution after solve
Array<Real> master_rhs_solution;
/// mumps data
DMUMPS_STRUC_C mumps_data;
/// Rank of the current process
UInt prank;
/// matrix release at last solve
UInt last_profile_release{UInt(-1)};
/// matrix release at last solve
UInt last_value_release{UInt(-1)};
/// check if the solver data are initialized
bool is_initialized{false};
/* ------------------------------------------------------------------------ */
/* Local types */
/* ------------------------------------------------------------------------ */
private:
SolverParallelMethod parallel_method;
// bool rhs_is_local;
enum SolverMumpsJob {
_smj_initialize = -1,
_smj_analyze = 1,
_smj_factorize = 2,
_smj_solve = 3,
_smj_analyze_factorize = 4,
_smj_factorize_solve = 5,
_smj_complete = 6, // analyze, factorize, solve
_smj_destroy = -2
};
};
} // namespace akantu
#endif /* AKANTU_SOLVER_MUMPS_HH_ */
diff --git a/src/solver/terms_to_assemble.hh b/src/solver/terms_to_assemble.hh
index bf5227e79..5964a9c41 100644
--- a/src/solver/terms_to_assemble.hh
+++ b/src/solver/terms_to_assemble.hh
@@ -1,99 +1,101 @@
/**
* @file terms_to_assemble.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Oct 11 2017
*
* @brief List of terms to assemble to a matrix
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TERMS_TO_ASSEMBLE_HH_
#define AKANTU_TERMS_TO_ASSEMBLE_HH_
namespace akantu {
class TermsToAssemble {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TermsToAssemble() = default;
virtual ~TermsToAssemble() = default;
class TermToAssemble {
public:
TermToAssemble(UInt i, UInt j) : _i(i), _j(j), val(0.) {}
inline TermToAssemble & operator=(Real val) {
this->val = val;
return *this;
}
inline TermToAssemble operator+=(Real val) {
this->val += val;
return *this;
}
inline operator Real() const { return val; }
inline UInt i() const { return _i; }
inline UInt j() const { return _j; }
private:
UInt _i, _j;
Real val;
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline TermToAssemble & operator()(UInt i, UInt j) {
terms.emplace_back(i, j);
return terms.back();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
using TermsContainer = std::vector<TermToAssemble>;
public:
using const_terms_iterator = TermsContainer::const_iterator;
const_terms_iterator begin() const { return terms.begin(); }
const_terms_iterator end() const { return terms.end(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
TermsContainer terms;
};
} // namespace akantu
#endif /* AKANTU_TERMS_TO_ASSEMBLE_HH_ */
diff --git a/src/synchronizer/communication_buffer.hh b/src/synchronizer/communication_buffer.hh
index 5a0a5b98a..48dd9193c 100644
--- a/src/synchronizer/communication_buffer.hh
+++ b/src/synchronizer/communication_buffer.hh
@@ -1,181 +1,183 @@
/**
* @file communication_buffer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Dec 11 2019
*
* @brief Buffer for packing and unpacking data
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#include <array>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATION_BUFFER_HH_
#define AKANTU_COMMUNICATION_BUFFER_HH_
namespace akantu {
template <bool is_static = true> class CommunicationBufferTemplated {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CommunicationBufferTemplated(UInt size) : buffer(size, 1, char()) {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
};
CommunicationBufferTemplated() : CommunicationBufferTemplated(0) {}
CommunicationBufferTemplated(const CommunicationBufferTemplated & other) =
delete;
CommunicationBufferTemplated &
operator=(const CommunicationBufferTemplated & other) = delete;
CommunicationBufferTemplated(CommunicationBufferTemplated && other) noexcept =
default;
virtual ~CommunicationBufferTemplated() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// reset to "empty"
inline void reset();
/// resize the internal buffer do not allocate on dynamic buffers
inline void resize(UInt size);
/// resize the internal buffer allocate always
inline void reserve(UInt size);
/// clear buffer context
inline void zero();
private:
inline void packResize(UInt size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline char * storage() { return buffer.storage(); };
inline const char * storage() const { return buffer.storage(); };
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// printing tool
template <typename T> inline std::string extractStream(UInt block_size);
/// packing data
template <typename T>
inline CommunicationBufferTemplated & operator<<(const T & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Vector<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated & operator<<(const Matrix<T> & to_pack);
template <typename T>
inline CommunicationBufferTemplated &
operator<<(const std::vector<T> & to_pack);
/// unpacking data
template <typename T>
inline CommunicationBufferTemplated & operator>>(T & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Vector<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(Matrix<T> & to_unpack);
template <typename T>
inline CommunicationBufferTemplated & operator>>(std::vector<T> & to_unpack);
inline CommunicationBufferTemplated & operator<<(const std::string & to_pack);
inline CommunicationBufferTemplated & operator>>(std::string & to_unpack);
private:
template <typename T> inline void packIterable(T & to_pack);
template <typename T> inline void unpackIterable(T & to_unpack);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
template <typename T> static inline UInt sizeInBuffer(const T & data);
template <typename T> static inline UInt sizeInBuffer(const Vector<T> & data);
template <typename T> static inline UInt sizeInBuffer(const Matrix<T> & data);
template <typename T>
static inline UInt sizeInBuffer(const std::vector<T> & data);
static inline UInt sizeInBuffer(const std::string & data);
/// return the size in bytes of the stored values
inline UInt getPackedSize() const { return ptr_pack - buffer.storage(); };
/// return the size in bytes of data left to be unpacked
inline UInt getLeftToUnpack() const {
return buffer.size() - (ptr_unpack - buffer.storage());
};
/// return the global size allocated
inline UInt size() const { return buffer.size(); };
/// is the buffer empty
inline bool empty() const {
return (getPackedSize() == 0) and (getLeftToUnpack() == 0);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// current position for packing
char * ptr_pack;
/// current position for unpacking
char * ptr_unpack;
/// storing buffer
Array<char> buffer;
};
using CommunicationBuffer = CommunicationBufferTemplated<true>;
using DynamicCommunicationBuffer = CommunicationBufferTemplated<false>;
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "communication_buffer_inline_impl.hh"
#endif /* AKANTU_COMMUNICATION_BUFFER_HH_ */
diff --git a/src/synchronizer/communication_buffer_inline_impl.hh b/src/synchronizer/communication_buffer_inline_impl.hh
index 80945ee0c..93bf84d4a 100644
--- a/src/synchronizer/communication_buffer_inline_impl.hh
+++ b/src/synchronizer/communication_buffer_inline_impl.hh
@@ -1,328 +1,331 @@
/**
* @file communication_buffer_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 14 2011
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Dec 04 2018
*
* @brief CommunicationBuffer inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include <cstring>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const T & /*unused*/) {
return sizeof(T);
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Vector<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt
CommunicationBufferTemplated<is_static>::sizeInBuffer(const Matrix<T> & data) {
UInt size = data.size() * sizeof(T);
return size;
}
template <bool is_static>
template <typename T>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::vector<T> & data) {
UInt size = data.size() * sizeof(T) + sizeof(size_t);
return size;
}
template <bool is_static>
inline UInt CommunicationBufferTemplated<is_static>::sizeInBuffer(
const std::string & data) {
UInt size = data.size() * sizeof(std::string::value_type) + sizeof(size_t);
return size;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::packResize(UInt size) {
if (not is_static) {
char * values = buffer.storage();
auto nb_packed = ptr_pack - values;
if (buffer.size() > nb_packed + size) {
return;
}
buffer.resize(nb_packed + size);
ptr_pack = buffer.storage() + nb_packed;
ptr_unpack = buffer.storage() + (ptr_unpack - values);
}
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const T & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
std::memcpy(ptr_pack, reinterpret_cast<const char *>(&to_pack), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(T & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
alignas(alignof(T)) std::array<char, sizeof(T)> aligned_ptr;
memcpy(aligned_ptr.data(), ptr_unpack, size);
auto * tmp = reinterpret_cast<T *>(aligned_ptr.data());
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
to_unpack = *tmp;
// memcpy(reinterpret_cast<char *>(&to_unpack), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
/**
* Vector
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Vector<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Vector<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/**
* Matrix
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(const Matrix<T> & to_pack) {
UInt size = sizeInBuffer(to_pack);
packResize(size);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_pack + size),
"Packing too much data in the CommunicationBufferTemplated");
memcpy(ptr_pack, to_pack.storage(), size);
ptr_pack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(Matrix<T> & to_unpack) {
UInt size = sizeInBuffer(to_unpack);
AKANTU_DEBUG_ASSERT(
(buffer.storage() + buffer.size()) >= (ptr_unpack + size),
"Unpacking too much data in the CommunicationBufferTemplated");
memcpy(to_unpack.storage(), ptr_unpack, size);
ptr_unpack += size;
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void CommunicationBufferTemplated<is_static>::packIterable(T & to_pack) {
operator<<(size_t(to_pack.size()));
auto it = to_pack.begin();
auto end = to_pack.end();
for (; it != end; ++it) {
operator<<(*it);
}
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline void
CommunicationBufferTemplated<is_static>::unpackIterable(T & to_unpack) {
size_t size;
operator>>(size);
to_unpack.resize(size);
auto it = to_unpack.begin();
auto end = to_unpack.end();
for (; it != end; ++it) {
operator>>(*it);
}
}
/**
* std::vector<T>
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(
const std::vector<T> & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(
std::vector<T> & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/**
* std::string
*/
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator<<(
const std::string & to_pack) {
packIterable(to_pack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline CommunicationBufferTemplated<is_static> &
CommunicationBufferTemplated<is_static>::operator>>(std::string & to_unpack) {
unpackIterable(to_unpack);
return *this;
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
template <typename T>
inline std::string
CommunicationBufferTemplated<is_static>::extractStream(UInt block_size) {
std::stringstream str;
auto * ptr = reinterpret_cast<T *>(buffer.storage());
UInt sz = buffer.size() / sizeof(T);
UInt sz_block = block_size / sizeof(T);
UInt n_block = 0;
for (UInt i = 0; i < sz; ++i) {
if (i % sz_block == 0) {
str << std::endl << n_block << " ";
++n_block;
}
str << *ptr << " ";
++ptr;
}
return str.str();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::resize(UInt size) {
if (!is_static) {
buffer.resize(0, 0);
} else {
buffer.resize(size, 0);
}
reset();
#ifndef AKANTU_NDEBUG
zero();
#endif
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::reserve(UInt size) {
char * values = buffer.storage();
auto nb_packed = ptr_pack - values;
buffer.resize(size);
ptr_pack = buffer.storage() + nb_packed;
ptr_unpack = buffer.storage() + (ptr_unpack - values);
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::zero() {
buffer.zero();
}
/* -------------------------------------------------------------------------- */
template <bool is_static>
inline void CommunicationBufferTemplated<is_static>::reset() {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
} // namespace akantu
diff --git a/src/synchronizer/communication_descriptor.hh b/src/synchronizer/communication_descriptor.hh
index 78369f0e1..2d6b293d2 100644
--- a/src/synchronizer/communication_descriptor.hh
+++ b/src/synchronizer/communication_descriptor.hh
@@ -1,153 +1,155 @@
/**
* @file communication_descriptor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
+ * @date creation: Fri Dec 02 2016
* @date last modification: Thu Jan 25 2018
*
* @brief Implementation of the helper classes for the synchronizer
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "communication_request.hh"
#include "communication_tag.hh"
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATION_DESCRIPTOR_HH_
#define AKANTU_COMMUNICATION_DESCRIPTOR_HH_
namespace akantu {
/* ------------------------------------------------------------------------ */
enum CommunicationSendRecv { _send, _recv, _csr_not_defined };
/* -------------------------------------------------------------------------- */
struct CommunicationSRType {
using type = CommunicationSendRecv;
static const type _begin_ = _send;
static const type _end_ = _csr_not_defined;
};
using send_recv_t = safe_enum<CommunicationSRType>;
namespace {
send_recv_t iterate_send_recv{};
}
/* ------------------------------------------------------------------------ */
class Communication {
public:
explicit Communication(const CommunicationSendRecv & type = _csr_not_defined)
: _type(type) {}
Communication(const Communication &) = delete;
Communication & operator=(const Communication &) = delete;
void resize(UInt size) {
this->_size = size;
this->_buffer.resize(size);
}
inline const CommunicationSendRecv & type() const { return this->_type; }
inline const UInt & size() const { return this->_size; }
inline const CommunicationRequest & request() const { return this->_request; }
inline CommunicationRequest & request() { return this->_request; }
inline const CommunicationBuffer & buffer() const { return this->_buffer; }
inline CommunicationBuffer & buffer() { return this->_buffer; }
private:
UInt _size{0};
CommunicationBuffer _buffer;
CommunicationRequest _request;
CommunicationSendRecv _type;
};
template <class Entity> class Communications;
/* ------------------------------------------------------------------------ */
template <class Entity> class CommunicationDescriptor {
public:
CommunicationDescriptor(Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications,
const SynchronizationTag & tag, UInt proc);
CommunicationDescriptor(const CommunicationDescriptor &) = default;
CommunicationDescriptor &
operator=(const CommunicationDescriptor &) = default;
/// get the quantity of data in the buffer
UInt getNbData() { return communication.size(); }
/// set the quantity of data in the buffer
void setNbData(UInt size) { communication.resize(size); }
/// get the corresponding tag
const SynchronizationTag & getTag() const { return tag; }
/// get the data buffer
CommunicationBuffer & getBuffer();
/// get the corresponding request
CommunicationRequest & getRequest();
/// get the communication scheme
const Array<Entity> & getScheme();
/// reset the buffer before pack or after unpack
void resetBuffer();
/// pack data for entities in the buffer
void packData(const DataAccessor<Entity> & accessor);
/// unpack data for entities from the buffer
void unpackData(DataAccessor<Entity> & accessor);
/// posts asynchronous send requests
void postSend(int hash_id);
/// posts asynchronous receive requests
void postRecv(int hash_id);
/// free the request
void freeRequest();
UInt getProc() { return proc; }
protected:
Communication & communication;
const Array<Entity> & scheme;
Communications<Entity> & communications;
const SynchronizationTag & tag;
UInt proc;
UInt rank;
UInt counter;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#include "communication_descriptor_tmpl.hh"
#endif /* AKANTU_COMMUNICATION_DESCRIPTOR_HH_ */
diff --git a/src/synchronizer/communication_descriptor_tmpl.hh b/src/synchronizer/communication_descriptor_tmpl.hh
index 24369fe01..262cc4d87 100644
--- a/src/synchronizer/communication_descriptor_tmpl.hh
+++ b/src/synchronizer/communication_descriptor_tmpl.hh
@@ -1,151 +1,153 @@
/**
* @file communication_descriptor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
+ * @date creation: Fri Dec 02 2016
* @date last modification: Thu Jan 25 2018
*
* @brief implementation of CommunicationDescriptor
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_
#define AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Implementations */
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationDescriptor<Entity>::CommunicationDescriptor(
Communication & communication, Array<Entity> & scheme,
Communications<Entity> & communications, const SynchronizationTag & tag,
UInt proc)
: communication(communication), scheme(scheme),
communications(communications), tag(tag), proc(proc),
rank(communications.getCommunicator().whoAmI()) {
counter = communications.getCounter(tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationBuffer & CommunicationDescriptor<Entity>::getBuffer() {
return communication.buffer();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
CommunicationRequest & CommunicationDescriptor<Entity>::getRequest() {
return communication.request();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void CommunicationDescriptor<Entity>::freeRequest() {
const auto & comm = communications.getCommunicator();
// comm.test(communication.request());
comm.freeCommunicationRequest(communication.request());
communications.decrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const Array<Entity> & CommunicationDescriptor<Entity>::getScheme() {
return scheme;
}
template <class Entity> void CommunicationDescriptor<Entity>::resetBuffer() {
this->communication.buffer().reset();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::packData(
const DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _send,
"Cannot pack data on communication that is not of type _send");
accessor.packData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::unpackData(
DataAccessor<Entity> & accessor) {
AKANTU_DEBUG_ASSERT(
communication.type() == _recv,
"Cannot unpack data from communication that is not of type _recv");
accessor.unpackData(communication.buffer(), scheme, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postSend(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _send,
"Cannot send a communication that is not of type _send");
Tag comm_tag = Tag::genTag(rank, counter, tag, hash_id);
AKANTU_DEBUG_ASSERT(communication.buffer().getPackedSize() ==
communication.size(),
"a problem have been introduced with "
<< "false sent sizes declaration "
<< communication.buffer().getPackedSize()
<< " != " << communication.size());
AKANTU_DEBUG_INFO("Posting send to proc " << proc << " (tag: " << tag << " - "
<< communication.size()
<< " data to send) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncSend(communication.buffer(),
proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void CommunicationDescriptor<Entity>::postRecv(int hash_id) {
AKANTU_DEBUG_ASSERT(communication.type() == _recv,
"Cannot receive data for communication ("
<< communication.type()
<< ")that is not of type _recv");
Tag comm_tag = Tag::genTag(proc, counter, tag, hash_id);
AKANTU_DEBUG_INFO("Posting receive from proc "
<< proc << " (tag: " << tag << " - " << communication.size()
<< " data to receive) "
<< " [ " << comm_tag << " ]");
CommunicationRequest & request = communication.request();
request = communications.getCommunicator().asyncReceive(
communication.buffer(), proc, comm_tag);
communications.incrementPending(tag, communication.type());
}
} // namespace akantu
#endif /* AKANTU_COMMUNICATION_DESCRIPTOR_TMPL_HH_ */
diff --git a/src/synchronizer/communication_request.hh b/src/synchronizer/communication_request.hh
index 58e88bd22..dc571e6e5 100644
--- a/src/synchronizer/communication_request.hh
+++ b/src/synchronizer/communication_request.hh
@@ -1,111 +1,113 @@
/**
* @file communication_request.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Tue Nov 07 2017
*
* @brief empty class just for inheritance
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_REAL_STATIC_COMMUNICATOR_HH_
#define AKANTU_REAL_STATIC_COMMUNICATOR_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
class InternalCommunicationRequest {
public:
InternalCommunicationRequest(UInt source, UInt dest);
virtual ~InternalCommunicationRequest();
virtual void printself(std::ostream & stream, int indent = 0) const;
AKANTU_GET_MACRO(Source, source, UInt);
AKANTU_GET_MACRO(Destination, destination, UInt);
private:
UInt source;
UInt destination;
UInt id;
static UInt counter;
};
/* -------------------------------------------------------------------------- */
class CommunicationRequest {
public:
CommunicationRequest(
std::shared_ptr<InternalCommunicationRequest> request = nullptr)
: request(std::move(request)) {}
virtual ~CommunicationRequest() = default;
virtual void free() { request.reset(); }
void printself(std::ostream & stream, int indent = 0) const {
request->printself(stream, indent);
};
UInt getSource() const { return request->getSource(); }
UInt getDestination() const { return request->getDestination(); }
bool isFreed() const { return request == nullptr; }
InternalCommunicationRequest & getInternal() { return *request; }
private:
std::shared_ptr<InternalCommunicationRequest> request;
};
/* -------------------------------------------------------------------------- */
class CommunicationStatus {
public:
AKANTU_GET_MACRO(Source, source, Int);
UInt size() const { return size_; }
AKANTU_GET_MACRO(Tag, tag, Int);
AKANTU_SET_MACRO(Source, source, Int);
AKANTU_SET_MACRO(Size, size_, UInt);
AKANTU_SET_MACRO(Tag, tag, Int);
private:
Int source{0};
UInt size_{0};
Int tag{0};
};
/* -------------------------------------------------------------------------- */
/// Datatype to pack pairs for MPI_{MIN,MAX}LOC
template <typename T1, typename T2> struct SCMinMaxLoc {
T1 min_max;
T2 loc;
};
} // namespace akantu
#endif /* AKANTU_REAL_STATIC_COMMUNICATOR_HH_ */
diff --git a/src/synchronizer/communication_tag.hh b/src/synchronizer/communication_tag.hh
index caab2255c..3716a5b0d 100644
--- a/src/synchronizer/communication_tag.hh
+++ b/src/synchronizer/communication_tag.hh
@@ -1,126 +1,129 @@
/**
* @file communication_tag.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Mon Feb 10 2020
*
* @brief Description of the communication tags
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATION_TAG_HH_
#define AKANTU_COMMUNICATION_TAG_HH_
namespace akantu {
/**
* tag = |__________20_________|___8____|_4_|
* | proc | num mes| ct|
*/
class Tag {
public:
Tag() = default;
Tag(int val) : tag(val) {}
Tag(int val, int hash) : tag(val), hash(hash) {}
operator int() const {
return int(max_tag == 0 ? tag : (uint32_t(tag) % max_tag));
}
/// generates a tag
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag) {
int _tag = ((((proc & 0xFFFFF) << 12) + ((msg_count & 0xFF) << 4) +
((int)tag & 0xF)));
Tag t(_tag);
return t;
}
/// generates a tag and hashes it
template <typename CommTag>
static inline Tag genTag(int proc, UInt msg_count, CommTag tag, int hash) {
Tag t = genTag(proc, msg_count, tag);
t.tag = t.tag ^ hash;
t.hash = hash;
return t;
}
virtual void printself(std::ostream & stream, int /*unused*/) const {
int t = tag;
stream << "TAG(";
if (hash != 0) {
t = t ^ hash;
}
stream << (t >> 12) << ":" << (t >> 4 & 0xFF) << ":" << (t & 0xF) << " -> "
<< std::hex << "0x" << int(*this);
if (hash != 0) {
stream << " {hash: 0x" << hash << "}";
}
stream << " [0x" << max_tag << "]";
stream << ")" << std::dec;
}
enum CommTags : int {
_sizes = 1,
_connectivity = 2,
_data = 3,
_partitions = 4,
_nb_nodes = 5,
_nodes = 6,
_coordinates = 7,
_nodes_type = 8,
_mesh_data = 9,
_element_group = 10,
_node_group = 11,
_modify_scheme = 12,
_gather_initialization = 1,
_gather = 2,
_scatter = 3,
_synchronize = 15,
_reduce,
_periodic_slaves,
_periodic_nodes,
};
private:
static void setMaxTag(int _max_tag) { max_tag = _max_tag; }
friend void initialize(const std::string & /*input_file*/, int & /*argc*/,
char **& /*argv*/);
private:
int tag{0};
int hash{0};
static int max_tag;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const Tag & _this) {
_this.printself(stream, 0);
return stream;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_COMMUNICATION_TAG_HH_ */
diff --git a/src/synchronizer/communications.hh b/src/synchronizer/communications.hh
index 365eb662c..e4c945cb7 100644
--- a/src/synchronizer/communications.hh
+++ b/src/synchronizer/communications.hh
@@ -1,275 +1,277 @@
/**
* @file communications.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Fri Jul 24 2020
*
* @brief Class handling the pending communications and the communications
* schemes
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_descriptor.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATIONS_HH_
#define AKANTU_COMMUNICATIONS_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications {
public:
using Scheme = Array<Entity>;
protected:
using CommunicationPerProcs = std::map<UInt, Communication>;
using CommunicationsPerTags =
std::map<SynchronizationTag, CommunicationPerProcs>;
using CommunicationSchemes = std::map<UInt, Scheme>;
using Request = std::map<UInt, std::vector<CommunicationRequest>>;
friend class CommunicationDescriptor<Entity>;
public:
using scheme_iterator = typename CommunicationSchemes::iterator;
using const_scheme_iterator = typename CommunicationSchemes::const_iterator;
/* ------------------------------------------------------------------------ */
class iterator;
class tag_iterator;
/* ------------------------------------------------------------------------ */
public:
CommunicationPerProcs & getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
bool hasPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
UInt getPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
iterator begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
iterator end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
iterator waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void incrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void decrementPending(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
void freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
Scheme & createScheme(UInt proc, const CommunicationSendRecv & sr);
void resetSchemes(const CommunicationSendRecv & sr);
/* ------------------------------------------------------------------------ */
void setCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size, const CommunicationSendRecv & sr);
public:
explicit Communications(const Communicator & communicator);
explicit Communications(const Communications & other);
/* ------------------------------------------------------------------------ */
void swapSendRecv();
/* ------------------------------------------------------------------------ */
class IterableCommunicationDesc {
public:
IterableCommunicationDesc(Communications & communications,
SynchronizationTag tag, CommunicationSendRecv sr)
: communications(communications), tag(tag), sr(sr) {}
auto begin() { return communications.begin(tag, sr); }
auto end() { return communications.end(tag, sr); }
private:
Communications & communications;
SynchronizationTag tag;
CommunicationSendRecv sr;
};
auto iterateRecv(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _recv);
}
auto iterateSend(const SynchronizationTag & tag) {
return IterableCommunicationDesc(*this, tag, _send);
}
/* ------------------------------------------------------------------------ */
// iterator begin_send(const SynchronizationTag & tag);
// iterator end_send(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
// iterator begin_recv(const SynchronizationTag & tag);
// iterator end_recv(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
class IterableTags {
public:
explicit IterableTags(Communications & communications)
: communications(communications) {}
decltype(auto) begin() { return communications.begin_tag(); }
decltype(auto) end() { return communications.end_tag(); }
private:
Communications & communications;
};
decltype(auto) iterateTags() { return IterableTags(*this); }
tag_iterator begin_tag();
tag_iterator end_tag();
/* ------------------------------------------------------------------------ */
bool hasCommunication(const SynchronizationTag & tag) const;
void incrementCounter(const SynchronizationTag & tag);
UInt getCounter(const SynchronizationTag & tag) const;
bool hasCommunicationSize(const SynchronizationTag & tag) const;
void invalidateSizes();
/* ------------------------------------------------------------------------ */
bool hasPendingRecv(const SynchronizationTag & tag) const;
bool hasPendingSend(const SynchronizationTag & tag) const;
const auto & getCommunicator() const;
/* ------------------------------------------------------------------------ */
iterator waitAnyRecv(const SynchronizationTag & tag);
iterator waitAnySend(const SynchronizationTag & tag);
void waitAllRecv(const SynchronizationTag & tag);
void waitAllSend(const SynchronizationTag & tag);
void freeSendRequests(const SynchronizationTag & tag);
void freeRecvRequests(const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
class IterableSchemes {
public:
IterableSchemes(Communications & communications, CommunicationSendRecv sr)
: communications(communications), sr(sr) {}
decltype(auto) begin() { return communications.begin_scheme(sr); }
decltype(auto) end() { return communications.end_scheme(sr); }
private:
Communications & communications;
CommunicationSendRecv sr;
};
class ConstIterableSchemes {
public:
ConstIterableSchemes(const Communications & communications,
CommunicationSendRecv sr)
: communications(communications), sr(sr) {}
decltype(auto) begin() const { return communications.begin_scheme(sr); }
decltype(auto) end() const { return communications.end_scheme(sr); }
private:
const Communications & communications;
CommunicationSendRecv sr;
};
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) {
return IterableSchemes(*this, sr);
}
decltype(auto) iterateSchemes(const CommunicationSendRecv & sr) const {
return ConstIterableSchemes(*this, sr);
}
decltype(auto) iterateSendSchemes() { return IterableSchemes(*this, _send); }
decltype(auto) iterateSendSchemes() const {
return ConstIterableSchemes(*this, _send);
}
decltype(auto) iterateRecvSchemes() { return IterableSchemes(*this, _recv); }
decltype(auto) iterateRecvSchemes() const {
return ConstIterableSchemes(*this, _recv);
}
scheme_iterator begin_scheme(const CommunicationSendRecv & sr);
scheme_iterator end_scheme(const CommunicationSendRecv & sr);
const_scheme_iterator begin_scheme(const CommunicationSendRecv & sr) const;
const_scheme_iterator end_scheme(const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_send_scheme();
scheme_iterator end_send_scheme();
const_scheme_iterator begin_send_scheme() const;
const_scheme_iterator end_send_scheme() const;
/* ------------------------------------------------------------------------ */
scheme_iterator begin_recv_scheme();
scheme_iterator end_recv_scheme();
const_scheme_iterator begin_recv_scheme() const;
const_scheme_iterator end_recv_scheme() const;
/* ------------------------------------------------------------------------ */
Scheme & createSendScheme(UInt proc);
Scheme & createRecvScheme(UInt proc);
/* ------------------------------------------------------------------------ */
Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr);
const Scheme & getScheme(UInt proc, const CommunicationSendRecv & sr) const;
/* ------------------------------------------------------------------------ */
void resetSchemes();
/* ------------------------------------------------------------------------ */
void setSendCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void setRecvCommunicationSize(const SynchronizationTag & tag, UInt proc,
UInt size);
void initializeCommunications(const SynchronizationTag & tag);
protected:
CommunicationSchemes schemes[2];
CommunicationsPerTags communications[2];
std::map<SynchronizationTag, UInt> comm_counter;
std::map<SynchronizationTag, UInt> pending_communications[2];
std::map<SynchronizationTag, bool> comm_size_computed;
const Communicator & communicator;
};
} // namespace akantu
#include "communications_tmpl.hh"
#endif /* AKANTU_COMMUNICATIONS_HH_ */
diff --git a/src/synchronizer/communications_tmpl.hh b/src/synchronizer/communications_tmpl.hh
index 27c13c5d1..623f28cbe 100644
--- a/src/synchronizer/communications_tmpl.hh
+++ b/src/synchronizer/communications_tmpl.hh
@@ -1,552 +1,554 @@
/**
* @file communications_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Fri Jul 24 2020
*
* @brief Implementation of Communications
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATIONS_TMPL_HH_
#define AKANTU_COMMUNICATIONS_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communicator & communicator)
: communicator(communicator) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communications & other)
: communicator(other.communicator) {
for (auto sr : iterate_send_recv) {
for (const auto & scheme_pair : other.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & other_scheme = scheme_pair.second;
auto & scheme = this->createScheme(proc, sr);
scheme.copy(other_scheme);
}
}
this->invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::swapSendRecv() {
std::swap(schemes[_send], schemes[_recv]);
}
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::iterator {
using communication_iterator =
typename std::map<UInt, Communication>::iterator;
public:
iterator() : communications(nullptr) {}
iterator(scheme_iterator scheme_it, communication_iterator comm_it,
Communications<Entity> & communications,
const SynchronizationTag & tag)
: scheme_it(scheme_it), comm_it(comm_it), communications(&communications),
tag(tag) {}
iterator(const iterator & other) = default;
iterator(iterator && other) noexcept = default;
iterator & operator=(const iterator & other) = default;
iterator & operator=(iterator && other) noexcept = default;
iterator & operator++() {
++scheme_it;
++comm_it;
return *this;
}
CommunicationDescriptor<Entity> operator*() {
AKANTU_DEBUG_ASSERT(
scheme_it->first == comm_it->first,
"The two iterators are not in phase, something wrong"
<< " happened, time to take out your favorite debugger ("
<< scheme_it->first << " != " << comm_it->first << ")");
return CommunicationDescriptor<Entity>(comm_it->second, scheme_it->second,
*communications, tag,
scheme_it->first);
}
bool operator==(const iterator & other) const {
return scheme_it == other.scheme_it && comm_it == other.comm_it;
}
bool operator!=(const iterator & other) const {
return scheme_it != other.scheme_it || comm_it != other.comm_it;
}
private:
scheme_iterator scheme_it;
communication_iterator comm_it;
Communications<Entity> * communications;
SynchronizationTag tag;
};
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::tag_iterator {
using internal_iterator = std::map<SynchronizationTag, UInt>::const_iterator;
public:
tag_iterator(const internal_iterator & it) : it(it) {}
tag_iterator & operator++() {
++it;
return *this;
}
SynchronizationTag operator*() { return it->first; }
bool operator==(const tag_iterator & other) const { return it == other.it; }
bool operator!=(const tag_iterator & other) const { return it != other.it; }
private:
internal_iterator it;
};
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::CommunicationPerProcs &
Communications<Entity>::getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto comm_it = this->communications[sr].find(tag);
if (comm_it == this->communications[sr].end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No known communications for the tag: " << tag);
}
return comm_it->second;
}
/* ---------------------------------------------------------------------- */
template <class Entity>
UInt Communications<Entity>::getPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
const std::map<SynchronizationTag, UInt> & pending =
pending_communications[sr];
auto it = pending.find(tag);
if (it == pending.end()) {
return 0;
}
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
bool Communications<Entity>::hasPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
return this->hasCommunication(tag) && (this->getPending(tag, sr) != 0);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].begin(), comms.begin(), *this, tag);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].end(), comms.end(), *this, tag);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
auto & request = it->second.request();
if (!request.isFreed()) {
requests.push_back(request);
}
}
UInt req_id = Communicator::waitAny(requests);
if (req_id != UInt(-1)) {
auto & request = requests[req_id];
UInt proc = sr == _recv ? request.getSource() : request.getDestination();
return iterator(this->schemes[sr].find(proc), comms.find(proc), *this, tag);
}
return this->end(tag, sr);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
requests.push_back(it->second.request());
}
Communicator::waitAll(requests);
}
template <class Entity>
void Communications<Entity>::incrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
++(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::decrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
--(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
iterator it = this->begin(tag, sr);
iterator end = this->end(tag, sr);
for (; it != end; ++it) {
(*it).freeRequest();
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createScheme(UInt proc,
const CommunicationSendRecv & sr) {
// scheme_iterator it = schemes[sr].find(proc);
// if (it != schemes[sr].end()) {
// AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
// "Communication scheme("
// << sr
// << ") already created for proc: " <<
// proc);
// }
return schemes[sr][proc];
}
template <class Entity>
void Communications<Entity>::resetSchemes(const CommunicationSendRecv & sr) {
auto it = this->schemes[sr].begin();
auto end = this->schemes[sr].end();
for (; it != end; ++it) {
it->second.resize(0);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size,
const CommunicationSendRecv & sr) {
// accessor that fails if it does not exists
comm_size_computed[tag] = true; // TODO: need perhaps to be split based on sr
auto & comms = this->communications[sr];
auto & comms_per_tag = comms.at(tag);
comms_per_tag.at(proc).resize(size);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::initializeCommunications(
const SynchronizationTag & tag) {
for (auto t : send_recv_t{}) {
pending_communications[t].insert(std::make_pair(tag, 0));
auto & comms = this->communications[t];
auto & comms_per_tag =
comms.insert(std::make_pair(tag, CommunicationPerProcs()))
.first->second;
for (const auto & pair : this->schemes[t]) {
comms_per_tag.emplace(std::piecewise_construct,
std::forward_as_tuple(pair.first),
std::forward_as_tuple(t));
}
}
comm_counter.insert(std::make_pair(tag, 0));
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::begin_tag() {
return tag_iterator(comm_counter.begin());
}
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::end_tag() {
return tag_iterator(comm_counter.end());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_send_scheme() {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_send_scheme() {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_send_scheme() const {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_send_scheme() const {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_recv_scheme() {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_recv_scheme() {
return this->end_scheme(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_recv_scheme() const {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_recv_scheme() const {
return this->end_scheme(_recv);
}
/* ------------------------------------------------------------------------ */
template <class Entity>
bool Communications<Entity>::hasCommunication(
const SynchronizationTag & tag) const {
return (communications[_send].find(tag) != communications[_send].end());
}
template <class Entity>
void Communications<Entity>::incrementCounter(const SynchronizationTag & tag) {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
++(it->second);
}
template <class Entity>
UInt Communications<Entity>::getCounter(const SynchronizationTag & tag) const {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
return it->second;
}
template <class Entity>
bool Communications<Entity>::hasCommunicationSize(
const SynchronizationTag & tag) const {
auto it = comm_size_computed.find(tag);
if (it == comm_size_computed.end()) {
return false;
}
return it->second;
}
template <class Entity> void Communications<Entity>::invalidateSizes() {
for (auto && pair : comm_size_computed) {
pair.second = false;
}
}
template <class Entity>
bool Communications<Entity>::hasPendingRecv(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _recv);
}
template <class Entity>
bool Communications<Entity>::hasPendingSend(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _send);
}
template <class Entity>
const auto & Communications<Entity>::getCommunicator() const {
return communicator;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnyRecv(const SynchronizationTag & tag) {
return this->waitAny(tag, _recv);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnySend(const SynchronizationTag & tag) {
return this->waitAny(tag, _send);
}
template <class Entity>
void Communications<Entity>::waitAllRecv(const SynchronizationTag & tag) {
this->waitAll(tag, _recv);
}
template <class Entity>
void Communications<Entity>::waitAllSend(const SynchronizationTag & tag) {
this->waitAll(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeSendRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeRecvRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createSendScheme(UInt proc) {
return createScheme(proc, _send);
}
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createRecvScheme(UInt proc) {
return createScheme(proc, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::resetSchemes() {
resetSchemes(_send);
resetSchemes(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc, const CommunicationSendRecv & sr) {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc,
const CommunicationSendRecv & sr) const {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setSendCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _send);
}
template <class Entity>
void Communications<Entity>::setRecvCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _recv);
}
} // namespace akantu
#endif /* AKANTU_COMMUNICATIONS_TMPL_HH_ */
diff --git a/src/synchronizer/communicator.cc b/src/synchronizer/communicator.cc
index 9f49130f5..43c7e2474 100644
--- a/src/synchronizer/communicator.cc
+++ b/src/synchronizer/communicator.cc
@@ -1,190 +1,192 @@
/**
* @file communicator.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Mon Feb 05 2018
+ * @date last modification: Wed Jun 05 2019
*
* @brief implementation of the common part of the static communicator
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
#if defined(AKANTU_USE_MPI)
int MPICommunicatorData::is_externaly_initialized = 0;
#endif
UInt InternalCommunicationRequest::counter = 0;
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::InternalCommunicationRequest(UInt source,
UInt dest)
: source(source), destination(dest) {
this->id = counter++;
}
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::~InternalCommunicationRequest() = default;
/* -------------------------------------------------------------------------- */
void InternalCommunicationRequest::printself(std::ostream & stream,
int indent) const {
std::string space(indent, AKANTU_INDENT);
stream << space << "CommunicationRequest [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + source : " << source << std::endl;
stream << space << " + destination : " << destination << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
Communicator::~Communicator() {
auto * event = new FinalizeCommunicatorEvent(*this);
this->sendEvent(*event);
delete event;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator() {
AKANTU_DEBUG_IN();
if (!static_communicator) {
int nb_args = 0;
char ** null = nullptr;
static_communicator =
std::make_unique<Communicator>(nb_args, null, private_member{});
}
AKANTU_DEBUG_OUT();
return *static_communicator;
}
/* -------------------------------------------------------------------------- */
Communicator & Communicator::getStaticCommunicator(int & argc, char **& argv) {
if (!static_communicator) {
static_communicator =
std::make_unique<Communicator>(argc, argv, private_member{});
}
return getStaticCommunicator();
}
} // namespace akantu
#ifdef AKANTU_USE_MPI
#include "communicator_mpi_inline_impl.hh"
#else
#include "communicator_dummy_inline_impl.hh"
#endif
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Template instantiation */
/* -------------------------------------------------------------------------- */
#define AKANTU_COMM_INSTANTIATE(T) \
template void Communicator::probe<T>(Int sender, Int tag, \
CommunicationStatus & status) const; \
template bool Communicator::asyncProbe<T>( \
Int sender, Int tag, CommunicationStatus & status) const; \
template void Communicator::sendImpl<T>( \
const T * buffer /*NOLINT*/, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
template void Communicator::receiveImpl<T>(T * buffer /*NOLINT*/, Int size, \
Int sender, Int tag) const; \
template CommunicationRequest Communicator::asyncSendImpl<T>( \
const T * buffer /*NOLINT*/, Int size, Int receiver, Int tag, \
const CommunicationMode & mode) const; \
template CommunicationRequest Communicator::asyncReceiveImpl<T>( \
T * buffer /* NOLINT */, Int size, Int sender, Int tag) const; \
template void Communicator::allGatherImpl<T>(T * values /*NOLINT*/, \
int nb_values) const; \
template void Communicator::allGatherVImpl<T>(T * values /*NOLINT*/, \
int * nb_values) const; \
template void Communicator::gatherImpl<T>(T * values /*NOLINT*/, \
int nb_values, int root) const; \
template void Communicator::gatherImpl<T>( \
T * values /*NOLINT*/, int nb_values, T * gathered /*NOLINT*/, \
int nb_gathered) const; \
template void Communicator::gatherVImpl<T>(T * values /*NOLINT*/, \
int * nb_values, int root) const; \
template void Communicator::broadcastImpl<T>(T * values /*NOLINT*/, \
int nb_values, int root) const; \
template void Communicator::allReduceImpl<T>( \
T * values /*NOLINT*/, int nb_values, SynchronizerOperation op) const; \
template void Communicator::scanImpl<T>(T * values /*NOLINT*/, \
T * /*NOLINT*/, int nb_values, \
SynchronizerOperation op) const; \
template void Communicator::exclusiveScanImpl<T>( \
T * values /*NOLINT*/, T * /*NOLINT*/, int nb_values, \
SynchronizerOperation op) const
#define MIN_MAX_REAL SCMinMaxLoc<Real, int>
#if !defined(DOXYGEN)
AKANTU_COMM_INSTANTIATE(bool);
AKANTU_COMM_INSTANTIATE(Real);
AKANTU_COMM_INSTANTIATE(UInt);
AKANTU_COMM_INSTANTIATE(Int);
AKANTU_COMM_INSTANTIATE(char);
AKANTU_COMM_INSTANTIATE(NodeFlag);
AKANTU_COMM_INSTANTIATE(MIN_MAX_REAL);
#if AKANTU_INTEGER_SIZE > 4
AKANTU_COMM_INSTANTIATE(int);
#endif
#endif
// template void Communicator::send<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template void Communicator::receive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template CommunicationRequest
// Communicator::asyncSend<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
// template CommunicationRequest
// Communicator::asyncReceive<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
// template void Communicator::probe<SCMinMaxLoc<Real, int>>(
// Int sender, Int tag, CommunicationStatus & status);
// template void Communicator::allGather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values);
// template void Communicator::allGatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values);
// template void Communicator::gather<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::gatherV<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int * nb_values, int root);
// template void Communicator::broadcast<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values, int root);
// template void Communicator::allReduce<SCMinMaxLoc<Real, int>>(
// SCMinMaxLoc<Real, int> * values, int nb_values,
// const SynchronizerOperation & op);
} // namespace akantu
diff --git a/src/synchronizer/communicator.hh b/src/synchronizer/communicator.hh
index d1ff00126..3c30f7bf1 100644
--- a/src/synchronizer/communicator.hh
+++ b/src/synchronizer/communicator.hh
@@ -1,559 +1,561 @@
/**
* @file communicator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 15 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Class handling the parallel communications
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_event_handler_manager.hh"
#include "communication_buffer.hh"
#include "communication_request.hh"
#include "communicator_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STATIC_COMMUNICATOR_HH_
#define AKANTU_STATIC_COMMUNICATOR_HH_
namespace akantu {
namespace debug {
class CommunicationException : public Exception {
public:
CommunicationException()
: Exception("An exception happen during a communication process.") {}
};
} // namespace debug
/// @enum SynchronizerOperation reduce operation that the synchronizer can
/// perform
enum class SynchronizerOperation {
_sum,
_min,
_max,
_prod,
_land,
_band,
_lor,
_bor,
_lxor,
_bxor,
_min_loc,
_max_loc,
_null
};
enum class CommunicationMode { _auto, _synchronous, _ready };
namespace {
int _any_source = -1;
}
} // namespace akantu
namespace akantu {
struct CommunicatorInternalData {
virtual ~CommunicatorInternalData() = default;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class Communicator : public EventHandlerManager<CommunicatorEventHandler> {
struct private_member {};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Communicator(int & argc, char **& argv, const private_member & /*m*/);
Communicator(const private_member & /*unused*/ = private_member{});
~Communicator() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Point to Point */
/* ------------------------------------------------------------------------ */
template <typename T>
void probe(Int sender, Int tag, CommunicationStatus & status) const;
template <typename T>
bool asyncProbe(Int sender, Int tag, CommunicationStatus & status) const;
/* ------------------------------------------------------------------------ */
template <typename T>
inline void receive(Array<T> & values, Int sender, Int tag) const {
return this->receiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline void receive(std::vector<T> & values, Int sender, Int tag) const {
return this->receiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor>
inline void
receive(Tensor & values, Int sender, Int tag,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
inline void receive(CommunicationBufferTemplated<true> & values, Int sender,
Int tag) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
inline void receive(CommunicationBufferTemplated<false> & values, Int sender,
Int tag) const {
CommunicationStatus status;
this->probe<char>(sender, tag, status);
values.reserve(status.size());
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <typename T>
inline void
receive(T & values, Int sender, Int tag,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
return this->receiveImpl(&values, 1, sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
send(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(),
values.size() * values.getNbComponent(), receiver,
tag, mode);
}
template <typename T>
inline void
send(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.data(), values.size(), receiver, tag, mode);
}
template <typename Tensor>
inline void
send(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <bool is_static>
inline void
send(const CommunicationBufferTemplated<is_static> & values, Int receiver,
Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <typename T>
inline void send(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
return this->sendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest
asyncSend(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(),
values.size() * values.getNbComponent(),
receiver, tag, mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.data(), values.size(), receiver, tag,
mode);
}
template <typename Tensor>
inline CommunicationRequest
asyncSend(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <bool is_static>
inline CommunicationRequest
asyncSend(const CommunicationBufferTemplated<is_static> & values,
Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
return this->asyncSendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncReceive(Array<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline CommunicationRequest asyncReceive(std::vector<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor,
typename = std::enable_if_t<aka::is_tensor<Tensor>::value>>
inline CommunicationRequest asyncReceive(Tensor & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncReceive(CommunicationBufferTemplated<is_static> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
/* ------------------------------------------------------------------------ */
/* Collectives */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
allReduce(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->allReduceImpl(values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
allReduce(Tensor & values,
SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
this->allReduceImpl(values.storage(), values.size(), op);
}
template <typename T>
inline void
allReduce(T & values, SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->allReduceImpl(&values, 1, op);
}
template <typename T>
inline void
scan(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->scanImpl(values.storage(), values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
scan(Tensor & values, SynchronizerOperation op,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
this->scanImpl(values.storage(), values.storage(), values.size(), op);
}
template <typename T>
inline void scan(T & values,
SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->scanImpl(&values, &values, 1, op);
}
template <typename T>
inline void
exclusiveScan(Array<T> & values,
SynchronizerOperation op = SynchronizerOperation::_sum) const {
this->exclusiveScanImpl(values.storage(), values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
exclusiveScan(Tensor & values,
SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
this->exclusiveScanImpl(values.storage(), values.storage(), values.size(),
op);
}
template <typename T>
inline void
exclusiveScan(T & values,
SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->exclusiveScanImpl(&values, &values, 1, op);
}
template <typename T>
inline void
exclusiveScan(T & values, T & result,
SynchronizerOperation op = SynchronizerOperation::_sum,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->exclusiveScanImpl(&values, &result, 1, op);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void allGather(Array<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(getNbProc()) == values.size(),
"The array size is not correct");
this->allGatherImpl(values.storage(), values.getNbComponent());
}
template <typename Tensor,
typename = std::enable_if_t<aka::is_tensor<Tensor>::value>>
inline void allGather(Tensor & values) const {
AKANTU_DEBUG_ASSERT(values.size() / getNbProc() > 0,
"The vector size is not correct");
this->allGatherImpl(values.storage(), values.size() / getNbProc());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allGatherV(Array<T> & values, const Array<Int> & sizes) const {
this->allGatherVImpl(values.storage(), sizes.storage());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void reduce(Array<T> & values, SynchronizerOperation op,
int root = 0) const {
this->reduceImpl(values.storage(), values.size() * values.getNbComponent(),
op, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor>
inline void
gather(Tensor & values, int root = 0,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
this->gatherImpl(values.storage(), values.getNbComponent(), root);
}
template <typename T>
inline void
gather(T values, int root = 0,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->gatherImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor, typename T>
inline void
gather(Tensor & values, Array<T> & gathered,
std::enable_if_t<aka::is_tensor<Tensor>::value> * /*unused*/ =
nullptr) const {
AKANTU_DEBUG_ASSERT(values.size() == gathered.getNbComponent(),
"The array size is not correct");
gathered.resize(getNbProc());
this->gatherImpl(values.data(), values.size(), gathered.storage(),
gathered.getNbComponent());
}
template <typename T>
inline void
gather(T values, Array<T> & gathered,
std::enable_if_t<std::is_arithmetic<T>::value> * /*unused*/ =
nullptr) const {
this->gatherImpl(&values, 1, gathered.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gatherV(Array<T> & values, const Array<Int> & sizes,
int root = 0) const {
this->gatherVImpl(values.storage(), sizes.storage(), root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void broadcast(Array<T> & values, int root = 0) const {
this->broadcastImpl(values.storage(),
values.size() * values.getNbComponent(), root);
}
template <typename T>
inline void broadcast(std::vector<T> & values, int root = 0) const {
this->broadcastImpl(values.data(), values.size(), root);
}
inline void broadcast(CommunicationBufferTemplated<true> & buffer,
int root = 0) const {
this->broadcastImpl(buffer.storage(), buffer.size(), root);
}
inline void broadcast(CommunicationBufferTemplated<false> & buffer,
int root = 0) const {
UInt buffer_size = buffer.size();
this->broadcastImpl(&buffer_size, 1, root);
if (whoAmI() != root) {
buffer.reserve(buffer_size);
}
if (buffer_size == 0) {
return;
}
this->broadcastImpl(buffer.storage(), buffer.size(), root);
}
template <typename T> inline void broadcast(T & values, int root = 0) const {
this->broadcastImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
void barrier() const;
CommunicationRequest asyncBarrier() const;
/* ------------------------------------------------------------------------ */
/* Request handling */
/* ------------------------------------------------------------------------ */
static bool test(CommunicationRequest & request);
static bool testAll(std::vector<CommunicationRequest> & request);
static void wait(CommunicationRequest & request);
static void waitAll(std::vector<CommunicationRequest> & requests);
static UInt waitAny(std::vector<CommunicationRequest> & requests);
static inline void freeCommunicationRequest(CommunicationRequest & request);
static inline void
freeCommunicationRequest(std::vector<CommunicationRequest> & requests);
template <typename T, typename MsgProcessor>
inline void
receiveAnyNumber(std::vector<CommunicationRequest> & send_requests,
MsgProcessor && processor, Int tag) const;
protected:
template <typename T>
void
sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
void receiveImpl(T * buffer, Int size, Int sender, Int tag) const;
template <typename T>
CommunicationRequest asyncSendImpl(
const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
CommunicationRequest asyncReceiveImpl(T * buffer, Int size, Int sender,
Int tag) const;
template <typename T>
void allReduceImpl(T * values, int nb_values, SynchronizerOperation op) const;
template <typename T>
void scanImpl(T * values, T * results, int nb_values,
SynchronizerOperation op) const;
template <typename T>
void exclusiveScanImpl(T * values, T * results, int nb_values,
SynchronizerOperation op) const;
template <typename T> void allGatherImpl(T * values, int nb_values) const;
template <typename T> void allGatherVImpl(T * values, int * nb_values) const;
template <typename T>
void reduceImpl(T * values, int nb_values, SynchronizerOperation op,
int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered = 0) const;
template <typename T>
void gatherVImpl(T * values, int * nb_values, int root = 0) const;
template <typename T>
void broadcastImpl(T * values, int nb_values, int root = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
Int getNbProc() const;
Int whoAmI() const;
static Communicator & getStaticCommunicator();
static Communicator & getStaticCommunicator(int & argc, char **& argv);
int getMaxTag() const;
int getMinTag() const;
AKANTU_GET_MACRO(CommunicatorData, (*communicator_data), decltype(auto));
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
static std::unique_ptr<Communicator> static_communicator;
protected:
std::unique_ptr<CommunicatorInternalData> communicator_data;
};
inline std::ostream & operator<<(std::ostream & stream,
const CommunicationRequest & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "communicator_inline_impl.hh"
#endif /* AKANTU_STATIC_COMMUNICATOR_HH_ */
diff --git a/src/synchronizer/communicator_dummy_inline_impl.hh b/src/synchronizer/communicator_dummy_inline_impl.hh
index 28a0d7083..632742b9f 100644
--- a/src/synchronizer/communicator_dummy_inline_impl.hh
+++ b/src/synchronizer/communicator_dummy_inline_impl.hh
@@ -1,150 +1,152 @@
/**
* @file communicator_dummy_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 07 2017
- * @date last modification: Fri Nov 10 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Dummy communicator to make everything work im sequential
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <type_traits>
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & /*unused*/) {}
Communicator::Communicator(const private_member & /*unused*/) {}
template <typename T>
void Communicator::sendImpl(const T * /*unused*/, Int /*unused*/,
Int /*unused*/, Int /*unused*/,
const CommunicationMode & /*unused*/) const {}
template <typename T>
void Communicator::receiveImpl(T * /*unused*/, Int /*unused*/, Int /*unused*/,
Int /*unused*/) const {}
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T * /*unused*/, Int /*unused*/,
Int /*unused*/, Int /*unused*/,
const CommunicationMode & /*unused*/) const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
CommunicationRequest
Communicator::asyncReceiveImpl(T * /*unused*/, Int /*unused*/, Int /*unused*/,
Int /*unused*/) const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
void Communicator::probe(Int /*unused*/, Int /*unused*/,
CommunicationStatus & /*unused*/) const {}
template <typename T>
bool Communicator::asyncProbe(Int /*unused*/, Int /*unused*/,
CommunicationStatus & /*unused*/) const {
return true;
}
bool Communicator::test(CommunicationRequest & /*unused*/) { return true; }
bool Communicator::testAll(std::vector<CommunicationRequest> & /*unused*/) {
return true;
}
void Communicator::wait(CommunicationRequest & /*unused*/) {}
void Communicator::waitAll(std::vector<CommunicationRequest> & /*unused*/) {}
UInt Communicator::waitAny(std::vector<CommunicationRequest> & /*unused*/) {
return UInt(-1);
}
void Communicator::barrier() const {}
CommunicationRequest Communicator::asyncBarrier() const {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T>
void Communicator::reduceImpl(T * /*unused*/, int /*unused*/,
SynchronizerOperation /*unused*/,
int /*unused*/) const {}
template <typename T>
void Communicator::allReduceImpl(T * /*unused*/, int /*unused*/,
SynchronizerOperation /*unused*/) const {}
template <typename T>
void Communicator::scanImpl(T * values, T * result, int n,
SynchronizerOperation /*unused*/) const {
if (values == result) {
return;
}
std::copy_n(values, n, result);
}
template <typename T>
void Communicator::exclusiveScanImpl(T * /*values*/, T * result, int n,
SynchronizerOperation /*unused*/) const {
std::fill_n(result, n, T());
}
template <typename T>
inline void Communicator::allGatherImpl(T * /*unused*/, int /*unused*/) const {}
template <typename T>
inline void Communicator::allGatherVImpl(T * /*unused*/,
int * /*unused*/) const {}
template <typename T>
inline void Communicator::gatherImpl(T * /*unused*/, int /*unused*/,
int /*unused*/) const {}
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int /*unused*/) const {
static_assert(std::is_trivially_copyable<T>{},
"Cannot send this type of data");
std::memcpy(gathered, values, nb_values);
}
template <typename T>
inline void Communicator::gatherVImpl(T * /*unused*/, int * /*unused*/,
int /*unused*/) const {}
template <typename T>
inline void Communicator::broadcastImpl(T * /*unused*/, int /*unused*/,
int /*unused*/) const {}
int Communicator::getMaxTag() const { return std::numeric_limits<int>::max(); }
int Communicator::getMinTag() const { return 0; }
Int Communicator::getNbProc() const { return 1; }
Int Communicator::whoAmI() const { return 0; }
} // namespace akantu
diff --git a/src/synchronizer/communicator_event_handler.hh b/src/synchronizer/communicator_event_handler.hh
index f4bfffc81..ab8fcb8e1 100644
--- a/src/synchronizer/communicator_event_handler.hh
+++ b/src/synchronizer/communicator_event_handler.hh
@@ -1,60 +1,62 @@
/**
* @file communicator_event_handler.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 15 2017
*
* @brief Event handler of the communicator
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_
#define AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_
namespace akantu {
class Communicator;
struct FinalizeCommunicatorEvent {
explicit FinalizeCommunicatorEvent(const Communicator & comm)
: communicator(comm) {}
const Communicator & communicator;
};
class CommunicatorEventHandler {
public:
virtual ~CommunicatorEventHandler() = default;
virtual void onCommunicatorFinalize() = 0;
private:
inline void sendEvent(const FinalizeCommunicatorEvent & /*unused*/) {
this->onCommunicatorFinalize();
}
template <class EventHandler> friend class EventHandlerManager;
};
} // namespace akantu
#endif /* AKANTU_COMMUNICATOR_EVENT_HANDLER_HH_ */
diff --git a/src/synchronizer/communicator_inline_impl.hh b/src/synchronizer/communicator_inline_impl.hh
index 921bc339e..74dc26591 100644
--- a/src/synchronizer/communicator_inline_impl.hh
+++ b/src/synchronizer/communicator_inline_impl.hh
@@ -1,99 +1,101 @@
/**
* @file communicator_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 02 2016
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Thu Mar 11 2021
*
* @brief implementation of inline functions
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_
#define AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void
Communicator::freeCommunicationRequest(CommunicationRequest & request) {
request.free();
}
/* -------------------------------------------------------------------------- */
inline void Communicator::freeCommunicationRequest(
std::vector<CommunicationRequest> & requests) {
std::vector<CommunicationRequest>::iterator it;
for (it = requests.begin(); it != requests.end(); ++it) {
it->free();
}
}
/* -------------------------------------------------------------------------- */
template <typename T, typename MsgProcessor>
inline void Communicator::receiveAnyNumber(
std::vector<CommunicationRequest> & send_requests,
MsgProcessor && processor, Int tag) const {
CommunicationRequest barrier_request;
bool got_all{false};
bool are_send_finished{false};
if (getNbProc() == 1) {
return;
}
AKANTU_DEBUG_INFO("Sending " << send_requests.size()
<< " messages and checking for receives TAG["
<< tag << "]");
while (not got_all) {
bool are_receives_ready = true;
while (are_receives_ready) {
CommunicationStatus status;
are_receives_ready = asyncProbe<T>(_any_source, tag, status);
if (are_receives_ready) {
AKANTU_DEBUG_INFO("Receiving message from " << status.getSource());
Array<T> receive_buffer(status.size(), 1);
receive(receive_buffer, status.getSource(), tag);
std::forward<MsgProcessor>(processor)(status.getSource(),
receive_buffer);
}
}
if (not are_send_finished) {
are_send_finished = testAll(send_requests);
if (are_send_finished) {
AKANTU_DEBUG_INFO("All messages send, checking for more receives");
barrier_request = asyncBarrier();
}
}
if (are_send_finished) {
got_all = test(barrier_request);
}
}
AKANTU_DEBUG_INFO("Finished receiving");
}
} // namespace akantu
#endif /* AKANTU_STATIC_COMMUNICATOR_INLINE_IMPL_HH_ */
diff --git a/src/synchronizer/communicator_mpi_inline_impl.hh b/src/synchronizer/communicator_mpi_inline_impl.hh
index 5ecd98144..b3ff61814 100644
--- a/src/synchronizer/communicator_mpi_inline_impl.hh
+++ b/src/synchronizer/communicator_mpi_inline_impl.hh
@@ -1,509 +1,511 @@
/**
* @file communicator_mpi_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 07 2017
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief StaticCommunicatorMPI implementation
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
#include <type_traits>
#include <unordered_map>
#include <vector>
/* -------------------------------------------------------------------------- */
#include <mpi.h>
/* -------------------------------------------------------------------------- */
#if (defined(__GNUC__) || defined(__GNUG__))
#if AKA_GCC_VERSION < 60000
namespace std {
template <> struct hash<akantu::SynchronizerOperation> {
using argument_type = akantu::SynchronizerOperation;
size_t operator()(const argument_type & e) const noexcept {
auto ue = underlying_type_t<argument_type>(e);
return uh(ue);
}
private:
const hash<underlying_type_t<argument_type>> uh{};
};
} // namespace std
#endif
#endif
namespace akantu {
class CommunicationRequestMPI : public InternalCommunicationRequest {
public:
CommunicationRequestMPI(UInt source, UInt dest)
: InternalCommunicationRequest(source, dest),
request(std::make_unique<MPI_Request>()) {}
MPI_Request & getMPIRequest() { return *request; };
private:
std::unique_ptr<MPI_Request> request;
};
namespace {
template <typename T> inline MPI_Datatype getMPIDatatype();
MPI_Op getMPISynchronizerOperation(SynchronizerOperation op) {
std::unordered_map<SynchronizerOperation, MPI_Op> _operations{
{SynchronizerOperation::_sum, MPI_SUM},
{SynchronizerOperation::_min, MPI_MIN},
{SynchronizerOperation::_max, MPI_MAX},
{SynchronizerOperation::_prod, MPI_PROD},
{SynchronizerOperation::_land, MPI_LAND},
{SynchronizerOperation::_band, MPI_BAND},
{SynchronizerOperation::_lor, MPI_LOR},
{SynchronizerOperation::_bor, MPI_BOR},
{SynchronizerOperation::_lxor, MPI_LXOR},
{SynchronizerOperation::_bxor, MPI_BXOR},
{SynchronizerOperation::_min_loc, MPI_MINLOC},
{SynchronizerOperation::_max_loc, MPI_MAXLOC},
{SynchronizerOperation::_null, MPI_OP_NULL}};
return _operations[op];
}
template <typename T> MPI_Datatype inline getMPIDatatype() {
return MPI_DATATYPE_NULL;
}
#define SPECIALIZE_MPI_DATATYPE(type, mpi_type) \
template <> MPI_Datatype inline getMPIDatatype<type>() { return mpi_type; }
#define COMMA ,
SPECIALIZE_MPI_DATATYPE(char, MPI_CHAR)
SPECIALIZE_MPI_DATATYPE(std::uint8_t, MPI_UINT8_T)
SPECIALIZE_MPI_DATATYPE(float, MPI_FLOAT)
SPECIALIZE_MPI_DATATYPE(double, MPI_DOUBLE)
SPECIALIZE_MPI_DATATYPE(long double, MPI_LONG_DOUBLE)
SPECIALIZE_MPI_DATATYPE(signed int, MPI_INT)
SPECIALIZE_MPI_DATATYPE(unsigned int, MPI_UNSIGNED)
SPECIALIZE_MPI_DATATYPE(signed long int, MPI_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long int, MPI_UNSIGNED_LONG)
SPECIALIZE_MPI_DATATYPE(signed long long int, MPI_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long long int, MPI_UNSIGNED_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<double COMMA int>, MPI_DOUBLE_INT)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<float COMMA int>, MPI_FLOAT_INT)
SPECIALIZE_MPI_DATATYPE(bool, MPI_CXX_BOOL)
template <> MPI_Datatype inline getMPIDatatype<NodeFlag>() {
return getMPIDatatype<std::underlying_type_t<NodeFlag>>();
}
inline int getMPISource(int src) {
if (src == _any_source) {
return MPI_ANY_SOURCE;
}
return src;
}
decltype(auto) convertRequests(std::vector<CommunicationRequest> & requests) {
std::vector<MPI_Request> mpi_requests(requests.size());
for (auto && request_pair : zip(requests, mpi_requests)) {
auto && req = std::get<0>(request_pair);
auto && mpi_req = std::get<1>(request_pair);
mpi_req = aka::as_type<CommunicationRequestMPI>(req.getInternal())
.getMPIRequest();
}
return mpi_requests;
}
} // namespace
// this is ugly but shorten the code a lot
#define MPIDATA \
(*reinterpret_cast<MPICommunicatorData *>(communicator_data.get()))
/* -------------------------------------------------------------------------- */
/* Implementation */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & m)
: Communicator(m) {}
/* -------------------------------------------------------------------------- */
Communicator::Communicator(const private_member & /*unused*/)
: communicator_data(std::make_unique<MPICommunicatorData>()) {
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Send(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_synchronous:
MPI_Ssend(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_ready:
MPI_Rsend(buffer, size, type, receiver, tag, communicator);
break;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::receiveImpl(T * buffer, Int size, Int sender,
Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status status;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Recv(buffer, size, type, getMPISource(sender), tag, communicator,
&status);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(whoAmI(), receiver);
MPI_Request & req = request->getMPIRequest();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Isend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_synchronous:
MPI_Issend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_ready:
MPI_Irsend(buffer, size, type, receiver, tag, communicator, &req);
break;
}
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest Communicator::asyncReceiveImpl(T * buffer, Int size,
Int sender, Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(sender, whoAmI());
MPI_Datatype type = getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
MPI_Irecv(buffer, size, type, getMPISource(sender), tag, communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::probe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
MPI_Probe(getMPISource(sender), tag, communicator, &mpi_status);
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool Communicator::asyncProbe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
int test;
MPI_Iprobe(getMPISource(sender), tag, communicator, &test, &mpi_status);
if (not test) {
return false;
}
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
return true;
}
/* -------------------------------------------------------------------------- */
bool Communicator::test(CommunicationRequest & request) {
MPI_Status status;
int flag;
auto & req_mpi = aka::as_type<CommunicationRequestMPI>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Test(&req, &flag, &status);
return flag != 0;
}
/* -------------------------------------------------------------------------- */
bool Communicator::testAll(std::vector<CommunicationRequest> & requests) {
// int are_finished;
// auto && mpi_requests = convertRequests(requests);
// MPI_Testall(mpi_requests.size(), mpi_requests.data(), &are_finished,
// MPI_STATUSES_IGNORE);
// return are_finished;
for (auto & request : requests) {
if (not test(request)) {
return false;
}
}
return true;
}
/* -------------------------------------------------------------------------- */
void Communicator::wait(CommunicationRequest & request) {
MPI_Status status;
auto & req_mpi = aka::as_type<CommunicationRequestMPI>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Wait(&req, &status);
}
/* -------------------------------------------------------------------------- */
void Communicator::waitAll(std::vector<CommunicationRequest> & requests) {
auto && mpi_requests = convertRequests(requests);
MPI_Waitall(mpi_requests.size(), mpi_requests.data(), MPI_STATUSES_IGNORE);
}
/* -------------------------------------------------------------------------- */
UInt Communicator::waitAny(std::vector<CommunicationRequest> & requests) {
auto && mpi_requests = convertRequests(requests);
int pos;
MPI_Waitany(mpi_requests.size(), mpi_requests.data(), &pos,
MPI_STATUSES_IGNORE);
if (pos != MPI_UNDEFINED) {
return pos;
}
return UInt(-1);
}
/* -------------------------------------------------------------------------- */
void Communicator::barrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Barrier(communicator);
}
/* -------------------------------------------------------------------------- */
CommunicationRequest Communicator::asyncBarrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
auto * request = new CommunicationRequestMPI(0, 0);
MPI_Request & req = request->getMPIRequest();
MPI_Ibarrier(communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::reduceImpl(T * values, int nb_values,
SynchronizerOperation op, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Reduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), root, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allReduceImpl(T * values, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allreduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::scanImpl(T * values, T * result, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
if (values == result) {
values = reinterpret_cast<T *>(MPI_IN_PLACE);
}
MPI_Scan(values, result, nb_values, type, getMPISynchronizerOperation(op),
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::exclusiveScanImpl(T * values, T * result, int nb_values,
SynchronizerOperation op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
if (values == result) {
values = reinterpret_cast<T *>(MPI_IN_PLACE);
}
MPI_Exscan(values, result, nb_values, type, getMPISynchronizerOperation(op),
communicator);
if (whoAmI() == 0) {
result[0] = T();
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherImpl(T * values, int nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgather(MPI_IN_PLACE, nb_values, type, values, nb_values, type,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherVImpl(T * values, int * nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
std::vector<int> displs(getNbProc());
displs[0] = 0;
for (int i = 1; i < getNbProc(); ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgatherv(MPI_IN_PLACE, *nb_values, type, values, nb_values,
displs.data(), type, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T * send_buf = nullptr;
T * recv_buf = nullptr;
if (whoAmI() == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_values, type, root,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T * send_buf = values;
T * recv_buf = gathered;
if (nb_gathered == 0) {
nb_gathered = nb_values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_gathered, type,
whoAmI(), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherVImpl(T * values, int * nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
int * displs = nullptr;
auto psize = getNbProc();
auto prank = whoAmI();
if (prank == root) {
displs = new int[psize];
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
}
T * send_buf = nullptr;
T * recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gatherv(send_buf, *nb_values, type, recv_buf, nb_values, displs, type,
root, communicator);
if (prank == root) {
delete[] displs;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::broadcastImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Bcast(values, nb_values, type, root, communicator);
}
/* -------------------------------------------------------------------------- */
int Communicator::getMaxTag() const { return MPIDATA.getMaxTag(); }
int Communicator::
getMinTag() // NOLINT(readability-convert-member-functions-to-static)
const {
return 0;
}
/* -------------------------------------------------------------------------- */
Int Communicator::getNbProc() const { return MPIDATA.size(); }
Int Communicator::whoAmI() const { return MPIDATA.rank(); }
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.cc b/src/synchronizer/data_accessor.cc
index 75f6e98de..4e13401f1 100644
--- a/src/synchronizer/data_accessor.cc
+++ b/src/synchronizer/data_accessor.cc
@@ -1,156 +1,158 @@
/**
* @file data_accessor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief data accessors constructor functions
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackNodalDataHelper(
Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
UInt nb_component = data.getNbComponent();
UInt nb_nodes_per_element = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt * conn = nullptr;
for (const auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
conn = mesh.getConnectivity(el.type, el.ghost_type).storage();
nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
}
UInt el_offset = el.element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_conn = conn[el_offset + n];
Vector<T> data_vect(data.storage() + offset_conn * nb_component,
nb_component);
if (pack_helper) {
buffer << data_vect;
} else {
buffer >> data_vect;
}
}
}
}
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
void DataAccessor<Element>::packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem) {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt nb_component = 0;
Array<T> * vect = nullptr;
for (const auto & el : element) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
nb_quad_per_elem =
per_quadrature_point_data
? fem.getNbIntegrationPoints(el.type, el.ghost_type)
: 1;
nb_component = vect->getNbComponent();
}
Vector<T> data(vect->storage() +
el.element * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem);
if (pack_helper) {
buffer << data;
} else {
buffer >> data;
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void DataAccessor<UInt>::packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
T * data_ptr = data.storage();
for (const auto & dof : dofs) {
if (pack_helper) {
buffer << data_ptr[dof];
} else {
buffer >> data_ptr[dof];
}
}
}
/* -------------------------------------------------------------------------- */
#define DECLARE_HELPERS(T) \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void DataAccessor<Element>::packUnpackNodalDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<Element> & elements, const Mesh & mesh); \
template void \
DataAccessor<Element>::packUnpackElementalDataHelper<T, false>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<Element>::packUnpackElementalDataHelper<T, true>( \
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer, \
const Array<Element> & element, bool per_quadrature_point_data, \
const FEEngine & fem); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, true>( \
Array<T> & data, CommunicationBuffer & buffer, \
const Array<UInt> & dofs); \
template void DataAccessor<UInt>::packUnpackDOFDataHelper<T, false>( \
Array<T> & data, CommunicationBuffer & buffer, const Array<UInt> & dofs)
/* -------------------------------------------------------------------------- */
DECLARE_HELPERS(Real);
DECLARE_HELPERS(UInt);
DECLARE_HELPERS(bool);
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.hh b/src/synchronizer/data_accessor.hh
index 5eada7b04..df3370722 100644
--- a/src/synchronizer/data_accessor.hh
+++ b/src/synchronizer/data_accessor.hh
@@ -1,352 +1,354 @@
/**
* @file data_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
- * @date last modification: Sun Feb 04 2018
+ * @date last modification: Fri Apr 09 2021
*
* @brief Interface of accessors for pack_unpack system
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DATA_ACCESSOR_HH_
#define AKANTU_DATA_ACCESSOR_HH_
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
class DataAccessorBase {
public:
DataAccessorBase() = default;
virtual ~DataAccessorBase() = default;
};
template <class T> class DataAccessor : public virtual DataAccessorBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DataAccessor() = default;
~DataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief get the number of data to exchange for a given array of T
* (elements or dofs) and a given akantu::SynchronizationTag
*/
virtual UInt getNbData(const Array<T> & elements,
const SynchronizationTag & tag) const = 0;
/**
* @brief pack the data for a given array of T (elements or dofs) and a given
* akantu::SynchronizationTag
*/
virtual void packData(CommunicationBuffer & buffer, const Array<T> & element,
const SynchronizationTag & tag) const = 0;
/**
* @brief unpack the data for a given array of T (elements or dofs) and a
* given akantu::SynchronizationTag
*/
virtual void unpackData(CommunicationBuffer & buffer,
const Array<T> & element,
const SynchronizationTag & tag) = 0;
};
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<Element> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void
packUnpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh);
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
static void packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem);
/* ------------------------------------------------------------------------ */
template <typename T>
static void
packNodalDataHelper(const Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, true>(const_cast<Array<T> &>(data), buffer,
elements, mesh);
}
template <typename T>
static inline void
unpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, false>(data, buffer, elements, mesh);
}
/* ------------------------------------------------------------------------ */
template <typename T>
static inline void
packElementalDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements,
per_quadrature_point, fem);
}
template <typename T>
static inline void
unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, false>(data_to_unpack, buffer, elements,
per_quadrature_point, fem);
}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<UInt> : public virtual DataAccessorBase {
public:
DataAccessor() = default;
~DataAccessor() override = default;
virtual UInt getNbData(const Array<UInt> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs);
template <typename T>
static inline void packDOFDataHelper(const Array<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, true>(const_cast<Array<T> &>(data_to_pack),
buffer, dofs);
}
template <typename T>
static inline void unpackDOFDataHelper(Array<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, false>(data_to_unpack, buffer, dofs);
}
};
/* -------------------------------------------------------------------------- */
template <typename T> class AddOperation {
public:
inline T operator()(T & a, T & b) { return a + b; };
};
template <typename T> class IdentityOperation {
public:
inline T & operator()(T & /*unused*/, T & b) { return b; };
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <class Entity, template <class> class Op, class T>
class ReduceDataAccessor : public virtual DataAccessor<Entity> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ReduceDataAccessor(Array<T> & data, const SynchronizationTag & tag)
: data(data), tag(tag) {}
~ReduceDataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Entity> & entities,
const SynchronizationTag & tag) const override {
if (tag != this->tag) {
return 0;
}
Vector<T> tmp(data.getNbComponent());
return entities.size() * CommunicationBuffer::sizeInBuffer(tmp);
}
/* ------------------------------------------------------------------------ */
void packData(CommunicationBuffer & buffer, const Array<Entity> & entities,
const SynchronizationTag & tag) const override {
if (tag != this->tag) {
return;
}
auto data_it = data.begin(data.getNbComponent());
for (auto el : entities) {
buffer << Vector<T>(data_it[el]);
}
}
/* ------------------------------------------------------------------------ */
void unpackData(CommunicationBuffer & buffer, const Array<Entity> & entities,
const SynchronizationTag & tag) override {
if (tag != this->tag) {
return;
}
auto data_it = data.begin(data.getNbComponent());
for (auto el : entities) {
Vector<T> unpacked(data.getNbComponent());
Vector<T> vect(data_it[el]);
buffer >> unpacked;
vect = oper(vect, unpacked);
}
}
protected:
/// data to (un)pack
Array<T> & data;
/// Tag to consider
SynchronizationTag tag;
/// reduction operator
Op<Vector<T>> oper;
};
/* -------------------------------------------------------------------------- */
template <class T>
using SimpleUIntDataAccessor = ReduceDataAccessor<UInt, IdentityOperation, T>;
/* -------------------------------------------------------------------------- */
template <class T>
class SimpleElementDataAccessor : public virtual DataAccessor<Element> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SimpleElementDataAccessor(ElementTypeMapArray<T> & data,
const SynchronizationTag & tag)
: data(data), tag(tag) {}
~SimpleElementDataAccessor() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag != this->tag)
return 0;
Int size = 0;
for (auto & el : elements) {
auto && data_type = data(el.type, el.ghost_type);
size += sizeof(T) * data_type.getNbComponent();
}
return size;
}
/* ------------------------------------------------------------------------ */
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag != this->tag)
return;
for (auto & el : elements) {
auto && data_type = data(el.type, el.ghost_type);
for (auto c : arange(data_type.getNbComponent())) {
const auto & data_per_element = data_type(el.element, c);
buffer << data_per_element;
}
}
}
/* ------------------------------------------------------------------------ */
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag != this->tag)
return;
for (auto & el : elements) {
auto && data_type = data(el.type, el.ghost_type);
for (auto c : arange(data_type.getNbComponent())) {
auto & data_per_element = data_type(el.element, c);
buffer >> data_per_element;
}
}
}
protected:
/// data to (un)pack
ElementTypeMapArray<T> & data;
/// Tag to consider
SynchronizationTag tag;
};
} // namespace akantu
#endif /* AKANTU_DATA_ACCESSOR_HH_ */
diff --git a/src/synchronizer/dof_synchronizer.cc b/src/synchronizer/dof_synchronizer.cc
index cd5f28ae1..93a63872a 100644
--- a/src/synchronizer/dof_synchronizer.cc
+++ b/src/synchronizer/dof_synchronizer.cc
@@ -1,229 +1,231 @@
/**
* @file dof_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Tue Feb 06 2018
+ * @date last modification: Fri Jul 24 2020
*
* @brief DOF synchronizing object implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_synchronizer.hh"
#include "aka_iterators.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A DOFSynchronizer needs a mesh and the number of degrees of freedom
* per node to be created. In the constructor computes the local and global dof
* number for each dof. The member
* proc_informations (std vector) is resized with the number of mpi
* processes. Each entry in the vector is a PerProcInformations object
* that contains the interactions of the current mpi process (prank) with the
* mpi process corresponding to the position of that entry. Every
* ProcInformations object contains one array with the dofs that have
* to be sent to prank and a second one with dofs that willl be received form
* prank.
* This information is needed for the asychronous communications. The
* constructor sets up this information.
*/
DOFSynchronizer::DOFSynchronizer(DOFManagerDefault & dof_manager, const ID & id)
: SynchronizerImpl<UInt>(dof_manager.getCommunicator(), id),
dof_manager(dof_manager) {
std::vector<ID> dof_ids = dof_manager.getDOFIDs();
// Transfers nodes to global equation numbers in new schemes
for (const ID & dof_id : dof_ids) {
registerDOFs(dof_id);
}
}
/* -------------------------------------------------------------------------- */
DOFSynchronizer::~DOFSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::registerDOFs(const ID & dof_id) {
if (this->nb_proc == 1) {
return;
}
if (dof_manager.getSupportType(dof_id) != _dst_nodal) {
return;
}
const auto & equation_numbers = dof_manager.getLocalEquationsNumbers(dof_id);
const auto & associated_nodes = dof_manager.getDOFsAssociatedNodes(dof_id);
const auto & node_synchronizer = dof_manager.getMesh().getNodeSynchronizer();
const auto & node_communications = node_synchronizer.getCommunications();
auto transcode_node_to_global_dof_scheme =
[this, &associated_nodes, &equation_numbers](
auto && it, auto && end, const CommunicationSendRecv & sr) -> void {
for (; it != end; ++it) {
auto & scheme = communications.createScheme(it->first, sr);
const auto & node_scheme = it->second;
for (auto & node : node_scheme) {
auto an_begin = associated_nodes.begin();
auto an_it = an_begin;
auto an_end = associated_nodes.end();
std::vector<UInt> global_dofs_per_node;
while ((an_it = std::find(an_it, an_end, node)) != an_end) {
UInt pos = an_it - an_begin;
UInt local_eq_num = equation_numbers(pos);
UInt global_eq_num =
dof_manager.localToGlobalEquationNumber(local_eq_num);
global_dofs_per_node.push_back(global_eq_num);
++an_it;
}
std::sort(global_dofs_per_node.begin(), global_dofs_per_node.end());
std::transform(global_dofs_per_node.begin(), global_dofs_per_node.end(),
global_dofs_per_node.begin(), [this](UInt g) -> UInt {
UInt l = dof_manager.globalToLocalEquationNumber(g);
return l;
});
for (auto & leqnum : global_dofs_per_node) {
scheme.push_back(leqnum);
}
}
}
};
for (auto sr : send_recv_t{}) {
auto ncs_it = node_communications.begin_scheme(sr);
auto ncs_end = node_communications.end_scheme(sr);
transcode_node_to_global_dof_scheme(ncs_it, ncs_end, sr);
}
entities_changed = true;
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::fillEntityToSend(Array<UInt> & dofs_to_send) {
UInt nb_dofs = dof_manager.getLocalSystemSize();
this->entities_from_root.zero();
dofs_to_send.resize(0);
for (UInt d : arange(nb_dofs)) {
if (not dof_manager.isLocalOrMasterDOF(d)) {
continue;
}
entities_from_root.push_back(d);
}
for (auto d : entities_from_root) {
UInt global_dof = dof_manager.localToGlobalEquationNumber(d);
dofs_to_send.push_back(global_dof);
}
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::onNodesAdded(const Array<UInt> & /*nodes_list*/) {
auto dof_ids = dof_manager.getDOFIDs();
for (auto sr : iterate_send_recv) {
for (auto && data : communications.iterateSchemes(sr)) {
auto & scheme = data.second;
scheme.resize(0);
}
}
for (auto & dof_id : dof_ids) {
registerDOFs(dof_id);
}
// const auto & node_synchronizer =
// dof_manager.getMesh().getNodeSynchronizer(); const auto &
// node_communications = node_synchronizer.getCommunications();
// std::map<UInt, std::vector<UInt>> nodes_per_proc[2];
// for (auto sr : iterate_send_recv) {
// for (auto && data : node_communications.iterateSchemes(sr)) {
// auto proc = data.first;
// const auto & scheme = data.second;
// for (auto node : scheme) {
// nodes_per_proc[sr][proc].push_back(node);
// }
// }
// }
// std::map<UInt, std::vector<UInt>> dofs_per_proc[2];
// for (auto & dof_id : dof_ids) {
// const auto & associated_nodes =
// dof_manager.getDOFsAssociatedNodes(dof_id); const auto &
// local_equation_numbers =
// dof_manager.getEquationsNumbers(dof_id);
// for (auto tuple : zip(associated_nodes, local_equation_numbers)) {
// UInt assoc_node;
// UInt local_eq_num;
// std::tie(assoc_node, local_eq_num) = tuple;
// for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
// ++sr_it) {
// for (auto & pair : nodes_per_proc[*sr_it]) {
// if (std::find(pair.second.end(), pair.second.end(), assoc_node) !=
// pair.second.end()) {
// dofs_per_proc[*sr_it][pair.first].push_back(local_eq_num);
// }
// }
// }
// }
// }
// for (auto sr_it = send_recv_t::begin(); sr_it != send_recv_t::end();
// ++sr_it) {
// for (auto & pair : dofs_per_proc[*sr_it]) {
// std::sort(pair.second.begin(), pair.second.end(),
// [this](UInt la, UInt lb) -> bool {
// UInt ga = dof_manager.localToGlobalEquationNumber(la);
// UInt gb = dof_manager.localToGlobalEquationNumber(lb);
// return ga < gb;
// });
// auto & scheme = communications.getScheme(pair.first, *sr_it);
// scheme.resize(0);
// for (auto leq : pair.second) {
// scheme.push_back(leq);
// }
// }
// }
this->entities_changed = true;
}
} // namespace akantu
diff --git a/src/synchronizer/dof_synchronizer.hh b/src/synchronizer/dof_synchronizer.hh
index b458785e6..169bca2b1 100644
--- a/src/synchronizer/dof_synchronizer.hh
+++ b/src/synchronizer/dof_synchronizer.hh
@@ -1,83 +1,85 @@
/**
* @file dof_synchronizer.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Mar 04 2020
*
* @brief Synchronize Array of DOFs
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class DOFManagerDefault;
} // namespace akantu
#ifndef AKANTU_DOF_SYNCHRONIZER_HH_
#define AKANTU_DOF_SYNCHRONIZER_HH_
namespace akantu {
class DOFSynchronizer : public SynchronizerImpl<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFSynchronizer(DOFManagerDefault & dof_manager,
const ID & id = "dof_synchronizer");
~DOFSynchronizer() override;
virtual void registerDOFs(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void onNodesAdded(const Array<UInt> & nodes);
protected:
Int getRank(const UInt & /*node*/) const final { AKANTU_TO_IMPLEMENT(); }
/// list the entities to send to root process
void fillEntityToSend(Array<UInt> & dofs_to_send) override;
inline UInt canScatterSize() override;
inline UInt gatheredSize() override;
inline UInt localToGlobalEntity(const UInt & local) override;
private:
/// information on the dofs
DOFManagerDefault & dof_manager;
};
} // namespace akantu
#include "dof_synchronizer_inline_impl.hh"
#endif /* AKANTU_DOF_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/dof_synchronizer_inline_impl.hh b/src/synchronizer/dof_synchronizer_inline_impl.hh
index 423549412..ac3b3d6d5 100644
--- a/src/synchronizer/dof_synchronizer_inline_impl.hh
+++ b/src/synchronizer/dof_synchronizer_inline_impl.hh
@@ -1,60 +1,62 @@
/**
* @file dof_synchronizer_inline_impl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Mar 04 2020
*
* @brief DOFSynchronizer inline implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_
#define AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt DOFSynchronizer::canScatterSize() {
return dof_manager.getLocalSystemSize();
}
/* -------------------------------------------------------------------------- */
inline UInt DOFSynchronizer::gatheredSize() {
return dof_manager.getSystemSize();
}
inline UInt DOFSynchronizer::localToGlobalEntity(const UInt & local) {
return dof_manager.localToGlobalEquationNumber(local);
}
} // namespace akantu
#endif /* AKANTU_DOF_SYNCHRONIZER_INLINE_IMPL_HH_ */
diff --git a/src/synchronizer/element_info_per_processor.cc b/src/synchronizer/element_info_per_processor.cc
index 69877a1d8..044e56b75 100644
--- a/src/synchronizer/element_info_per_processor.cc
+++ b/src/synchronizer/element_info_per_processor.cc
@@ -1,125 +1,127 @@
/**
* @file element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Helper class to distribute a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_info_per_processor.hh"
#include "communicator.hh"
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ElementInfoPerProc::ElementInfoPerProc(ElementSynchronizer & synchronizer,
UInt message_cnt, UInt root,
ElementType type)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
rank(synchronizer.getCommunicator().whoAmI()),
nb_proc(synchronizer.getCommunicator().getNbProc()), root(root),
type(type), message_count(message_cnt), mesh(synchronizer.getMesh()),
comm(synchronizer.getCommunicator()) {}
/* -------------------------------------------------------------------------- */
bool ElementInfoPerProc::synchronize() {
auto need_synchronize = needSynchronize();
if (need_synchronize) {
synchronizeConnectivities();
synchronizePartitions();
synchronizeTags();
synchronizeGroups();
}
return need_synchronize;
}
/* -------------------------------------------------------------------------- */
void ElementInfoPerProc::fillCommunicationScheme(
const Array<UInt> & partition) {
AKANTU_DEBUG_IN();
Element element;
element.type = this->type;
auto & communications = this->synchronizer.getCommunications();
auto part = partition.begin();
std::map<UInt, Array<Element>> send_array_per_proc;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part;
++part;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p, ++part) {
UInt proc = *part;
AKANTU_DEBUG(dblAccessory,
"Must send : " << element << " to proc " << proc);
send_array_per_proc[proc].push_back(element);
}
}
for (auto & send_schemes : send_array_per_proc) {
if (send_schemes.second.empty()) {
continue;
}
auto & scheme = communications.createSendScheme(send_schemes.first);
scheme.append(send_schemes.second);
}
std::map<UInt, Array<Element>> recv_array_per_proc;
for (UInt gel = 0; gel < nb_ghost_element; ++gel, ++part) {
UInt proc = *part;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory,
"Must recv : " << element << " from proc " << proc);
recv_array_per_proc[proc].push_back(element);
}
for (auto & recv_schemes : recv_array_per_proc) {
if (recv_schemes.second.empty()) {
continue;
}
auto & scheme = communications.createRecvScheme(recv_schemes.first);
scheme.append(recv_schemes.second);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/element_info_per_processor.hh b/src/synchronizer/element_info_per_processor.hh
index fd3d677ac..7503a598f 100644
--- a/src/synchronizer/element_info_per_processor.hh
+++ b/src/synchronizer/element_info_per_processor.hh
@@ -1,150 +1,152 @@
/**
* @file element_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communication_buffer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_
#define AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_
namespace akantu {
class ElementSynchronizer;
class Communicator;
class MeshPartition;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementInfoPerProc : protected MeshAccessor {
public:
ElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type);
bool synchronize();
protected:
virtual void synchronizeConnectivities() = 0;
virtual void synchronizePartitions() = 0;
virtual void synchronizeTags() = 0;
virtual void synchronizeGroups() = 0;
virtual bool needSynchronize() = 0;
protected:
void fillCommunicationScheme(const Array<UInt> & partition);
template <class CommunicationBuffer>
void fillElementGroupsFromBuffer(CommunicationBuffer & buffer);
template <typename T, typename BufferType>
void fillMeshDataTemplated(BufferType & buffer, const std::string & tag_name,
UInt nb_component);
template <typename BufferType>
void fillMeshData(BufferType & buffer, const std::string & tag_name,
const MeshDataTypeCode & type_code, UInt nb_component);
protected:
ElementSynchronizer & synchronizer;
UInt rank{0};
UInt nb_proc{1};
UInt root{0};
ElementType type{_not_defined};
UInt nb_tags{0};
UInt nb_nodes_per_element{0};
UInt nb_element{0};
UInt nb_local_element{0};
UInt nb_ghost_element{0};
UInt message_count{0};
Mesh & mesh;
const Communicator & comm;
};
/* -------------------------------------------------------------------------- */
class MasterElementInfoPerProc : public ElementInfoPerProc {
public:
MasterElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type,
const MeshPartition & partition);
protected:
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
bool needSynchronize() override { return type != _not_defined; }
protected:
template <typename T>
void fillTagBufferTemplated(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
void fillTagBuffer(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
private:
const MeshPartition & partition;
Vector<UInt> all_nb_local_element;
Vector<UInt> all_nb_ghost_element;
Vector<UInt> all_nb_element_to_send;
};
/* -------------------------------------------------------------------------- */
class SlaveElementInfoPerProc : public ElementInfoPerProc {
public:
SlaveElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root);
protected:
void synchronizeConnectivities() override;
void synchronizePartitions() override;
void synchronizeTags() override;
void synchronizeGroups() override;
bool needSynchronize() override;
private:
UInt nb_element_to_receive{0};
};
} // namespace akantu
#include "element_info_per_processor_tmpl.hh"
#endif /* AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH_ */
diff --git a/src/synchronizer/element_info_per_processor_tmpl.hh b/src/synchronizer/element_info_per_processor_tmpl.hh
index febb3e794..2ab1e7bce 100644
--- a/src/synchronizer/element_info_per_processor_tmpl.hh
+++ b/src/synchronizer/element_info_per_processor_tmpl.hh
@@ -1,146 +1,148 @@
/**
* @file element_info_per_processor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Nov 12 2020
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_
#define AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, typename BufferType>
void ElementInfoPerProc::fillMeshDataTemplated(BufferType & buffer,
const std::string & tag_name,
UInt nb_component) {
AKANTU_DEBUG_ASSERT(this->mesh.getNbElement(this->type) == nb_local_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_not_ghost."
<< " Got " << nb_local_element << " values, expected "
<< mesh.getNbElement(this->type));
mesh.getElementalData<T>(tag_name);
Array<T> & data = mesh.getElementalDataArrayAlloc<T>(
tag_name, this->type, _not_ghost, nb_component);
data.resize(nb_local_element);
/// unpacking the data, element by element
for (UInt i(0); i < nb_local_element; ++i) {
for (UInt j(0); j < nb_component; ++j) {
buffer >> data(i, j);
}
}
AKANTU_DEBUG_ASSERT(mesh.getNbElement(this->type, _ghost) == nb_ghost_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_ghost."
<< " Got " << nb_ghost_element << " values, expected "
<< mesh.getNbElement(this->type, _ghost));
Array<T> & data_ghost = mesh.getElementalDataArrayAlloc<T>(
tag_name, this->type, _ghost, nb_component);
data_ghost.resize(nb_ghost_element);
/// unpacking the ghost data, element by element
for (UInt j(0); j < nb_ghost_element; ++j) {
for (UInt k(0); k < nb_component; ++k) {
buffer >> data_ghost(j, k);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename BufferType>
void ElementInfoPerProc::fillMeshData(BufferType & buffer,
const std::string & tag_name,
const MeshDataTypeCode & type_code,
UInt nb_component) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
fillMeshDataTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffer, tag_name, \
nb_component); \
break; \
}
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not determine the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void ElementInfoPerProc::fillElementGroupsFromBuffer(
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (auto ghost_type : ghost_types) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
el.ghost_type = ghost_type;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, ghost_type),
"The mesh does not have the element " << e);
for (auto && group : element_to_group) {
mesh.getElementGroup(group).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH_ */
diff --git a/src/synchronizer/element_synchronizer.cc b/src/synchronizer/element_synchronizer.cc
index 772e32982..c2d65a1ad 100644
--- a/src/synchronizer/element_synchronizer.cc
+++ b/src/synchronizer/element_synchronizer.cc
@@ -1,293 +1,295 @@
/**
* @file element_synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Sep 01 2010
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of a communicator using a static_communicator for
* real
* send/receive
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
#if defined(AKANTU_MODULE)
#define AKANTU_MODULE_SAVE_ AKANTU_MODULE
#undef AKANTU_MODULE
#endif
#define AKANTU_MODULE element_synchronizer
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(Mesh & mesh, const ID & id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(mesh.getCommunicator(), id),
mesh(mesh), element_to_prank("element_to_prank", id) {
AKANTU_DEBUG_IN();
if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::ElementSynchronizer(const ElementSynchronizer & other,
const ID & id,
bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<Element>(other, id), mesh(other.mesh),
element_to_prank("element_to_prank", id) {
AKANTU_DEBUG_IN();
element_to_prank.copy(other.element_to_prank);
if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementSynchronizer::~ElementSynchronizer() = default;
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::substituteElements(
const std::map<Element, Element> & old_to_new_elements) {
auto found_element_end = old_to_new_elements.end();
// substitute old elements with new ones
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto & el : list) {
auto found_element_it = old_to_new_elements.find(el);
if (found_element_it != found_element_end) {
el = found_element_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsChanged(
const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) {
// create a map to link old elements to new ones
std::map<Element, Element> old_to_new_elements;
for (UInt el = 0; el < old_elements_list.size(); ++el) {
AKANTU_DEBUG_ASSERT(old_to_new_elements.find(old_elements_list(el)) ==
old_to_new_elements.end(),
"The same element cannot appear twice in the list");
old_to_new_elements[old_elements_list(el)] = new_elements_list(el);
}
substituteElements(old_to_new_elements);
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::onElementsRemoved(
const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & /*unused*/) {
AKANTU_DEBUG_IN();
this->filterScheme([&](auto && element) {
return std::find(element_to_remove.begin(), element_to_remove.end(),
element) == element_to_remove.end();
});
this->renumberElements(new_numbering);
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::buildElementToPrank() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true, _default_value = rank);
/// assign prank to all ghost elements
for (auto && scheme : communications.iterateSchemes(_recv)) {
auto & recv = scheme.second;
auto proc = scheme.first;
for (auto & element : recv) {
element_to_prank(element) = proc;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Int ElementSynchronizer::getRank(const Element & element) const {
if (not element_to_prank.exists(element.type, element.ghost_type)) {
// Nicolas: Ok This is nasty I know....
const_cast<ElementSynchronizer *>(this)->buildElementToPrank();
}
return element_to_prank(element);
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::renumberElements(
const ElementTypeMapArray<UInt> & new_numbering) {
for (auto && sr : iterate_send_recv) {
for (auto && scheme_pair : communications.iterateSchemes(sr)) {
auto & list = scheme_pair.second;
for (auto && el : list) {
if (new_numbering.exists(el.type, el.ghost_type)) {
el.element = new_numbering(el);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt ElementSynchronizer::sanityCheckDataSize(const Array<Element> & elements,
const SynchronizationTag & tag,
bool from_comm_desc) const {
UInt size = SynchronizerImpl<Element>::sanityCheckDataSize(elements, tag,
from_comm_desc);
// global connectivities;
size += mesh.getNbNodesPerElementList(elements) * sizeof(UInt);
// barycenters
size += (elements.size() * mesh.getSpatialDimension() * sizeof(Real));
return size;
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::packSanityCheckData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & /*tag*/) const {
for (auto && element : elements) {
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element, barycenter);
buffer << barycenter;
const auto & conns = mesh.getConnectivity(element.type, element.ghost_type);
for (auto n : arange(conns.getNbComponent())) {
buffer << mesh.getNodeGlobalId(conns(element.element, n));
}
}
}
/* -------------------------------------------------------------------------- */
void ElementSynchronizer::unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag,
UInt proc, UInt rank) const {
auto spatial_dimension = mesh.getSpatialDimension();
std::set<SynchronizationTag> skip_conn_tags{
SynchronizationTag::_smmc_facets_conn,
SynchronizationTag::_giu_global_conn};
bool is_skip_tag_conn = skip_conn_tags.find(tag) != skip_conn_tags.end();
for (auto && element : elements) {
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element, barycenter_loc);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
auto dist = barycenter_loc.distance(barycenter);
if (not Math::are_float_equal(dist, 0.)) {
AKANTU_EXCEPTION("Unpacking an unknown value for the element "
<< element << "(barycenter " << barycenter_loc
<< " != buffer " << barycenter << ") [" << dist
<< "] - tag: " << tag << " comm from " << proc << " to "
<< rank);
}
const auto & conns = mesh.getConnectivity(element.type, element.ghost_type);
Vector<UInt> global_conn(conns.getNbComponent());
Vector<UInt> local_global_conn(conns.getNbComponent());
auto is_same = true;
for (auto n : arange(global_conn.size())) {
buffer >> global_conn(n);
auto node = conns(element.element, n);
local_global_conn(n) = mesh.getNodeGlobalId(node);
is_same &= is_skip_tag_conn or mesh.isPureGhostNode(node) or
(local_global_conn(n) == global_conn(n));
}
if (not is_same) {
AKANTU_DEBUG_WARNING(
"The connectivity of the element "
<< element << " " << local_global_conn
<< " does not match the connectivity of the equivalent "
"element on proc "
<< proc << " " << global_conn << " in communication with tag "
<< tag);
}
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#if defined(AKANTU_MODULE_SAVE_)
#undef AKANTU_MODULE
#define AKANTU_MODULE AKANTU_MODULE_SAVE_
#undef AKANTU_MODULE_SAVE_
#endif
diff --git a/src/synchronizer/element_synchronizer.hh b/src/synchronizer/element_synchronizer.hh
index e772094dd..34f6e9de1 100644
--- a/src/synchronizer/element_synchronizer.hh
+++ b/src/synchronizer/element_synchronizer.hh
@@ -1,200 +1,202 @@
/**
* @file element_synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Mar 04 2020
*
* @brief Main element synchronizer
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_ELEMENT_SYNCHRONIZER_HH_
#define AKANTU_ELEMENT_SYNCHRONIZER_HH_
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "mesh_partition.hh"
#include "synchronizer_impl.hh"
namespace akantu {
class Mesh;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer : public SynchronizerImpl<Element>,
public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
ElementSynchronizer(const ElementSynchronizer & other,
const ID & id = "element_synchronizer_copy",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
public:
~ElementSynchronizer() override;
friend class ElementInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/// mesh event handler onElementsChanged
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
/// mesh event handler onRemovedElement
void onElementsRemoved(const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
protected:
/// remove elements from the synchronizer without renumbering them
void removeElements(const Array<Element> & element_to_remove);
/// renumber the elements in the synchronizer
void renumberElements(const ElementTypeMapArray<UInt> & new_numbering);
/// build processor to element correspondence
void buildElementToPrank();
protected:
/// fill the nodes type vector
void fillNodesType(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name, ElementType el_type,
const Array<UInt> & partition_num);
template <typename T>
void fillTagBufferTemplated(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
ElementType el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
void fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name, ElementType el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
/// function that handels the MeshData to be split (root side)
static void synchronizeTagsSend(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
ElementType type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the MeshData to be split (other nodes)
static void synchronizeTagsRecv(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
ElementType type,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
ElementType type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
ElementType type);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsMaster(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsSlaves(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
template <class CommunicationBuffer>
static void fillNodeGroupsFromBuffer(ElementSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer);
/// substitute elements in the send and recv arrays
void
substituteElements(const std::map<Element, Element> & old_to_new_elements);
/* ------------------------------------------------------------------------ */
/* Sanity checks */
/* ------------------------------------------------------------------------ */
UInt sanityCheckDataSize(const Array<Element> & elements,
const SynchronizationTag & tag,
bool from_comm_desc = true) const override;
void packSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/) const override;
void unpackSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Element> & /*elements*/,
const SynchronizationTag & /*tag*/, UInt /*proc*/,
UInt /*rank*/) const override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
AKANTU_GET_MACRO(ElementToRank, element_to_prank,
const ElementTypeMapArray<Int> &);
Int getRank(const Element & element) const final;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// reference to the underlying mesh
Mesh & mesh;
friend class FacetSynchronizer;
ElementTypeMapArray<Int> element_to_prank;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* AKANTU_ELEMENT_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/facet_synchronizer.cc b/src/synchronizer/facet_synchronizer.cc
index 9359a7110..e3c13d589 100644
--- a/src/synchronizer/facet_synchronizer.cc
+++ b/src/synchronizer/facet_synchronizer.cc
@@ -1,226 +1,228 @@
/**
* @file facet_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Fri Jan 26 2018
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Facet synchronizer for parallel simulations with cohesive elments
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "facet_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_MODULE)
#define AKANTU_MODULE_SAVE_ AKANTU_MODULE
#undef AKANTU_MODULE
#endif
#define AKANTU_MODULE facet_synchronizer
namespace akantu {
/* -------------------------------------------------------------------------- */
FacetSynchronizer::FacetSynchronizer(
Mesh & mesh, const ElementSynchronizer & element_synchronizer,
const ID & id)
: ElementSynchronizer(mesh, id) {
auto spatial_dimension = mesh.getSpatialDimension();
element_to_prank.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = _ghost, _with_nb_element = true,
_default_value = rank);
// Build element to prank
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(_recv)) {
auto proc = std::get<0>(scheme_pair);
const auto & scheme = std::get<1>(scheme_pair);
for (auto && elem : scheme) {
const auto & facet_to_element =
mesh.getSubelementToElement(elem.type, elem.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[elem.element];
for (UInt f = 0; f < facets.size(); ++f) {
const auto & facet = facets(f);
if (facet == ElementNull) {
continue;
}
if (facet.ghost_type == _not_ghost) {
continue;
}
auto & facet_rank = element_to_prank(facet);
if ((proc < UInt(facet_rank)) || (UInt(facet_rank) == rank)) {
facet_rank = proc;
}
}
}
}
ElementTypeMapArray<UInt> facet_global_connectivities(
"facet_global_connectivities", id);
facet_global_connectivities.initialize(
mesh, _spatial_dimension = spatial_dimension - 1, _with_nb_element = true,
_with_nb_nodes_per_element = true);
mesh.getGlobalConnectivity(facet_global_connectivities);
// \TODO perhaps a global element numbering might be useful here...
for (auto type : facet_global_connectivities.elementTypes(_spatial_dimension =
_all_dimensions,
_element_kind = _ek_not_defined, _ghost_type = _not_ghost)) {
auto & conn = facet_global_connectivities(type, _not_ghost);
auto conn_view = make_view(conn, conn.getNbComponent());
std::for_each(conn_view.begin(), conn_view.end(), [&](auto & conn) {
std::sort(conn.storage(), conn.storage() + conn.size());
});
}
/// init facet check tracking
ElementTypeMapArray<bool> facet_checked("facet_checked", id);
std::map<UInt, ElementTypeMapArray<UInt>> recv_connectivities;
/// Generate the recv scheme and connnectivities to send to the other
/// processors
for (auto && scheme_pair :
element_synchronizer.communications.iterateSchemes(_recv)) {
facet_checked.initialize(mesh, _spatial_dimension = spatial_dimension - 1,
_ghost_type = _ghost, _with_nb_element = true,
_default_value = false);
auto proc = scheme_pair.first;
const auto & elements = scheme_pair.second;
auto & facet_scheme = communications.createScheme(proc, _recv);
// this creates empty arrays...
auto & connectivities_for_proc = recv_connectivities[proc];
connectivities_for_proc.setID(
id + ":connectivities_for_proc:" + std::to_string(proc));
connectivities_for_proc.initialize(
mesh, _spatial_dimension = spatial_dimension - 1,
_with_nb_nodes_per_element = true, _ghost_type = _ghost);
// for every element in the element synchronizer communication scheme,
// check the facets to see if they should be communicated and create a
// connectivity array to match with the one other processors might send
for (auto && element : elements) {
const auto & facet_to_element =
mesh.getSubelementToElement(element.type, element.ghost_type);
Vector<Element> facets = facet_to_element.begin(
facet_to_element.getNbComponent())[element.element];
for (UInt f = 0; f < facets.size(); ++f) {
auto & facet = facets(f);
// exclude no valid facets
if (facet == ElementNull) {
continue;
}
// exclude _ghost facet from send scheme and _not_ghost from receive
if (facet.ghost_type != _ghost) {
continue;
}
// exclude facet from other processors then the one of current
// interest in case of receive scheme
if (UInt(element_to_prank(facet)) != proc) {
continue;
}
auto & checked = facet_checked(facet);
// skip already checked facets
if (checked) {
continue;
}
checked = true;
facet_scheme.push_back(facet);
auto & global_conn =
facet_global_connectivities(facet.type, facet.ghost_type);
Vector<UInt> conn =
global_conn.begin(global_conn.getNbComponent())[facet.element];
std::sort(conn.storage(), conn.storage() + conn.size());
connectivities_for_proc(facet.type, facet.ghost_type).push_back(conn);
}
}
}
std::vector<CommunicationRequest> send_requests;
/// do every communication by element type
for (auto && type : mesh.elementTypes(spatial_dimension - 1)) {
for (auto && pair : recv_connectivities) {
auto proc = std::get<0>(pair);
const auto & connectivities_for_proc = std::get<1>(pair);
auto && tag = Tag::genTag(proc, type, 1337);
send_requests.push_back(
communicator.asyncSend(connectivities_for_proc(type, _ghost), proc,
tag, CommunicationMode::_synchronous));
}
auto nb_nodes_per_facet = Mesh::getNbNodesPerElement(type);
communicator.receiveAnyNumber<UInt>(
send_requests,
[&](auto && proc, auto && message) {
auto & local_connectivities =
facet_global_connectivities(type, _not_ghost);
auto & send_scheme = communications.createScheme(proc, _send);
auto conn_view = make_view(local_connectivities, nb_nodes_per_facet);
auto conn_begin = conn_view.begin();
auto conn_end = conn_view.end();
for (const auto & c_to_match :
make_view(message, nb_nodes_per_facet)) {
auto it = std::find(conn_begin, conn_end, c_to_match);
if (it != conn_end) {
auto facet = Element{type, UInt(it - conn_begin), _not_ghost};
send_scheme.push_back(facet);
} else {
AKANTU_EXCEPTION("No local facet found to send to proc "
<< proc << " corresponding to " << c_to_match);
}
}
},
Tag::genTag(rank, type, 1337));
}
}
} // namespace akantu
#if defined(AKANTU_MODULE_SAVE_)
#undef AKANTU_MODULE
#define AKANTU_MODULE AKANTU_MODULE_SAVE_
#undef AKANTU_MODULE_SAVE_
#endif
diff --git a/src/synchronizer/facet_synchronizer.hh b/src/synchronizer/facet_synchronizer.hh
index e7beec804..19a42c195 100644
--- a/src/synchronizer/facet_synchronizer.hh
+++ b/src/synchronizer/facet_synchronizer.hh
@@ -1,95 +1,113 @@
/**
* @file facet_synchronizer.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Facet synchronizer for parallel simulations with cohesive elments
*
*
- * Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
+
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_FACET_SYNCHRONIZER_HH_
#define AKANTU_FACET_SYNCHRONIZER_HH_
namespace akantu {
class FacetSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FacetSynchronizer(Mesh & mesh,
const ElementSynchronizer & element_synchronizer,
const ID & id = "facet_synchronizer");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// update distributed synchronizer after elements' insertion
void
updateDistributedSynchronizer(ElementSynchronizer & distributed_synchronizer,
DataAccessor<Element> & data_accessor,
const Mesh & mesh_cohesive);
protected:
/// update elements list based on facets list
void updateElementList(Array<Element> * elements,
const Array<Element> * facets,
const Mesh & mesh_cohesive);
/// setup facet synchronization
void
setupFacetSynchronization(ElementSynchronizer & distributed_synchronizer);
/// build send facet arrays
void buildSendElementList(
const Array<ElementTypeMapArray<UInt> *> & send_connectivity,
const Array<ElementTypeMapArray<UInt> *> & recv_connectivity,
const Array<ElementTypeMapArray<UInt> *> & temp_send_element);
/// build recv facet arrays
void buildRecvElementList(
const Array<ElementTypeMapArray<UInt> *> & temp_recv_element);
/// get facets' global connectivity for a list of elements
template <GhostType ghost_facets>
inline void getFacetGlobalConnectivity(
const ElementSynchronizer & distributed_synchronizer,
const ElementTypeMapArray<UInt> & rank_to_facet,
const Array<Element> * elements,
Array<ElementTypeMapArray<UInt> *> & connectivity,
Array<ElementTypeMapArray<UInt> *> & facets);
/// initialize ElementTypeMap containing correspondance between
/// facets and processors
void initRankToFacet(ElementTypeMapArray<UInt> & rank_to_facet);
/// find which processor a facet is assigned to
void buildRankToFacet(ElementTypeMapArray<UInt> & rank_to_facet,
const Array<Element> * elements);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ElementTypeMapArray<UInt> facet_to_rank;
};
} // namespace akantu
#include "facet_synchronizer_inline_impl.hh"
#endif /* AKANTU_FACET_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/facet_synchronizer_inline_impl.hh b/src/synchronizer/facet_synchronizer_inline_impl.hh
index 977db56cf..0d1e221b5 100644
--- a/src/synchronizer/facet_synchronizer_inline_impl.hh
+++ b/src/synchronizer/facet_synchronizer_inline_impl.hh
@@ -1,30 +1,32 @@
/**
* @file facet_synchronizer_inline_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Tue Nov 07 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Tue Dec 04 2018
*
* @brief facet synchronizer inline implementation
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
diff --git a/src/synchronizer/grid_synchronizer.cc b/src/synchronizer/grid_synchronizer.cc
index 59d4f30d2..55316802b 100644
--- a/src/synchronizer/grid_synchronizer.cc
+++ b/src/synchronizer/grid_synchronizer.cc
@@ -1,485 +1,487 @@
/**
* @file grid_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief implementation of the grid synchronizer
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#include "aka_grid_dynamic.hh"
#include "communicator.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class E>
void GridSynchronizer::createGridSynchronizer(const SpatialGrid<E> & grid) {
AKANTU_DEBUG_IN();
const Communicator & comm = this->mesh.getCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
if (nb_proc == 1) {
return;
}
UInt spatial_dimension = this->mesh.getSpatialDimension();
BBox my_bounding_box(spatial_dimension);
const auto & lower = grid.getLowerBounds();
const auto & upper = grid.getUpperBounds();
const auto & spacing = grid.getSpacing();
my_bounding_box.getLowerBounds() = lower - spacing;
my_bounding_box.getUpperBounds() = upper + spacing;
AKANTU_DEBUG_INFO(
"Exchange of bounding box to detect the overlapping regions.");
auto && bboxes = my_bounding_box.allGather(comm);
std::vector<bool> intersects_proc(nb_proc);
std::fill(intersects_proc.begin(), intersects_proc.end(), true);
Matrix<Int> first_cells(spatial_dimension, nb_proc);
Matrix<Int> last_cells(spatial_dimension, nb_proc);
std::map<UInt, ElementTypeMapArray<UInt>> element_per_proc;
// check the overlapping between my box and the one from other processors
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank) {
continue;
}
const auto & proc_bounding_box = bboxes[p];
auto intersection = my_bounding_box.intersection(proc_bounding_box);
Vector<Int> first_cell_p = first_cells(p);
Vector<Int> last_cell_p = last_cells(p);
intersects_proc[p] = intersection;
if (intersects_proc[p]) {
for (UInt s = 0; s < spatial_dimension; ++s) {
first_cell_p(s) = grid.getCellID(intersection.getLowerBounds()(s), s);
last_cell_p(s) = grid.getCellID(intersection.getUpperBounds()(s), s);
}
}
// create the list of cells in the overlapping
using CellID = typename SpatialGrid<E>::CellID;
std::vector<CellID> cell_ids;
if (intersects_proc[p]) {
AKANTU_DEBUG_INFO("I intersects with processor " << p);
CellID cell_id(spatial_dimension);
// for (UInt i = 0; i < spatial_dimension; ++i) {
// if(first_cell_p[i] != 0) --first_cell_p[i];
// if(last_cell_p[i] != 0) ++last_cell_p[i];
// }
for (Int fd = first_cell_p(0); fd <= last_cell_p(0); ++fd) {
cell_id.setID(0, fd);
if (spatial_dimension == 1) {
cell_ids.push_back(cell_id);
} else {
for (Int sd = first_cell_p(1); sd <= last_cell_p(1); ++sd) {
cell_id.setID(1, sd);
if (spatial_dimension == 2) {
cell_ids.push_back(cell_id);
} else {
for (Int ld = first_cell_p(2); ld <= last_cell_p(2); ++ld) {
cell_id.setID(2, ld);
cell_ids.push_back(cell_id);
}
}
}
}
}
// get the list of elements in the cells of the overlapping
std::set<Element> to_send;
for (auto & cur_cell_id : cell_ids) {
auto & cell = grid.getCell(cur_cell_id);
for (auto & element : cell) {
to_send.insert(element);
}
}
AKANTU_DEBUG_INFO("I have prepared " << to_send.size()
<< " elements to send to processor "
<< p);
auto & scheme = this->getCommunications().createSendScheme(p);
std::stringstream sstr;
sstr << "element_per_proc_" << p;
element_per_proc.emplace(
std::piecewise_construct, std::forward_as_tuple(p),
std::forward_as_tuple(sstr.str(), id));
ElementTypeMapArray<UInt> & elempproc = element_per_proc[p];
for (auto elem : to_send) {
ElementType type = elem.type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
// /!\ this part must be slow due to the access in the
// ElementTypeMapArray<UInt>
if (!elempproc.exists(type, _not_ghost)) {
elempproc.alloc(0, nb_nodes_per_element, type, _not_ghost);
}
Vector<UInt> global_connect(nb_nodes_per_element);
Vector<UInt> local_connect = mesh.getConnectivity(type).begin(
nb_nodes_per_element)[elem.element];
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
global_connect(i) = mesh.getNodeGlobalId(local_connect(i));
AKANTU_DEBUG_ASSERT(
global_connect(i) < mesh.getNbGlobalNodes(),
"This global node send in the connectivity does not seem correct "
<< global_connect(i) << " corresponding to "
<< local_connect(i) << " from element " << elem.element);
}
elempproc(type).push_back(global_connect);
scheme.push_back(elem);
}
}
}
AKANTU_DEBUG_INFO("I have finished to compute intersection,"
<< " no it's time to communicate with my neighbors");
/**
* Sending loop, sends the connectivity asynchronously to all concerned proc
*/
std::vector<CommunicationRequest> isend_requests;
Tensor3<UInt> space(2, _max_element_type, nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank) {
continue;
}
if (not intersects_proc[p]) {
continue;
}
Matrix<UInt> info_proc = space(p);
auto & elempproc = element_per_proc[p];
UInt count = 0;
for (auto type : elempproc.elementTypes(_all_dimensions, _not_ghost)) {
Array<UInt> & conn = elempproc(type, _not_ghost);
Vector<UInt> info = info_proc((UInt)type);
info[0] = (UInt)type;
info[1] = conn.size() * conn.getNbComponent();
AKANTU_DEBUG_INFO(
"I have " << conn.size() << " elements of type " << type
<< " to send to processor " << p << " (communication tag : "
<< Tag::genTag(my_rank, count, DATA_TAG) << ")");
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
if (info[1] != 0) {
isend_requests.push_back(comm.asyncSend<UInt>(
conn, p, Tag::genTag(my_rank, count, DATA_TAG)));
}
++count;
}
Vector<UInt> info = info_proc((UInt)_not_defined);
info[0] = (UInt)_not_defined;
info[1] = 0;
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
}
/**
* Receives the connectivity and store them in the ghosts elements
*/
MeshAccessor mesh_accessor(mesh);
auto & global_nodes_ids = mesh_accessor.getNodesGlobalIds();
auto & nodes_type = mesh_accessor.getNodesFlags();
std::vector<CommunicationRequest> isend_nodes_requests;
Vector<UInt> nb_nodes_to_recv(nb_proc);
UInt nb_total_nodes_to_recv = 0;
UInt nb_current_nodes = global_nodes_ids.size();
NewNodesEvent new_nodes;
NewElementsEvent new_elements;
std::map<UInt, std::vector<UInt>> ask_nodes_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
nb_nodes_to_recv(p) = 0;
if (p == my_rank) {
continue;
}
if (!intersects_proc[p]) {
continue;
}
auto & scheme = this->getCommunications().createRecvScheme(p);
ask_nodes_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0));
auto & ask_nodes = ask_nodes_per_proc[p];
UInt count = 0;
ElementType type = _not_defined;
do {
Vector<UInt> info(2);
comm.receive(info, p, Tag::genTag(p, count, SIZE_TAG));
type = (ElementType)info[0];
if (type == _not_defined) {
break;
}
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = info[1] / nb_nodes_per_element;
Array<UInt> tmp_conn(nb_element, nb_nodes_per_element);
tmp_conn.zero();
if (info[1] != 0) {
comm.receive<UInt>(tmp_conn, p, Tag::genTag(p, count, DATA_TAG));
}
AKANTU_DEBUG_INFO("I will receive "
<< nb_element << " elements of type "
<< ElementType(info[0]) << " from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, count, DATA_TAG) << ")");
auto & ghost_connectivity = mesh_accessor.getConnectivity(type, _ghost);
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
UInt nb_ghost_element = ghost_connectivity.size();
Element element{type, 0, _ghost};
Vector<UInt> conn(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
UInt nb_node_to_ask_for_elem = 0;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt gn = tmp_conn(el, n);
UInt ln = global_nodes_ids.find(gn);
AKANTU_DEBUG_ASSERT(gn < mesh.getNbGlobalNodes(),
"This global node seems not correct "
<< gn << " from element " << el << " node "
<< n);
if (ln == UInt(-1)) {
global_nodes_ids.push_back(gn);
nodes_type.push_back(NodeFlag::_pure_ghost); // pure ghost node
ln = nb_current_nodes;
new_nodes.getList().push_back(ln);
++nb_current_nodes;
ask_nodes.push_back(gn);
++nb_node_to_ask_for_elem;
}
conn[n] = ln;
}
// all the nodes are already known locally, the element should
// already exists
auto c = UInt(-1);
if (nb_node_to_ask_for_elem == 0) {
c = ghost_connectivity.find(conn);
element.element = c;
}
if (c == UInt(-1)) {
element.element = nb_ghost_element;
++nb_ghost_element;
ghost_connectivity.push_back(conn);
ghost_counter.push_back(1);
new_elements.getList().push_back(element);
} else {
++ghost_counter(c);
}
scheme.push_back(element);
}
count++;
} while (type != _not_defined);
AKANTU_DEBUG_INFO("I have "
<< ask_nodes.size()
<< " missing nodes for elements coming from processor "
<< p << " (communication tag : "
<< Tag::genTag(my_rank, 0, ASK_NODES_TAG) << ")");
ask_nodes.push_back(UInt(-1));
isend_nodes_requests.push_back(
comm.asyncSend(ask_nodes, p, Tag::genTag(my_rank, 0, ASK_NODES_TAG)));
nb_nodes_to_recv(p) = ask_nodes.size() - 1;
nb_total_nodes_to_recv += nb_nodes_to_recv(p);
}
Communicator::waitAll(isend_requests);
Communicator::freeCommunicationRequest(isend_requests);
/**
* Sends requested nodes to proc
*/
auto & nodes = const_cast<Array<Real> &>(mesh.getNodes());
UInt nb_nodes = nodes.size();
std::vector<CommunicationRequest> isend_coordinates_requests;
std::map<UInt, Array<Real>> nodes_to_send_per_proc;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank || !intersects_proc[p]) {
continue;
}
Array<UInt> asked_nodes;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Waiting list of nodes to send to processor "
<< p << "(communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.probe<UInt>(p, Tag::genTag(p, 0, ASK_NODES_TAG), status);
UInt nb_nodes_to_send = status.size();
asked_nodes.resize(nb_nodes_to_send);
AKANTU_DEBUG_INFO("I have " << nb_nodes_to_send - 1
<< " nodes to send to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
AKANTU_DEBUG_INFO("Getting list of nodes to send to processor "
<< p << " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.receive(asked_nodes, p, Tag::genTag(p, 0, ASK_NODES_TAG));
nb_nodes_to_send--;
asked_nodes.resize(nb_nodes_to_send);
nodes_to_send_per_proc.emplace(std::piecewise_construct,
std::forward_as_tuple(p),
std::forward_as_tuple(0, spatial_dimension));
auto & nodes_to_send = nodes_to_send_per_proc[p];
auto node_it = nodes.begin(spatial_dimension);
for (UInt n = 0; n < nb_nodes_to_send; ++n) {
UInt ln = global_nodes_ids.find(asked_nodes(n));
AKANTU_DEBUG_ASSERT(ln != UInt(-1), "The node ["
<< asked_nodes(n)
<< "] requested by proc " << p
<< " was not found locally!");
nodes_to_send.push_back(node_it + ln);
}
if (nb_nodes_to_send != 0) {
AKANTU_DEBUG_INFO("Sending the "
<< nb_nodes_to_send << " nodes to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
isend_coordinates_requests.push_back(comm.asyncSend(
nodes_to_send, p, Tag::genTag(my_rank, 0, SEND_NODES_TAG)));
}
#if not defined(AKANTU_NDEBUG)
else {
AKANTU_DEBUG_INFO("No nodes to send to processor " << p);
}
#endif
}
Communicator::waitAll(isend_nodes_requests);
Communicator::freeCommunicationRequest(isend_nodes_requests);
nodes.resize(nb_total_nodes_to_recv + nb_nodes);
for (UInt p = 0; p < nb_proc; ++p) {
if ((p != my_rank) && (nb_nodes_to_recv(p) > 0)) {
AKANTU_DEBUG_INFO("Receiving the "
<< nb_nodes_to_recv(p) << " nodes from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
Vector<Real> nodes_to_recv(nodes.storage() + nb_nodes * spatial_dimension,
nb_nodes_to_recv(p) * spatial_dimension);
comm.receive(nodes_to_recv, p, Tag::genTag(p, 0, SEND_NODES_TAG));
nb_nodes += nb_nodes_to_recv(p);
}
#if not defined(AKANTU_NDEBUG)
else {
if (p != my_rank) {
AKANTU_DEBUG_INFO("No nodes to receive from processor " << p);
}
}
#endif
}
Communicator::waitAll(isend_coordinates_requests);
Communicator::freeCommunicationRequest(isend_coordinates_requests);
mesh.sendEvent(new_nodes);
mesh.sendEvent(new_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template void GridSynchronizer::createGridSynchronizer<IntegrationPoint>(
const SpatialGrid<IntegrationPoint> & grid);
template void GridSynchronizer::createGridSynchronizer<Element>(
const SpatialGrid<Element> & grid);
} // namespace akantu
diff --git a/src/synchronizer/grid_synchronizer.hh b/src/synchronizer/grid_synchronizer.hh
index 7a2483fe8..1be656981 100644
--- a/src/synchronizer/grid_synchronizer.hh
+++ b/src/synchronizer/grid_synchronizer.hh
@@ -1,101 +1,103 @@
/**
* @file grid_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 08 2017
*
* @brief Synchronizer based on spatial grid
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_GRID_SYNCHRONIZER_HH_
#define AKANTU_GRID_SYNCHRONIZER_HH_
namespace akantu {
class Mesh;
template <class T> class SpatialGrid;
class GridSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id = "grid_synchronizer",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register,
const ID & id = "grid_synchronizer",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~GridSynchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/**
*Create the Grid Synchronizer:
*Compute intersection and send info to neighbours that will be stored in
*ghosts elements
*/
template <typename E>
void createGridSynchronizer(const SpatialGrid<E> & grid);
protected:
/// Define the tags that will be used in the send and receive instructions
enum CommTags {
SIZE_TAG = 0,
DATA_TAG = 1,
ASK_NODES_TAG = 2,
SEND_NODES_TAG = 3
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "grid_synchronizer_tmpl.hh"
#endif /* AKANTU_GRID_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/grid_synchronizer_tmpl.hh b/src/synchronizer/grid_synchronizer_tmpl.hh
index 0eb0b1cb2..58b17773c 100644
--- a/src/synchronizer/grid_synchronizer_tmpl.hh
+++ b/src/synchronizer/grid_synchronizer_tmpl.hh
@@ -1,74 +1,76 @@
/**
* @file grid_synchronizer_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 06 2017
* @date last modification: Wed Aug 09 2017
*
* @brief implementation of the templated part of the grid syncrhonizers
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#ifndef AKANTU_GRID_SYNCHRONIZER_TMPL_HH_
#define AKANTU_GRID_SYNCHRONIZER_TMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename E>
GridSynchronizer::GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: ElementSynchronizer(mesh, id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
this->createGridSynchronizer(grid);
AKANTU_DEBUG_OUT();
}
template <typename E>
GridSynchronizer::GridSynchronizer(
Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, const ID & id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: GridSynchronizer(mesh, grid, id, register_to_event_manager,
event_priority) {
AKANTU_DEBUG_IN();
// Register the tags if any
for (const auto & tag : tags_to_register) {
synchronizer_registry.registerSynchronizer(*this, tag);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* AKANTU_GRID_SYNCHRONIZER_TMPL_HH_ */
diff --git a/src/synchronizer/master_element_info_per_processor.cc b/src/synchronizer/master_element_info_per_processor.cc
index 9df05f725..871728443 100644
--- a/src/synchronizer/master_element_info_per_processor.cc
+++ b/src/synchronizer/master_element_info_per_processor.cc
@@ -1,453 +1,455 @@
/**
* @file master_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu Nov 12 2020
*
* @brief Helper class to distribute a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "element_group.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_iterators.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
#include <tuple>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
MasterElementInfoPerProc::MasterElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root,
ElementType type, const MeshPartition & partition)
: ElementInfoPerProc(synchronizer, message_cnt, root, type),
partition(partition), all_nb_local_element(nb_proc, 0),
all_nb_ghost_element(nb_proc, 0), all_nb_element_to_send(nb_proc, 0) {
Vector<UInt> size(5);
size(0) = (UInt)type;
if (type != _not_defined) {
nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
nb_element = mesh.getNbElement(type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
this->all_nb_local_element[partition_num(el)]++;
for (auto part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part) {
this->all_nb_ghost_element[*part]++;
}
this->all_nb_element_to_send[partition_num(el)] +=
ghost_partition.getNbCols(el) + 1;
}
/// tag info
auto && tag_names = this->mesh.getTagNames(type);
this->nb_tags = tag_names.size();
size(4) = nb_tags;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
size(1) = this->all_nb_local_element[p];
size(2) = this->all_nb_ghost_element[p];
size(3) = this->all_nb_element_to_send[p];
AKANTU_DEBUG_INFO(
"Sending connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_sizes)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_sizes));
} else {
this->nb_local_element = this->all_nb_local_element[p];
this->nb_ghost_element = this->all_nb_ghost_element[p];
}
}
} else {
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending empty connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_sizes)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_sizes));
}
}
}
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizeConnectivities() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->nb_proc);
const auto & connectivities =
this->mesh.getConnectivity(this->type, _not_ghost);
/// copying the local connectivity
for (auto && part_conn :
zip(partition_num,
make_view(connectivities, this->nb_nodes_per_element))) {
auto && part = std::get<0>(part_conn);
auto && conn = std::get<1>(part_conn);
for (UInt i = 0; i < conn.size(); ++i) {
buffers[part].push_back(conn[i]);
}
}
/// copying the connectivity of ghost element
for (auto && tuple :
enumerate(make_view(connectivities, this->nb_nodes_per_element))) {
auto && el = std::get<0>(tuple);
auto && conn = std::get<1>(tuple);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part) {
UInt proc = *part;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[proc].push_back(conn[i]);
}
}
}
#ifndef AKANTU_NDEBUG
for (auto p : arange(this->nb_proc)) {
UInt size = this->nb_nodes_per_element *
(this->all_nb_local_element[p] + this->all_nb_ghost_element[p]);
AKANTU_DEBUG_ASSERT(
buffers[p].size() == size,
"The connectivity data packed in the buffer are not correct");
}
#endif
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest> requests;
for (auto p : arange(this->nb_proc)) {
if (p == this->root) {
continue;
}
auto && tag =
Tag::genTag(this->rank, this->message_count, Tag::_connectivity);
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
Array<UInt> & old_nodes = this->getNodesGlobalIds();
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh, buffers[root], all_nb_local_element[root],
all_nb_ghost_element[root], type, old_nodes);
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizePartitions() {
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->partition.getNbPartition());
/// splitting the partition information to send them to processors
Vector<UInt> count_by_proc(nb_proc, 0);
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num(el);
buffers[proc].push_back(ghost_partition.getNbCols(el));
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[proc].push_back(*part);
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part, ++i) {
buffers[*part].push_back(partition_num(el));
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
AKANTU_DEBUG_ASSERT(buffers[p].size() == (this->all_nb_ghost_element[p] +
this->all_nb_element_to_send[p]),
"Data stored in the buffer are most probably wrong");
}
#endif
std::vector<CommunicationRequest> requests;
/// last data to compute the communication scheme
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->root) {
continue;
}
auto && tag =
Tag::genTag(this->rank, this->message_count, Tag::_partitions);
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("
<< tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(buffers[this->rank]);
}
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/// tag info
auto tag_names = mesh.getTagNames(type);
// Make sure the tags are sorted (or at least not in random order),
// because they come from a map !!
std::sort(tag_names.begin(), tag_names.end());
// Sending information about the tags in mesh_data: name, data type and
// number of components of the underlying array associated to the current
// type
DynamicCommunicationBuffer mesh_data_sizes_buffer;
for (auto && tag_name : tag_names) {
mesh_data_sizes_buffer << tag_name;
mesh_data_sizes_buffer << mesh.getTypeCode(tag_name);
mesh_data_sizes_buffer << mesh.getNbComponent(tag_name, type);
}
AKANTU_DEBUG_INFO(
"Broadcasting the size of the information about the mesh data tags: ("
<< mesh_data_sizes_buffer.size() << ").");
AKANTU_DEBUG_INFO(
"Broadcasting the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer, root);
if (mesh_data_sizes_buffer.empty()) {
return;
}
// Sending the actual data to each processor
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Type code of the current tag (i.e. the tag named *names_it)
this->fillTagBuffer(buffers, tag_name);
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == root) {
continue;
}
auto && tag = Tag::genTag(this->rank, this->message_count, Tag::_mesh_data);
AKANTU_DEBUG_INFO("Sending " << buffers[p].size()
<< " bytes of mesh data to proc " << p
<< " TAG(" << tag << ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
// Loop over each tag for the current type
for (auto && tag_name : tag_names) {
// Reinitializing the mesh data on the master
this->fillMeshData(buffers[root], tag_name, mesh.getTypeCode(tag_name),
mesh.getNbComponent(tag_name, type));
}
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void MasterElementInfoPerProc::fillTagBufferTemplated(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
const auto & data = mesh.getElementalDataArray<T>(tag_name, type);
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
// Not possible to use the iterator because it potentially triggers the
// creation of complex
// type templates (such as akantu::Vector< std::vector<Element> > which don't
// implement the right interface
// (e.g. operator<< in that case).
// typename Array<T>::template const_iterator< Vector<T> > data_it =
// data.begin(data.getNbComponent());
// typename Array<T>::template const_iterator< Vector<T> > data_end =
// data.end(data.getNbComponent());
const T * data_it = data.storage();
const T * data_end = data.storage() + data.size() * data.getNbComponent();
const UInt * part = partition_num.storage();
/// copying the data, element by element
for (; data_it != data_end; ++part) {
for (UInt j(0); j < data.getNbComponent(); ++j, ++data_it) {
buffers[*part] << *data_it;
}
}
data_it = data.storage();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end;
data_it += data.getNbComponent(), ++el) {
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
for (UInt j(0); j < data.getNbComponent(); ++j) {
buffers[proc] << data_it[j];
}
}
}
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::fillTagBuffer(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
this->fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffers, \
tag_name); \
break; \
}
MeshDataTypeCode data_type_code = mesh.getTypeCode(tag_name);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
using ElementToGroup = std::vector<std::vector<std::string>>;
ElementToGroup element_to_group(nb_element);
for (auto & eg : mesh.iterateElementGroups()) {
const auto & name = eg.getName();
for (const auto & element : eg.getElements(type, _not_ghost)) {
element_to_group[element].push_back(name);
}
eg.clear(type, _not_ghost);
}
const auto & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const auto & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
/// copying the data, element by element
for (auto && pair : zip(partition_num, element_to_group)) {
buffers[std::get<0>(pair)] << std::get<1>(pair);
}
/// copying the data for the ghost element
for (auto && pair : enumerate(element_to_group)) {
auto && el = std::get<0>(pair);
auto it = ghost_partition.begin(el);
auto end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
buffers[proc] << std::get<1>(pair);
}
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->rank) {
continue;
}
auto && tag = Tag::genTag(this->rank, p, Tag::_element_group);
AKANTU_DEBUG_INFO("Sending element groups to proc " << p << " TAG(" << tag
<< ")");
requests.push_back(comm.asyncSend(buffers[p], p, tag));
}
this->fillElementGroupsFromBuffer(buffers[this->rank]);
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/mpi_communicator_data.hh b/src/synchronizer/mpi_communicator_data.hh
index 571d5d3e3..756ce87d8 100644
--- a/src/synchronizer/mpi_communicator_data.hh
+++ b/src/synchronizer/mpi_communicator_data.hh
@@ -1,139 +1,142 @@
/**
* @file mpi_communicator_data.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
- * @date last modification: Mon Feb 05 2018
+ * @date last modification: Tue Jun 16 2020
*
* @brief Wrapper on MPI types to have a better separation between libraries
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wliteral-suffix"
#endif
#endif
#include <mpi.h>
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic pop
#endif
#endif
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_MPI_TYPE_WRAPPER_HH_
#define AKANTU_MPI_TYPE_WRAPPER_HH_
namespace akantu {
class MPICommunicatorData : public CommunicatorInternalData {
public:
MPICommunicatorData() {
MPI_Initialized(&is_externaly_initialized);
if (is_externaly_initialized == 0) {
MPI_Init(nullptr, nullptr); // valid according to the spec
}
MPI_Comm_create_errhandler(MPICommunicatorData::errorHandler,
&error_handler);
MPI_Comm_set_errhandler(MPI_COMM_WORLD, error_handler);
setMPICommunicator(MPI_COMM_WORLD);
}
~MPICommunicatorData() override {
if (is_externaly_initialized == 0) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
MPI_Errhandler_free(&error_handler);
MPI_Finalize();
}
}
inline void setMPICommunicator(MPI_Comm comm) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
communicator = comm;
MPI_Comm_get_errhandler(comm, &save_error_handler);
MPI_Comm_set_errhandler(comm, error_handler);
}
inline int rank() const {
int prank;
MPI_Comm_rank(communicator, &prank);
return prank;
}
inline int size() const {
int psize;
MPI_Comm_size(communicator, &psize);
return psize;
}
inline MPI_Comm getMPICommunicator() const { return communicator; }
static int getMaxTag() {
int flag;
int * value;
// not defined on derived intra-communicator
MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_TAG_UB, &value, &flag);
AKANTU_DEBUG_ASSERT(flag, "No attribute MPI_TAG_UB.");
return *value;
}
private:
MPI_Comm communicator{MPI_COMM_WORLD};
MPI_Errhandler save_error_handler{MPI_ERRORS_ARE_FATAL};
static int is_externaly_initialized;
/* ------------------------------------------------------------------------ */
MPI_Errhandler error_handler;
static void
errorHandler(MPI_Comm * /*comm*/,
int * error_code, // NOLINT(readability-non-const-parameter)
...) {
char error_string[MPI_MAX_ERROR_STRING];
int str_len;
MPI_Error_string(*error_code, error_string, &str_len);
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"MPI failed with the error code "
<< *error_code << ": \"" << error_string
<< "\"");
}
};
} // namespace akantu
#endif /* AKANTU_MPI_TYPE_WRAPPER_HH_ */
diff --git a/src/synchronizer/node_info_per_processor.cc b/src/synchronizer/node_info_per_processor.cc
index eeee66941..cd4f62d73 100644
--- a/src/synchronizer/node_info_per_processor.cc
+++ b/src/synchronizer/node_info_per_processor.cc
@@ -1,846 +1,848 @@
/**
* @file node_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Please type the brief for file: Helper classes to create the
* distributed synchronizer and distribute a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_info_per_processor.hh"
#include "communicator.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeInfoPerProc::NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
comm(synchronizer.getCommunicator()), rank(comm.whoAmI()),
nb_proc(comm.getNbProc()), root(root), mesh(synchronizer.getMesh()),
spatial_dimension(synchronizer.getMesh().getSpatialDimension()),
message_count(message_cnt) {}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::synchronize() {
synchronizeNodes();
synchronizeTypes();
synchronizeGroups();
synchronizePeriodicity();
synchronizeTags();
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void NodeInfoPerProc::fillNodeGroupsFromBuffer(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector<std::vector<std::string>> node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const auto & global_nodes = mesh.getGlobalNodesIds();
for (auto && data : enumerate(global_nodes)) {
for (const auto & node : node_to_group[std::get<1>(data)]) {
mesh.getNodeGroup(node).add(std::get<0>(data), false);
}
}
for (auto && ng_data : mesh.iterateNodeGroups()) {
ng_data.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodesType() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
auto & nodes_flags = this->getNodesFlags();
Array<UInt> nodes_set(nb_nodes);
nodes_set.set(0);
enum NodeSet {
NORMAL_SET = 1,
GHOST_SET = 2,
};
Array<bool> already_seen(nb_nodes, 1, false);
for (auto gt : ghost_types) {
UInt set = NORMAL_SET;
if (gt == _ghost) {
set = GHOST_SET;
}
already_seen.set(false);
for (auto && type :
mesh.elementTypes(_all_dimensions, gt, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, gt);
for (const auto & conn :
make_view(connectivity, connectivity.getNbComponent())) {
for (UInt n = 0; n < conn.size(); ++n) {
AKANTU_DEBUG_ASSERT(conn(n) < nb_nodes,
"Node " << conn(n)
<< " bigger than number of nodes "
<< nb_nodes);
if (!already_seen(conn(n))) {
nodes_set(conn(n)) += set;
already_seen(conn(n)) = true;
}
}
}
}
}
nodes_flags.resize(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
if (nodes_set(i) == NORMAL_SET) {
nodes_flags(i) = NodeFlag::_normal;
} else if (nodes_set(i) == GHOST_SET) {
nodes_flags(i) = NodeFlag::_pure_ghost;
} else if (nodes_set(i) == (GHOST_SET + NORMAL_SET)) {
nodes_flags(i) = NodeFlag::_master;
} else {
AKANTU_EXCEPTION("Gni ?");
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillCommunicationScheme(const Array<UInt> & master_info) {
AKANTU_DEBUG_IN();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
{ // send schemes
std::map<UInt, Array<UInt>> send_array_per_proc;
for (const auto & send_info : make_view(master_info, 2)) {
send_array_per_proc[send_info(0)].push_back(send_info(1));
}
for (auto & send_schemes : send_array_per_proc) {
auto & scheme = communications.createSendScheme(send_schemes.first);
auto & sends = send_schemes.second;
std::sort(sends.begin(), sends.end());
std::transform(sends.begin(), sends.end(), sends.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(sends);
AKANTU_DEBUG_INFO("Proc " << rank << " has " << sends.size()
<< " nodes to send to to proc "
<< send_schemes.first);
}
}
{ // receive schemes
std::map<UInt, Array<UInt>> recv_array_per_proc;
for (auto node : arange(mesh.getNbNodes())) {
if (mesh.isSlaveNode(node)) {
recv_array_per_proc[mesh.getNodePrank(node)].push_back(
mesh.getNodeGlobalId(node));
}
}
for (auto & recv_schemes : recv_array_per_proc) {
auto & scheme = communications.createRecvScheme(recv_schemes.first);
auto & recvs = recv_schemes.second;
std::sort(recvs.begin(), recvs.end());
std::transform(recvs.begin(), recvs.end(), recvs.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(recvs);
AKANTU_DEBUG_INFO("Proc " << rank << " will receive " << recvs.size()
<< " nodes from proc " << recv_schemes.first);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillPeriodicPairs(const Array<UInt> & global_pairs,
std::vector<UInt> & missing_nodes) {
this->wipePeriodicInfo();
auto & nodes_flags = this->getNodesFlags();
auto checkIsLocal = [&](auto && global_node) {
auto && node = mesh.getNodeLocalId(global_node);
if (node == UInt(-1)) {
auto & global_nodes = this->getNodesGlobalIds();
node = global_nodes.size();
global_nodes.push_back(global_node);
nodes_flags.push_back(NodeFlag::_pure_ghost);
missing_nodes.push_back(global_node);
std::cout << "Missing node " << node << std::endl;
}
return node;
};
for (auto && pairs : make_view(global_pairs, 2)) {
UInt slave = checkIsLocal(pairs(0));
UInt master = checkIsLocal(pairs(1));
this->addPeriodicSlave(slave, master);
}
this->markMeshPeriodic();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::receiveMissingPeriodic(
DynamicCommunicationBuffer & buffer) {
auto & nodes = this->getNodes();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
std::size_t nb_nodes;
buffer >> nb_nodes;
for (auto _ [[gnu::unused]] : arange(nb_nodes)) {
Vector<Real> pos(spatial_dimension);
Int prank;
buffer >> pos;
buffer >> prank;
UInt node = nodes.size();
this->setNodePrank(node, prank);
nodes.push_back(pos);
auto & scheme = communications.createRecvScheme(prank);
scheme.push_back(node);
}
while (buffer.getLeftToUnpack() != 0) {
Int prank;
UInt gnode;
buffer >> gnode;
buffer >> prank;
auto node = mesh.getNodeLocalId(gnode);
AKANTU_DEBUG_ASSERT(node != UInt(-1),
"I cannot send the node "
<< gnode << " to proc " << prank
<< " because it is note a local node");
auto & scheme = communications.createSendScheme(prank);
scheme.push_back(node);
}
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodalData(DynamicCommunicationBuffer & buffer,
const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, _, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
auto & nodal_data = \
mesh.getNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(tag_name); \
nodal_data.resize(mesh.getNbNodes()); \
for (auto && data : make_view(nodal_data)) { \
buffer >> data; \
} \
break; \
}
MeshDataTypeCode data_type_code =
mesh.getTypeCode(tag_name, MeshDataType::_nodal);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MasterNodeInfoPerProc::MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root),
all_nodes(0, synchronizer.getMesh().getSpatialDimension()) {
UInt nb_global_nodes = this->mesh.getNbGlobalNodes();
this->comm.broadcast(nb_global_nodes, this->root);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeNodes() {
this->nodes_per_proc.resize(nb_proc);
this->nb_nodes_per_proc.resize(nb_proc);
Array<Real> local_nodes(0, spatial_dimension);
Array<Real> & nodes = this->getNodes();
all_nodes.copy(nodes);
nodes_pranks.resize(nodes.size(), UInt(-1));
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
Array<Real> * nodes_to_send{nullptr};
Array<UInt> & nodespp = nodes_per_proc[p];
if (p != root) {
nodes_to_send = new Array<Real>(0, spatial_dimension);
AKANTU_DEBUG_INFO("Receiving number of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_nb_nodes));
comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_nb_nodes));
nodespp.resize(nb_nodes);
this->nb_nodes_per_proc(p) = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_nodes));
comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_nodes));
} else {
Array<UInt> & local_ids = this->getNodesGlobalIds();
this->nb_nodes_per_proc(p) = local_ids.size();
nodespp.copy(local_ids);
nodes_to_send = &local_nodes;
}
/// get the coordinates for the selected nodes
for (const auto & node : nodespp) {
Vector<Real> coord(nodes.storage() + spatial_dimension * node,
spatial_dimension);
nodes_to_send->push_back(coord);
}
if (p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_coordinates));
comm.send(*nodes_to_send, p,
Tag::genTag(this->rank, 0, Tag::_coordinates));
delete nodes_to_send;
}
}
/// construct the local nodes coordinates
nodes.copy(local_nodes);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTypes() {
// <global_id, <proc, local_id> >
std::multimap<UInt, std::pair<UInt, UInt>> nodes_to_proc;
std::vector<Array<NodeFlag>> nodes_flags_per_proc(nb_proc);
std::vector<Array<Int>> nodes_prank_per_proc(nb_proc);
if (mesh.isPeriodic()) {
all_periodic_flags.copy(this->getNodesFlags());
}
// arrays containing pairs of (proc, node)
std::vector<Array<UInt>> nodes_to_send_per_proc(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
nodes_flags_per_proc[p].resize(nb_nodes_per_proc(p), NodeFlag(0xFF));
nodes_prank_per_proc[p].resize(nb_nodes_per_proc(p), -1);
}
this->fillNodesType();
auto is_master = [](auto && flag) {
return (flag & NodeFlag::_shared_mask) == NodeFlag::_master;
};
auto is_local = [](auto && flag) {
return (flag & NodeFlag::_shared_mask) == NodeFlag::_normal;
};
for (auto p : arange(nb_proc)) {
auto & nodes_flags = nodes_flags_per_proc[p];
if (p != root) {
AKANTU_DEBUG_INFO(
"Receiving first nodes types from proc "
<< p << " "
<< Tag::genTag(this->rank, this->message_count, Tag::_nodes_type));
comm.receive(nodes_flags, p, Tag::genTag(p, 0, Tag::_nodes_type));
} else {
nodes_flags.copy(this->getNodesFlags());
}
// stack all processors claiming to be master for a node
for (auto local_node : arange(nb_nodes_per_proc(p))) {
auto global_node = nodes_per_proc[p](local_node);
if (is_master(nodes_flags(local_node))) {
nodes_to_proc.insert(
std::make_pair(global_node, std::make_pair(p, local_node)));
} else if (is_local(nodes_flags(local_node))) {
nodes_pranks[global_node] = p;
}
}
}
for (auto i : arange(mesh.getNbGlobalNodes())) {
auto it_range = nodes_to_proc.equal_range(i);
if (it_range.first == nodes_to_proc.end() || it_range.first->first != i) {
continue;
}
// pick the first processor out of the multi-map as the actual master
UInt master_proc = (it_range.first)->second.first;
nodes_pranks[i] = master_proc;
for (auto && data : range(it_range.first, it_range.second)) {
auto proc = data.second.first;
auto node = data.second.second;
if (proc != master_proc) {
// store the info on all the slaves for a given master
nodes_flags_per_proc[proc](node) = NodeFlag::_slave;
nodes_to_send_per_proc[master_proc].push_back(proc);
nodes_to_send_per_proc[master_proc].push_back(i);
}
}
}
/// Fills the nodes prank per proc
for (auto && data : zip(arange(nb_proc), nodes_per_proc, nodes_prank_per_proc,
nodes_flags_per_proc)) {
for (auto && node_data :
zip(std::get<1>(data), std::get<2>(data), std::get<3>(data))) {
if (std::get<2>(node_data) == NodeFlag::_normal) {
std::get<1>(node_data) = std::get<0>(data);
} else {
std::get<1>(node_data) = nodes_pranks(std::get<0>(node_data));
}
}
}
std::vector<CommunicationRequest> requests_send_type;
std::vector<CommunicationRequest> requests_send_master_info;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
auto tag0 = Tag::genTag(this->rank, 0, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes types to proc " << p << " " << tag0);
requests_send_type.push_back(
comm.asyncSend(nodes_flags_per_proc[p], p, tag0));
auto tag2 = Tag::genTag(this->rank, 2, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes pranks to proc " << p << " " << tag2);
requests_send_type.push_back(
comm.asyncSend(nodes_prank_per_proc[p], p, tag2));
auto & nodes_to_send = nodes_to_send_per_proc[p];
auto tag1 = Tag::genTag(this->rank, 1, Tag::_nodes_type);
AKANTU_DEBUG_INFO("Sending nodes master info to proc " << p << " "
<< tag1);
requests_send_master_info.push_back(
comm.asyncSend(nodes_to_send, p, tag1));
} else {
this->getNodesFlags().copy(nodes_flags_per_proc[p]);
for (auto && data : enumerate(nodes_prank_per_proc[p])) {
auto node = std::get<0>(data);
if (not(mesh.isMasterNode(node) or mesh.isLocalNode(node))) {
this->setNodePrank(node, std::get<1>(data));
}
}
this->fillCommunicationScheme(nodes_to_send_per_proc[root]);
}
}
Communicator::waitAll(requests_send_type);
Communicator::freeCommunicationRequest(requests_send_type);
Communicator::waitAll(requests_send_master_info);
Communicator::freeCommunicationRequest(requests_send_master_info);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
using NodeToGroup = std::vector<std::vector<std::string>>;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
for (auto & ng : mesh.iterateNodeGroups()) {
std::string name = ng.getName();
for (auto && node : ng.getNodes()) {
node_to_group[node].push_back(name);
}
ng.clear();
}
buffer << node_to_group;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == this->rank) {
continue;
}
AKANTU_DEBUG_INFO("Sending node groups to proc "
<< p << " "
<< Tag::genTag(this->rank, p, Tag::_node_group));
requests.push_back(comm.asyncSend(
buffer, p, Tag::genTag(this->rank, p, Tag::_node_group)));
}
this->fillNodeGroupsFromBuffer(buffer);
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizePeriodicity() {
bool is_periodic = mesh.isPeriodic();
comm.broadcast(is_periodic, root);
if (not is_periodic) {
return;
}
std::vector<CommunicationRequest> requests;
std::vector<Array<UInt>> periodic_info_to_send_per_proc;
for (auto p : arange(nb_proc)) {
periodic_info_to_send_per_proc.emplace_back(0, 2);
auto && periodic_info = periodic_info_to_send_per_proc.back();
for (UInt proc_local_node : arange(nb_nodes_per_proc(p))) {
UInt global_node = nodes_per_proc[p](proc_local_node);
if ((all_periodic_flags[global_node] & NodeFlag::_periodic_mask) ==
NodeFlag::_periodic_slave) {
periodic_info.push_back(
Vector<UInt>{global_node, mesh.getPeriodicMaster(global_node)});
}
}
if (p == root) {
continue;
}
auto && tag = Tag::genTag(this->rank, p, Tag::_periodic_slaves);
AKANTU_DEBUG_INFO("Sending periodic info to proc " << p << " " << tag);
requests.push_back(comm.asyncSend(periodic_info, p, tag));
}
CommunicationStatus status;
std::vector<DynamicCommunicationBuffer> buffers(nb_proc);
std::vector<std::vector<UInt>> proc_missings(nb_proc);
auto nodes_it = all_nodes.begin(spatial_dimension);
for (UInt p = 0; p < nb_proc; ++p) {
auto & proc_missing = proc_missings[p];
if (p != root) {
auto && tag = Tag::genTag(p, 0, Tag::_periodic_nodes);
comm.probe<UInt>(p, tag, status);
proc_missing.resize(status.size());
comm.receive(proc_missing, p, tag);
} else {
fillPeriodicPairs(periodic_info_to_send_per_proc[root], proc_missing);
}
auto & buffer = buffers[p];
buffer.reserve((spatial_dimension * sizeof(Real) + sizeof(Int)) *
proc_missing.size());
buffer << proc_missing.size();
for (auto && node : proc_missing) {
buffer << *(nodes_it + node);
buffer << nodes_pranks(node);
}
}
for (UInt p = 0; p < nb_proc; ++p) {
for (auto && node : proc_missings[p]) {
auto & buffer = buffers[nodes_pranks(node)];
buffer << node;
buffer << p;
}
}
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
auto && tag_send = Tag::genTag(p, 1, Tag::_periodic_nodes);
requests.push_back(comm.asyncSend(buffers[p], p, tag_send));
} else {
receiveMissingPeriodic(buffers[p]);
}
}
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::fillTagBuffers(
std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, _, elem) \
case MeshDataTypeCode::BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
auto & nodal_data = \
mesh.getNodalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(tag_name); \
for (auto && data : enumerate(nodes_per_proc)) { \
auto proc = std::get<0>(data); \
auto & nodes = std::get<1>(data); \
auto & buffer = buffers[proc]; \
for (auto & node : nodes) { \
for (auto i : arange(nodal_data.getNbComponent())) { \
buffer << nodal_data(node, i); \
} \
} \
} \
break; \
}
MeshDataTypeCode data_type_code =
mesh.getTypeCode(tag_name, MeshDataType::_nodal);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
} // namespace akantu
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTags() {
/// tag info
auto tag_names = mesh.getTagNames();
DynamicCommunicationBuffer tags_buffer;
for (auto && tag_name : tag_names) {
tags_buffer << tag_name;
tags_buffer << mesh.getTypeCode(tag_name, MeshDataType::_nodal);
tags_buffer << mesh.getNbComponent(tag_name);
}
AKANTU_DEBUG_INFO(
"Broadcasting the information about the nodes mesh data tags: ("
<< tags_buffer.size() << ").");
comm.broadcast(tags_buffer, root);
for (auto && tag_data : enumerate(tag_names)) {
auto tag_count = std::get<0>(tag_data);
auto & tag_name = std::get<1>(tag_data);
std::vector<DynamicCommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
buffers.resize(nb_proc);
fillTagBuffers(buffers, tag_name);
for (auto && data : enumerate(buffers)) {
auto && proc = std::get<0>(data);
auto & buffer = std::get<1>(data);
if (proc == root) {
fillNodalData(buffer, tag_name);
} else {
auto && tag = Tag::genTag(this->rank, tag_count, Tag::_mesh_data);
requests.push_back(comm.asyncSend(buffer, proc, tag));
}
}
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
}
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
SlaveNodeInfoPerProc::SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = 0;
comm.broadcast(nb_global_nodes, root);
this->setNbGlobalNodes(nb_global_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeNodes() {
AKANTU_DEBUG_INFO("Sending list of nodes to proc "
<< root << " " << Tag::genTag(this->rank, 0, Tag::_nb_nodes)
<< " " << Tag::genTag(this->rank, 0, Tag::_nodes));
Array<UInt> & local_ids = this->getNodesGlobalIds();
Array<Real> & nodes = this->getNodes();
UInt nb_nodes = local_ids.size();
comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_nb_nodes));
comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_nodes));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes.resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_coordinates));
comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_coordinates));
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTypes() {
this->fillNodesType();
auto & nodes_flags = this->getNodesFlags();
AKANTU_DEBUG_INFO("Sending first nodes types to proc "
<< root << ""
<< Tag::genTag(this->rank, 0, Tag::_nodes_type));
comm.send(nodes_flags, root, Tag::genTag(this->rank, 0, Tag::_nodes_type));
AKANTU_DEBUG_INFO("Receiving nodes types from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_nodes_type));
comm.receive(nodes_flags, root, Tag::genTag(root, 0, Tag::_nodes_type));
Array<Int> nodes_prank(nodes_flags.size());
AKANTU_DEBUG_INFO("Receiving nodes pranks from proc "
<< root << " " << Tag::genTag(root, 2, Tag::_nodes_type));
comm.receive(nodes_prank, root, Tag::genTag(root, 2, Tag::_nodes_type));
for (auto && data : enumerate(nodes_prank)) {
auto node = std::get<0>(data);
if (not(mesh.isMasterNode(node) or mesh.isLocalNode(node))) {
this->setNodePrank(node, std::get<1>(data));
}
}
AKANTU_DEBUG_INFO("Receiving nodes master info from proc "
<< root << " " << Tag::genTag(root, 1, Tag::_nodes_type));
CommunicationStatus status;
comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_nodes_type), status);
Array<UInt> nodes_master_info(status.size());
comm.receive(nodes_master_info, root, Tag::genTag(root, 1, Tag::_nodes_type));
this->fillCommunicationScheme(nodes_master_info);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Receiving node groups from proc "
<< root << " "
<< Tag::genTag(root, this->rank, Tag::_node_group));
DynamicCommunicationBuffer buffer;
comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_node_group));
this->fillNodeGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizePeriodicity() {
bool is_periodic;
comm.broadcast(is_periodic, root);
if (not is_periodic) {
return;
}
CommunicationStatus status;
auto && tag = Tag::genTag(root, this->rank, Tag::_periodic_slaves);
comm.probe<UInt>(root, tag, status);
Array<UInt> periodic_info(status.size() / 2, 2);
comm.receive(periodic_info, root, tag);
std::vector<UInt> proc_missing;
fillPeriodicPairs(periodic_info, proc_missing);
auto && tag_missing_request =
Tag::genTag(this->rank, 0, Tag::_periodic_nodes);
comm.send(proc_missing, root, tag_missing_request);
DynamicCommunicationBuffer buffer;
auto && tag_missing = Tag::genTag(this->rank, 1, Tag::_periodic_nodes);
comm.receive(buffer, root, tag_missing);
receiveMissingPeriodic(buffer);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTags() {
DynamicCommunicationBuffer tags_buffer;
comm.broadcast(tags_buffer, root);
std::vector<std::string> tag_names;
while (tags_buffer.getLeftToUnpack() > 0) {
std::string name;
MeshDataTypeCode code;
UInt nb_components;
tags_buffer >> name;
tags_buffer >> code;
tags_buffer >> nb_components;
mesh.registerNodalData(name, nb_components, code);
tag_names.push_back(name);
}
for (auto && tag_data : enumerate(tag_names)) {
auto tag_count = std::get<0>(tag_data);
auto & tag_name = std::get<1>(tag_data);
DynamicCommunicationBuffer buffer;
auto && tag = Tag::genTag(this->root, tag_count, Tag::_mesh_data);
comm.receive(buffer, this->root, tag);
fillNodalData(buffer, tag_name);
}
}
} // namespace akantu
diff --git a/src/synchronizer/node_info_per_processor.hh b/src/synchronizer/node_info_per_processor.hh
index b548a9a1b..1b51003ef 100644
--- a/src/synchronizer/node_info_per_processor.hh
+++ b/src/synchronizer/node_info_per_processor.hh
@@ -1,128 +1,130 @@
/**
* @file node_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communication_buffer.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NODE_INFO_PER_PROCESSOR_HH_
#define AKANTU_NODE_INFO_PER_PROCESSOR_HH_
namespace akantu {
class NodeSynchronizer;
class Communicator;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
class NodeInfoPerProc : protected MeshAccessor {
public:
NodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt, UInt root);
void synchronize();
protected:
virtual void synchronizeNodes() = 0;
virtual void synchronizeTypes() = 0;
virtual void synchronizeGroups() = 0;
virtual void synchronizePeriodicity() = 0;
virtual void synchronizeTags() = 0;
protected:
template <class CommunicationBuffer>
void fillNodeGroupsFromBuffer(CommunicationBuffer & buffer);
void fillNodesType();
void fillCommunicationScheme(const Array<UInt> & /*master_info*/);
void fillNodalData(DynamicCommunicationBuffer & buffer,
const std::string & tag_name);
void fillPeriodicPairs(const Array<UInt> & /*global_pairs*/,
std::vector<UInt> & /*missing_nodes*/);
void receiveMissingPeriodic(DynamicCommunicationBuffer & /*buffer*/);
protected:
NodeSynchronizer & synchronizer;
const Communicator & comm;
UInt rank;
UInt nb_proc;
UInt root;
Mesh & mesh;
UInt spatial_dimension;
UInt message_count;
};
/* -------------------------------------------------------------------------- */
class MasterNodeInfoPerProc : public NodeInfoPerProc {
public:
MasterNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
void synchronizePeriodicity() override;
void synchronizeTags() override;
private:
void fillTagBuffers(std::vector<DynamicCommunicationBuffer> & buffers,
const std::string & tag_name);
/// get the list of nodes to send and send them
std::vector<Array<UInt>> nodes_per_proc;
Array<UInt> nb_nodes_per_proc;
Array<Real> all_nodes;
Array<NodeFlag> all_periodic_flags;
Array<Int> nodes_pranks;
};
/* -------------------------------------------------------------------------- */
class SlaveNodeInfoPerProc : public NodeInfoPerProc {
public:
SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeNodes() override;
void synchronizeTypes() override;
void synchronizeGroups() override;
void synchronizePeriodicity() override;
void synchronizeTags() override;
private:
};
} // namespace akantu
#endif /* AKANTU_NODE_INFO_PER_PROCESSOR_HH_ */
diff --git a/src/synchronizer/node_synchronizer.cc b/src/synchronizer/node_synchronizer.cc
index 4f873197f..874c54d55 100644
--- a/src/synchronizer/node_synchronizer.cc
+++ b/src/synchronizer/node_synchronizer.cc
@@ -1,246 +1,248 @@
/**
* @file node_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Wed Nov 15 2017
+ * @date last modification: Wed Dec 09 2020
*
* @brief Implementation of the node synchronizer
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
NodeSynchronizer::NodeSynchronizer(Mesh & mesh, const ID & id,
const bool register_to_event_manager,
EventHandlerPriority event_priority)
: SynchronizerImpl<UInt>(mesh.getCommunicator(), id),
mesh(mesh) {
AKANTU_DEBUG_IN();
if (register_to_event_manager) {
this->mesh.registerEventHandler(*this, event_priority);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NodeSynchronizer::~NodeSynchronizer() = default;
/* -------------------------------------------------------------------------- */
Int NodeSynchronizer::getRank(const UInt & node) const {
return this->mesh.getNodePrank(node);
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::onNodesAdded(const Array<UInt> & /*nodes_list*/,
const NewNodesEvent & /*unused*/) {
std::map<UInt, std::vector<UInt>> nodes_per_proc;
// recreates fully the schemes due to changes of global ids
// \TODO add an event to handle global id changes
for (auto && data : communications.iterateSchemes(_recv)) {
auto & scheme = data.second;
scheme.resize(0);
}
for (auto && local_id : arange(mesh.getNbNodes())) {
if (not mesh.isSlaveNode(local_id)) {
continue; // local, master or pure ghost
}
auto global_id = mesh.getNodeGlobalId(local_id);
auto proc = mesh.getNodePrank(local_id);
AKANTU_DEBUG_ASSERT(
proc != -1,
"The node " << local_id << " does not have a valid associated prank");
nodes_per_proc[proc].push_back(global_id);
auto & scheme = communications.createScheme(proc, _recv);
scheme.push_back(local_id);
}
std::vector<CommunicationRequest> send_requests;
for (auto && pair : communications.iterateSchemes(_recv)) {
auto proc = pair.first;
AKANTU_DEBUG_ASSERT(proc != UInt(-1),
"For real I should send something to proc -1");
// if proc not in nodes_per_proc this should insert an empty array to send
send_requests.push_back(communicator.asyncSend(
nodes_per_proc[proc], proc, Tag::genTag(rank, proc, 0xcafe)));
}
for (auto && data : communications.iterateSchemes(_send)) {
auto proc = data.first;
auto & scheme = data.second;
CommunicationStatus status;
auto tag = Tag::genTag(proc, rank, 0xcafe);
communicator.probe<UInt>(proc, tag, status);
scheme.resize(status.size());
communicator.receive(scheme, proc, tag);
std::transform(scheme.begin(), scheme.end(), scheme.begin(),
[&](auto & gnode) { return mesh.getNodeLocalId(gnode); });
}
// communicator.receiveAnyNumber<UInt>(
// send_requests,
// [&](auto && proc, auto && nodes) {
// auto & scheme = communications.createScheme(proc, _send);
// scheme.resize(nodes.size());
// for (auto && data : enumerate(nodes)) {
// auto global_id = std::get<1>(data);
// auto local_id = mesh.getNodeLocalId(global_id);
// AKANTU_DEBUG_ASSERT(local_id != UInt(-1),
// "The global node " << global_id
// << "is not known on rank "
// << rank);
// scheme[std::get<0>(data)] = local_id;
// }
// },
// Tag::genTag(rank, count, 0xcafe));
// ++count;
Communicator::waitAll(send_requests);
Communicator::freeCommunicationRequest(send_requests);
this->entities_changed = true;
}
/* -------------------------------------------------------------------------- */
UInt NodeSynchronizer::sanityCheckDataSize(const Array<UInt> & nodes,
const SynchronizationTag & tag,
bool from_comm_desc) const {
UInt size =
SynchronizerImpl<UInt>::sanityCheckDataSize(nodes, tag, from_comm_desc);
// global id
if (tag != SynchronizationTag::_giu_global_conn) {
size += sizeof(UInt) * nodes.size();
}
// flag
size += sizeof(NodeFlag) * nodes.size();
// positions
size += mesh.getSpatialDimension() * sizeof(Real) * nodes.size();
return size;
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::packSanityCheckData(
CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag & tag) const {
auto dim = mesh.getSpatialDimension();
for (auto && node : nodes) {
if (tag != SynchronizationTag::_giu_global_conn) {
buffer << mesh.getNodeGlobalId(node);
}
buffer << mesh.getNodeFlag(node);
buffer << Vector<Real>(mesh.getNodes().begin(dim)[node]);
}
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & tag,
UInt proc, UInt rank) const {
auto dim = mesh.getSpatialDimension();
#ifndef AKANTU_NDEBUG
auto periodic = [&](auto && flag) { return flag & NodeFlag::_periodic_mask; };
auto distrib = [&](auto && flag) { return flag & NodeFlag::_shared_mask; };
#endif
for (auto && node : nodes) {
if (tag != SynchronizationTag::_giu_global_conn) {
UInt global_id;
buffer >> global_id;
AKANTU_DEBUG_ASSERT(global_id == mesh.getNodeGlobalId(node),
"The nodes global ids do not match: "
<< global_id
<< " != " << mesh.getNodeGlobalId(node));
}
NodeFlag flag;
buffer >> flag;
AKANTU_DEBUG_ASSERT(
(periodic(flag) == periodic(mesh.getNodeFlag(node))) and
(((distrib(flag) == NodeFlag::_master) and
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_slave)) or // master to slave
((distrib(flag) == NodeFlag::_slave) and
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_master)) or // reverse comm slave to master
(distrib(mesh.getNodeFlag(node)) ==
NodeFlag::_pure_ghost or // pure ghost nodes
distrib(flag) == NodeFlag::_pure_ghost)),
"The node flags: " << flag << " and " << mesh.getNodeFlag(node));
Vector<Real> pos_remote(dim);
buffer >> pos_remote;
Vector<Real> pos(mesh.getNodes().begin(dim)[node]);
auto dist = pos_remote.distance(pos);
if (not Math::are_float_equal(dist, 0.)) {
AKANTU_EXCEPTION("Unpacking an unknown value for the node "
<< node << "(position " << pos << " != buffer "
<< pos_remote << ") [" << dist << "] - tag: " << tag
<< " comm from " << proc << " to " << rank);
}
}
}
/* -------------------------------------------------------------------------- */
void NodeSynchronizer::fillEntityToSend(Array<UInt> & nodes_to_send) {
UInt nb_nodes = mesh.getNbNodes();
this->entities_from_root.clear();
nodes_to_send.resize(0);
for (UInt n : arange(nb_nodes)) {
if (not mesh.isLocalOrMasterNode(n)) {
continue;
}
entities_from_root.push_back(n);
}
for (auto n : entities_from_root) {
UInt global_node = mesh.getNodeGlobalId(n);
nodes_to_send.push_back(global_node);
}
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/node_synchronizer.hh b/src/synchronizer/node_synchronizer.hh
index 04efb149e..b85d1d246 100644
--- a/src/synchronizer/node_synchronizer.hh
+++ b/src/synchronizer/node_synchronizer.hh
@@ -1,112 +1,114 @@
/**
* @file node_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue Nov 08 2016
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Wed Mar 04 2020
*
* @brief Synchronizer for nodal information
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NODE_SYNCHRONIZER_HH_
#define AKANTU_NODE_SYNCHRONIZER_HH_
namespace akantu {
class NodeSynchronizer : public MeshEventHandler,
public SynchronizerImpl<UInt> {
public:
NodeSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
~NodeSynchronizer() override;
UInt sanityCheckDataSize(const Array<UInt> & nodes,
const SynchronizationTag & tag,
bool from_comm_desc) const override;
void packSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & /*tag*/) const override;
void unpackSanityCheckData(CommunicationBuffer & buffer,
const Array<UInt> & nodes,
const SynchronizationTag & tag, UInt proc,
UInt rank) const override;
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & /*unused*/,
const NewNodesEvent & /*unused*/) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & /*unused*/,
const Array<UInt> & /*unused*/,
const RemovedNodesEvent & /*unused*/) override {}
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & /*unused*/,
const NewElementsEvent & /*unused*/) override {}
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const RemovedElementsEvent & /*unused*/) override {}
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & /*unused*/,
const Array<Element> & /*unused*/,
const ElementTypeMapArray<UInt> & /*unused*/,
const ChangedElementsEvent & /*unused*/) override {}
/* ------------------------------------------------------------------------ */
NodeSynchronizer & operator=(const NodeSynchronizer & other) {
copySchemes(other);
return *this;
}
friend class NodeInfoPerProc;
protected:
void fillEntityToSend(Array<UInt> & nodes_to_send) override;
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
inline UInt canScatterSize() override;
inline UInt gatheredSize() override;
inline UInt localToGlobalEntity(const UInt & local) override;
protected:
Int getRank(const UInt & node) const final;
protected:
Mesh & mesh;
};
} // namespace akantu
#include "node_synchronizer_inline_impl.hh"
#endif /* AKANTU_NODE_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/node_synchronizer_inline_impl.hh b/src/synchronizer/node_synchronizer_inline_impl.hh
index 41cfaf626..6eb13ce6d 100644
--- a/src/synchronizer/node_synchronizer_inline_impl.hh
+++ b/src/synchronizer/node_synchronizer_inline_impl.hh
@@ -1,55 +1,59 @@
/**
* @file node_synchronizer_inline_impl.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mar jan 14 2020
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Wed Mar 04 2020
*
- * @brief A Documented file.
+ * @brief Synchronizer for nodal information
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
#define AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::canScatterSize() {
return mesh.getNbNodes();
}
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::gatheredSize() {
return mesh.getNbGlobalNodes();
}
/* -------------------------------------------------------------------------- */
inline UInt NodeSynchronizer::localToGlobalEntity(const UInt & local) {
return mesh.getNodeGlobalId(local);
}
} // akantu
#endif // AKANTU_NODE_SYNCHRONIZER_INLINE_IMPL_HH_
diff --git a/src/synchronizer/periodic_node_synchronizer.cc b/src/synchronizer/periodic_node_synchronizer.cc
index 6389c0e08..9ba529d05 100644
--- a/src/synchronizer/periodic_node_synchronizer.cc
+++ b/src/synchronizer/periodic_node_synchronizer.cc
@@ -1,131 +1,135 @@
/**
* @file periodic_node_synchronizer.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue May 29 2018
+ * @date creation: Wed May 30 2018
+ * @date last modification: Fri Jul 24 2020
*
- * @brief Implementation of the periodic node synchronizer
+ * @brief Implementation of the periodic node synchronizer
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "periodic_node_synchronizer.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
PeriodicNodeSynchronizer::PeriodicNodeSynchronizer(
Mesh & mesh, const ID & id,
const bool register_to_event_manager, EventHandlerPriority event_priority)
: NodeSynchronizer(mesh, id + ":masters",
register_to_event_manager, event_priority) {}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::update() {
static int count = 0;
const auto & masters_to_slaves = this->mesh.getPeriodicMasterSlaves();
masters_list.resize(0);
masters_list.reserve(masters_to_slaves.size());
slaves_list.resize(0);
slaves_list.reserve(masters_to_slaves.size());
reset();
std::set<UInt> masters_to_receive;
for (auto && data : masters_to_slaves) {
auto master = std::get<0>(data);
auto slave = std::get<1>(data);
masters_list.push_back(master);
slaves_list.push_back(slave);
if (not(mesh.isMasterNode(master) or mesh.isLocalNode(master))) {
masters_to_receive.insert(master);
}
}
if (not mesh.isDistributed() or nb_proc == 1) {
return;
}
std::map<Int, Array<UInt>> buffers;
for (auto node : masters_to_receive) {
auto && proc = mesh.getNodePrank(node);
auto && scheme = this->communications.createRecvScheme(proc);
scheme.push_back(node);
buffers[proc].push_back(mesh.getNodeGlobalId(node));
}
auto tag = Tag::genTag(0, count, Tag::_modify_scheme);
std::vector<CommunicationRequest> requests;
for (auto && data : buffers) {
auto proc = std::get<0>(data);
auto & buffer = std::get<1>(data);
requests.push_back(communicator.asyncSend(buffer, proc, tag,
CommunicationMode::_synchronous));
std::cout << "Recv from proc : " << proc << " -> "
<< this->communications.getScheme(proc, _recv).size()
<< std::endl;
}
communicator.receiveAnyNumber<UInt>(
requests,
[&](auto && proc, auto && msg) {
auto && scheme = this->communications.createSendScheme(proc);
for (auto node : msg) {
scheme.push_back(mesh.getNodeLocalId(node));
}
std::cout << "Send to proc : " << proc << " -> " << scheme.size()
<< " [" << tag << "]" << std::endl;
},
tag);
++count;
}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::synchronizeOnceImpl(
DataAccessor<UInt> & data_accessor, const SynchronizationTag & tag) const {
NodeSynchronizer::synchronizeOnceImpl(data_accessor, tag);
auto size = data_accessor.getNbData(masters_list, tag);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, masters_list, tag);
data_accessor.unpackData(buffer, slaves_list, tag);
}
/* -------------------------------------------------------------------------- */
void PeriodicNodeSynchronizer::waitEndSynchronizeImpl(
DataAccessor<UInt> & data_accessor, const SynchronizationTag & tag) {
NodeSynchronizer::waitEndSynchronizeImpl(data_accessor, tag);
auto size = data_accessor.getNbData(masters_list, tag);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, masters_list, tag);
data_accessor.unpackData(buffer, slaves_list, tag);
}
} // namespace akantu
diff --git a/src/synchronizer/periodic_node_synchronizer.hh b/src/synchronizer/periodic_node_synchronizer.hh
index 42ec94824..b928bd82e 100644
--- a/src/synchronizer/periodic_node_synchronizer.hh
+++ b/src/synchronizer/periodic_node_synchronizer.hh
@@ -1,92 +1,96 @@
/**
* @file periodic_node_synchronizer.hh
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Tue May 29 2018
+ * @date creation: Wed May 30 2018
+ * @date last modification: Fri Jul 24 2020
*
- * @brief PeriodicNodeSynchronizer definition
+ * @brief PeriodicNodeSynchronizer definition
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_
#define AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_
namespace akantu {
class PeriodicNodeSynchronizer : public NodeSynchronizer {
public:
PeriodicNodeSynchronizer(
Mesh & mesh, const ID & id = "periodic_node_synchronizer", bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void update();
/// Uses the synchronizer to perform a reduction on the vector
template <template <class> class Op, typename T>
void reduceSynchronizeWithPBCSlaves(Array<T> & array) const;
/// synchronize ghosts without state
void synchronizeOnceImpl(DataAccessor<UInt> & data_accessor,
const SynchronizationTag & tag) const override;
// /// asynchronous synchronization of ghosts
// void asynchronousSynchronizeImpl(const DataAccessor<UInt> & data_accessor,
// const SynchronizationTag & tag) override;
/// wait end of asynchronous synchronization of ghosts
void waitEndSynchronizeImpl(DataAccessor<UInt> & data_accessor,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// NodeSynchronizer master_to_slaves_synchronizer;
Array<UInt> masters_list;
Array<UInt> slaves_list;
};
/* -------------------------------------------------------------------------- */
template <template <class> class Op, typename T>
void PeriodicNodeSynchronizer::reduceSynchronizeWithPBCSlaves(
Array<T> & array) const {
ReduceDataAccessor<UInt, Op, T> data_accessor(array,
SynchronizationTag::_whatever);
auto size =
data_accessor.getNbData(slaves_list, SynchronizationTag::_whatever);
CommunicationBuffer buffer(size);
data_accessor.packData(buffer, slaves_list, SynchronizationTag::_whatever);
data_accessor.unpackData(buffer, masters_list, SynchronizationTag::_whatever);
this->reduceSynchronizeArray<Op>(array);
}
} // namespace akantu
#endif /* AKANTU_PERIODIC_NODE_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/slave_element_info_per_processor.cc b/src/synchronizer/slave_element_info_per_processor.cc
index b0f8e94d0..0e3b22467 100644
--- a/src/synchronizer/slave_element_info_per_processor.cc
+++ b/src/synchronizer/slave_element_info_per_processor.cc
@@ -1,193 +1,195 @@
/**
* @file slave_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 16 2016
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Fri Jul 24 2020
*
* @brief Helper class to distribute a mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SlaveElementInfoPerProc::SlaveElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root)
: ElementInfoPerProc(synchronizer, message_cnt, root, _not_defined) {
Vector<UInt> size(5);
comm.receive(size, this->root,
Tag::genTag(this->root, this->message_count, Tag::_sizes));
this->type = (ElementType)size[0];
this->nb_local_element = size[1];
this->nb_ghost_element = size[2];
this->nb_element_to_receive = size[3];
this->nb_tags = size[4];
if (this->type != _not_defined) {
this->nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
}
}
/* -------------------------------------------------------------------------- */
bool SlaveElementInfoPerProc::needSynchronize() {
return this->type != _not_defined;
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeConnectivities() {
Array<UInt> local_connectivity(
(this->nb_local_element + this->nb_ghost_element) *
this->nb_nodes_per_element);
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(
local_connectivity, this->root,
Tag::genTag(this->root, this->message_count, Tag::_connectivity));
auto & old_nodes = this->getNodesGlobalIds();
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(this->mesh, local_connectivity,
this->nb_local_element, this->nb_ghost_element,
this->type, old_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizePartitions() {
Array<UInt> local_partitions(this->nb_element_to_receive +
this->nb_ghost_element * 2);
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
this->comm.receive(local_partitions, this->root,
Tag::genTag(root, this->message_count, Tag::_partitions));
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(local_partitions);
}
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
DynamicCommunicationBuffer mesh_data_sizes_buffer;
comm.broadcast(mesh_data_sizes_buffer, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: "
<< mesh_data_sizes_buffer.size());
if (mesh_data_sizes_buffer.empty()) {
return;
}
AKANTU_DEBUG_INFO("Receiving the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
std::vector<std::string> tag_names;
std::vector<MeshDataTypeCode> tag_type_codes;
std::vector<UInt> tag_nb_component;
tag_names.resize(nb_tags);
tag_type_codes.resize(nb_tags);
tag_nb_component.resize(nb_tags);
CommunicationBuffer mesh_data_buffer;
UInt type_code_int;
for (UInt i(0); i < nb_tags; ++i) {
mesh_data_sizes_buffer >> tag_names[i];
mesh_data_sizes_buffer >> type_code_int;
tag_type_codes[i] = static_cast<MeshDataTypeCode>(type_code_int);
mesh_data_sizes_buffer >> tag_nb_component[i];
}
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
CommunicationStatus mesh_data_comm_status;
AKANTU_DEBUG_INFO("Checking size of data to receive for mesh data TAG("
<< Tag::genTag(root, this->message_count, Tag::_mesh_data)
<< ")");
comm.probe<char>(root,
Tag::genTag(root, this->message_count, Tag::_mesh_data),
mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.size());
AKANTU_DEBUG_INFO("Receiving "
<< mesh_data_buffer_size << " bytes of mesh data TAG("
<< Tag::genTag(root, this->message_count, Tag::_mesh_data)
<< ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer, root,
Tag::genTag(root, this->message_count, Tag::_mesh_data));
// Loop over each tag for the current type
UInt k(0);
for (; names_it != names_end; ++names_it, ++k) {
this->fillMeshData(mesh_data_buffer, *names_it, tag_type_codes[k],
tag_nb_component[k]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc "
<< root << " TAG("
<< Tag::genTag(root, my_rank, Tag::_element_group) << ")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, Tag::_element_group),
status);
CommunicationBuffer buffer(status.size());
comm.receive(buffer, root, Tag::genTag(root, my_rank, Tag::_element_group));
this->fillElementGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/synchronizer.cc b/src/synchronizer/synchronizer.cc
index 280bbc47f..5bf27d221 100644
--- a/src/synchronizer/synchronizer.cc
+++ b/src/synchronizer/synchronizer.cc
@@ -1,54 +1,56 @@
/**
* @file synchronizer.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Wed Nov 15 2017
*
* @brief implementation of the common part
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <functional>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Synchronizer::Synchronizer(const Communicator & comm, const ID & id)
: communicator(comm) {
int max_tag = comm.getMaxTag();
this->hash_id = std::hash<std::string>()(id);
if (max_tag != 0) {
this->hash_id = this->hash_id % max_tag;
}
this->nb_proc = communicator.getNbProc();
this->rank = communicator.whoAmI();
}
} // namespace akantu
diff --git a/src/synchronizer/synchronizer.hh b/src/synchronizer/synchronizer.hh
index 66040e359..84cf96eab 100644
--- a/src/synchronizer/synchronizer.hh
+++ b/src/synchronizer/synchronizer.hh
@@ -1,127 +1,130 @@
/**
* @file synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Mar 04 2020
*
* @brief Common interface for synchronizers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SYNCHRONIZER_HH_
#define AKANTU_SYNCHRONIZER_HH_
namespace akantu {
class Communicator;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Base class for synchronizers */
/* -------------------------------------------------------------------------- */
class Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Synchronizer(const Communicator & comm, const ID & id = "synchronizer");
Synchronizer(const Synchronizer & other) = default;
virtual ~Synchronizer() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronous communications form slaves to master
template <class DataAccessor>
void slaveReductionOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts without state
template <class DataAccessor>
void synchronizeOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts
template <class DataAccessor>
void synchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// asynchronous synchronization of ghosts
template <class DataAccessor>
void asynchronousSynchronize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
template <class DataAccessor>
void waitEndSynchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// compute buffer size for a given tag and data accessor
template <class DataAccessor>
void computeBufferSize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Communicator, communicator, const Communicator &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the synchronizer
ID id;
/// hashed version of the id
int hash_id;
/// message counter per tag
std::map<SynchronizationTag, UInt> tag_counter;
/// the static memory instance
const Communicator & communicator;
/// nb processors in the communicator
UInt nb_proc;
/// rank in the communicator
UInt rank;
};
} // namespace akantu
#include "synchronizer_tmpl.hh"
#endif /* AKANTU_SYNCHRONIZER_HH_ */
diff --git a/src/synchronizer/synchronizer_impl.hh b/src/synchronizer/synchronizer_impl.hh
index 576544014..16b0d04ff 100644
--- a/src/synchronizer/synchronizer_impl.hh
+++ b/src/synchronizer/synchronizer_impl.hh
@@ -1,216 +1,218 @@
/**
* @file synchronizer_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Wed Mar 04 2020
*
* @brief Implementation of the generic part of synchronizers
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communications.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SYNCHRONIZER_IMPL_HH_
#define AKANTU_SYNCHRONIZER_IMPL_HH_
namespace akantu {
template <class Entity> class SynchronizerImpl : public Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerImpl(const Communicator & communicator,
const ID & id = "synchronizer");
SynchronizerImpl(const SynchronizerImpl & other, const ID & id);
~SynchronizerImpl() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
void communicateOnce(
const std::tuple<CommunicationSendRecv, CommunicationSendRecv> &
send_recv_schemes,
const Tag::CommTags & comm_tag, DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
public:
/// synchronous synchronization without state
virtual void slaveReductionOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// synchronous synchronization without state
virtual void synchronizeOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// asynchronous synchronization of ghosts
virtual void
asynchronousSynchronizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
virtual void waitEndSynchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// compute all buffer sizes
virtual void
computeAllBufferSizes(const DataAccessor<Entity> & data_accessor);
/// compute buffer size for a given tag and data accessor
virtual void computeBufferSizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
virtual void synchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
this->asynchronousSynchronizeImpl(data_accessor, tag);
this->waitEndSynchronizeImpl(data_accessor, tag);
}
/* ------------------------------------------------------------------------ */
/// reset send and recv element lists
void reset();
/// extract the elements that have a true predicate from in_synchronizer and
/// store them in the current synchronizer
template <typename Pred>
void split(SynchronizerImpl & in_synchronizer, Pred && pred);
/// update schemes in a synchronizer
template <typename Updater> void updateSchemes(Updater && scheme_updater);
/// filter the send scheme and let the other processor now about iterate
template <typename Pred> void filterScheme(Pred && pred);
/// flip send and receive schemes
void swapSendRecv();
/// copy the schemes of an other communicator.
SynchronizerImpl & operator=(const SynchronizerImpl & other);
/// gather data on the predefined root process (master version)
template <typename T>
void gather(const Array<T> & to_gather, Array<T> & gathered);
/// gather data on the predefined root process (slave version)
template <typename T> void gather(const Array<T> & to_gather);
/// scatter data from the predefined root process (master version)
template <typename T>
void scatter(Array<T> & scattered, const Array<T> & to_scatter);
/// scatter data from the predefined root process (slave version)
template <typename T> void scatter(Array<T> & scattered);
template <typename T>
void synchronizeArray(Array<T> & array) const;
/// Uses the synchronizer to perform a reduction on the vector
template <template <class> class Op, typename T>
void reduceSynchronizeArray(Array<T> & array) const;
protected:
/// copy schemes
void copySchemes(const SynchronizerImpl & other);
/// check if dof changed set on at least one processor
inline bool hasChanged();
/// init the scheme for scatter and gather operation, need extra memory
inline void initScatterGatherCommunicationScheme();
/// list the entities to send to root process
virtual void fillEntityToSend(Array<Entity> & /*entities_to_send*/) {
AKANTU_TO_IMPLEMENT();
}
virtual Entity localToGlobalEntity(const Entity & /*local*/) {
AKANTU_TO_IMPLEMENT();
}
virtual UInt canScatterSize() {
AKANTU_TO_IMPLEMENT();
}
virtual UInt gatheredSize() {
AKANTU_TO_IMPLEMENT();
}
public:
/* ------------------------------------------------------------------------ */
virtual UInt sanityCheckDataSize(const Array<Entity> & elements,
const SynchronizationTag & tag,
bool is_comm_desc = true) const;
virtual void
packSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void
unpackSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void packSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Entity> & /*elements*/,
const SynchronizationTag & /*tag*/) const {}
virtual void unpackSanityCheckData(CommunicationBuffer & /*buffer*/,
const Array<Entity> & /*elements*/,
const SynchronizationTag & /*tag*/,
UInt /*proc*/, UInt /*rank*/) const {}
public:
AKANTU_GET_MACRO(Communications, communications,
const Communications<Entity> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(Communications, communications,
Communications<Entity> &);
virtual Int getRank(const Entity & entity) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// information on the communications
Communications<Entity> communications;
/// did the scheme change, this is to recreate the scatter/gather data if
/// needed
bool entities_changed{true};
/// Root processor for scatter/gather operations
Int root{0};
/// entities coming/going from/to root
Array<Entity> entities_from_root;
/// entities received from slaves proc (only on master)
std::map<UInt, Array<Entity>> master_receive_entities;
};
} // namespace akantu
#include "synchronizer_impl_tmpl.hh"
#endif /* AKANTU_SYNCHRONIZER_IMPL_HH_ */
diff --git a/src/synchronizer/synchronizer_impl_tmpl.hh b/src/synchronizer/synchronizer_impl_tmpl.hh
index a6a317fdc..7bfe86d43 100644
--- a/src/synchronizer/synchronizer_impl_tmpl.hh
+++ b/src/synchronizer/synchronizer_impl_tmpl.hh
@@ -1,867 +1,869 @@
/**
* @file synchronizer_impl_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Wed Dec 09 2020
*
* @brief Implementation of the SynchronizerImpl
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const Communicator & comm,
const ID & id)
: Synchronizer(comm, id), communications(comm) {}
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity>::SynchronizerImpl(const SynchronizerImpl & other,
const ID & id)
: Synchronizer(other), communications(other.communications) {
this->id = id;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::communicateOnce(
const std::tuple<CommunicationSendRecv, CommunicationSendRecv> &
send_recv_schemes,
const Tag::CommTags & comm_tag, DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
// no need to synchronize
if (this->nb_proc == 1) {
return;
}
CommunicationSendRecv send_dir;
CommunicationSendRecv recv_dir;
std::tie(send_dir, recv_dir) = send_recv_schemes;
using CommunicationRequests = std::vector<CommunicationRequest>;
using CommunicationBuffers = std::map<UInt, CommunicationBuffer>;
CommunicationRequests send_requests;
CommunicationRequests recv_requests;
CommunicationBuffers send_buffers;
CommunicationBuffers recv_buffers;
auto postComm = [&](const auto & sr, auto & buffers,
auto & requests) -> void {
for (auto && pair : communications.iterateSchemes(sr)) {
auto & proc = pair.first;
const auto & scheme = pair.second;
if (scheme.empty()) {
continue;
}
auto & buffer = buffers[proc];
auto buffer_size = data_accessor.getNbData(scheme, tag);
if (buffer_size == 0) {
continue;
}
#ifndef AKANTU_NDEBUG
buffer_size += this->sanityCheckDataSize(scheme, tag, false);
#endif
buffer.resize(buffer_size);
if (sr == recv_dir) {
requests.push_back(communicator.asyncReceive(
buffer, proc,
Tag::genTag(this->rank, UInt(tag), comm_tag, this->hash_id)));
} else {
#ifndef AKANTU_NDEBUG
this->packSanityCheckData(buffer, scheme, tag);
#endif
data_accessor.packData(buffer, scheme, tag);
AKANTU_DEBUG_ASSERT(
buffer.getPackedSize() == buffer.size(),
"The data accessor did not pack all the data it "
"promised in communication with tag "
<< tag << " (Promised: " << buffer.size()
<< "bytes, packed: " << buffer.getPackedSize() << "bytes [avg: "
<< Real(buffer.size() - buffer.getPackedSize()) / scheme.size()
<< "bytes per entity missing])");
send_requests.push_back(communicator.asyncSend(
buffer, proc,
Tag::genTag(proc, UInt(tag), comm_tag, this->hash_id)));
}
}
};
// post the receive requests
postComm(recv_dir, recv_buffers, recv_requests);
// post the send data requests
postComm(send_dir, send_buffers, send_requests);
// treat the receive requests
UInt request_ready;
while ((request_ready = Communicator::waitAny(recv_requests)) != UInt(-1)) {
auto & req = recv_requests[request_ready];
auto proc = req.getSource();
auto & buffer = recv_buffers[proc];
const auto & scheme = this->communications.getScheme(proc, recv_dir);
#ifndef AKANTU_NDEBUG
this->unpackSanityCheckData(buffer, scheme, tag, proc, this->rank);
#endif
data_accessor.unpackData(buffer, scheme, tag);
AKANTU_DEBUG_ASSERT(
buffer.getLeftToUnpack() == 0,
"The data accessor ignored some data in communication with tag "
<< tag);
req.free();
recv_requests.erase(recv_requests.begin() + request_ready);
}
Communicator::waitAll(send_requests);
Communicator::freeCommunicationRequest(send_requests);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::slaveReductionOnceImpl(
DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
communicateOnce(std::make_tuple(_recv, _send), Tag::_reduce, data_accessor,
tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::synchronizeOnceImpl(
DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const {
communicateOnce(std::make_tuple(_send, _recv), Tag::_synchronize,
data_accessor, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::asynchronousSynchronizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (not this->communications.hasCommunicationSize(tag)) {
this->computeBufferSize(data_accessor, tag);
}
this->communications.incrementCounter(tag);
// Posting the receive -------------------------------------------------------
if (this->communications.hasPendingRecv(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must still be some pending receive communications."
<< " Tag is " << tag << " Cannot start new ones");
}
for (auto && comm_desc : this->communications.iterateRecv(tag)) {
comm_desc.postRecv(this->hash_id);
}
// Posting the sends -------------------------------------------------------
if (communications.hasPendingSend(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"There must be some pending sending communications."
<< " Tag is " << tag);
}
for (auto && comm_desc : this->communications.iterateSend(tag)) {
comm_desc.resetBuffer();
#ifndef AKANTU_NDEBUG
this->packSanityCheckData(comm_desc);
#endif
comm_desc.packData(data_accessor);
comm_desc.postSend(this->hash_id);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::waitEndSynchronizeImpl(
DataAccessor<Entity> & data_accessor, const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
if (this->communications.begin(tag, _recv) !=
this->communications.end(tag, _recv) &&
!this->communications.hasPendingRecv(tag)) {
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"No pending communication with the tag \""
<< tag);
}
#endif
auto recv_end = this->communications.end(tag, _recv);
decltype(recv_end) recv_it;
while ((recv_it = this->communications.waitAnyRecv(tag)) != recv_end) {
auto && comm_desc = *recv_it;
#ifndef AKANTU_NDEBUG
this->unpackSanityCheckData(comm_desc);
#endif
comm_desc.unpackData(data_accessor);
comm_desc.resetBuffer();
comm_desc.freeRequest();
}
this->communications.waitAllSend(tag);
this->communications.freeSendRequests(tag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeAllBufferSizes(
const DataAccessor<Entity> & data_accessor) {
for (auto && tag : this->communications.iterateTags()) {
this->computeBufferSize(data_accessor, tag);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::computeBufferSizeImpl(
const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (not this->communications.hasCommunication(tag)) {
this->communications.initializeCommunications(tag);
AKANTU_DEBUG_ASSERT(communications.hasCommunication(tag) == true,
"Communications where not properly initialized");
}
for (auto sr : iterate_send_recv) {
for (auto && pair : this->communications.iterateSchemes(sr)) {
auto proc = pair.first;
const auto & scheme = pair.second;
UInt size = 0;
#ifndef AKANTU_NDEBUG
size += this->sanityCheckDataSize(scheme, tag);
#endif
size += data_accessor.getNbData(scheme, tag);
AKANTU_DEBUG_INFO("I have "
<< size << "(" << printMemorySize<char>(size) << " - "
<< scheme.size() << " element(s)) data to "
<< std::string(sr == _recv ? "receive from" : "send to")
<< proc << " for tag " << tag);
this->communications.setCommunicationSize(tag, proc, size, sr);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity> void SynchronizerImpl<Entity>::reset() {
AKANTU_DEBUG_IN();
communications.resetSchemes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Pred>
void SynchronizerImpl<Entity>::split(SynchronizerImpl<Entity> & in_synchronizer,
Pred && pred) {
AKANTU_DEBUG_IN();
auto filter_list = [&](auto & list, auto & new_list) {
auto copy = list;
list.resize(0);
new_list.resize(0);
for (auto && entity : copy) {
if (std::forward<Pred>(pred)(entity)) {
new_list.push_back(entity);
} else {
list.push_back(entity);
}
}
};
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair :
in_synchronizer.communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto & new_scheme = communications.createScheme(proc, sr);
filter_list(scheme, new_scheme);
}
}
in_synchronizer.communications.invalidateSizes();
communications.invalidateSizes();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Updater>
void SynchronizerImpl<Entity>::updateSchemes(Updater && scheme_updater) {
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair : communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
std::forward<Updater>(scheme_updater)(scheme, proc, sr);
}
}
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <typename Entity>
template <typename Pred>
void SynchronizerImpl<Entity>::filterScheme(Pred && pred) {
std::vector<CommunicationRequest> requests;
std::unordered_map<UInt, Array<UInt>> keep_entities;
auto filter_list = [](const auto & keep, auto & list) {
Array<Entity> new_list;
for (const auto & keep_entity : keep) {
const Entity & entity = list(keep_entity);
new_list.push_back(entity);
}
list.copy(new_list);
};
// loop over send_schemes
for (auto & scheme_pair : communications.iterateSchemes(_recv)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto & keep_entity = keep_entities[proc];
for (auto && entity : enumerate(scheme)) {
if (pred(std::get<1>(entity))) {
keep_entity.push_back(std::get<0>(entity));
}
}
auto tag = Tag::genTag(this->rank, 0, Tag::_modify_scheme);
AKANTU_DEBUG_INFO("I have " << keep_entity.size()
<< " elements to still receive from processor "
<< proc << " (communication tag : " << tag
<< ")");
filter_list(keep_entity, scheme);
requests.push_back(communicator.asyncSend(keep_entity, proc, tag));
}
// clean the receive scheme
for (auto & scheme_pair : communications.iterateSchemes(_send)) {
auto proc = scheme_pair.first;
auto & scheme = scheme_pair.second;
auto tag = Tag::genTag(proc, 0, Tag::_modify_scheme);
AKANTU_DEBUG_INFO("Waiting list of elements to keep from processor "
<< proc << " (communication tag : " << tag << ")");
CommunicationStatus status;
communicator.probe<UInt>(proc, tag, status);
Array<UInt> keep_entity(status.size(), 1, "keep_element");
AKANTU_DEBUG_INFO("I have "
<< keep_entity.size()
<< " elements to keep in my send list to processor "
<< proc << " (communication tag : " << tag << ")");
communicator.receive(keep_entity, proc, tag);
filter_list(keep_entity, scheme);
}
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
communications.invalidateSizes();
}
/* -------------------------------------------------------------------------- */
template <class Entity> void SynchronizerImpl<Entity>::swapSendRecv() {
communications.swapSendRecv();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::copySchemes(const SynchronizerImpl & other) {
reset();
for (auto sr : iterate_send_recv) {
for (auto & scheme_pair : other.communications.iterateSchemes(sr)) {
auto proc = scheme_pair.first;
auto & other_scheme = scheme_pair.second;
auto & scheme = communications.createScheme(proc, sr);
scheme.copy(other_scheme);
}
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
SynchronizerImpl<Entity> &
SynchronizerImpl<Entity>::operator=(const SynchronizerImpl & other) {
copySchemes(other);
return *this;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
UInt SynchronizerImpl<Entity>::sanityCheckDataSize(
const Array<Entity> & /*unused*/, const SynchronizationTag & /*unused*/,
bool is_comm_desc) const {
if (not is_comm_desc) {
return 0;
}
UInt size = 0;
size += sizeof(SynchronizationTag); // tag
size += sizeof(UInt); // comm_desc.getNbData();
size += sizeof(UInt); // comm_desc.getProc();
size += sizeof(this->rank); // mesh.getCommunicator().whoAmI();
return size;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::packSanityCheckData(
CommunicationDescriptor<Entity> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
buffer << comm_desc.getTag();
buffer << comm_desc.getNbData();
buffer << comm_desc.getProc();
buffer << this->rank;
const auto & tag = comm_desc.getTag();
const auto & send_element = comm_desc.getScheme();
this->packSanityCheckData(buffer, send_element, tag);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::unpackSanityCheckData(
CommunicationDescriptor<Entity> & comm_desc) const {
auto & buffer = comm_desc.getBuffer();
const auto & tag = comm_desc.getTag();
auto nb_data = comm_desc.getNbData();
auto proc = comm_desc.getProc();
auto rank = this->rank;
decltype(nb_data) recv_nb_data;
decltype(proc) recv_proc;
decltype(rank) recv_rank;
SynchronizationTag t;
buffer >> t;
buffer >> recv_nb_data;
buffer >> recv_proc;
buffer >> recv_rank;
AKANTU_DEBUG_ASSERT(
t == tag, "The tag received does not correspond to the tag expected");
AKANTU_DEBUG_ASSERT(
nb_data == recv_nb_data,
"The nb_data received does not correspond to the nb_data expected");
AKANTU_DEBUG_ASSERT(UInt(recv_rank) == proc,
"The rank received does not correspond to the proc");
AKANTU_DEBUG_ASSERT(recv_proc == UInt(rank),
"The proc received does not correspond to the rank");
auto & recv_element = comm_desc.getScheme();
this->unpackSanityCheckData(buffer, recv_element, tag, proc, rank);
}
/* -------------------------------------------------------------------------- */
template <class Entity> bool SynchronizerImpl<Entity>::hasChanged() {
communicator.allReduce(entities_changed, SynchronizerOperation::_lor);
return entities_changed;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void SynchronizerImpl<Entity>::initScatterGatherCommunicationScheme() {
if (this->nb_proc == 1) {
entities_changed = false;
AKANTU_DEBUG_OUT();
return;
}
AKANTU_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void SynchronizerImpl<UInt>::initScatterGatherCommunicationScheme() {
AKANTU_DEBUG_IN();
if (this->nb_proc == 1) {
entities_changed = false;
AKANTU_DEBUG_OUT();
return;
}
this->entities_from_root.clear();
this->master_receive_entities.clear();
Array<UInt> entities_to_send;
fillEntityToSend(entities_to_send);
std::vector<CommunicationRequest> requests;
if (this->rank == UInt(this->root)) {
master_receive_entities[this->root].copy(entities_to_send);
Array<UInt> nb_entities_per_proc(this->nb_proc);
communicator.gather(entities_to_send.size(), nb_entities_per_proc);
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(this->root)) {
continue;
}
auto & receive_per_proc = master_receive_entities[p];
receive_per_proc.resize(nb_entities_per_proc(p));
if (nb_entities_per_proc(p) == 0) {
continue;
}
requests.push_back(communicator.asyncReceive(
receive_per_proc, p,
Tag::genTag(p, 0, Tag::_gather_initialization, this->hash_id)));
}
} else {
communicator.gather(entities_to_send.size(), this->root);
AKANTU_DEBUG(dblDebug, "I have " << entities_to_send.size()
<< " entities to send to master proc");
if (not entities_to_send.empty()) {
requests.push_back(communicator.asyncSend(
entities_to_send, this->root,
Tag::genTag(this->rank, 0, Tag::_gather_initialization,
this->hash_id)));
}
}
entities_changed = false;
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::gather(const Array<T> & to_gather,
Array<T> & gathered) {
if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
}
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(to_gather.size() == this->canScatterSize(),
"The array to gather does not have the correct size");
AKANTU_DEBUG_ASSERT(gathered.size() == this->gatheredSize(),
"The gathered array does not have the correct size");
if (this->nb_proc == 1) {
gathered.copy(to_gather, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == UInt(this->root)) {
continue;
}
auto receive_it = this->master_receive_entities.find(p);
AKANTU_DEBUG_ASSERT(receive_it != this->master_receive_entities.end(),
"Could not find the receive list for dofs of proc "
<< p);
const auto & receive_entities = receive_it->second;
if (receive_entities.empty()) {
continue;
}
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_entities.size() * to_gather.getNbComponent() *
sizeof(T));
AKANTU_DEBUG_INFO(
"Preparing to receive data for "
<< receive_entities.size() << " entities from processor " << p << " "
<< Tag::genTag(p, this->root, Tag::_gather, this->hash_id));
requests.push_back(communicator.asyncReceive(
buffer, p, Tag::genTag(p, this->root, Tag::_gather, this->hash_id)));
}
auto data_gathered_it = gathered.begin(to_gather.getNbComponent());
{ // copy master data
auto data_to_gather_it = to_gather.begin(to_gather.getNbComponent());
for (auto local_entity : entities_from_root) {
UInt global_entity = localToGlobalEntity(local_entity);
Vector<T> entity_data_gathered = data_gathered_it[global_entity];
Vector<T> entity_data_to_gather = data_to_gather_it[local_entity];
entity_data_gathered = entity_data_to_gather;
}
}
auto rr = UInt(-1);
while ((rr = Communicator::waitAny(requests)) != UInt(-1)) {
auto & request = requests[rr];
auto sender = request.getSource();
AKANTU_DEBUG_ASSERT(this->master_receive_entities.find(sender) !=
this->master_receive_entities.end() &&
buffers.find(sender) != buffers.end(),
"Missing infos concerning proc " << sender);
const auto & receive_entities =
this->master_receive_entities.find(sender)->second;
auto & buffer = buffers[sender];
for (auto global_entity : receive_entities) {
Vector<T> entity_data = data_gathered_it[global_entity];
buffer >> entity_data;
}
requests.erase(requests.begin() + rr);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::gather(const Array<T> & to_gather) {
AKANTU_DEBUG_IN();
if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
}
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(to_gather.size() == this->canScatterSize(),
"The array to gather does not have the correct size");
if (this->entities_from_root.empty()) {
AKANTU_DEBUG_OUT();
return;
}
CommunicationBuffer buffer(this->entities_from_root.size() *
to_gather.getNbComponent() * sizeof(T));
auto data_it = to_gather.begin(to_gather.getNbComponent());
for (auto entity : this->entities_from_root) {
Vector<T> data = data_it[entity];
buffer << data;
}
AKANTU_DEBUG_INFO("Gathering data for "
<< to_gather.size() << " dofs on processor " << this->root
<< " "
<< Tag::genTag(this->rank, 0, Tag::_gather, this->hash_id));
communicator.send(buffer, this->root,
Tag::genTag(this->rank, 0, Tag::_gather, this->hash_id));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::scatter(Array<T> & scattered,
const Array<T> & to_scatter) {
AKANTU_DEBUG_IN();
if (this->hasChanged()) {
initScatterGatherCommunicationScheme();
}
AKANTU_DEBUG_ASSERT(this->rank == UInt(this->root),
"This function cannot be called on a slave processor");
AKANTU_DEBUG_ASSERT(scattered.size() == this->canScatterSize(),
"The scattered array does not have the correct size");
AKANTU_DEBUG_ASSERT(to_scatter.size() == this->gatheredSize(),
"The array to scatter does not have the correct size");
if (this->nb_proc == 1) {
scattered.copy(to_scatter, true);
AKANTU_DEBUG_OUT();
return;
}
std::map<UInt, CommunicationBuffer> buffers;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
auto data_to_scatter_it = to_scatter.begin(to_scatter.getNbComponent());
if (p == this->rank) {
auto data_scattered_it = scattered.begin(to_scatter.getNbComponent());
// copy the data for the local processor
for (auto local_entity : entities_from_root) {
auto global_entity = localToGlobalEntity(local_entity);
Vector<T> entity_data_to_scatter = data_to_scatter_it[global_entity];
Vector<T> entity_data_scattered = data_scattered_it[local_entity];
entity_data_scattered = entity_data_to_scatter;
}
continue;
}
const auto & receive_entities =
this->master_receive_entities.find(p)->second;
// prepare the send buffer
CommunicationBuffer & buffer = buffers[p];
buffer.resize(receive_entities.size() * scattered.getNbComponent() *
sizeof(T));
// pack the data
for (auto global_entity : receive_entities) {
Vector<T> entity_data_to_scatter = data_to_scatter_it[global_entity];
buffer << entity_data_to_scatter;
}
// send the data
requests.push_back(communicator.asyncSend(
buffer, p, Tag::genTag(p, 0, Tag::_scatter, this->hash_id)));
}
// wait a clean communications
Communicator::waitAll(requests);
Communicator::freeCommunicationRequest(requests);
// synchronize slave and ghost nodes
synchronizeArray(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::scatter(Array<T> & scattered) {
AKANTU_DEBUG_IN();
if (this->hasChanged()) {
this->initScatterGatherCommunicationScheme();
}
AKANTU_DEBUG_ASSERT(this->rank != UInt(this->root),
"This function cannot be called on the root processor");
AKANTU_DEBUG_ASSERT(scattered.size() == this->canScatterSize(),
"The scattered array does not have the correct size");
// prepare the data
auto data_scattered_it = scattered.begin(scattered.getNbComponent());
CommunicationBuffer buffer(this->entities_from_root.size() *
scattered.getNbComponent() * sizeof(T));
// receive the data
communicator.receive(
buffer, this->root,
Tag::genTag(this->rank, 0, Tag::_scatter, this->hash_id));
// unpack the data
for (auto local_entity : entities_from_root) {
Vector<T> data_scattered(data_scattered_it[local_entity]);
buffer >> data_scattered;
}
// synchronize the ghosts
synchronizeArray(scattered);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <typename T>
void SynchronizerImpl<Entity>::synchronizeArray(Array<T> & array) const {
static_assert(std::is_same<Entity, UInt>::value,
"Not implemented for other type than UInt");
SimpleUIntDataAccessor<T> data_accessor(array, SynchronizationTag::_whatever);
this->synchronizeOnce(data_accessor, SynchronizationTag::_whatever);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
template <template <class> class Op, typename T>
void SynchronizerImpl<Entity>::reduceSynchronizeArray(Array<T> & array) const {
static_assert(std::is_same<Entity, UInt>::value,
"Not implemented for other type than UInt");
ReduceDataAccessor<UInt, Op, T> data_accessor(array,
SynchronizationTag::_whatever);
this->slaveReductionOnceImpl(data_accessor, SynchronizationTag::_whatever);
this->synchronizeArray(array);
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/synchronizer_registry.cc b/src/synchronizer/synchronizer_registry.cc
index f9387db0c..d04579393 100644
--- a/src/synchronizer/synchronizer_registry.cc
+++ b/src/synchronizer/synchronizer_registry.cc
@@ -1,119 +1,121 @@
/**
* @file synchronizer_registry.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Wed Nov 15 2017
*
* @brief Registry of synchronizers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "synchronizer_registry.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::SynchronizerRegistry() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::~SynchronizerRegistry() {
AKANTU_DEBUG_IN();
synchronizers.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerDataAccessor(
DataAccessorBase & data_accessor) {
this->data_accessor = &data_accessor;
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::synchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
it->second->synchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::asynchronousSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
(*it).second->asynchronousSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::waitEndSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (auto it = range.first; it != range.second; ++it) {
(*it).second->waitEndSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
synchronizers.insert(
std::pair<SynchronizationTag, Synchronizer *>(tag, &synchronizer));
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/synchronizer/synchronizer_registry.hh b/src/synchronizer/synchronizer_registry.hh
index 0a6bd2424..f38030471 100644
--- a/src/synchronizer/synchronizer_registry.hh
+++ b/src/synchronizer/synchronizer_registry.hh
@@ -1,89 +1,91 @@
/**
* @file synchronizer_registry.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
- * @date last modification: Sun Dec 03 2017
+ * @date last modification: Wed Nov 15 2017
*
* @brief Registry of synchronizers
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SYNCHRONIZER_REGISTRY_HH_
#define AKANTU_SYNCHRONIZER_REGISTRY_HH_
namespace akantu {
class DataAccessorBase;
class Synchronizer;
} // namespace akantu
namespace akantu {
class SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerRegistry();
virtual ~SynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize operation
void synchronize(SynchronizationTag tag);
/// asynchronous synchronization
void asynchronousSynchronize(SynchronizationTag tag);
/// wait end of asynchronous synchronization
void waitEndSynchronize(SynchronizationTag tag);
/// register a new synchronization
void registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag);
/// Register a different data accessor.
void registerDataAccessor(DataAccessorBase & data_accessor);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
using Tag2Sync = std::multimap<SynchronizationTag, Synchronizer *>;
/// list of registered synchronization
Tag2Sync synchronizers;
/// data accessor that will permit to do the pack/unpack things
DataAccessorBase * data_accessor{nullptr};
};
} // namespace akantu
#endif /* AKANTU_SYNCHRONIZER_REGISTRY_HH_ */
diff --git a/src/synchronizer/synchronizer_tmpl.hh b/src/synchronizer/synchronizer_tmpl.hh
index 1dc55d4cd..3311e7bb5 100644
--- a/src/synchronizer/synchronizer_tmpl.hh
+++ b/src/synchronizer/synchronizer_tmpl.hh
@@ -1,136 +1,138 @@
/**
* @file synchronizer_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 07 2016
- * @date last modification: Thu May 11 2017
+ * @date creation: Fri Dec 02 2016
+ * @date last modification: Mon Feb 26 2018
*
* @brief Implementation of the helper classes for the synchronizer
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "data_accessor.hh"
#include "synchronizer.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_SYNCHRONIZER_TMPL_HH_
#define AKANTU_SYNCHRONIZER_TMPL_HH_
namespace akantu {
template <class DataAccessorT>
void Synchronizer::slaveReductionOnce(DataAccessorT & data_accessor,
const SynchronizationTag & tag) const {
if (const auto * synch_el =
dynamic_cast<const SynchronizerImpl<Element> *>(this)) {
synch_el->slaveReductionOnceImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (const auto * synch_dof =
dynamic_cast<const SynchronizerImpl<UInt> *>(this)) {
synch_dof->slaveReductionOnceImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
template <class DataAccessorT>
void Synchronizer::synchronizeOnce(DataAccessorT & data_accessor,
const SynchronizationTag & tag) const {
if (const auto * synch_el =
dynamic_cast<const SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeOnceImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (const auto * synch_dof =
dynamic_cast<const SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeOnceImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// synchronize ghosts
template <class DataAccessorT>
void Synchronizer::synchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->synchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->synchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::asynchronousSynchronize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->asynchronousSynchronizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/* -------------------------------------------------------------------------- */
template <class DataAccessorT>
void Synchronizer::waitEndSynchronize(DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->waitEndSynchronizeImpl(
dynamic_cast<DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
/// compute buffer size for a given tag and data accessor
template <class DataAccessorT>
void Synchronizer::computeBufferSize(const DataAccessorT & data_accessor,
const SynchronizationTag & tag) {
if (auto * synch_el = dynamic_cast<SynchronizerImpl<Element> *>(this)) {
synch_el->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<Element> &>(data_accessor), tag);
} else if (auto * synch_dof = dynamic_cast<SynchronizerImpl<UInt> *>(this)) {
synch_dof->computeBufferSizeImpl(
dynamic_cast<const DataAccessor<UInt> &>(data_accessor), tag);
} else {
AKANTU_EXCEPTION("You synchronizer is not of a known type");
}
}
} // namespace akantu
#endif /* AKANTU_SYNCHRONIZER_TMPL_HH_ */
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index ac29527d9..61a3b3509 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,72 +1,74 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Mon Feb 12 2018
+# @date last modification: Thu Sep 24 2020
#
# @brief configuration for tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
include_directories(
${AKANTU_INCLUDE_DIRS}
${AKANTU_EXTERNAL_LIB_INCLUDE_DIR}
)
set(AKANTU_TESTS_FILES CACHE INTERNAL "")
#===============================================================================
# List of tests
#===============================================================================
add_akantu_test(test_common "Test the common part of Akantu")
add_akantu_test(test_fe_engine "Test finite element functionalties")
add_akantu_test(test_mesh_utils "Test mesh utils")
add_akantu_test(test_mesh "Test mesh")
add_akantu_test(test_model "Test model objects")
add_akantu_test(test_solver "Test solver function")
add_akantu_test(test_io "Test the IO modules")
add_akantu_test(test_contact "Test the contact part of Akantu")
add_akantu_test(test_geometry "Test the geometry module of Akantu")
add_akantu_test(test_synchronizer "Test synchronizers")
add_akantu_test(test_python_interface "Test python interface")
package_add_files_to_package(
cmake/akantu_test_driver.sh
cmake/AkantuTestsMacros.cmake
)
package_is_activated(parallel _is_parallel)
if (_is_parallel)
option(AKANTU_TESTS_ALWAYS_USE_MPI "Defines if sequential tests should also use MPIEXEC" FALSE)
mark_as_advanced(AKANTU_TESTS_ALWAYS_USE_MPI)
endif()
package_is_activated(gbenchmark _has_gbenchmark)
if (_has_gbenchmark)
add_subdirectory(benchmark)
endif()
diff --git a/test/ci/codeclimate/codeclimate-clang-tidy/lib/command.py b/test/ci/codeclimate/codeclimate-clang-tidy/lib/command.py
index ad8c6de0e..8c1c746d1 100644
--- a/test/ci/codeclimate/codeclimate-clang-tidy/lib/command.py
+++ b/test/ci/codeclimate/codeclimate-clang-tidy/lib/command.py
@@ -1,74 +1,87 @@
+
+""" command.py: command to run clang-tidy in codeclimate"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import json
import os
import re
class Command:
"""Returns command line arguments by parsing codeclimate config file."""
def __init__(self, config, workspace):
self.config = config
self._workspace = workspace
def build(self):
command = ['/usr/src/app/bin/run-clang-tidy',
'-clang-tidy-binary',
'/usr/bin/clang-tidy']
if 'checks' in self.config:
checks = self.config["checks"]
if not isinstance(checks, list):
command.extend(['-checks', f'\'{checks}\''])
else:
command.extend(['-checks', f'\'{",".join(checks)}\''])
if 'config' in self.config:
command.extend(['-config', self.config["config"]])
if 'header-filter' in self.config:
command.extend(['-header-filter', self.config["header-file"]])
extra_args = []
if 'extra-arg' in self.config:
tmp_extra_args = self.config['extra-arg']
if not isinstance(extra_args, list):
tmp_extra_args = [extra_args]
extra_args = []
includes_re = re.compile(r'-I(.*)')
for arg in tmp_extra_args:
match = includes_re.match(arg)
if match:
path = os.path.abspath(match.group(1))
extra_args.append(f'-I{path}')
else:
extra_args.append(arg)
if 'compilation-database-path' in self.config:
for arg in extra_args:
command.extend(['-extra-arg', arg])
if 'compilation-database-path' in self.config:
command.extend(['-p', self.config['compilation-database-path']])
else:
include_flags = ' -I'.join(self._workspace.include_paths)
compile_commands = []
for file_ in self._workspace.files:
cmd = {
'directory': os.path.dirname(file_),
'file': file_,
'command': f'/usr/bin/clang++ {include_flags} {" ".join(extra_args)} -c {file_} -o dummy.o', # noqa
}
compile_commands.append(cmd)
location = '/tmp'
compile_database = os.path.join(location, 'compile_commands.json')
with open(compile_database, 'w') as db:
json.dump(compile_commands, db)
command.extend(['-p', location])
command.extend([f'{path}.*' if os.path.isdir(path) else path
for path in self._workspace.paths])
return command
diff --git a/test/ci/codeclimate/codeclimate-clang-tidy/lib/issue_formatter.py b/test/ci/codeclimate/codeclimate-clang-tidy/lib/issue_formatter.py
index 4b0ec3308..ad81b761c 100644
--- a/test/ci/codeclimate/codeclimate-clang-tidy/lib/issue_formatter.py
+++ b/test/ci/codeclimate/codeclimate-clang-tidy/lib/issue_formatter.py
@@ -1,92 +1,104 @@
+""" issue_formatter.py: issue_formater for clang-tidy in codeclimate (inspired
+from cpp-check)"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import hashlib
import os
class IssueFormatter:
CLASSIFICATIONS = {
'bugprone': {
'categories': ['Bug Risk'],
'severity': 'major',
},
'modernize': {
'categories': ['Clarity', 'Compatibility', 'Style'],
'severity': 'info'
},
'mpi': {
'categories': ['Bug Risk', 'Performance'],
'severity': 'critical',
},
'openmp': {
'categories': ['Bug Risk', 'Performance'],
'severity': 'critical',
},
'performance': {
'categories': ['Performance'],
'severity': 'minor',
},
'readability': {
'categories': ['Clarity', 'Style'],
'severity': 'info'
},
}
def _get_classifiaction(self, type_):
categories = ['Bug Risk']
severity = 'blocker'
if type_ in self.CLASSIFICATIONS:
categories = self.CLASSIFICATIONS[type_]['categories']
severity = self.CLASSIFICATIONS[type_]['severity']
elif type_[0] == 'clang':
if type_[1] == 'diagnostic':
categories = ['Bug Risk']
severity = 'blocker'
elif type_[1] == 'analyzer':
categories = ['Bug Risk']
severity = 'major'
return (categories, severity)
def __init__(self, issue):
self.issue_dict = issue
def format(self):
self.issue_dict['file'] = os.path.relpath(self.issue_dict['file'])
issue = {
'type': 'issue',
'check_name': self.issue_dict['type'],
'description': self.issue_dict['detail'],
'location': {
"path": self.issue_dict['file'],
"lines": {
"begin": int(self.issue_dict['line']),
"end": int(self.issue_dict['line']),
},
"positions": {
"begin": {
"line": int(self.issue_dict['line']),
"column": int(self.issue_dict['column']),
},
"end": {
"line": int(self.issue_dict['line']),
"column": int(self.issue_dict['column']),
},
},
},
}
if 'content' in self.issue_dict:
issue['content'] = {
'body': '```\n' +
'\n'.join(self.issue_dict['content']) +
'\n```'
}
-
+
issue['fingerprint'] = hashlib.md5(
'{file}:{line}:{column}:{type}'.format(**self.issue_dict).encode()
).hexdigest()
type_ = self.issue_dict['type'].split('-')[0]
issue['categories'], issue['severity'] = self._get_classifiaction(type_)
return issue
diff --git a/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py b/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
index eed340983..98097e29b 100644
--- a/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
+++ b/test/ci/codeclimate/codeclimate-clang-tidy/lib/runner.py
@@ -1,102 +1,114 @@
+"""runner.py: runner for clang-tidy in codeclimate (inspired from cpp-check)"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import json
import subprocess
import sys
import re
import os
try:
from termcolor import colored
except ImportError:
def colored(text, color):
return text
from command import Command
from issue_formatter import IssueFormatter
from workspace import Workspace
class Runner:
CONFIG_FILE_PATH = '/config.json'
"""Runs clang-tidy, collects and reports results."""
def __init__(self):
self._config_file_path = self.CONFIG_FILE_PATH
self._config = {}
self._decode_config()
self._ansi_escape = re.compile(r'\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])')
self._issue_parse = re.compile(r'(?P<file>.*\.(cc|hh)):(?P<line>[0-9]+):(?P<column>[0-9]+): (warning|error): (?P<detail>.*) \[(?P<type>.*)\]') # noqa
self._issues_fpr = []
self._workspace = Workspace(self._config.get('include_paths', []))
self._files = self._workspace.files
self._include_paths = self._workspace.include_paths
def run(self):
if not len(self._files) > 0:
return
self._print_debug(f'[clang-tidy] analyzing {len(self._files)} files')
command = Command(self._config, self._workspace).build()
self._print_debug(f'[clang-tidy] command: {command}')
self._generate_issues(command)
def _decode_config(self):
self._print_debug(f"Decoding config file {self._config_file_path}")
contents = ""
with open(self._config_file_path, "r") as config:
contents = config.read()
self._config = json.loads(contents)
self._print_debug(f'[clang-tidy] config: {self._config}')
def _print_issue(self, issue):
issue_ = IssueFormatter(issue).format()
path = os.path.dirname(os.path.abspath(issue_["location"]["path"]))
if path not in self._include_paths:
return
if issue_['fingerprint'] in self._issues_fpr:
return
self._issues_fpr.append(issue_['fingerprint'])
print('{}\0'.format(json.dumps(issue_)))
def _generate_issues(self, command):
issue = None
for line in self._run_command(command):
clean_line = self._ansi_escape.sub('', line)
match = self._issue_parse.match(clean_line)
if match:
if issue is not None:
self._print_issue(issue)
issue = match.groupdict()
elif issue:
if 'content' in issue:
issue['content'].append(line)
else:
issue['content'] = [line]
self._print_issue(issue)
def _run_command(self, command):
popen = subprocess.Popen(command,
stdout=subprocess.PIPE,
universal_newlines=True)
for stdout_line in iter(popen.stdout.readline, ""):
self._print_debug(stdout_line)
yield stdout_line
popen.stdout.close()
return_code = popen.wait()
if return_code:
self._print_debug(
f"[clang-tidy] {command} ReturnCode {return_code}")
# raise subprocess.CalledProcessError(return_code, command)
def _print_debug(self, message):
print(message, file=sys.stderr, flush=True)
diff --git a/test/ci/codeclimate/codeclimate-clang-tidy/lib/workspace.py b/test/ci/codeclimate/codeclimate-clang-tidy/lib/workspace.py
index 29685c3db..864a72e40 100644
--- a/test/ci/codeclimate/codeclimate-clang-tidy/lib/workspace.py
+++ b/test/ci/codeclimate/codeclimate-clang-tidy/lib/workspace.py
@@ -1,40 +1,54 @@
+
+""" workspace.py: workspace for clang-tidy in codeclimate (inspired from cpp-
+check)"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import os
class Workspace:
def __init__(self, include_paths, suffixes=['.c', '.cpp', '.cc', '.cxx']):
self._include_paths = include_paths
self._suffixes = suffixes
@property
def files(self):
paths = self._walk()
return [path for path in paths
if self._should_include(path)]
@property
def include_paths(self):
paths = self._walk()
return [path for path in paths if os.path.isdir(path)]
@property
def paths(self):
return [path for path in self._include_paths
if self._should_include(path) or os.path.isdir(path)]
def _should_include(self, name):
_, ext = os.path.splitext(name)
return ext in self._suffixes
def _walk(self):
paths = []
for path in self._include_paths:
if os.path.isdir(path):
for root, dirs, files in os.walk(path):
paths.extend([os.path.join(root, dir_) for dir_ in dirs])
paths.extend([os.path.join(root, file_) for file_ in files])
else:
paths.append(path)
return [os.path.abspath(path) for path in paths]
diff --git a/test/ci/includes_for_ci/aka_config.hh b/test/ci/includes_for_ci/aka_config.hh
index 737661d83..3b02f7015 100644
--- a/test/ci/includes_for_ci/aka_config.hh
+++ b/test/ci/includes_for_ci/aka_config.hh
@@ -1,90 +1,100 @@
/**
- * @file aka_config.hh.in
+ * @file aka_config.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Sun Sep 26 2010
- * @date last modification: Thu Jan 25 2018
+ * @date creation: Mon Feb 08 2021
+ * @date last modification: Mon Feb 08 2021
*
* @brief Compilation time configuration of Akantu
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_CONFIG_HH_
#define AKANTU_AKA_CONFIG_HH_
#define AKANTU_VERSION_MAJOR 4
#define AKANTU_VERSION_MINOR 0
#define AKANTU_VERSION_PATCH 0
#define AKANTU_VERSION (AKANTU_VERSION_MAJOR * 10000 \
+ AKANTU_VERSION_MINOR * 100 \
+ AKANTU_VERSION_PATCH)
namespace akantu {
using Real = double;
using Int = int;
using UInt = unsigned int;
} // akantu
#define AKANTU_INTEGER_SIZE 4
#define AKANTU_FLOAT_SIZE 8
/* #undef AKANTU_HAS_STRDUP */
/* #undef AKANTU_USE_BLAS */
#define AKANTU_USE_LAPACK
#define AKANTU_PARALLEL
#define AKANTU_USE_MPI
#define AKANTU_USE_SCOTCH
/* #undef AKANTU_USE_PTSCOTCH */
/* #undef AKANTU_SCOTCH_NO_EXTERN */
#define AKANTU_IMPLICIT
#define AKANTU_USE_MUMPS
/* #undef AKANTU_USE_PETSC */
#define AKANTU_USE_IOHELPER
/* #undef AKANTU_USE_QVIEW */
/* #undef AKANTU_USE_BLACKDYNAMITE */
#define AKANTU_USE_PYBIND11
/* #undef AKANTU_USE_OBSOLETE_GETTIMEOFDAY */
/* #undef AKANTU_EXTRA_MATERIALS */
/* #undef AKANTU_STUDENTS_EXTRA_PACKAGE */
#define AKANTU_DAMAGE_NON_LOCAL
#define AKANTU_SOLID_MECHANICS
#define AKANTU_STRUCTURAL_MECHANICS
#define AKANTU_HEAT_TRANSFER
#define AKANTU_PYTHON_INTERFACE
#define AKANTU_COHESIVE_ELEMENT
/* #undef AKANTU_PARALLEL_COHESIVE_ELEMENT */
/* #undef AKANTU_IGFEM */
/* #undef AKANTU_USE_CGAL */
/* #undef AKANTU_EMBEDDED */
// Debug tools
/* #undef AKANTU_NDEBUG */
/* #undef AKANTU_DEBUG_TOOLS */
#define READLINK_COMMAND /bin/readlink
#define ADDR2LINE_COMMAND /usr/bin/addr2line
#endif /* AKANTU_AKA_CONFIG_HH_ */
diff --git a/test/ci/includes_for_ci/aka_element_classes_info.hh b/test/ci/includes_for_ci/aka_element_classes_info.hh
index b13600d44..c00436f70 100644
--- a/test/ci/includes_for_ci/aka_element_classes_info.hh
+++ b/test/ci/includes_for_ci/aka_element_classes_info.hh
@@ -1,373 +1,376 @@
/**
- * @file aka_element_classes_info.hh.in
+ * @file aka_element_classes_info.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 19 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Mon Feb 08 2021
*
* @brief Declaration of the enums for the element classes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_
#define AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element Types */
/* -------------------------------------------------------------------------- */
/// @enum ElementType type of elements
enum ElementType {
_not_defined,
_cohesive_1d_2,
_cohesive_2d_4,
_cohesive_2d_6,
_cohesive_3d_12,
_cohesive_3d_16,
_cohesive_3d_6,
_cohesive_3d_8,
_point_1,
_segment_2,
_segment_3,
_triangle_3,
_triangle_6,
_quadrangle_4,
_quadrangle_8,
_tetrahedron_4,
_tetrahedron_10,
_pentahedron_6,
_pentahedron_15,
_hexahedron_8,
_hexahedron_20,
_bernoulli_beam_2,
_bernoulli_beam_3,
_discrete_kirchhoff_triangle_18,
_max_element_type
};
#define AKANTU_ek_cohesive_ELEMENT_TYPE \
(_cohesive_1d_2) \
(_cohesive_2d_4) \
(_cohesive_2d_6) \
(_cohesive_3d_12) \
(_cohesive_3d_16) \
(_cohesive_3d_6) \
(_cohesive_3d_8)
#define AKANTU_ek_regular_ELEMENT_TYPE \
(_point_1) \
(_segment_2) \
(_segment_3) \
(_triangle_3) \
(_triangle_6) \
(_quadrangle_4) \
(_quadrangle_8) \
(_tetrahedron_4) \
(_tetrahedron_10) \
(_pentahedron_6) \
(_pentahedron_15) \
(_hexahedron_8) \
(_hexahedron_20)
#define AKANTU_ek_structural_ELEMENT_TYPE \
(_bernoulli_beam_2) \
(_bernoulli_beam_3) \
(_discrete_kirchhoff_triangle_18)
#define AKANTU_ALL_ELEMENT_TYPE \
AKANTU_ek_cohesive_ELEMENT_TYPE \
AKANTU_ek_regular_ELEMENT_TYPE \
AKANTU_ek_structural_ELEMENT_TYPE
/* -------------------------------------------------------------------------- */
/* Element Kinds */
/* -------------------------------------------------------------------------- */
#define AKANTU_COHESIVE_KIND (_ek_cohesive)
#define AKANTU_REGULAR_KIND (_ek_regular)
#define AKANTU_STRUCTURAL_KIND (_ek_structural)
#define AKANTU_ELEMENT_KIND \
AKANTU_COHESIVE_KIND \
AKANTU_REGULAR_KIND \
AKANTU_STRUCTURAL_KIND
enum ElementKind {
BOOST_PP_SEQ_ENUM(AKANTU_ELEMENT_KIND),
_ek_not_defined
};
/* -------------------------------------------------------------------------- */
struct ElementKind_def {
using type = ElementKind;
static const type _begin_ = BOOST_PP_SEQ_HEAD(AKANTU_ELEMENT_KIND);
static const type _end_ = _ek_not_defined;
};
using element_kind_t = safe_enum<ElementKind_def> ;
/* -------------------------------------------------------------------------- */
/// @enum GeometricalType type of element potentially contained in a Mesh
enum GeometricalType {
_gt_cohesive_1d_2,
_gt_cohesive_2d_4,
_gt_cohesive_2d_6,
_gt_cohesive_3d_12,
_gt_cohesive_3d_16,
_gt_cohesive_3d_6,
_gt_cohesive_3d_8,
_gt_point,
_gt_segment_2,
_gt_segment_3,
_gt_triangle_3,
_gt_triangle_6,
_gt_quadrangle_4,
_gt_quadrangle_8,
_gt_tetrahedron_4,
_gt_tetrahedron_10,
_gt_hexahedron_8,
_gt_hexahedron_20,
_gt_pentahedron_6,
_gt_pentahedron_15,
_gt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Interpolation Types */
/* -------------------------------------------------------------------------- */
#define AKANTU_INTERPOLATION_TYPES \
(_itp_lagrange_point_1) \
(_itp_lagrange_segment_2) \
(_itp_lagrange_segment_3) \
(_itp_lagrange_triangle_3) \
(_itp_lagrange_triangle_6) \
(_itp_lagrange_quadrangle_4) \
(_itp_serendip_quadrangle_8) \
(_itp_lagrange_tetrahedron_4) \
(_itp_lagrange_tetrahedron_10) \
(_itp_lagrange_hexahedron_8) \
(_itp_serendip_hexahedron_20) \
(_itp_lagrange_pentahedron_6) \
(_itp_lagrange_pentahedron_15)\
(_itp_hermite_2) \
(_itp_bernoulli_beam_2) \
(_itp_bernoulli_beam_3) \
(_itp_discrete_kirchhoff_triangle_6) \
(_itp_discrete_kirchhoff_triangle_18)
/// @enum InterpolationType type of elements
enum InterpolationType {
BOOST_PP_SEQ_ENUM(AKANTU_INTERPOLATION_TYPES),
_itp_not_defined
};
/* -------------------------------------------------------------------------- */
/* Some sub types less probable to change */
/* -------------------------------------------------------------------------- */
/// @enum GeometricalShapeType types of shapes to define the contains
/// function in the element classes
enum GeometricalShapeType {
_gst_point,
_gst_triangle,
_gst_square,
_gst_prism,
_gst_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum GaussIntegrationType classes of types using common
/// description of the gauss point position and weights
enum GaussIntegrationType {
_git_point,
_git_segment,
_git_triangle,
_git_tetrahedron,
_git_pentahedron,
_git_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum InterpolationKind the family of interpolation types
enum InterpolationKind {
_itk_lagrangian,
_itk_structural,
_itk_not_defined
};
/* -------------------------------------------------------------------------- */
// BOOST PART: TOUCH ONLY IF YOU KNOW WHAT YOU ARE DOING
#define AKANTU_BOOST_CASE_MACRO(r, macro, _type) \
case _type: { \
macro(_type); \
break; \
}
#define AKANTU_BOOST_LIST_SWITCH(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
default: { \
AKANTU_ERROR("Type (" \
<< var /* NOLINT */ << ") not handled by this function"); \
} \
} \
} while (0)
#define AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, var) \
do { \
switch (var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
case _not_defined: /* FALLTHRU */ \
case _max_element_type: \
break; \
} \
} while (0)
#define AKANTU_BOOST_ELEMENT_SWITCH(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH(macro1, list1, type)
#define AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH_NO_DEFAULT(macro1, list1, type)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH_NO_DEFAULT(macro) \
AKANTU_BOOST_ELEMENT_SWITCH_NO_DEFAULT(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_LIST_MACRO(r, macro, type) macro(type)
#define AKANTU_BOOST_APPLY_ON_LIST(macro, list) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_GET_ELEMENT_LIST(kind) AKANTU##kind##_ELEMENT_TYPE
#define AKANTU_BOOST_KIND_ELEMENT_SWITCH(macro, kind) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, AKANTU_GET_ELEMENT_LIST(kind))
// BOOST_PP_SEQ_TO_LIST does not exists in Boost < 1.49
#define AKANTU_GENERATE_KIND_LIST(seq) \
BOOST_PP_TUPLE_TO_LIST(BOOST_PP_SEQ_SIZE(seq), BOOST_PP_SEQ_TO_TUPLE(seq))
#define AKANTU_ELEMENT_KIND_BOOST_LIST \
AKANTU_GENERATE_KIND_LIST(AKANTU_ELEMENT_KIND)
#define AKANTU_BOOST_ALL_KIND_LIST(macro, list) \
BOOST_PP_LIST_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_KIND(macro) \
AKANTU_BOOST_ALL_KIND_LIST(macro, AKANTU_ELEMENT_KIND_BOOST_LIST)
#define AKANTU_BOOST_ALL_KIND_SWITCH(macro) \
AKANTU_BOOST_LIST_SWITCH(macro, AKANTU_ELEMENT_KIND, kind)
#define AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_cohesive_ELEMENT_TYPE)
#define AKANTU_BOOST_COHESIVE_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_cohesive_ELEMENT_TYPE)
#define AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_regular_ELEMENT_TYPE)
#define AKANTU_BOOST_REGULAR_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_regular_ELEMENT_TYPE)
#define AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ek_structural_ELEMENT_TYPE)
#define AKANTU_BOOST_STRUCTURAL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ek_structural_ELEMENT_TYPE)
// /// define kept for compatibility reasons (they are most probably not needed
// /// anymore) \todo check if they can be removed
// #define AKANTU_REGULAR_ELEMENT_TYPE AKANTU_ek_regular_ELEMENT_TYPE
// #define AKANTU_COHESIVE_ELEMENT_TYPE AKANTU_ek_cohesive_ELEMENT_TYPE
// #define AKANTU_STRUCTURAL_ELEMENT_TYPE AKANTU_ek_structural_ELEMENT_TYPE
// #define AKANTU_IGFEM_ELEMENT_TYPE AKANTU_ek_igfem_ELEMENT_TYPE
/* -------------------------------------------------------------------------- */
/* Lists of interests for FEEngineTemplate functions */
/* -------------------------------------------------------------------------- */
#define AKANTU_FE_ENGINE_LIST_ASSEMBLE_FIELDS \
AKANTU_GENERATE_KIND_LIST((_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES_DERIVATIVES \
AKANTU_GENERATE_KIND_LIST((_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES \
AKANTU_GENERATE_KIND_LIST((_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_INTERPOLATE \
AKANTU_GENERATE_KIND_LIST((_ek_regular))
#define AKANTU_FE_ENGINE_LIST_LAGRANGE_BASE \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular))
#define AKANTU_FE_ENGINE_LIST_INVERSE_MAP \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular))
#define AKANTU_FE_ENGINE_LIST_INTERPOLATE_ON_INTEGRATION_POINTS \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_GRADIENT_ON_INTEGRATION_POINTS \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_GET_SHAPES_DERIVATIVES \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular) \
(_ek_structural))
#define AKANTU_FE_ENGINE_LIST_CONTAINS \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular))
#define AKANTU_FE_ENGINE_LIST_COMPUTE_NORMALS_ON_INTEGRATION_POINTS \
AKANTU_GENERATE_KIND_LIST((_ek_cohesive) \
(_ek_regular))
} // akantu
#endif /* AKANTU_AKA_ELEMENT_CLASSES_INFO_HH_ */
#include "aka_element_classes_info_inline_impl.hh"
diff --git a/test/ci/includes_for_ci/aka_fortran_mangling.hh b/test/ci/includes_for_ci/aka_fortran_mangling.hh
index d27b675b2..e6da111ec 100644
--- a/test/ci/includes_for_ci/aka_fortran_mangling.hh
+++ b/test/ci/includes_for_ci/aka_fortran_mangling.hh
@@ -1,16 +1,47 @@
+/**
+ * @file aka_fortran_mangling.hh
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Feb 08 2021
+ * @date last modification: Mon Feb 08 2021
+ *
+ * @brief Copy of the auto generated aka_fortran_mangling.hh
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
#ifndef AKA_FC_HEADER_INCLUDED
#define AKA_FC_HEADER_INCLUDED
/* Mangling for Fortran global symbols without underscores. */
#define AKA_FC_GLOBAL(name,NAME) name##_
/* Mangling for Fortran global symbols with underscores. */
#define AKA_FC_GLOBAL_(name,NAME) name##_
/* Mangling for Fortran module symbols without underscores. */
#define AKA_FC_MODULE(mod_name,name, mod_NAME,NAME) __##mod_name##_MOD_##name
/* Mangling for Fortran module symbols with underscores. */
#define AKA_FC_MODULE_(mod_name,name, mod_NAME,NAME) __##mod_name##_MOD_##name
#endif
diff --git a/test/ci/includes_for_ci/material_list.hh b/test/ci/includes_for_ci/material_list.hh
index 21440bce2..52659cd7f 100644
--- a/test/ci/includes_for_ci/material_list.hh
+++ b/test/ci/includes_for_ci/material_list.hh
@@ -1,46 +1,56 @@
/**
- * @file material_list.hh.in
+ * @file material_list.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 01 2010
- * @date last modification: Wed Feb 03 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Feb 08 2021
*
* @brief List of materials and all includes
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * @section LICENSE
*
- * Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_LIST_HH__
#define __AKANTU_MATERIAL_LIST_HH__
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
/* Material includes */
/* -------------------------------------------------------------------------- */
#include "material_cohesive_includes.hh"
#include "material_non_local_includes.hh"
#include "material_core_includes.hh"
/* -------------------------------------------------------------------------- */
/* Material list */
/* -------------------------------------------------------------------------- */
#define AKANTU_MATERIAL_LIST \
AKANTU_COHESIVE_MATERIAL_LIST \
AKANTU_DAMAGE_NON_LOCAL_MATERIAL_LIST \
AKANTU_CORE_MATERIAL_LIST \
// leave an empty line after the list
#endif /* __AKANTU_MATERIAL_LIST_HH__ */
diff --git a/test/ci/scripts/clang-tidy2code-quality.py b/test/ci/scripts/clang-tidy2code-quality.py
index 1f5c5e615..1a8e5841e 100644
--- a/test/ci/scripts/clang-tidy2code-quality.py
+++ b/test/ci/scripts/clang-tidy2code-quality.py
@@ -1,80 +1,92 @@
#!/usr/bin/env python3
+"""clang-tidy2code-quality.py: Conversion of clang-tidy output 2
+code-quality"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import re
import os
import hashlib
import json
import sys
# 7-bit C1 ANSI sequences
ansi_escape = re.compile(r'''
\x1B # ESC
(?: # 7-bit C1 Fe (except CSI)
[@-Z\\-_]
| # or [ for CSI, followed by a control sequence
\[
[0-?]* # Parameter bytes
[ -/]* # Intermediate bytes
[@-~] # Final byte
)
''', re.VERBOSE)
re_log_parse = re.compile(
r'(?P<file>.*\.(cc|hh)):(?P<line>[0-9]+):(?P<column>[0-9]+): warning: (?P<detail>.*) \[(?P<type>.*)\]' # noqa
)
categories = {
"bugprone": "Bug Risk",
"modernize": "Clarity",
"mpi": "Bug Risk",
"openmp": "Bug Risk",
"performance": "Performance",
"readability": "Clarity",
}
issues = {}
with open('clang-tidy-all-out.log', 'r') as log:
for line in log:
clean_line = ansi_escape.sub('', line)
match = re_log_parse.match(clean_line)
if match:
line_dict = match.groupdict()
line_dict['file'] = os.path.relpath(line_dict['file'])
line_dict['fingerprint'] = hashlib.md5(
'{file}:{line}:{column}:{type}'.format(**line_dict).encode()
).hexdigest()
issue = {
'type': 'issue',
'description': line_dict['detail'],
'fingerprint': line_dict['fingerprint'],
'location': {
"path": line_dict['file'],
"lines": {
"begin": int(line_dict['line']),
"end": int(line_dict['line']),
},
"positions": {
"begin": {
"line": int(line_dict['line']),
"column": int(line_dict['column']),
},
},
},
'severity': 'minor',
}
category = line_dict['type'].split('-')[0]
if category in categories:
issue['category'] = categories[category]
# use a dictionnary to avoid duplicates
issues[issue['fingerprint']] = issue
issues = list(issues.values())
json.dump(issues, sys.stdout)
diff --git a/test/python_fe/__init__.py b/test/python_fe/__init__.py
index c778de567..1678b5708 100644
--- a/test/python_fe/__init__.py
+++ b/test/python_fe/__init__.py
@@ -1,34 +1,47 @@
+
+""" __init__.py: Python module to test the fe_engine"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
import sys as __aka_sys
def export(definition):
"""
Decorator to export definitions from sub-modules to the top-level package
:param definition: definition to be exported
:return: definition
"""
__module = __aka_sys.modules[definition.__module__]
__pkg = __aka_sys.modules[__module.__package__]
__pkg.__dict__[definition.__name__] = definition
if '__all__' not in __pkg.__dict__:
__pkg.__dict__['__all__'] = []
__pkg.__all__.append(definition.__name__)
return definition
try:
from termcolor import colored
except ImportError:
# noinspection PyUnusedLocal
def colored(string, *args, **kwargs):
return string
__all__ = ['colored']
-from . import truss_fe # NOQA: F401
-from . import static_solver # NOQA: F401
-from . import dynamic_solver # NOQA: F401
+from . import truss_fe # NOQA: E402
+from . import static_solver # NOQA: E402
+from . import dynamic_solver # NOQA: E402
diff --git a/test/python_fe/dynamic_solver.py b/test/python_fe/dynamic_solver.py
index 42d9e532c..dbfdc916b 100644
--- a/test/python_fe/dynamic_solver.py
+++ b/test/python_fe/dynamic_solver.py
@@ -1,101 +1,102 @@
+""" dynamic_solver.py: dynamic solver for test purposes"""
# ------------------------------------------------------------------------------
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
+__license__ = "LGPLv3"
# ------------------------------------------------------------------------------
import copy
import numpy.linalg as npl
import scipy.sparse as sp
import scipy.sparse.linalg as spl
from . import export
from . import fe
@export
class DynamicSolver(fe.Solver):
def __init__(self, model, **kwargs):
opt = copy.copy(kwargs)
self._delta_t = opt.pop("delta_t", 0.001)
self._alpha = opt.pop("alpha", 1./2.)
self._beta = opt.pop("beta", 1./2.)
self._type = opt.pop("type", 'disp')
self._tolerance = opt.pop("tolerance", 1e-10)
self._max_nloops = opt.pop("max_iterations", 100)
self._model = model
self._J = sp.csr_matrix(self._model.K.shape)
self._coeff = {'disp': {'disp': 1.,
'velo': 1. / (self._alpha * self._delta_t),
'acce': 1. / (self._alpha * self._beta * self._delta_t ** 2)}, # NOQA: E501
'velo': {'disp': self._alpha * self._delta_t,
'velo': 1.,
'acce': 1. / (self._beta * self._delta_t)},
'acce': {'disp': self._alpha * self._beta * self._delta_t ** 2, # NOQA: E501
'velo': self._beta * self._delta_t,
'acce': 1.}}
def _assembleResidual(self):
self._r = self._model.f_ext - self._model.f_int - \
self._model.M * self._model.a
C = self._model.C
if C is not None:
self._r -= C * self._model.v
def _predictor(self):
self._model.u += self._delta_t * self._model.v + \
self._delta_t ** 2 / 2. * self._model.a
self._model.v += self._delta_t * self._model.a
def _corrector(self, delta_):
self._model.u += self._coeff[self._type]['disp'] * delta_
self._model.v += self._coeff[self._type]['velo'] * delta_
self._model.a += self._coeff[self._type]['acce'] * delta_
def _assembleJacobian(self):
K = self._model.K
e = self._coeff[self._type]['disp']
self._J = e * K
C = self._model.C
if C is not None:
d = self._coeff[self._type]['velo']
self._J += d * C
M = self._model.M
if M is not None:
c = self._coeff[self._type]['acce']
self._J += c * M
self._model.applyDirichletBC()
self._zero_rows(self._J, self._model.blocked)
def solveStep(self):
self._predictor()
self._nloops = 0
converged = False
while not converged:
self._assembleJacobian()
self._assembleResidual()
delta_ = spl.spsolve(self._J, self._r)
self._corrector(delta_)
self._nloops += 1
error = npl.norm(delta_)
converged = error < self._tolerance or \
self._nloops > self._max_nloops
print("{0} {1} -> {2}".format(error, self._nloops, converged))
if self._nloops >= self._max_nloops:
raise ValueError('The solver did not converge')
@property
def nloops(self):
return self._nloops
diff --git a/test/python_fe/fe.py b/test/python_fe/fe.py
index e80e3f872..784530962 100644
--- a/test/python_fe/fe.py
+++ b/test/python_fe/fe.py
@@ -1,60 +1,60 @@
-# ------------------------------------------------------------------------------
+""" fe.py: feengine testers"""
+
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
import abc
class Solver(metaclass=abc.ABCMeta):
@abc.abstractmethod
def solveStep(self):
pass
def _zero_rows(self, A, rows):
for r in rows:
diag = A[r, r]
# zeros the lines defined in b
A.data[A.indptr[r]:A.indptr[r + 1]] = 0.
A[r, r] = diag
class Model(metaclass=abc.ABCMeta):
@abc.abstractmethod
def applyDirichletBC(self):
pass
@abc.abstractmethod
def f_int(self):
pass
@property
@abc.abstractmethod
def f_ext(self):
pass
@property
@abc.abstractmethod
def K(self):
pass
@property
@abc.abstractmethod
def M(self):
pass
@property
@abc.abstractmethod
def C(self):
pass
@property
@abc.abstractmethod
def blocked(self):
pass
diff --git a/test/python_fe/static_solver.py b/test/python_fe/static_solver.py
index 201e725e1..658a12ceb 100644
--- a/test/python_fe/static_solver.py
+++ b/test/python_fe/static_solver.py
@@ -1,36 +1,37 @@
+""" static_solver.py: static solver for test purposes"""
# ------------------------------------------------------------------------------
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
+__license__ = "LGPLv3"
# ------------------------------------------------------------------------------
import copy
import scipy.sparse.linalg as spl
from . import export
from . import fe
@export
class StaticSolver(fe.Solver):
def __init__(self, model):
self._model = model
def _assembleResidual(self):
self._r = self._model.f_ext - self._model.f_int
def _assembleJacobian(self):
self._J = copy.copy(self._model.K)
self._model.applyDirichletBC()
self._zero_rows(self._J, self._model.blocked)
def solveStep(self):
self._assembleJacobian()
self._assembleResidual()
x = spl.spsolve(self._J, self._r)
self._model.u += x
diff --git a/test/python_fe/truss_fe.py b/test/python_fe/truss_fe.py
index 757a49c7a..c609303b9 100644
--- a/test/python_fe/truss_fe.py
+++ b/test/python_fe/truss_fe.py
@@ -1,132 +1,133 @@
+""" truss_fe.py: truss tester"""
# ------------------------------------------------------------------------------
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
+__license__ = "LGPLv3"
# ------------------------------------------------------------------------------
-import numpy as np
import copy
+import numpy as np
import scipy.sparse as sp
from . import export
from . import fe
@export
class TrussFE(fe.Model):
def __init__(self, **kwargs):
opt = copy.copy(kwargs)
self._A = opt.pop("A", 1.)
self._E = opt.pop("E", 1.)
self._L = opt.pop("L", 1.)
self._rho = opt.pop("rho", 1.)
self._F = opt.pop("F", {-10: [-1]})
self._blocked = opt.pop("blocked", ([0], [0]))
self._Ne = opt.pop("Ne", 1)
self._Le = self._L / self._Ne
self._F_ext = np.zeros((self._Ne + 1))
self._F_int = np.zeros((self._Ne + 1))
self._u = np.zeros((self._Ne + 1))
self._v = np.zeros((self._Ne + 1))
self._a = np.zeros((self._Ne + 1))
self.assembleMass()
def assembleMass(self):
Me = np.array([[2., 1.],
[1., 2.]])
Me *= self._rho * self._A * self._Le / 6
self._M = sp.lil_matrix((self._Ne + 1, self._Ne + 1))
for i in range(self._Ne):
self._M[i:i+2, i:i+2] += Me
self._M = self._M.tocsr()
def assembleStiffness(self):
Ke = np.array([[1., -1.],
[-1., 1.]])
Ke *= self._E * self._A / self._Le
self._K = sp.lil_matrix((self._Ne + 1, self._Ne + 1))
for i in range(self._Ne):
self._K[i:i+2, i:i+2] += Ke
self._K = self._K.tocsr()
def applyNeumannBC(self):
for force, nodes in self._F.items():
self._F_ext[nodes] = force
def applyDirichletBC(self):
for i, b in enumerate(self._blocked[0]):
self._u[b] = self._blocked[1][i]
def computeInternalForces(self):
self._F_int = self._K * self._u
@property
def K(self):
self.assembleStiffness()
return self._K
@property
def M(self):
return self._M
@property
def C(self):
return None
@property
def u(self):
self.applyDirichletBC()
return self._u
@u.setter
def u(self, x):
self._u = x
self.applyDirichletBC()
@property
def v(self):
return self._v
@v.setter
def v(self, v_):
self._v = v_
@property
def a(self):
return self._a
@a.setter
def a(self, a_):
self._a = a_
@property
def f_int(self):
self.computeInternalForces()
return self._F_int
@property
def f_ext(self):
self.applyNeumannBC()
return self._F_ext
@f_ext.setter
def f_ext(self, f):
self._F_ext = f
@property
def blocked(self):
return self._blocked[0]
@property
def Le(self):
return self._Le
diff --git a/test/test_common/CMakeLists.txt b/test/test_common/CMakeLists.txt
index 3365f7019..ba1ddb301 100644
--- a/test/test_common/CMakeLists.txt
+++ b/test/test_common/CMakeLists.txt
@@ -1,36 +1,46 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Tue Dec 05 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed May 27 2020
#
# @brief configurations for common tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(test_grid_mesh circle.geo 2 1)
register_test(test_grid test_grid.cc
DEPENDS test_grid_mesh
PACKAGE core)
#register_test(test_types test_types.cc PACKAGE core)
register_gtest_sources(SOURCES test_csr.cc PACKAGE core)
register_gtest_sources(SOURCES test_array.cc PACKAGE core)
register_gtest_sources(SOURCES test_tensors.cc PACKAGE core)
register_gtest_sources(SOURCES test_voigt_helper.cc PACKAGE core)
register_gtest_test(test_common)
diff --git a/test/test_common/test_array.cc b/test/test_common/test_array.cc
index 10baffdca..9b89586af 100644
--- a/test/test_common/test_array.cc
+++ b/test/test_common/test_array.cc
@@ -1,289 +1,292 @@
/**
* @file test_array.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Nov 09 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Test the arry class
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <aka_array.hh>
#include <aka_types.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <memory>
#include <typeindex>
#include <typeinfo>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
class NonTrivial {
public:
NonTrivial() = default;
NonTrivial(int a) : a(a){};
bool operator==(const NonTrivial & rhs) { return a == rhs.a; }
int a{0};
};
bool operator==(const int & a, const NonTrivial & rhs) { return a == rhs.a; }
std::ostream & operator<<(std::ostream & stream, const NonTrivial & _this) {
stream << _this.a;
return stream;
}
/* -------------------------------------------------------------------------- */
using TestTypes = ::testing::Types<Real, UInt, NonTrivial>;
/* -------------------------------------------------------------------------- */
::testing::AssertionResult AssertType(const char * /*a_expr*/,
const char * /*b_expr*/,
const std::type_info & a,
const std::type_info & b) {
if (std::type_index(a) == std::type_index(b))
return ::testing::AssertionSuccess();
return ::testing::AssertionFailure()
<< debug::demangle(a.name()) << " != " << debug::demangle(b.name())
<< ") are different";
}
/* -------------------------------------------------------------------------- */
template <typename T> class ArrayConstructor : public ::testing::Test {
protected:
using type = T;
void SetUp() override { type_str = debug::demangle(typeid(T).name()); }
template <typename... P> decltype(auto) construct(P &&... params) {
return std::make_unique<Array<T>>(std::forward<P>(params)...);
}
protected:
std::string type_str;
};
TYPED_TEST_SUITE(ArrayConstructor, TestTypes, );
TYPED_TEST(ArrayConstructor, ConstructDefault1) {
auto array = this->construct();
EXPECT_EQ(0, array->size());
EXPECT_EQ(1, array->getNbComponent());
EXPECT_STREQ("", array->getID().c_str());
}
TYPED_TEST(ArrayConstructor, ConstructDefault2) {
auto array = this->construct(1000);
EXPECT_EQ(1000, array->size());
EXPECT_EQ(1, array->getNbComponent());
EXPECT_STREQ("", array->getID().c_str());
}
TYPED_TEST(ArrayConstructor, ConstructDefault3) {
auto array = this->construct(1000, 10);
EXPECT_EQ(1000, array->size());
EXPECT_EQ(10, array->getNbComponent());
EXPECT_STREQ("", array->getID().c_str());
}
TYPED_TEST(ArrayConstructor, ConstructDefault4) {
auto array = this->construct(1000, 10, "test");
EXPECT_EQ(1000, array->size());
EXPECT_EQ(10, array->getNbComponent());
EXPECT_STREQ("test", array->getID().c_str());
}
TYPED_TEST(ArrayConstructor, ConstructDefault5) {
auto array = this->construct(1000, 10, 1);
EXPECT_EQ(1000, array->size());
EXPECT_EQ(10, array->getNbComponent());
EXPECT_EQ(1, array->operator()(10, 6));
EXPECT_STREQ("", array->getID().c_str());
}
// TYPED_TEST(ArrayConstructor, ConstructDefault6) {
// typename TestFixture::type defaultv[2] = {0, 1};
// auto array = this->construct(1000, 2, defaultv);
// EXPECT_EQ(1000, array->size());
// EXPECT_EQ(2, array->getNbComponent());
// EXPECT_EQ(1, array->operator()(10, 1));
// EXPECT_EQ(0, array->operator()(603, 0));
// EXPECT_STREQ("", array->getID().c_str());
// }
/* -------------------------------------------------------------------------- */
template <typename T> class ArrayFixture : public ArrayConstructor<T> {
public:
void SetUp() override {
ArrayConstructor<T>::SetUp();
array = this->construct(1000, 10);
}
void TearDown() override { array.reset(nullptr); }
protected:
std::unique_ptr<Array<T>> array;
};
TYPED_TEST_SUITE(ArrayFixture, TestTypes, );
TYPED_TEST(ArrayFixture, Copy) {
Array<typename TestFixture::type> copy(*this->array);
EXPECT_EQ(1000, copy.size());
EXPECT_EQ(10, copy.getNbComponent());
EXPECT_NE(this->array->storage(), copy.storage());
}
TYPED_TEST(ArrayFixture, Set) {
auto & arr = *(this->array);
arr.set(12);
EXPECT_EQ(12, arr(156, 5));
EXPECT_EQ(12, arr(520, 7));
EXPECT_EQ(12, arr(999, 9));
}
TYPED_TEST(ArrayFixture, Resize) {
auto & arr = *(this->array);
auto * ptr = arr.storage();
arr.resize(0);
EXPECT_EQ(0, arr.size());
EXPECT_TRUE(arr.storage() == nullptr or arr.storage() == ptr);
EXPECT_LE(0, arr.getAllocatedSize());
arr.resize(3000);
EXPECT_EQ(3000, arr.size());
EXPECT_LE(3000, arr.getAllocatedSize());
ptr = arr.storage();
arr.resize(0);
EXPECT_EQ(0, arr.size());
EXPECT_TRUE(arr.storage() == nullptr or arr.storage() == ptr);
EXPECT_LE(0, arr.getAllocatedSize());
}
TYPED_TEST(ArrayFixture, PushBack) {
auto & arr = *(this->array);
auto * ptr = arr.storage();
arr.resize(0);
EXPECT_EQ(0, arr.size());
EXPECT_TRUE(arr.storage() == nullptr or arr.storage() == ptr);
EXPECT_LE(0, arr.getAllocatedSize());
arr.resize(3000);
EXPECT_EQ(3000, arr.size());
EXPECT_LE(3000, arr.getAllocatedSize());
ptr = arr.storage();
arr.resize(0);
EXPECT_EQ(0, arr.size());
EXPECT_TRUE(arr.storage() == nullptr or arr.storage() == ptr);
EXPECT_LE(0, arr.getAllocatedSize());
}
TYPED_TEST(ArrayFixture, ViewVector) {
auto && view = make_view(*this->array, 10);
EXPECT_NO_THROW(view.begin());
{
auto it = view.begin();
EXPECT_EQ(10, it->size());
EXPECT_PRED_FORMAT2(AssertType, typeid(*it),
typeid(Vector<typename TestFixture::type>));
EXPECT_PRED_FORMAT2(AssertType, typeid(it[0]),
typeid(VectorProxy<typename TestFixture::type>));
}
}
TYPED_TEST(ArrayFixture, ViewMatrix) {
{
auto && view = make_view(*this->array, 2, 5);
EXPECT_NO_THROW(view.begin());
{
auto it = view.begin();
EXPECT_EQ(10, it->size());
EXPECT_EQ(2, it->size(0));
EXPECT_EQ(5, it->size(1));
EXPECT_PRED_FORMAT2(AssertType, typeid(*it),
typeid(Matrix<typename TestFixture::type>));
EXPECT_PRED_FORMAT2(AssertType, typeid(it[0]),
typeid(MatrixProxy<typename TestFixture::type>));
}
}
}
TYPED_TEST(ArrayFixture, ViewVectorWrong) {
auto && view = make_view(*this->array, 11);
EXPECT_THROW(view.begin(), debug::ArrayException);
}
TYPED_TEST(ArrayFixture, ViewMatrixWrong) {
auto && view = make_view(*this->array, 3, 7);
EXPECT_THROW(view.begin(), debug::ArrayException);
}
TYPED_TEST(ArrayFixture, ViewMatrixIter) {
std::size_t count = 0;
for (auto && mat : make_view(*this->array, 10, 10)) {
EXPECT_EQ(100, mat.size());
EXPECT_EQ(10, mat.size(0));
EXPECT_EQ(10, mat.size(1));
EXPECT_PRED_FORMAT2(AssertType, typeid(mat),
typeid(Matrix<typename TestFixture::type>));
++count;
}
EXPECT_EQ(100, count);
}
TYPED_TEST(ArrayFixture, ConstViewVector) {
const auto & carray = *this->array;
auto && view = make_view(carray, 10);
EXPECT_NO_THROW(view.begin());
{
auto it = view.begin();
EXPECT_EQ(10, it->size());
EXPECT_PRED_FORMAT2(AssertType, typeid(*it),
typeid(Vector<typename TestFixture::type>));
EXPECT_PRED_FORMAT2(AssertType, typeid(it[0]),
typeid(VectorProxy<typename TestFixture::type>));
}
}
} // namespace
diff --git a/test/test_common/test_csr.cc b/test/test_common/test_csr.cc
index c5403ab15..ca2eb48aa 100644
--- a/test/test_common/test_csr.cc
+++ b/test/test_common/test_csr.cc
@@ -1,101 +1,103 @@
/**
* @file test_csr.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jul 30 2012
- * @date last modification: Sun Dec 03 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sun Dec 03 2017
*
* @brief Test the CSR (compressed sparse row) data structure
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class TestCsrFixture : public ::testing::Test {
protected:
void SetUp() override {
csr.resizeRows(N);
csr.clearRows();
for (UInt i = 0; i < N; ++i) {
UInt nb_cols(UInt(rand() * double(N) / (RAND_MAX + 1.)));
nb_cols_per_row.push_back(nb_cols);
for (UInt j = 0; j < nb_cols; ++j) {
++csr.rowOffset(i);
}
}
csr.countToCSR();
csr.resizeCols();
csr.beginInsertions();
for (UInt i = 0; i < N; ++i) {
UInt nb_cols = nb_cols_per_row[i];
for (UInt j = 0; j < nb_cols; ++j) {
csr.insertInRow(i, nb_cols - j);
}
}
csr.endInsertions();
}
std::vector<UInt> nb_cols_per_row;
CSR<UInt> csr;
size_t N = 1000;
};
TEST_F(TestCsrFixture, CheckInsertion) { EXPECT_EQ(N, this->csr.getNbRows()); }
TEST_F(TestCsrFixture, Iteration) {
for (UInt i = 0; i < this->csr.getNbRows(); ++i) {
auto it = this->csr.begin(i);
auto end = this->csr.end(i);
UInt nb_cols = this->nb_cols_per_row[i];
for (; it != end; ++it) {
EXPECT_EQ(nb_cols, *it);
nb_cols--;
}
EXPECT_EQ(0, nb_cols);
}
}
TEST_F(TestCsrFixture, ReverseIteration) {
for (UInt i = 0; i < csr.getNbRows(); ++i) {
auto it = csr.rbegin(i);
auto end = csr.rend(i);
UInt nb_cols = nb_cols_per_row[i];
UInt j = nb_cols;
for (; it != end; --it) {
EXPECT_EQ((nb_cols - j + 1), *it);
j--;
}
EXPECT_EQ(0, j);
}
}
diff --git a/test/test_common/test_grid.cc b/test/test_common/test_grid.cc
index 420274b3a..c6c501073 100644
--- a/test/test_common/test_grid.cc
+++ b/test/test_common/test_grid.cc
@@ -1,83 +1,85 @@
/**
* @file test_grid.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jul 15 2010
- * @date last modification: Fri Dec 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Nov 02 2018
*
* @brief Test the grid object
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_grid_dynamic.hh"
#include "mesh.hh"
#include "mesh_io.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
const UInt spatial_dimension = 2;
akantu::initialize(argc, argv);
Mesh circle(spatial_dimension);
circle.read("circle.msh");
const auto & l = circle.getLocalLowerBounds();
const auto & u = circle.getLocalUpperBounds();
Real spacing[spatial_dimension] = {0.2, 0.2};
Vector<Real> s(spacing, spatial_dimension);
Vector<Real> c = u;
c += l;
c /= 2.;
SpatialGrid<Element> grid(spatial_dimension, s, c);
Vector<Real> bary(spatial_dimension);
Element el;
el.ghost_type = _not_ghost;
for (auto & type : circle.elementTypes(spatial_dimension)) {
UInt nb_element = circle.getNbElement(type);
el.type = type;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
circle.getBarycenter(el, bary);
grid.insert(el, bary);
}
}
std::cout << grid << std::endl;
Mesh mesh(spatial_dimension, "save");
grid.saveAsMesh(mesh);
mesh.write("grid.msh");
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_common/test_tensors.cc b/test/test_common/test_tensors.cc
index c219aa4ef..531f862cc 100644
--- a/test/test_common/test_tensors.cc
+++ b/test/test_common/test_tensors.cc
@@ -1,592 +1,594 @@
/**
* @file test_tensors.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Mon Jan 22 2018
+ * @date last modification: Tue Feb 05 2019
*
* @brief test the tensors types
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_iterators.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <gtest/gtest.h>
#include <memory>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
/* -------------------------------------------------------------------------- */
class TensorConstructorFixture : public ::testing::Test {
public:
void SetUp() override {
for (auto & r : reference) {
r = rand(); // google-test seeds srand()
}
}
void TearDown() override {}
template <typename V> void compareToRef(const V & v) {
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(reference[i], v.storage()[i]);
}
}
protected:
const int size_{24};
const std::array<int, 2> mat_size{{4, 6}};
// const std::array<int, 3> tens3_size{{4, 2, 3}};
std::array<double, 24> reference;
};
/* -------------------------------------------------------------------------- */
class TensorFixture : public TensorConstructorFixture {
public:
TensorFixture()
: vref(reference.data(), size_),
mref(reference.data(), mat_size[0], mat_size[1]) {}
protected:
Vector<double> vref;
Matrix<double> mref;
};
/* -------------------------------------------------------------------------- */
// Vector ----------------------------------------------------------------------
TEST_F(TensorConstructorFixture, VectorDefaultConstruct) {
Vector<double> v;
EXPECT_EQ(0, v.size());
EXPECT_EQ(nullptr, v.storage());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorConstructorFixture, VectorConstruct1) {
double r = rand();
Vector<double> v(size_, r);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(r, v(i));
EXPECT_DOUBLE_EQ(r, v[i]);
}
}
TEST_F(TensorConstructorFixture, VectorConstructWrapped) {
Vector<double> v(reference.data(), size_);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
for (int i = 0; i < size_; ++i) {
EXPECT_DOUBLE_EQ(reference[i], v(i));
EXPECT_DOUBLE_EQ(reference[i], v[i]);
}
}
TEST_F(TensorConstructorFixture, VectorConstructInitializer) {
Vector<double> v{0., 1., 2., 3., 4., 5.};
EXPECT_EQ(6, v.size());
EXPECT_EQ(false, v.isWrapped());
for (int i = 0; i < 6; ++i) {
EXPECT_DOUBLE_EQ(i, v(i));
}
}
TEST_F(TensorConstructorFixture, VectorConstructCopy1) {
Vector<double> vref(reference.data(), reference.size());
Vector<double> v(vref);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructCopy2) {
Vector<double> vref(reference.data(), reference.size());
Vector<double> v(vref, false);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructProxy1) {
VectorProxy<double> vref(reference.data(), reference.size());
EXPECT_EQ(size_, vref.size());
compareToRef(vref);
Vector<double> v(vref);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(true, v.isWrapped());
compareToRef(v);
}
TEST_F(TensorConstructorFixture, VectorConstructProxy2) {
Vector<double> vref(reference.data(), reference.size());
VectorProxy<double> v(vref);
EXPECT_EQ(size_, v.size());
compareToRef(v);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorEqual) {
Vector<double> v;
v = vref;
compareToRef(v);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorFixture, VectorEqualProxy) {
VectorProxy<double> vref_proxy(vref);
Vector<double> v;
v = vref;
compareToRef(v);
EXPECT_EQ(size_, v.size());
EXPECT_EQ(false, v.isWrapped());
}
TEST_F(TensorFixture, VectorEqualProxy2) {
Vector<double> v_store(size_, 0.);
VectorProxy<double> v(v_store);
v = vref;
compareToRef(v);
compareToRef(v_store);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorSet) {
Vector<double> v(vref);
compareToRef(v);
double r = rand();
v.set(r);
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(r, v[i]);
}
TEST_F(TensorFixture, VectorClear) {
Vector<double> v(vref);
compareToRef(v);
v.zero();
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0, v[i]);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, VectorDivide) {
Vector<double> v;
double r = rand();
v = vref / r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, v[i]);
}
TEST_F(TensorFixture, VectorMultiply1) {
Vector<double> v;
double r = rand();
v = vref * r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorMultiply2) {
Vector<double> v;
double r = rand();
v = r * vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorAddition) {
Vector<double> v;
v = vref + vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., v[i]);
}
TEST_F(TensorFixture, VectorSubstract) {
Vector<double> v;
v = vref - vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., v[i]);
}
TEST_F(TensorFixture, VectorDivideEqual) {
Vector<double> v(vref);
double r = rand();
v /= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, v[i]);
}
TEST_F(TensorFixture, VectorMultiplyEqual1) {
Vector<double> v(vref);
double r = rand();
v *= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, v[i]);
}
TEST_F(TensorFixture, VectorMultiplyEqual2) {
Vector<double> v(vref);
v *= v;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * reference[i], v[i]);
}
TEST_F(TensorFixture, VectorAdditionEqual) {
Vector<double> v(vref);
v += vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., v[i]);
}
TEST_F(TensorFixture, VectorSubstractEqual) {
Vector<double> v(vref);
v -= vref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., v[i]);
}
/* -------------------------------------------------------------------------- */
// Matrix ----------------------------------------------------------------------
TEST_F(TensorConstructorFixture, MatrixDefaultConstruct) {
Matrix<double> m;
EXPECT_EQ(0, m.size());
EXPECT_EQ(0, m.rows());
EXPECT_EQ(0, m.cols());
EXPECT_EQ(nullptr, m.storage());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorConstructorFixture, MatrixConstruct1) {
double r = rand();
Matrix<double> m(mat_size[0], mat_size[1], r);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
for (int i = 0; i < mat_size[0]; ++i) {
for (int j = 0; j < mat_size[1]; ++j) {
EXPECT_EQ(r, m(i, j));
EXPECT_EQ(r, m[i + j * mat_size[0]]);
}
}
}
TEST_F(TensorConstructorFixture, MatrixConstructWrapped) {
Matrix<double> m(reference.data(), mat_size[0], mat_size[1]);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(true, m.isWrapped());
for (int i = 0; i < mat_size[0]; ++i) {
for (int j = 0; j < mat_size[1]; ++j) {
EXPECT_DOUBLE_EQ(reference[i + j * mat_size[0]], m(i, j));
}
}
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructInitializer) {
Matrix<double> m{{0., 1., 2.}, {3., 4., 5.}};
EXPECT_EQ(6, m.size());
EXPECT_EQ(2, m.rows());
EXPECT_EQ(3, m.cols());
EXPECT_EQ(false, m.isWrapped());
int c = 0;
for (int i = 0; i < 2; ++i) {
for (int j = 0; j < 3; ++j, ++c) {
EXPECT_DOUBLE_EQ(c, m(i, j));
}
}
}
TEST_F(TensorConstructorFixture, MatrixConstructCopy1) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructCopy2) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructProxy1) {
MatrixProxy<double> mref(reference.data(), mat_size[0], mat_size[1]);
EXPECT_EQ(size_, mref.size());
EXPECT_EQ(mat_size[0], mref.size(0));
EXPECT_EQ(mat_size[1], mref.size(1));
compareToRef(mref);
Matrix<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(true, m.isWrapped());
compareToRef(m);
}
TEST_F(TensorConstructorFixture, MatrixConstructProxy2) {
Matrix<double> mref(reference.data(), mat_size[0], mat_size[1]);
MatrixProxy<double> m(mref);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.size(0));
EXPECT_EQ(mat_size[1], m.size(1));
compareToRef(m);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixEqual) {
Matrix<double> m;
m = mref;
compareToRef(m);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorFixture, MatrixEqualProxy1) {
MatrixProxy<double> mref_proxy(mref);
Matrix<double> m;
m = mref;
compareToRef(m);
EXPECT_EQ(size_, m.size());
EXPECT_EQ(mat_size[0], m.rows());
EXPECT_EQ(mat_size[1], m.cols());
EXPECT_EQ(false, m.isWrapped());
}
TEST_F(TensorFixture, MatrixEqualProxy2) {
Matrix<double> m_store(mat_size[0], mat_size[1], 0.);
MatrixProxy<double> m(m_store);
m = mref;
compareToRef(m);
compareToRef(m_store);
}
TEST_F(TensorFixture, MatrixEqualSlice) {
Matrix<double> m(mat_size[0], mat_size[1], 0.);
for (unsigned int i = 0; i < m.cols(); ++i)
m(i) = Vector<Real>(mref(i));
compareToRef(m);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixSet) {
Matrix<double> m(mref);
compareToRef(m);
double r = rand();
m.set(r);
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(r, m[i]);
}
TEST_F(TensorFixture, MatrixClear) {
Matrix<double> m(mref);
compareToRef(m);
m.zero();
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0, m[i]);
}
/* -------------------------------------------------------------------------- */
TEST_F(TensorFixture, MatrixDivide) {
Matrix<double> m;
double r = rand();
m = mref / r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiply1) {
Matrix<double> m;
double r = rand();
m = mref * r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiply2) {
Matrix<double> m;
double r = rand();
m = r * mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixAddition) {
Matrix<double> m;
m = mref + mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., m[i]);
}
TEST_F(TensorFixture, MatrixSubstract) {
Matrix<double> m;
m = mref - mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., m[i]);
}
TEST_F(TensorFixture, MatrixDivideEqual) {
Matrix<double> m(mref);
double r = rand();
m /= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] / r, m[i]);
}
TEST_F(TensorFixture, MatrixMultiplyEqual1) {
Matrix<double> m(mref);
double r = rand();
m *= r;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * r, m[i]);
}
TEST_F(TensorFixture, MatrixAdditionEqual) {
Matrix<double> m(mref);
m += mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(reference[i] * 2., m[i]);
}
TEST_F(TensorFixture, MatrixSubstractEqual) {
Matrix<double> m(mref);
m -= mref;
for (int i = 0; i < size_; ++i)
EXPECT_DOUBLE_EQ(0., m[i]);
}
TEST_F(TensorFixture, MatrixIterator) {
Matrix<double> m(mref);
UInt col_count = 0;
for (auto && col : m) {
Vector<Real> col_hand(m.storage() + col_count * m.rows(), m.rows());
Vector<Real> col_wrap(col);
auto comp = (col_wrap - col_hand).norm<L_inf>();
EXPECT_DOUBLE_EQ(0., comp);
++col_count;
}
}
TEST_F(TensorFixture, MatrixIteratorZip) {
Matrix<double> m1(mref);
Matrix<double> m2(mref);
UInt col_count = 0;
for (auto && col : zip(m1, m2)) {
Vector<Real> col1(std::get<0>(col));
Vector<Real> col2(std::get<1>(col));
auto comp = (col1 - col2).norm<L_inf>();
EXPECT_DOUBLE_EQ(0., comp);
++col_count;
}
}
#if defined(AKANTU_USE_LAPACK)
TEST_F(TensorFixture, MatrixEigs) {
Matrix<double> m{{0, 1, 0, 0}, {1., 0, 0, 0}, {0, 1, 0, 1}, {0, 0, 4, 0}};
Matrix<double> eig_vects(4, 4);
Vector<double> eigs(4);
m.eig(eigs, eig_vects);
Vector<double> eigs_ref{2, 1., -1., -2};
auto lambda_v = m * eig_vects;
for (int i = 0; i < 4; ++i) {
EXPECT_NEAR(eigs_ref(i), eigs(i), 1e-14);
for (int j = 0; j < 4; ++j) {
EXPECT_NEAR(lambda_v(i)(j), eigs(i) * eig_vects(i)(j), 1e-14);
}
}
}
#endif
/* -------------------------------------------------------------------------- */
} // namespace
diff --git a/test/test_common/test_types.cc b/test/test_common/test_types.cc
index 24be0eae3..ae0e23e24 100644
--- a/test/test_common/test_types.cc
+++ b/test/test_common/test_types.cc
@@ -1,354 +1,356 @@
/**
* @file test_types.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 15 2015
- * @date last modification: Wed Jun 14 2017
+ * @date last modification: Wed Jun 14 2017
*
* @brief Test the types declared in aka_types.hh
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
#include <iostream>
#include <sstream>
#include <stdexcept>
using namespace akantu;
const Real tolerance = 1e-15;
std::string itoa(UInt a) {
std::stringstream sstr;
sstr << a;
return sstr.str();
}
UInt testcounter = 0;
struct wrap_error : std::runtime_error {
wrap_error(const std::string & msg) : std::runtime_error(msg) {}
};
struct size_error : std::runtime_error {
size_error(const std::string & msg) : std::runtime_error(msg) {}
};
struct data_error : std::runtime_error {
data_error(const std::string & msg, UInt i)
: std::runtime_error(msg), index(i) {}
UInt index;
};
template <class type>
void compare_storages_with_ref(const type & a, Real * ref, UInt size, UInt line,
const std::string & txt) {
std::cout << std::setw(3) << (testcounter++) << ": " << std::setw(10) << txt
<< " - " << a << " - wrapped: " << std::boolalpha << a.isWrapped()
<< std::endl;
if (a.size() != size)
throw size_error("the size is not correct " + itoa(a.size()) +
" instead of " + itoa(size) +
" [Test at line: " + itoa(line) + "]");
Real * a_ptr = a.storage();
for (UInt i = 0; i < a.size(); ++i) {
if (!((std::abs(a_ptr[i]) < tolerance && std::abs(ref[i]) < tolerance) ||
std::abs((a_ptr[i] - ref[i]) / a_ptr[i]) < tolerance)) {
std::stringstream txt;
txt << " std::abs(" << a_ptr[i] << " - " << ref[i]
<< " [= " << std::abs(a_ptr[i] - ref[i]) << "] ) > " << tolerance;
throw data_error("storage differs at index " + itoa(i) +
" [Test at line: " + itoa(line) + "]" + txt.str(),
i);
}
}
if (a_ptr == ref && !a.isWrapped())
throw wrap_error(
"the storage should be wrapped but it is not [Test at line: " +
itoa(line) + "]");
if (a_ptr != ref && a.isWrapped())
throw wrap_error(
"the storage should not be wrapped but it is [Test at line: " +
itoa(line) + "]");
}
#define COMPARE(a, aref, txt) \
compare_storages_with_ref(a, aref, sizeof(aref) / sizeof(aref[0]), __LINE__, \
txt)
#define COMPARE_STORAGE(a, aref, txt) \
compare_storages_with_ref(a, aref.storage(), aref.size(), __LINE__, txt)
const UInt ref_size = 10;
// clang-format off
/* -------------------------------------------------------------------------- */
void test_constructor() {
std::cout << "=== Test constructors ===" << std::endl;
Real ref1[ref_size] = { 0. };
Real ref2[ref_size] = { 1563.58, 1563.58, 1563.58, 1563.58, 1563.58, 1563.58, 1563.58, 1563.58, 1563.58, 1563.58 };
Real ref3[ref_size] = { 23.1594, 79.6184, 77.9052, 47.9922, 12.8674, 37.1445, 64.8991, 80.3364, 98.4064, 73.7858 };
std::cout << "-- Vectors: " << std::endl;
Vector<Real> v0 = { 23.1594, 79.6184, 77.9052, 47.9922, 12.8674, 37.1445, 64.8991, 80.3364, 98.4064, 73.7858 };
; COMPARE ( v0, ref3, "init_list" );
Vector<Real> v1(ref_size); COMPARE ( v1, ref1, "normal" );
Vector<Real> v2(ref_size, 1563.58); COMPARE ( v2, ref2, "defval" );
Vector<Real> v3(ref3, ref_size); COMPARE ( v3, ref3, "wrapped" );
Vector<Real> v3dcw(v3); COMPARE ( v3dcw, ref3, "wdeepcopy" );
Vector<Real> v3scw(v3, false); COMPARE ( v3scw, ref3, "wshallow" );
Vector<Real> v3dc(v3dcw); COMPARE_STORAGE( v3dc, v3dcw, "deepcopy" );
Vector<Real> v3sc(v3dcw, false); COMPARE_STORAGE( v3sc, v3dcw, "shallow" );
VectorProxy<Real> vp1(ref3, ref_size);
Vector<Real> v4(vp1); COMPARE ( v4, ref3, "proxyptr" );
VectorProxy<Real> vp2(v3dcw);
Vector<Real> v5(vp2); COMPARE_STORAGE( v5, v3dcw, "proxyvdc" );
VectorProxy<Real> vp3(v3scw);
Vector<Real> v6(vp3); COMPARE ( v6, ref3, "proxyvsc" );
/* ------------------------------------------------------------------------ */
std::cout << "-- Matrices: " << std::endl;
Matrix<Real> m0 = {{23.1594, 37.1445},
{79.6184, 64.8991},
{77.9052, 80.3364},
{47.9922, 98.4064},
{12.8674, 73.7858}};
COMPARE ( m0, ref3 , "init_list" );
Matrix<Real> m1(5, 2); COMPARE ( m1, ref1 , "normal" );
Matrix<Real> m1t(2, 5); COMPARE ( m1t, ref1 , "tnormal" );
Matrix<Real> m2(5, 2, 1563.58); COMPARE ( m2, ref2 , "defval" );
Matrix<Real> m2t(2, 5, 1563.58); COMPARE ( m2t, ref2 , "tdefval" );
Matrix<Real> m3(ref3, 5, 2); COMPARE ( m3, ref3 , "wrapped" );
Matrix<Real> m3t(ref3, 2, 5); COMPARE ( m3t, ref3 , "twrapped" );
Matrix<Real> m3dcw(m3); COMPARE ( m3dcw, ref3 , "wdeepcopy" );
Matrix<Real> m3scw(m3, false); COMPARE ( m3scw, ref3 , "wshallow" );
Matrix<Real> m3dc(m3dcw); COMPARE_STORAGE( m3dc, m3dcw , "deepcopy" );
Matrix<Real> m3sc(m3dcw, false); COMPARE_STORAGE( m3sc, m3dcw , "shallow" );
Matrix<Real> m3tdcw(m3t); COMPARE (m3tdcw, ref3 , "twdeepcopy");
Matrix<Real> m3tscw(m3t, false); COMPARE (m3tscw, ref3 , "twshallow" );
Matrix<Real> m3tdc(m3tdcw); COMPARE_STORAGE( m3tdc, m3tdcw, "tdeepcopy" );
Matrix<Real> m3tsc(m3tdcw, false); COMPARE_STORAGE( m3tsc, m3tdcw, "tshallow" );
MatrixProxy<Real> mp1(ref3, 5, 2);
Matrix<Real> m4(mp1); COMPARE ( m4, ref3, "proxyptr" );
MatrixProxy<Real> mp2(m3dcw);
Matrix<Real> m5(mp2); COMPARE_STORAGE( m5, m3dcw, "proxyvdc" );
MatrixProxy<Real> mp3(m3scw);
Matrix<Real> m6(mp3); COMPARE ( m6, ref3, "proxyvsc" );
MatrixProxy<Real> mp1t(ref3, 2, 5);
Matrix<Real> m4t(mp1t); COMPARE ( m4t, ref3, "tproxyptr" );
MatrixProxy<Real> mp2t(m3tdcw);
Matrix<Real> m5t(mp2t); COMPARE_STORAGE( m5t, m3tdcw, "tproxyvdc" );
MatrixProxy<Real> mp3t(m3tscw);
Matrix<Real> m6t(mp3t); COMPARE ( m6t, ref3, "tproxyvsc" );
}
/* -------------------------------------------------------------------------- */
void test_equal_and_accessors() {
std::cout << "=== Test operator=() ===" << std::endl;
Real ref[ref_size] = { 23.1594, 79.6184, 77.9052, 47.9922, 12.8674, 37.1445, 64.8991, 80.3364, 98.4064, 73.7858 };
Real mod[ref_size] = { 98.7982, 72.1227, 19.7815, 57.6722, 47.1088, 14.9865, 13.3171, 62.7973, 33.9493, 98.3052 };
std::cout << "-- Vectors: " << std::endl;
Vector<Real> v (ref, ref_size);
Vector<Real> vm(mod, ref_size);
Vector<Real> vref1(v);
Vector<Real> v1;
v1 = vref1; COMPARE_STORAGE(v1, vref1, "simple=" );
for (UInt i = 0; i < ref_size; ++i) v1 (i) = mod[i]; COMPARE (v1, mod, "s_acces" );
COMPARE_STORAGE(vref1, v, "refcheck1");
Vector<Real> v2 = vref1; COMPARE_STORAGE(v2, vref1, "construc=");
for (UInt i = 0; i < ref_size; ++i) v2 (i) = mod[i]; COMPARE (v2, mod, "c_acces" );
COMPARE_STORAGE(vref1, v, "refcheck2");
Vector<Real> vref2(vref1, false);
Vector<Real> v1w;
v1w = vref2; COMPARE_STORAGE(v1w, vref1, "w_simple=" );
for (UInt i = 0; i < ref_size; ++i) v1w(i) = mod[i]; COMPARE (v1w, mod, "ws_acces" );
try { COMPARE(vref2, ref, "refcheck3"); } catch(wrap_error &) {}
Vector<Real> v2w = vref2; COMPARE_STORAGE(v2w, vref1, "w_constru=");
for (UInt i = 0; i < ref_size; ++i) v2w(i) = mod[i]; COMPARE (v2w, mod, "wc_acces" );
try { COMPARE(vref2, ref, "refcheck4"); } catch(wrap_error &) {}
VectorProxy<Real> vp1(vref1);
Vector<Real> v3;
v3 = vp1; COMPARE_STORAGE(v3, vref1, "p_simple=" );
for (UInt i = 0; i < ref_size; ++i) v3(i) = mod[i]; COMPARE (v3, mod, "ps_acces" );
COMPARE_STORAGE(vref1, v, "refcheck5");
Vector<Real> v4 = vp1; COMPARE_STORAGE(v4, vref1, "p_constru=");
for (UInt i = 0; i < ref_size; ++i) v4(i) = mod[i];
try { COMPARE(v4, mod, "pc_acces" ); } catch (wrap_error &) {}
COMPARE(vref1, mod, "refcheck6");
try { COMPARE(vref2, mod, "refcheck7"); } catch(wrap_error &) {}
vref2 = v;
VectorProxy<Real> vp2(vref2);
Vector<Real> v3w;
v3w = vp2; COMPARE_STORAGE(v3w, vref1, "pw_simpl=");
for (UInt i = 0; i < ref_size; ++i) v3w(i) = mod[i]; COMPARE (v3w, mod, "pws_acces");
try { COMPARE(vref2, ref, "refcheck8"); } catch(wrap_error &) {}
Vector<Real> v4w = vp2; COMPARE_STORAGE( v4w, vref1, "pw_constr=");
for (UInt i = 0; i < ref_size; ++i) v4w(i) = mod[i];
try { COMPARE(v4w, mod, "pwc_acces"); } catch (wrap_error &) {}
COMPARE_STORAGE(v4w, vref2, "refcheck9");
try { COMPARE(vref2, mod, "refcheck10"); } catch(wrap_error &) {}
vref1 = v;
Real store[ref_size] = {0., 0., 0., 0., 0., 0., 0., 0., 0., 0.};
Vector<Real> vs(store, 10);
VectorProxy<Real> vp3(vs);
vp3 = vref1;
try { COMPARE(vref1, store, "vp_equal_v"); } catch(wrap_error &) {}
// Vector<Real> vref3(vm);
// VectorProxy<Real> vp4 = vref3;
// vp3 = vp4;
// try { COMPARE(vs, mod, "vp_equal_vp"); } catch(wrap_error &) {}
/* ------------------------------------------------------------------------ */
std::cout << "-- Matrices: " << std::endl;
Matrix<Real> m (ref, 5, 2);
Matrix<Real> mt(ref, 2, 5);
Matrix<Real> m1 (5, 2);
Matrix<Real> m1t(2, 5);
for (UInt i = 0; i < 5; ++i) {
for (UInt j = 0; j < 2; ++j) {
m1(i, j) = ref[i + j*5];
m1t(j, i) = ref[j + i*2];
}
}
COMPARE_STORAGE( m1, m, "access" );
COMPARE_STORAGE(m1t, m, "t_access");
Matrix<Real> mm (mod, 5, 2);
Matrix<Real> mmt(mod, 2, 5);
Matrix<Real> m2(m);
Matrix<Real> m3(m);
for (UInt j = 0; j < 2; ++j) {
Vector<Real> v = m2(j);
for (UInt i = 0; i < 5; ++i)
v(i) = mm(i, j);
}
COMPARE_STORAGE(m2, mm, "slicing");
for (UInt j = 0; j < 2; ++j)
m3(j) = mm(j);
COMPARE_STORAGE(m3, mm, "slic_slic");
COMPARE(mm, mod, "refcheck");
Real mod_1[ref_size] = { 98.7982, 72.1227, 197.815, 57.6722, 47.1088, 14.9865, 13.3171, 627.973, 33.9493, 98.3052 };
Matrix<Real> m4 (mm);
m4 (2,0) = 197.815;
m4 (2,1) = 627.973;
COMPARE(m4, mod_1, "partial");
Matrix<Real> m4t(mmt);
m4t(0,1) = 197.815;
m4t(1,3) = 627.973;
COMPARE(m4t, mod_1, "t_partial");
}
/* -------------------------------------------------------------------------- */
void test_simple_operators() {
std::cout << "=== Test simple operation ===" << std::endl;
Real ref[ref_size] = { 23.1594, 79.6184, 77.9052, 47.9922, 12.8674, 37.1445, 64.8991, 80.3364, 98.4064, 73.7858 };
Real mod[ref_size] = { 98.7982, 72.1227, 19.7815, 57.6722, 47.1088, 14.9865, 13.3171, 62.7973, 33.9493, 98.3052 };
Real ref_div[ref_size] = { 1.163905920192984e+00, 4.001326766509196e+00,
3.915227661071464e+00, 2.411910744798472e+00,
6.466680068348578e-01, 1.866745401547894e+00,
3.261589104432606e+00, 4.037410795054780e+00,
4.945542265554328e+00, 3.708201829329581e+00 };
Real ref_tim[ref_size] = { 4.608257412000000e+02, 1.584246923200000e+03,
1.550157669600000e+03, 9.549487955999999e+02,
2.560355252000000e+02, 7.391012610000000e+02,
1.291362291800000e+03, 1.598533687200000e+03,
1.958090547200000e+03, 1.468189848400000e+03 };
Real ref_p_mod[ref_size] = { 1.219576000000000e+02, 1.517411000000000e+02,
9.768670000000000e+01, 1.056644000000000e+02,
5.997620000000001e+01, 5.213100000000000e+01,
7.821620000000000e+01, 1.431337000000000e+02,
1.323557000000000e+02, 1.720910000000000e+02 };
Real ref_m_mod[ref_size] = { -7.563879999999999e+01, 7.495699999999999e+00,
5.812369999999999e+01, -9.680000000000000e+00,
-3.424140000000000e+01, 2.215800000000000e+01,
5.158200000000001e+01, 1.753910000000000e+01,
6.445710000000000e+01, -2.451940000000000e+01 };
std::cout << "-- Vectors: " << std::endl;
Vector<Real> v (ref, ref_size);
Vector<Real> vm(mod, ref_size);
Vector<Real> vref(v);
Vector<Real> vmod(vm);
Vector<Real> v1 = vref / 19.898; COMPARE(v1, ref_div, "v / s" );
Vector<Real> v2 = vref * 19.898; COMPARE(v2, ref_tim, "v * s" );
Vector<Real> v3 = 19.898 * vref; COMPARE(v3, ref_tim, "s * v" );
Vector<Real> v4 = vref + vmod; COMPARE(v4, ref_p_mod, "v1 + v2" );
Vector<Real> v5 = vref - vmod; COMPARE(v5, ref_m_mod, "v1 - v2" );
Vector<Real> v6 = vref; v6 *= 19.898; COMPARE(v6, ref_tim, "v *= s" );
Vector<Real> v7 = vref; v7 /= 19.898; COMPARE(v7, ref_div, "v /= s" );
Vector<Real> v8 = vref; v8 += vmod; COMPARE(v8, ref_p_mod, "v1 += v2");
Vector<Real> v9 = vref; v9 -= vmod; COMPARE(v9, ref_m_mod, "v1 -= v2");
std::cout << "-- Matrices: " << std::endl;
Matrix<Real> m (ref, 5, 2);
Matrix<Real> mm(mod, 5, 2);
Matrix<Real> mref(m);
Matrix<Real> mmod(mm);
Matrix<Real> m1 = mref / 19.898; COMPARE(m1, ref_div, "m / s" );
Matrix<Real> m2 = mref * 19.898; COMPARE(m2, ref_tim, "m * s" );
Matrix<Real> m3 = 19.898 * mref; COMPARE(m3, ref_tim, "s * m" );
Matrix<Real> m4 = mref + mmod; COMPARE(m4, ref_p_mod, "m1 + m2" );
Matrix<Real> m5 = mref - mmod; COMPARE(m5, ref_m_mod, "m1 - m2" );
Matrix<Real> m6 = mref; m6 *= 19.898; COMPARE(m6, ref_tim, "m *= s" );
Matrix<Real> m7 = mref; m7 /= 19.898; COMPARE(m7, ref_div, "m /= s" );
Matrix<Real> m8 = mref; m8 += mmod; COMPARE(m8, ref_p_mod, "m1 += m2");
Matrix<Real> m9 = mref; m9 -= mmod; COMPARE(m9, ref_m_mod, "m1 -= m2");
}
// clang-format on
/* -------------------------------------------------------------------------- */
int main() {
test_constructor();
test_equal_and_accessors();
test_simple_operators();
return 0;
}
diff --git a/test/test_common/test_voigt_helper.cc b/test/test_common/test_voigt_helper.cc
index 33a9440b9..e9445d361 100644
--- a/test/test_common/test_voigt_helper.cc
+++ b/test/test_common/test_voigt_helper.cc
@@ -1,160 +1,164 @@
/**
* @file test_voigt_helper.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation mer nov 13 2019
+ * @date creation: Wed Nov 27 2019
+ * @date last modification: Wed Nov 18 2020
*
- * @brief unit tests for VoigtHelper
+ * @brief unit tests for VoigtHelper
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <aka_voigthelper.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
using namespace akantu;
template <class Dim_v> class VoigtHelperFixture : public ::testing::Test {
protected:
using voigt_h = VoigtHelper<Dim_v::value>;
constexpr static UInt dim = Dim_v::value;
VoigtHelperFixture() {
switch (this->dim) {
case 1: {
indices.push_back({0, 0});
matrix = Matrix<Real>{{10}};
vector = Vector<Real>{10};
vector_factor = Vector<Real>{10};
break;
}
case 2: {
indices.push_back({0, 0});
indices.push_back({1, 1});
indices.push_back({0, 1});
matrix = Matrix<Real>{{10, 33}, {0, 56}};
vector = Vector<Real>{10, 56, 33};
vector_factor = Vector<Real>{10, 56, 2 * 33};
break;
}
case 3: {
indices.push_back({0, 0});
indices.push_back({1, 1});
indices.push_back({2, 2});
indices.push_back({1, 2});
indices.push_back({0, 2});
indices.push_back({0, 1});
matrix = Matrix<Real>{{10, 33, 20}, {0, 56, 27}, {0, 0, 98}};
vector = Vector<Real>{10, 56, 98, 27, 20, 33};
vector_factor = Vector<Real>{10, 56, 98, 2 * 27, 2 * 20, 2 * 33};
break;
}
}
}
void SetUp() override {}
std::vector<std::pair<UInt, UInt>> indices;
Matrix<Real> matrix;
Vector<Real> vector;
Vector<Real> vector_factor;
};
template <UInt dim>
using spatial_dimension_t = std::integral_constant<UInt, dim>;
using TestTypes =
::testing::Types<spatial_dimension_t<1>, spatial_dimension_t<2>,
spatial_dimension_t<3>>;
TYPED_TEST_SUITE(VoigtHelperFixture, TestTypes, );
TYPED_TEST(VoigtHelperFixture, Size) {
using voigt_h = typename TestFixture::voigt_h;
switch (this->dim) {
case 1:
EXPECT_EQ(voigt_h::size, 1);
break;
case 2:
EXPECT_EQ(voigt_h::size, 3);
break;
case 3:
EXPECT_EQ(voigt_h::size, 6);
break;
}
}
TYPED_TEST(VoigtHelperFixture, Indicies) {
using voigt_h = typename TestFixture::voigt_h;
for (UInt I = 0; I < voigt_h::size; ++I) {
EXPECT_EQ(this->indices[I].first, voigt_h::vec[I][0]);
EXPECT_EQ(this->indices[I].second, voigt_h::vec[I][1]);
}
}
TYPED_TEST(VoigtHelperFixture, Factors) {
using voigt_h = typename TestFixture::voigt_h;
for (UInt I = 0; I < voigt_h::size; ++I) {
if (I < this->dim) {
EXPECT_EQ(voigt_h::factors[I], 1);
} else {
EXPECT_EQ(voigt_h::factors[I], 2);
}
}
}
TYPED_TEST(VoigtHelperFixture, MatrixToVoight) {
using voigt_h = typename TestFixture::voigt_h;
auto voigt = voigt_h::matrixToVoigt(this->matrix);
for (UInt I = 0; I < voigt_h::size; ++I) {
EXPECT_EQ(voigt(I), this->vector(I));
}
}
TYPED_TEST(VoigtHelperFixture, MatrixToVoightFactors) {
using voigt_h = typename TestFixture::voigt_h;
auto voigt = voigt_h::matrixToVoigtWithFactors(this->matrix);
for (UInt I = 0; I < voigt_h::size; ++I) {
EXPECT_EQ(voigt(I), this->vector_factor(I));
}
}
TYPED_TEST(VoigtHelperFixture, VoightToMatrix) {
using voigt_h = typename TestFixture::voigt_h;
auto matrix = voigt_h::voigtToMatrix(this->vector);
for (UInt i = 0; i < this->dim; ++i) {
for (UInt j = 0; j < this->dim; ++j) {
EXPECT_EQ(matrix(i, j), this->matrix(std::min(i, j), std::max(i, j)));
}
}
}
diff --git a/test/test_fe_engine/CMakeLists.txt b/test/test_fe_engine/CMakeLists.txt
index 7054e6381..fb99a4f21 100644
--- a/test/test_fe_engine/CMakeLists.txt
+++ b/test/test_fe_engine/CMakeLists.txt
@@ -1,129 +1,131 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Lucas Frerot <lucas.frerot@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jan 26 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Tue Jun 30 2020
#
# @brief configuration for FEM tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
function(register_fem_test operation type)
set(_target test_${operation}${type})
register_test(${_target}
SOURCES test_${operation}.cc
FILES_TO_COPY ${type}.msh
COMPILE_OPTIONS TYPE=${type}
PACKAGE core
)
endfunction()
#===============================================================================
macro(register_mesh_types package)
package_get_element_types(${package} _types)
foreach(_type ${_types})
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${_type}.msh)
list(APPEND _meshes ${_type}.msh)
else()
if(NOT ${_type} STREQUAL _point_1)
message("The mesh ${_type}.msh is missing, the fe_engine test cannot be activated without it")
endif()
endif()
endforeach()
endmacro(register_mesh_types)
set(_meshes)
register_mesh_types(core)
package_is_activated(structural_mechanics has_structural_mechanics)
if(has_structural_mechanics)
register_mesh_types(structural_mechanics)
endif()
# Tests for class MeshData
macro(register_typed_test test_name type value1 value2)
set(target test_${test_name}_${type})
register_test(${target}
SOURCES test_${test_name}.cc
COMPILE_OPTIONS "TYPE=${type};VALUE1=${value1};VALUE2=${value2}"
PACKAGE core
)
endmacro()
register_typed_test(mesh_data string \"5\" \"10\")
register_typed_test(mesh_data UInt 5 10)
add_mesh(test_boundary_msh cube.geo 3 1)
add_mesh(test_boundary_msh_physical_names cube_physical_names.geo 3 1)
register_test(test_mesh_boundary
SOURCES test_mesh_boundary.cc
DEPENDS test_boundary_msh test_boundary_msh_physical_names
PACKAGE core)
register_test(test_facet_element_mapping
SOURCES test_facet_element_mapping.cc
DEPENDS test_boundary_msh_physical_names
PACKAGE core)
register_gtest_sources(
SOURCES test_fe_engine_precomputation.cc
PACKAGE core python_interface
INCLUDE_DIRECTORIES ${PROJECT_SOURCE_DIR}/python
)
register_gtest_sources(
SOURCES test_fe_engine_precomputation_structural.cc
PACKAGE structural_mechanics
)
register_gtest_sources(
SOURCES test_fe_engine_gauss_integration.cc
PACKAGE core
)
register_gtest_sources(
SOURCES test_gradient.cc
PACKAGE core
)
register_gtest_sources(
SOURCES test_integrate.cc
PACKAGE core
)
register_gtest_sources(
SOURCES test_inverse_map.cc
PACKAGE core
)
register_gtest_test(test_fe_engine
FILES_TO_COPY ${_meshes})
diff --git a/test/test_fe_engine/py_engine/__init__.py b/test/test_fe_engine/py_engine/__init__.py
index ad166ecf8..d84690a04 100644
--- a/test/test_fe_engine/py_engine/__init__.py
+++ b/test/test_fe_engine/py_engine/__init__.py
@@ -1,6 +1,19 @@
+
+""" __init__.py: fe engine tester module"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
+
__all__ = []
from .py_engine import * # noqa: F401,F403
from . import py_engine as __pye # noqa: F401
__all__.append(__pye.__all__)
diff --git a/test/test_fe_engine/py_engine/py_engine.py b/test/test_fe_engine/py_engine/py_engine.py
index 27f8fa087..158820c3b 100644
--- a/test/test_fe_engine/py_engine/py_engine.py
+++ b/test/test_fe_engine/py_engine/py_engine.py
@@ -1,364 +1,363 @@
#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# ------------------------------------------------------------------------------
+""" py_engine.py: feengine tester"""
+
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
__all__ = ['Shapes']
import numpy as np
import numpy.polynomial.polynomial as poly
# pylint: disable=missing-docstring, invalid-name, too-many-instance-attributes
# flake8: noqa
class Shapes:
"""Python version of the shape functions for test purposes"""
# pylint: disable=bad-whitespace, line-too-long
NATURAL_COORDS = {
(1, 'quadrangle'): np.array([[-1.], [1.], [0.]]),
(2, 'quadrangle'): np.array([[-1., -1.], [ 1., -1.], [ 1., 1.], [-1., 1.],
[ 0., -1.], [ 1., 0.], [ 0., 1.], [-1., 0.]]),
(3, 'quadrangle'): np.array([[-1., -1., -1.], [ 1., -1., -1.], [ 1., 1., -1.], [-1., 1., -1.],
[-1., -1., 1.], [ 1., -1., 1.], [ 1., 1., 1.], [-1., 1., 1.],
[ 0., -1., -1.], [ 1., 0., -1.], [ 0., 1., -1.], [-1., 0., -1.],
[-1., -1., 0.], [ 1., -1., 0.], [ 1., 1., 0.], [-1., 1., 0.],
[ 0., -1., 1.], [ 1., 0., 1.], [ 0., 1., 1.], [-1., 0., 1.]]),
(2, 'triangle'): np.array([[0., 0.], [1., 0.], [0., 1], [.5, 0.], [.5, .5], [0., .5]]),
(3, 'triangle'): np.array([[0., 0., 0.], [1., 0., 0.], [0., 1., 0.], [0., 0., 1.],
[.5, 0., 0.], [.5, .5, 0.], [0., .5, 0.],
[0., 0., .5], [.5, 0., .5], [0., .5, .5]]),
(3, 'pentahedron'): np.array([[-1., 1., 0.], [-1., 0., 1.], [-1., 0., 0.],
[ 1., 1., 0.], [ 1., 0., 1.], [ 1., 0., 0.],
[-1., .5, .5], [-1., 0., .5], [-1., .5, 0.],
[ 0., 1., 0.], [ 0., 0., 1.], [ 0., 0., 0.],
[ 1., .5, .5], [ 1., 0., .5], [ 1., .5, 0.],
[ 0., .5, .5], [ 0., 0., .5], [ 0., .5, 0.]]),
}
QUADRATURE_W = {
(1, 'quadrangle', 1): np.array([2.]),
(1, 'quadrangle', 2): np.array([1., 1.]),
(2, 'triangle', 1): np.array([1./2.]),
(2, 'triangle', 2): np.array([1., 1., 1.])/6.,
(3, 'triangle', 1): np.array([1./6.]),
(3, 'triangle', 2): np.array([1., 1., 1., 1.])/24.,
(2, 'quadrangle', 1): np.array([1., 1., 1., 1.]),
(2, 'quadrangle', 2): np.array([1., 1., 1., 1.]),
(3, 'quadrangle', 1): np.array([1., 1., 1., 1.,
1., 1., 1., 1.]),
(3, 'quadrangle', 2): np.array([1., 1., 1., 1.,
1., 1., 1., 1.]),
(3, 'pentahedron', 1): np.array([1., 1., 1., 1., 1., 1.])/6.,
(3, 'pentahedron', 2): np.array([1., 1., 1., 1., 1., 1.])/6.,
}
_tet_a = (5. - np.sqrt(5.))/20.
_tet_b = (5. + 3.*np.sqrt(5.))/20.
QUADRATURE_G = {
(1, 'quadrangle', 1): np.array([[0.]]),
(1, 'quadrangle', 2): np.array([[-1.], [1.]])/np.sqrt(3.),
(2, 'triangle', 1): np.array([[1., 1.]])/3.,
(2, 'triangle', 2): np.array([[1./6., 1./6.], [2./3, 1./6], [1./6., 2./3.]]),
(3, 'triangle', 1): np.array([[1., 1., 1.]])/4.,
(3, 'triangle', 2): np.array([[_tet_a, _tet_a, _tet_a],
[_tet_b, _tet_a, _tet_a],
[_tet_a, _tet_b, _tet_a],
[_tet_a, _tet_a, _tet_b]]),
(2, 'quadrangle', 1): np.array([[-1., -1.], [ 1., -1.],
[-1., 1.], [ 1., 1.]])/np.sqrt(3.),
(2, 'quadrangle', 2): np.array([[-1., -1.], [ 1., -1.],
[-1., 1.], [ 1., 1.]])/np.sqrt(3.),
(3, 'quadrangle', 1): np.array([[-1., -1., -1.],
[ 1., -1., -1.],
[-1., 1., -1.],
[ 1., 1., -1.],
[-1., -1., 1.],
[ 1., -1., 1.],
[-1., 1., 1.],
[ 1., 1., 1.]])/np.sqrt(3.),
(3, 'quadrangle', 2): np.array([[-1., -1., -1.],
[ 1., -1., -1.],
[-1., 1., -1.],
[ 1., 1., -1.],
[-1., -1., 1.],
[ 1., -1., 1.],
[-1., 1., 1.],
[ 1., 1., 1.]])/np.sqrt(3.),
(3, 'pentahedron', 1): np.array([[-1./np.sqrt(3.), 1./6., 1./6.],
[-1./np.sqrt(3.), 2./3., 1./6.],
[-1./np.sqrt(3.), 1./6., 2./3.],
[ 1./np.sqrt(3.), 1./6., 1./6.],
[ 1./np.sqrt(3.), 2./3., 1./6.],
[ 1./np.sqrt(3.), 1./6., 2./3.]]),
(3, 'pentahedron', 2): np.array([[-1./np.sqrt(3.), 1./6., 1./6.],
[-1./np.sqrt(3.), 2./3., 1./6.],
[-1./np.sqrt(3.), 1./6., 2./3.],
[ 1./np.sqrt(3.), 1./6., 1./6.],
[ 1./np.sqrt(3.), 2./3., 1./6.],
[ 1./np.sqrt(3.), 1./6., 2./3.]]),
}
ELEMENT_TYPES = {
'_segment_2': ('quadrangle', 1, 'lagrange', 1, 2),
'_segment_3': ('quadrangle', 2, 'lagrange', 1, 3),
'_triangle_3': ('triangle', 1, 'lagrange', 2, 3),
'_triangle_6': ('triangle', 2, 'lagrange', 2, 6),
'_quadrangle_4': ('quadrangle', 1, 'serendip', 2, 4),
'_quadrangle_8': ('quadrangle', 2, 'serendip', 2, 8),
'_tetrahedron_4': ('triangle', 1, 'lagrange', 3, 4),
'_tetrahedron_10': ('triangle', 2, 'lagrange', 3, 10),
'_pentahedron_6': ('pentahedron', 1, 'lagrange', 3, 6),
'_pentahedron_15': ('pentahedron', 2, 'lagrange', 3, 15),
'_hexahedron_8': ('quadrangle', 1, 'serendip', 3, 8),
'_hexahedron_20': ('quadrangle', 2, 'serendip', 3, 20),
}
MONOMES = {(1, 'quadrangle'): np.array([[0], [1], [2], [3], [4], [5]]),
(2, 'triangle'): np.array([[0, 0], # 1
[1, 0], [0, 1], # x y
[2, 0], [1, 1], [0, 2]]), # x^2 x.y y^2
(2, 'quadrangle'): np.array([[0, 0],
[1, 0], [1, 1], [0, 1],
[2, 0], [2, 1], [1, 2], [0, 2]]),
(3, 'triangle'): np.array([[0, 0, 0],
[1, 0, 0], [0, 1, 0], [0, 0, 1],
[2, 0, 0], [1, 1, 0], [0, 2, 0], [0, 1, 1], [0, 0, 2],
[1, 0, 1]]),
(3, 'quadrangle'): np.array([[0, 0, 0],
[1, 0, 0], [0, 1, 0], [0, 0, 1],
[1, 1, 0], [1, 0, 1],
[0, 1, 1], [1, 1, 1],
[2, 0, 0], [0, 2, 0], [0, 0, 2],
[2, 1, 0], [2, 0, 1], [2, 1, 1],
[1, 2, 0], [0, 2, 1], [1, 2, 1],
[1, 0, 2], [0, 1, 2], [1, 1, 2]])}
SHAPES = {
(3, 'pentahedron', 1): np.array([
[[[ 0., 0.], [ 1., 0.]], [[ 0., 0.], [-1., 0.]]],
[[[ 0., 1.], [ 0., 0.]], [[ 0., -1.], [ 0., 0.]]],
[[[ 1., -1.], [-1., 0.]], [[-1., 1.], [ 1., 0.]]],
[[[ 0., 0.], [ 1., 0.]], [[ 0., 0.], [ 1., 0.]]],
[[[ 0., 1.], [ 0., 0.]], [[ 0., 1.], [ 0., 0.]]],
[[[ 1., -1.], [-1., 0.]], [[ 1., -1.], [-1., 0.]]]
])/2.,
(3, 'pentahedron', 2): np.array([
# 0
[[[ 0. , 0. , 0. ], [-1. , 0. , 0. ], [ 1. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0.5, 0. , 0. ], [-1. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0.5, 0. , 0. ], [ 0. , 0. , 0. ]]],
# 1
[[[ 0. , -1. , 1. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0.5, -1. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0.5, 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 2
[[[ 0. , -1. , 1. ], [-1. , 2. , 0. ], [ 1. , 0. , 0. ]],
[[-0.5, 1.5, -1. ], [ 1.5, -2. , 0. ], [-1. , 0. , 0. ]],
[[ 0.5, -0.5, 0. ], [-0.5, 0. , 0. ], [ 0. , 0. , 0. ]]],
# 3
[[[ 0. , 0. , 0. ], [-1. , 0. , 0. ], [ 1. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [-0.5, 0. , 0. ], [ 1. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0.5, 0. , 0. ], [ 0. , 0. , 0. ]]],
# 4
[[[ 0. , -1. , 1. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , -0.5, 1. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0.5, 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 5
[[[ 0. , -1. , 1. ], [-1. , 2. , 0. ], [ 1. , 0. , 0. ]],
[[ 0.5, -1.5, 1. ], [-1.5, 2. , 0. ], [ 1. , 0. , 0. ]],
[[ 0.5, -0.5, 0. ], [-0.5, 0. , 0. ], [ 0. , 0. , 0. ]]],
# 6
[[[ 0. , 0. , 0. ], [ 0. , 2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , -2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 7
[[[ 0. , 2. , -2. ], [ 0. , -2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , -2. , 2. ], [ 0. , 2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 8
[[[ 0. , 0. , 0. ], [ 2. , -2. , 0. ], [-2. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [-2. , 2. , 0. ], [ 2. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 9
[[[ 0. , 0. , 0. ], [ 1. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [-1. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 10
[[[ 0. , 1. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , -1. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 11
[[[ 1. , -1. , 0. ], [-1. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]],
[[-1. , 1. , 0. ], [ 1. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 12
[[[ 0. , 0. , 0. ], [ 0. , 2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 13
[[[ 0. , 2. , -2. ], [ 0. , -2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 2. , -2. ], [ 0. , -2. , 0. ], [ 0. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
# 14
[[[ 0. , 0. , 0. ], [ 2. , -2. , 0. ], [-2. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 2. , -2. , 0. ], [-2. , 0. , 0. ]],
[[ 0. , 0. , 0. ], [ 0. , 0. , 0. ], [ 0. , 0. , 0. ]]],
])}
# pylint: enable=bad-whitespace, line-too-long
def __init__(self, element):
self._shape, self._order, self._inter_poly, self._dim, \
self._nnodes = self.ELEMENT_TYPES[element]
self._ksi = self.NATURAL_COORDS[(self._dim, self._shape)][:self._nnodes]
self._g = self.QUADRATURE_G[(self._dim, self._shape, self._order)]
self._w = self.QUADRATURE_W[(self._dim, self._shape, self._order)]
self._poly_shape = ()
self._monome = []
def polyval(self, x, p):
if self._dim == 1:
return poly.polyval(x[0], p)
if self._dim == 2:
return poly.polyval2d(x[0], x[1], p)
if self._dim == 3:
return poly.polyval3d(x[0], x[1], x[2], p)
return None
def shape_from_monomes(self):
momo = self.MONOMES[(self._dim, self._shape)][:self._nnodes]
_shapes = list(momo[0])
for s, _ in enumerate(_shapes):
_shapes[s] = max(momo[:, s])+1
self._poly_shape = tuple(_shapes)
self._monome = []
for m in momo:
p = np.zeros(self._poly_shape)
p[tuple(m)] = 1
self._monome.append(p)
# evaluate polynomial constant for shapes
_x = self._ksi
_xe = np.zeros((self._nnodes, self._nnodes))
for n in range(self._nnodes):
_xe[:, n] = [self.polyval(_x[n], m) for m in self._monome]
_a = np.linalg.inv(_xe)
_n = np.zeros((self._nnodes,) + self._monome[0].shape)
# set shapes polynomials
for n in range(self._nnodes):
for m in range(len(self._monome)):
_n[n] += _a[n, m] * self._monome[m]
return _n
def compute_shapes(self):
if (self._dim, self._shape) in self.MONOMES:
return self.shape_from_monomes()
_n = self.SHAPES[(self._dim, self._shape, self._order)]
self._poly_shape = _n[0].shape
return _n
# pylint: disable=too-many-locals,too-many-branches
def precompute(self, **kwargs):
X = np.array(kwargs["X"], copy=False)
nb_element = X.shape[0]
X = X.reshape(nb_element, self._nnodes, self._dim)
_x = self._ksi
_n = self.compute_shapes()
# sanity check on shapes
for n in range(self._nnodes):
for m in range(self._nnodes):
v = self.polyval(_x[n], _n[m])
ve = 1. if n == m else 0.
test = np.isclose(v, ve)
if not test:
raise Exception("Most probably an error in the shapes evaluation")
# compute shapes derivatives
_b = np.zeros((self._dim, self._nnodes,) + self._poly_shape)
for d in range(self._dim):
for n in range(self._nnodes):
_der = poly.polyder(_n[n], axis=d)
_mshape = np.array(self._poly_shape)
_mshape[d] = _mshape[d] - _der.shape[d]
_mshape = tuple(_mshape)
_comp = np.zeros(_mshape)
if self._dim == 1:
_bt = np.hstack((_der, _comp))
else:
if d == 0:
_bt = np.vstack((_der, _comp))
if d == 1:
_bt = np.hstack((_der, _comp))
if d == 2:
_bt = np.dstack((_der, _comp))
_b[d, n] = _bt
_nb_quads = len(self._g)
_nq = np.zeros((_nb_quads, self._nnodes))
_bq = np.zeros((_nb_quads, self._dim, self._nnodes))
# evaluate shapes and shapes derivatives on gauss points
for q in range(_nb_quads):
_g = self._g[q]
for n in range(self._nnodes):
_nq[q, n] = self.polyval(_g, _n[n])
for d in range(self._dim):
_bq[q, d, n] = self.polyval(_g, _b[d, n])
_j = np.array(kwargs['j'], copy=False).reshape((nb_element, _nb_quads))
_B = np.array(kwargs['B'], copy=False).reshape((nb_element, _nb_quads,
self._nnodes, self._dim))
_N = np.array(kwargs['N'], copy=False).reshape((nb_element, _nb_quads, self._nnodes))
_Q = kwargs['Q']
if np.linalg.norm(_Q - self._g.T) > 1e-15:
raise Exception('Not using the same quadrature'
' points norm({0} - {1}) = {2}'.format(_Q, self._g.T,
np.linalg.norm(_Q - self._g.T)))
for e in range(nb_element):
for q in range(_nb_quads):
_J = np.matmul(_bq[q], X[e])
if np.linalg.norm(_N[e, q] - _nq[q]) > 1e-10:
print("{0},{1}".format(e, q))
print(_N[e, q])
print(_nq[q])
_N[e, q] = _nq[q]
_tmp = np.matmul(np.linalg.inv(_J), _bq[q])
_B[e, q] = _tmp.T
_j[e, q] = np.linalg.det(_J) * self._w[q]
diff --git a/test/test_fe_engine/test_facet_element_mapping.cc b/test/test_fe_engine/test_facet_element_mapping.cc
index 8c3a9569e..5864f3be9 100644
--- a/test/test_fe_engine/test_facet_element_mapping.cc
+++ b/test/test_fe_engine/test_facet_element_mapping.cc
@@ -1,126 +1,128 @@
/**
* @file test_facet_element_mapping.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
- * @date creation: Fri May 03 2013
- * @date last modification: Tue Nov 07 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Nov 02 2018
*
* @brief Test of the MeshData class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_error.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <string>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using namespace std;
int main(int argc, char * argv[]) {
// Testing the subelement-to-element mappings
UInt spatial_dimension(3);
akantu::initialize(argc, argv);
Mesh mesh(spatial_dimension, "my_mesh");
mesh.read("./cube_physical_names.msh");
typedef Array<std::vector<Element>> ElemToSubelemMapping;
typedef Array<Element> SubelemToElemMapping;
std::cout << "ELEMENT-SUBELEMENT MAPPING:" << std::endl;
for (auto ghost_type : ghost_types) {
std::cout << " "
<< "Ghost type: " << ghost_type << std::endl;
for (auto & type : mesh.elementTypes(spatial_dimension, ghost_type)) {
const SubelemToElemMapping & subelement_to_element =
mesh.getSubelementToElement(type, ghost_type);
std::cout << " "
<< " "
<< "Element type: " << type << std::endl;
std::cout << " "
<< " "
<< " "
<< "subelement_to_element:" << std::endl;
subelement_to_element.printself(std::cout, 8);
for (UInt i(0); i < subelement_to_element.size(); ++i) {
std::cout << " ";
for (UInt j(0); j < mesh.getNbFacetsPerElement(type); ++j) {
if (subelement_to_element(i, j) != ElementNull) {
std::cout << subelement_to_element(i, j);
std::cout << ", ";
} else {
std::cout << "ElementNull"
<< ", ";
}
}
std::cout << "for element " << i << std::endl;
}
}
for (auto & type : mesh.elementTypes(spatial_dimension - 1, ghost_type)) {
const ElemToSubelemMapping & element_to_subelement =
mesh.getElementToSubelement(type, ghost_type);
std::cout << " "
<< " "
<< "Element type: " << type << std::endl;
std::cout << " "
<< " "
<< " "
<< "element_to_subelement:" << std::endl;
element_to_subelement.printself(std::cout, 8);
for (UInt i(0); i < element_to_subelement.size(); ++i) {
const std::vector<Element> & vec = element_to_subelement(i);
std::cout << " ";
std::cout << "item " << i << ": [ ";
if (vec.size() > 0) {
for (UInt j(0); j < vec.size(); ++j) {
if (vec[j] != ElementNull) {
std::cout << vec[j] << ", ";
} else {
std::cout << "ElementNull"
<< ", ";
}
}
} else {
std::cout << "empty, ";
}
std::cout << "]"
<< ", " << std::endl;
}
std::cout << std::endl;
}
}
return 0;
}
diff --git a/test/test_fe_engine/test_fe_engine_fixture.hh b/test/test_fe_engine/test_fe_engine_fixture.hh
index c3662b687..c58211439 100644
--- a/test/test_fe_engine/test_fe_engine_fixture.hh
+++ b/test/test_fe_engine/test_fe_engine_fixture.hh
@@ -1,111 +1,114 @@
/**
* @file test_fe_engine_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Fixture for feengine tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <element_class.hh>
#include <fe_engine.hh>
#include <integrator_gauss.hh>
#include <shape_lagrange.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_FE_ENGINE_FIXTURE_HH_
#define AKANTU_TEST_FE_ENGINE_FIXTURE_HH_
using namespace akantu;
/// Generic class for FEEngine tests
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind = _ek_regular>
class TestFEMBaseFixture : public ::testing::Test {
public:
static constexpr const ElementType type = type_::value;
static constexpr const size_t dim = ElementClass<type>::getSpatialDimension();
using FEM = FEEngineTemplate<IntegratorGauss, shape_t, kind>;
/// Setup reads mesh corresponding to element type and initializes an FEEngine
void SetUp() override {
const auto dim = this->dim;
mesh = std::make_unique<Mesh>(dim);
std::stringstream meshfilename;
meshfilename << type << ".msh";
this->readMesh(meshfilename.str());
lower = mesh->getLowerBounds();
upper = mesh->getUpperBounds();
nb_element = this->mesh->getNbElement(type);
fem = std::make_unique<FEM>(*mesh, dim, "my_fem");
nb_quadrature_points_total =
GaussIntegrationElement<type>::getNbQuadraturePoints() * nb_element;
SCOPED_TRACE(std::to_string(type));
}
void TearDown() override {
fem.reset(nullptr);
mesh.reset(nullptr);
}
/// Should be reimplemented if further treatment of the mesh is needed
virtual void readMesh(std::string file_name) { mesh->read(file_name); }
protected:
std::unique_ptr<FEM> fem;
std::unique_ptr<Mesh> mesh;
UInt nb_element;
UInt nb_quadrature_points_total;
Vector<Real> lower;
Vector<Real> upper;
};
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind>
constexpr const ElementType TestFEMBaseFixture<type_, shape_t, kind>::type;
template <typename type_, template <ElementKind> class shape_t,
ElementKind kind>
constexpr const size_t TestFEMBaseFixture<type_, shape_t, kind>::dim;
/* -------------------------------------------------------------------------- */
/// Base class for test with Lagrange FEEngine and regular elements
template <typename type_>
using TestFEMFixture = TestFEMBaseFixture<type_, ShapeLagrange, _ek_regular>;
/* -------------------------------------------------------------------------- */
using fe_engine_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestFEMFixture, fe_engine_types, );
#endif /* AKANTU_TEST_FE_ENGINE_FIXTURE_HH_ */
diff --git a/test/test_fe_engine/test_fe_engine_gauss_integration.cc b/test/test_fe_engine/test_fe_engine_gauss_integration.cc
index e9ea2dde8..bf89c1160 100644
--- a/test/test_fe_engine/test_fe_engine_gauss_integration.cc
+++ b/test/test_fe_engine/test_fe_engine_gauss_integration.cc
@@ -1,153 +1,155 @@
/**
* @file test_fe_engine_gauss_integration.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 24 2016
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief test integration on elements, this test consider that mesh is a cube
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
/* -------------------------------------------------------------------------- */
template <size_t t> using degree_t = std::integral_constant<size_t, t>;
/* -------------------------------------------------------------------------- */
using TestDegreeTypes = std::tuple<degree_t<0>, degree_t<1>, degree_t<2>,
degree_t<3>, degree_t<4>, degree_t<5>>;
std::array<Polynomial<5>, 3> global_polys{
{{0.40062394, 0.13703225, 0.51731446, 0.87830084, 0.5410543, 0.71842292},
{0.41861835, 0.11080576, 0.49874043, 0.49077504, 0.85073835, 0.66259755},
{0.92620845, 0.7503478, 0.62962232, 0.31662719, 0.64069644, 0.30878135}}};
template <typename T>
class TestGaussIntegrationFixture
: public TestFEMFixture<std::tuple_element_t<0, T>> {
protected:
using parent = TestFEMFixture<std::tuple_element_t<0, T>>;
static constexpr size_t degree{std::tuple_element_t<1, T>::value};
public:
TestGaussIntegrationFixture() : integration_points_pos(0, parent::dim) {}
void SetUp() override {
parent::SetUp();
this->fem->initShapeFunctions();
auto integration_points =
this->fem->getIntegrator().template getIntegrationPoints <
parent::type,
degree == 0 ? 1 : degree > ();
nb_integration_points = integration_points.cols();
auto shapes_size = ElementClass<parent::type>::getShapeSize();
Array<Real> shapes(0, shapes_size);
this->fem->getShapeFunctions()
.template computeShapesOnIntegrationPoints<parent::type>(
this->mesh->getNodes(), integration_points, shapes, _not_ghost);
auto vect_size = this->nb_integration_points * this->nb_element;
integration_points_pos.resize(vect_size);
this->fem->getShapeFunctions()
.template interpolateOnIntegrationPoints<parent::type>(
this->mesh->getNodes(), integration_points_pos, this->dim, shapes);
for (size_t d = 0; d < this->dim; ++d) {
polys[d] = global_polys[d].extract(degree);
}
}
void testIntegrate() {
std::stringstream sstr;
sstr << this->type << ":" << this->degree;
SCOPED_TRACE(sstr.str().c_str());
auto vect_size = this->nb_integration_points * this->nb_element;
Array<Real> polynomial(vect_size);
size_t dim = parent::dim;
for (size_t d = 0; d < dim; ++d) {
auto poly = this->polys[d];
for (auto && pair :
zip(polynomial, make_view(this->integration_points_pos, dim))) {
auto && p = std::get<0>(pair);
auto & x = std::get<1>(pair);
p = poly(x(d));
}
auto res =
this->fem->getIntegrator()
.template integrate<parent::type, (degree == 0 ? 1 : degree)>(
polynomial);
auto expect = poly.integrate(this->lower(d), this->upper(d));
for (size_t o = 0; o < dim; ++o) {
if (o == d)
continue;
expect *= this->upper(d) - this->lower(d);
}
EXPECT_NEAR(expect, res, 5e-14);
}
}
protected:
UInt nb_integration_points;
std::array<Array<Real>, parent::dim> polynomial;
Array<Real> integration_points_pos;
std::array<Polynomial<5>, 3> polys;
};
template <typename T> constexpr size_t TestGaussIntegrationFixture<T>::degree;
/* -------------------------------------------------------------------------- */
/* Tests */
/* -------------------------------------------------------------------------- */
TYPED_TEST_SUITE_P(TestGaussIntegrationFixture);
TYPED_TEST_P(TestGaussIntegrationFixture, ArbitraryOrder) {
this->testIntegrate();
}
REGISTER_TYPED_TEST_SUITE_P(TestGaussIntegrationFixture, ArbitraryOrder);
using TestTypes = gtest_list_t<
tuple_split_t<50, cross_product_t<TestElementTypes, TestDegreeTypes>>>;
INSTANTIATE_TYPED_TEST_SUITE_P(Split1, TestGaussIntegrationFixture, TestTypes, );
using TestTypesTail = gtest_list_t<
tuple_split_tail_t<50, cross_product_t<TestElementTypes, TestDegreeTypes>>>;
INSTANTIATE_TYPED_TEST_SUITE_P(Split2, TestGaussIntegrationFixture,
TestTypesTail, );
} // namespace
diff --git a/test/test_fe_engine/test_fe_engine_precomputation.cc b/test/test_fe_engine/test_fe_engine_precomputation.cc
index e7c6a5f35..b1f5f2fe8 100644
--- a/test/test_fe_engine/test_fe_engine_precomputation.cc
+++ b/test/test_fe_engine/test_fe_engine_precomputation.cc
@@ -1,113 +1,115 @@
/**
* @file test_fe_engine_precomputation.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jun 14 2010
- * @date last modification: Mon Feb 19 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 18 2020
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "py_aka_array.hh"
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <pybind11/embed.h>
#include <pybind11/numpy.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace py = pybind11;
using namespace py::literals;
template <class T> decltype(auto) make_proxy(Array<T> & array) {
return detail::ArrayProxy<T>(array);
}
template <typename type_>
class TestFEMPyFixture : public TestFEMFixture<type_> {
using parent = TestFEMFixture<type_>;
public:
void SetUp() override {
parent::SetUp();
const auto & connectivities = this->mesh->getConnectivity(this->type);
const auto & nodes = this->mesh->getNodes().begin(this->dim);
coordinates = std::make_unique<Array<Real>>(
connectivities.size(), connectivities.getNbComponent() * this->dim);
for (auto && tuple :
zip(make_view(connectivities, connectivities.getNbComponent()),
make_view(*coordinates, this->dim,
connectivities.getNbComponent()))) {
const auto & conn = std::get<0>(tuple);
const auto & X = std::get<1>(tuple);
for (auto s : arange(conn.size())) {
Vector<Real>(X(s)) = Vector<Real>(nodes[conn(s)]);
}
}
}
void TearDown() override {
parent::TearDown();
coordinates.reset(nullptr);
}
protected:
std::unique_ptr<Array<Real>> coordinates;
};
TYPED_TEST_SUITE(TestFEMPyFixture, fe_engine_types, );
TYPED_TEST(TestFEMPyFixture, Precompute) {
SCOPED_TRACE(std::to_string(this->type));
this->fem->initShapeFunctions();
const auto & N = this->fem->getShapeFunctions().getShapes(this->type);
const auto & B =
this->fem->getShapeFunctions().getShapesDerivatives(this->type);
const auto & j = this->fem->getIntegrator().getJacobians(this->type);
// Array<Real> ref_N(this->nb_quadrature_points_total, N.getNbComponent());
// Array<Real> ref_B(this->nb_quadrature_points_total, B.getNbComponent());
Array<Real> ref_j(this->nb_quadrature_points_total, j.getNbComponent());
auto ref_N(N);
auto ref_B(B);
py::module py_engine = py::module::import("py_engine");
auto py_shape = py_engine.attr("Shapes")(py::str(std::to_string(this->type)));
auto kwargs = py::dict("N"_a = ref_N, "B"_a = ref_B, "j"_a = ref_j,
"X"_a = *this->coordinates,
"Q"_a = this->fem->getIntegrationPoints(this->type));
auto ret = py_shape.attr("precompute")(**kwargs);
auto check = [&](auto & ref_A, auto & A, const auto & id) {
SCOPED_TRACE(std::to_string(this->type) + " " + id);
for (auto && n : zip(make_view(ref_A, ref_A.getNbComponent()),
make_view(A, A.getNbComponent()))) {
auto diff = (std::get<0>(n) - std::get<1>(n)).template norm<L_inf>();
EXPECT_NEAR(0., diff, 1e-10);
}
};
check(ref_N, N, "N");
check(ref_B, B, "B");
check(ref_j, j, "j");
}
diff --git a/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_2.cc b/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_2.cc
index cfbc59b87..c48285fed 100644
--- a/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_2.cc
+++ b/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_2.cc
@@ -1,152 +1,154 @@
/**
* @file test_fe_engine_precomputation_bernoulli_2.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jun 14 2010
- * @date last modification: Thu Jan 25 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Jan 25 2018
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator_gauss.hh"
#include "shape_structural.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <functional>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
Matrix<Real> globalToLocalRotation(Real theta) {
// clang-format off
return {{ std::cos(theta), std::sin(theta), 0},
{-std::sin(theta), std::cos(theta), 0},
{ 0, 0, 1}};
// clang-format on
}
Vector<Real> axialReference(Real xq) {
return {(1. - xq) / 2, 0, 0, (1. + xq) / 2, 0, 0};
}
Vector<Real> bendingReference(Real xq) {
return {0,
1. / 4. * Math::pow<2>(xq - 1) * (xq + 2),
1. / 4. * Math::pow<2>(xq - 1) * (xq + 1),
0,
1. / 4. * Math::pow<2>(xq + 1) * (2 - xq),
1. / 4. * Math::pow<2>(xq + 1) * (xq - 1)};
}
Vector<Real> bendingRotationReference(Real xq) {
return {0, 3. / 4. * (xq * xq - 1), 1. / 4. * (3 * xq * xq - 2 * xq - 1),
0, 3. / 4. * (1 - xq * xq), 1. / 4. * (3 * xq * xq + 2 * xq - 1)};
}
bool testBending(const Array<Real> & shape_functions, UInt shape_line_index,
std::function<Vector<Real>(Real)> reference) {
Real xq = -1. / std::sqrt(3.);
// Testing values for bending rotations shapes on quadrature points
for (auto && N : make_view(shape_functions, 3, 6)) {
auto Nt = N.transpose();
Vector<Real> N_bending = Nt(shape_line_index);
auto bending_reference = reference(xq);
if (!Math::are_vector_equal(6, N_bending.storage(),
bending_reference.storage()))
return false;
xq *= -1;
}
std::cout.flush();
return true;
}
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
// debug::setDebugLevel(dblTest);
constexpr ElementType type = _bernoulli_beam_2;
UInt dim = ElementClass<type>::getSpatialDimension();
Mesh mesh(dim);
// creating nodes
Vector<Real> node = {0, 0};
mesh.getNodes().push_back(node);
node = {3. / 5., 4. / 5.};
mesh.getNodes().push_back(node);
node = {2 * 3. / 5., 0};
mesh.getNodes().push_back(node);
mesh.addConnectivityType(type);
auto & connectivity = mesh.getConnectivity(type);
// creating elements
Vector<UInt> elem = {0, 1};
connectivity.push_back(elem);
elem = {1, 2};
connectivity.push_back(elem);
elem = {0, 2};
connectivity.push_back(elem);
using FE = FEEngineTemplate<IntegratorGauss, ShapeStructural, _ek_structural>;
using ShapeStruct = ShapeStructural<_ek_structural>;
auto fem = std::make_unique<FE>(mesh, dim, "test_fem");
fem->initShapeFunctions();
auto & shape = dynamic_cast<const ShapeStruct &>(fem->getShapeFunctions());
Array<Real> angles;
angles.push_back(std::atan(4. / 3.));
angles.push_back(-std::atan(4. / 3.));
angles.push_back(0);
/// Testing the rotation matrices
for (auto && tuple : zip(make_view(shape.getRotations(type), 3, 3), angles)) {
auto && rotation = std::get<0>(tuple);
auto theta = std::get<1>(tuple);
auto reference = globalToLocalRotation(theta);
if (!Math::are_vector_equal(9, reference.storage(), rotation.storage()))
return 1;
}
auto & shape_functions = shape.getShapes(type);
if (!testBending(shape_functions, 0, axialReference))
return 1;
// if (!testBending(shape_functions, 1, bendingReference))
// return 1;
// if (!testBending(shape_functions, 2, bendingRotationReference))
// return 1;
std::cout.flush();
finalize();
return 0;
}
diff --git a/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_3.cc b/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_3.cc
index bc00ada49..e676e35bf 100644
--- a/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_3.cc
+++ b/test/test_fe_engine/test_fe_engine_precomputation_bernoulli_3.cc
@@ -1,104 +1,107 @@
/**
* @file test_fe_engine_precomputation_bernoulli_3.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jan 24 2018
+ * @date last modification: Wed Sep 12 2018
*
* @brief test of the fem class
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator_gauss.hh"
#include "shape_structural.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <functional>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/**
* Reference: p. 285, example 5.7 - A First Course in the Finite Elements Method
* Logan, 6th Edition, 2016
* ISBN-13: 978-1-305-63734-4
*/
Matrix<Real> rotationReference() {
return {{3. / 13, 4. / 13, 12. / 13},
{-4. / 5, 3. / 5, 0},
{-36. / 65, -48. / 65, 5. / 13}};
}
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
// debug::setDebugLevel(dblTest);
constexpr ElementType type = _bernoulli_beam_3;
UInt dim = ElementClass<type>::getSpatialDimension();
Mesh mesh(dim);
// Pushing nodes
Vector<Real> node = {0, 0, 0};
mesh.getNodes().push_back(node);
node = {3, 4, 12};
mesh.getNodes().push_back(node);
// Pushing connectivity
mesh.addConnectivityType(type);
auto & connectivity = mesh.getConnectivity(type);
Vector<UInt> elem = {0, 1};
connectivity.push_back(elem);
// Pushing normals
auto & normals = mesh.registerElementalData<Real>("extra_normal")
.alloc(0, dim, type, _not_ghost);
Vector<Real> normal = {-36. / 65, -48. / 65, 5. / 13};
normals.push_back(normal);
normals.push_back(normal);
using FE = FEEngineTemplate<IntegratorGauss, ShapeStructural, _ek_structural>;
using ShapeStruct = ShapeStructural<_ek_structural>;
auto fem = std::make_unique<FE>(mesh, dim, "test_fem");
fem->initShapeFunctions();
auto & shape = dynamic_cast<const ShapeStruct &>(fem->getShapeFunctions());
Matrix<Real> rot_ref = rotationReference();
Matrix<Real> solution(6, 6);
solution.block(rot_ref, 0, 0);
solution.block(rot_ref, 3, 3);
for (auto && rot : make_view(shape.getRotations(type), 6, 6)) {
if (!Math::are_vector_equal(6 * 6, solution.storage(), rot.storage()))
return 1;
}
/// TODO check shape functions and shape derivatives
finalize();
return 0;
}
diff --git a/test/test_fe_engine/test_fe_engine_precomputation_structural.cc b/test/test_fe_engine/test_fe_engine_precomputation_structural.cc
index 9ec326434..8432b740f 100644
--- a/test/test_fe_engine/test_fe_engine_precomputation_structural.cc
+++ b/test/test_fe_engine/test_fe_engine_precomputation_structural.cc
@@ -1,125 +1,127 @@
/**
* @file test_fe_engine_precomputation_structural.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 26 2018
- * @date last modification: Mon Feb 19 2018
+ * @date last modification: Wed Sep 12 2018
*
* @brief test of the structural precomputations
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator_gauss.hh"
#include "shape_structural.hh"
#include "test_fe_engine_structural_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
// Need a special fixture for the extra normal
class TestBernoulliB3
: public TestFEMStructuralFixture<element_type_t<_bernoulli_beam_3>> {
using parent = TestFEMStructuralFixture<element_type_t<_bernoulli_beam_3>>;
public:
/// Load the mesh and provide extra normal direction
void readMesh(std::string filename) override {
parent::readMesh(filename);
auto & normals = this->mesh->getElementalData<Real>("extra_normal")
.alloc(0, dim, type, _not_ghost);
Vector<Real> normal = {-36. / 65, -48. / 65, 5. / 13};
normals.push_back(normal);
}
};
/* -------------------------------------------------------------------------- */
/// Type alias
using TestBernoulliB2 =
TestFEMStructuralFixture<element_type_t<_bernoulli_beam_2>>;
using TestDKT18 =
TestFEMStructuralFixture<element_type_t<_discrete_kirchhoff_triangle_18>>;
/* -------------------------------------------------------------------------- */
/// Solution for 2D rotation matrices
Matrix<Real> globalToLocalRotation(Real theta) {
auto c = std::cos(theta);
auto s = std::sin(theta);
return {{c, s, 0}, {-s, c, 0}, {0, 0, 1}};
}
/* -------------------------------------------------------------------------- */
TEST_F(TestBernoulliB2, PrecomputeRotations) {
this->fem->initShapeFunctions();
using ShapeStruct = ShapeStructural<_ek_structural>;
auto & shape = dynamic_cast<const ShapeStruct &>(fem->getShapeFunctions());
auto & rot = shape.getRotations(type);
Real a = std::atan(4. / 3);
std::vector<Real> angles = {a, -a, 0};
Math::setTolerance(1e-15);
for (auto && tuple : zip(make_view(rot, ndof, ndof), angles)) {
auto rotation = std::get<0>(tuple);
auto angle = std::get<1>(tuple);
auto rotation_error = (rotation - globalToLocalRotation(angle)).norm<L_2>();
EXPECT_NEAR(rotation_error, 0., Math::getTolerance());
}
}
/* -------------------------------------------------------------------------- */
TEST_F(TestBernoulliB3, PrecomputeRotations) {
this->fem->initShapeFunctions();
using ShapeStruct = ShapeStructural<_ek_structural>;
auto & shape = dynamic_cast<const ShapeStruct &>(fem->getShapeFunctions());
auto & rot = shape.getRotations(type);
Matrix<Real> ref = {{3. / 13, 4. / 13, 12. / 13},
{-4. / 5, 3. / 5, 0},
{-36. / 65, -48. / 65, 5. / 13}};
Matrix<Real> solution{ndof, ndof};
solution.block(ref, 0, 0);
solution.block(ref, dim, dim);
// The default tolerance is too much, really
Math::setTolerance(1e-15);
for (auto & rotation : make_view(rot, ndof, ndof)) {
auto rotation_error = (rotation - solution).norm<L_2>();
EXPECT_NEAR(rotation_error, 0., Math::getTolerance());
}
}
/* -------------------------------------------------------------------------- */
TEST_F(TestDKT18, DISABLED_PrecomputeRotations) {
this->fem->initShapeFunctions();
using ShapeStruct = ShapeStructural<_ek_structural>;
auto & shape = dynamic_cast<const ShapeStruct &>(fem->getShapeFunctions());
auto & rot = shape.getRotations(type);
for (auto & rotation : make_view(rot, ndof, ndof)) {
std::cout << rotation << "\n";
}
std::cout.flush();
}
diff --git a/test/test_fe_engine/test_fe_engine_structural_fixture.hh b/test/test_fe_engine/test_fe_engine_structural_fixture.hh
index 6dcd943ff..78d8eb0a3 100644
--- a/test/test_fe_engine/test_fe_engine_structural_fixture.hh
+++ b/test/test_fe_engine/test_fe_engine_structural_fixture.hh
@@ -1,63 +1,65 @@
/**
* @file test_fe_engine_structural_fixture.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Fri Aug 20 2010
- * @date last modification: Fri Jan 26 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jun 12 2019
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io_msh_struct.hh"
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_
#define AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_
using namespace akantu;
/// Base class for structural FEEngine tests with structural elements
template <typename type_>
class TestFEMStructuralFixture
: public TestFEMBaseFixture<type_, ShapeStructural, _ek_structural> {
using parent = TestFEMBaseFixture<type_, ShapeStructural, _ek_structural>;
public:
static const UInt ndof = ElementClass<parent::type>::getNbDegreeOfFreedom();
/// Need to tell the mesh to load structural elements
void readMesh(std::string file_name) override {
this->mesh->read(file_name, _miot_gmsh_struct);
}
};
template <typename type_> const UInt TestFEMStructuralFixture<type_>::ndof;
// using types = gtest_list_t<TestElementTypes>;
// TYPED_TEST_SUITE(TestFEMFixture, types);
#endif /* AKANTU_TEST_FE_ENGINE_STRUCTURAL_FIXTURE_HH_ */
diff --git a/test/test_fe_engine/test_gradient.cc b/test/test_fe_engine/test_gradient.cc
index 0e1a5d895..7eb6d6965 100644
--- a/test/test_fe_engine/test_gradient.cc
+++ b/test/test_fe_engine/test_gradient.cc
@@ -1,102 +1,104 @@
/**
* @file test_gradient.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
- * @date creation: Fri Sep 03 2010
- * @date last modification: Mon Feb 19 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Feb 19 2018
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section DESCRIPTION
*
* This code is computing the gradient of a linear field and check that it gives
* a constant result. It also compute the gradient the coordinates of the mesh
* and check that it gives the identity
*
*/
/* -------------------------------------------------------------------------- */
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
TYPED_TEST(TestFEMFixture, GradientPoly) {
this->fem->initShapeFunctions();
Real alpha[2][3] = {{13, 23, 31}, {11, 7, 5}};
const auto dim = this->dim;
const auto type = this->type;
const auto & position = this->fem->getMesh().getNodes();
Array<Real> const_val(this->fem->getMesh().getNbNodes(), 2, "const_val");
for (auto && pair : zip(make_view(position, dim), make_view(const_val, 2))) {
auto & pos = std::get<0>(pair);
auto & const_ = std::get<1>(pair);
const_.set(0.);
for (UInt d = 0; d < dim; ++d) {
const_(0) += alpha[0][d] * pos(d);
const_(1) += alpha[1][d] * pos(d);
}
}
/// compute the gradient
Array<Real> grad_on_quad(this->nb_quadrature_points_total, 2 * dim,
"grad_on_quad");
this->fem->gradientOnIntegrationPoints(const_val, grad_on_quad, 2, type);
/// check the results
for (auto && grad : make_view(grad_on_quad, 2, dim)) {
for (UInt d = 0; d < dim; ++d) {
EXPECT_NEAR(grad(0, d), alpha[0][d], 5e-13);
EXPECT_NEAR(grad(1, d), alpha[1][d], 5e-13);
}
}
}
TYPED_TEST(TestFEMFixture, GradientPositions) {
this->fem->initShapeFunctions();
const auto dim = this->dim;
const auto type = this->type;
UInt nb_quadrature_points =
this->fem->getNbIntegrationPoints(type) * this->nb_element;
Array<Real> grad_coord_on_quad(nb_quadrature_points, dim * dim,
"grad_coord_on_quad");
const auto & position = this->mesh->getNodes();
this->fem->gradientOnIntegrationPoints(position, grad_coord_on_quad, dim,
type);
auto I = Matrix<Real>::eye(UInt(dim));
for (auto && grad : make_view(grad_coord_on_quad, dim, dim)) {
auto diff = (I - grad).template norm<L_inf>();
EXPECT_NEAR(0., diff, 2e-14);
}
}
diff --git a/test/test_fe_engine/test_integrate.cc b/test/test_fe_engine/test_integrate.cc
index 5c1dd767e..819d78be8 100644
--- a/test/test_fe_engine/test_integrate.cc
+++ b/test/test_fe_engine/test_integrate.cc
@@ -1,72 +1,74 @@
/**
* @file test_integrate.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
- * @date creation: Fri Sep 03 2010
- * @date last modification: Mon Feb 19 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Feb 19 2018
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
TYPED_TEST(TestFEMFixture, IntegrateConstant) {
this->fem->initShapeFunctions();
const auto type = this->type;
const auto & position = this->fem->getMesh().getNodes();
Array<Real> const_val(position.size(), 2, "const_val");
Array<Real> val_on_quad(this->nb_quadrature_points_total, 2, "val_on_quad");
Vector<Real> value{1, 2};
for (auto && const_ : make_view(const_val, 2)) {
const_ = value;
}
// interpolate function on quadrature points
this->fem->interpolateOnIntegrationPoints(const_val, val_on_quad, 2, type);
// integrate function on elements
Array<Real> int_val_on_elem(this->nb_element, 2, "int_val_on_elem");
this->fem->integrate(val_on_quad, int_val_on_elem, 2, type);
// get global integration value
Vector<Real> sum{0., 0.};
for (auto && int_ : make_view(int_val_on_elem, 2)) {
sum += int_;
}
auto diff = (value - sum).template norm<L_inf>();
EXPECT_NEAR(0, diff, 1e-14);
}
diff --git a/test/test_fe_engine/test_interpolate.cc b/test/test_fe_engine/test_interpolate.cc
index fc0bb8042..f96ac62e2 100644
--- a/test/test_fe_engine/test_interpolate.cc
+++ b/test/test_fe_engine/test_interpolate.cc
@@ -1,71 +1,73 @@
/**
* @file test_interpolate.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Sep 03 2010
- * @date last modification: Tue Nov 14 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Nov 14 2017
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
TYPED_TEST(TestFEMFixture, InterpolateConstant) {
const auto type = this->type;
const auto & position = this->fem->getMesh().getNodes();
Array<Real> const_val(position.size(), 2, "const_val");
Array<Real> val_on_quad(this->nb_quadrature_points_total, 2, "val_on_quad");
Vector<Real> value{1, 2};
for (auto && const_ : make_view(const_val, 2)) {
const_ = value;
}
// interpolate function on quadrature points
this->fem->interpolateOnIntegrationPoints(const_val, val_on_quad, 2, type);
for (auto && int_ : make_view(val_on_quad, 2)) {
auto diff = (value - int_).template norm<L_inf>();
EXPECT_NEAR(0, diff, 1e-14);
}
}
// TYPED_TEST(TestFEMFixture, InterpolatePosition) {
// const auto dim = this->dim;
// const auto type = this->type;
// const auto & position = this->fem->getMesh().getNodes();
// Array<Real> coord_on_quad(this->nb_quadrature_points_total, dim,
// "coord_on_quad");
// this->fem->interpolateOnIntegrationPoints(position, coord_on_quad, dim,
// type);
// }
} // namespace
diff --git a/test/test_fe_engine/test_interpolate_bernoulli_beam_2.cc b/test/test_fe_engine/test_interpolate_bernoulli_beam_2.cc
index b99550d01..fb8d11e49 100644
--- a/test/test_fe_engine/test_interpolate_bernoulli_beam_2.cc
+++ b/test/test_fe_engine/test_interpolate_bernoulli_beam_2.cc
@@ -1,117 +1,119 @@
/**
* @file test_interpolate_bernoulli_beam_2.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Sat Jan 23 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sat Jan 23 2016
*
* @brief Test of the interpolation on the type _bernoulli_beam_2
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "fe_engine.hh"
#include "fe_engine_template.hh"
#include "integrator_gauss.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "shape_linked.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main() {
Mesh beams(2);
/* --------------------------------------------------------------------------
*/
// Defining the mesh
Array<Real> & nodes = const_cast<Array<Real> &>(beams.getNodes());
nodes.resize(4);
beams.addConnectivityType(_bernoulli_beam_2);
Array<UInt> & connectivity =
const_cast<Array<UInt> &>(beams.getConnectivity(_bernoulli_beam_2));
connectivity.resize(3);
for (UInt i = 0; i < 4; ++i) {
nodes(i, 0) = (i + 1) * 2;
nodes(i, 1) = 1;
}
for (UInt i = 0; i < 3; ++i) {
connectivity(i, 0) = i;
connectivity(i, 1) = i + 1;
}
akantu::MeshIOMSH mesh_io;
mesh_io.write("b_beam_2.msh", beams);
/* --------------------------------------------------------------------------
*/
// Interpolation
FEEngineTemplate<IntegratorGauss, ShapeLinked> * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLinked>(beams, 2);
fem->initShapeFunctions();
Array<Real> displ_on_nodes(4, 3);
Array<Real> displ_on_quad(0, 3);
for (UInt i = 0; i < 4; ++i) {
displ_on_nodes(i, 0) = (i + 1) * 2; // Definition of the displacement
displ_on_nodes(i, 1) = 0;
displ_on_nodes(i, 2) = 0;
}
fem->getShapeFunctions().interpolateOnControlPoints<_bernoulli_beam_2>(
displ_on_nodes, displ_on_quad, 3, _not_ghost, NULL, false, 0, 0, 0);
fem->getShapeFunctions().interpolateOnControlPoints<_bernoulli_beam_2>(
displ_on_nodes, displ_on_quad, 3, _not_ghost, NULL, false, 1, 1, 1);
fem->getShapeFunctions().interpolateOnControlPoints<_bernoulli_beam_2>(
displ_on_nodes, displ_on_quad, 3, _not_ghost, NULL, true, 2, 2, 1);
fem->getShapeFunctions().interpolateOnControlPoints<_bernoulli_beam_2>(
displ_on_nodes, displ_on_quad, 3, _not_ghost, NULL, false, 3, 2, 3);
fem->getShapeFunctions().interpolateOnControlPoints<_bernoulli_beam_2>(
displ_on_nodes, displ_on_quad, 3, _not_ghost, NULL, true, 4, 3, 3);
Real * don = displ_on_nodes.storage();
Real * doq = displ_on_quad.storage();
std::ofstream my_file("out.txt");
my_file << don << std::endl;
my_file << doq << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_fe_engine/test_inverse_map.cc b/test/test_fe_engine/test_inverse_map.cc
index 610799b6b..dfeaf3adc 100644
--- a/test/test_fe_engine/test_inverse_map.cc
+++ b/test/test_fe_engine/test_inverse_map.cc
@@ -1,69 +1,71 @@
/**
* @file test_inverse_map.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
- * @date creation: Fri Sep 03 2010
- * @date last modification: Mon Feb 19 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Mar 13 2018
*
* @brief test of the fem class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_fe_engine_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
TYPED_TEST(TestFEMFixture, InverseMap) {
this->fem->initShapeFunctions();
Matrix<Real> quad =
GaussIntegrationElement<TestFixture::type>::getQuadraturePoints();
const auto & position = this->fem->getMesh().getNodes();
/// get the quadrature points coordinates
Array<Real> coord_on_quad(quad.cols() * this->nb_element, this->dim,
"coord_on_quad");
this->fem->interpolateOnIntegrationPoints(position, coord_on_quad, this->dim,
this->type);
Vector<Real> natural_coords(this->dim);
auto length = (this->upper - this->lower).template norm<L_inf>();
for (auto && enum_ :
enumerate(make_view(coord_on_quad, this->dim, quad.cols()))) {
auto el = std::get<0>(enum_);
const auto & quads_coords = std::get<1>(enum_);
for (auto q : arange(quad.cols())) {
Vector<Real> quad_coord = quads_coords(q);
Vector<Real> ref_quad_coord = quad(q);
this->fem->inverseMap(quad_coord, el, this->type, natural_coords);
auto dis_normalized = ref_quad_coord.distance(natural_coords) / length;
EXPECT_NEAR(0., dis_normalized, 3.5e-11);
}
}
}
diff --git a/test/test_fe_engine/test_mesh_boundary.cc b/test/test_fe_engine/test_mesh_boundary.cc
index d4a5fd88c..feb6ba6f1 100644
--- a/test/test_fe_engine/test_mesh_boundary.cc
+++ b/test/test_fe_engine/test_mesh_boundary.cc
@@ -1,64 +1,66 @@
/**
* @file test_mesh_boundary.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
- * @date creation: Fri May 03 2013
- * @date last modification: Sun Aug 13 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sun Aug 13 2017
*
* @brief Thest the element groups
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
UInt spatialDimension(3);
akantu::initialize(argc, argv);
Mesh mesh(spatialDimension, "mesh_names");
std::cout << "Loading the mesh." << std::endl;
mesh.read("./cube_physical_names.msh");
std::cout << "Examining mesh:" << std::endl;
// Inspection of the number of boundaries
UInt nb_boundaries = mesh.getNbElementGroups(spatialDimension - 1);
AKANTU_DEBUG_INFO(nb_boundaries << " boundaries advertised by Mesh.");
if (nb_boundaries == 0) {
std::cout << "No boundary detected!" << std::endl;
return 1;
}
std::cout << (*dynamic_cast<GroupManager *>(&mesh)) << std::endl;
akantu::finalize();
return 0;
}
diff --git a/test/test_fe_engine/test_mesh_data.cc b/test/test_fe_engine/test_mesh_data.cc
index b09ce4ce3..6e9c746c4 100644
--- a/test/test_fe_engine/test_mesh_data.cc
+++ b/test/test_fe_engine/test_mesh_data.cc
@@ -1,85 +1,87 @@
/**
* @file test_mesh_data.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
- * @date creation: Fri May 03 2013
- * @date last modification: Wed Feb 03 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Jul 13 2015
*
* @brief Test of the MeshData class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <string>
#define QUOTES(x) #x
#define ADD_QUOTES(x) QUOTES(x)
#define CAT(x, y) x##_##y
#define CONCAT(x, y) CAT(x, y)
//#define TYPE std::string
//#define VALUE1 "abc"
//#define VALUE2 "qwe"
#define ELEMENT _triangle_6
#define NAME CONCAT(TYPE, data)
/* -------------------------------------------------------------------------- */
using namespace akantu;
using namespace std;
int main() {
std::cout << "Testing with type " << ADD_QUOTES(TYPE) << " and values "
<< ADD_QUOTES(VALUE1) << "," << ADD_QUOTES(VALUE2) << "..."
<< std::endl;
MeshData mesh_data;
ElementType elem_type = ELEMENT;
const std::string name = ADD_QUOTES(NAME);
Array<TYPE> & vec =
mesh_data.getElementalDataArrayAlloc<TYPE>(name, elem_type);
// XXX TO DELETE
// vec.copy(mesh_data.getElementalDataArrayAlloc<TYPE>(name, elem_type));
TYPE value[2] = {VALUE1, VALUE2};
vec.push_back(value[0]);
vec.push_back(value[1]);
for (UInt i(0); i < 2; i++) {
AKANTU_DEBUG_ASSERT(vec(i) == value[i], "The Array accessed through the "
"getElementDataArray method does "
"not contain the right value.");
}
std::cout << vec << std::endl;
std::cout << mesh_data.getTypeCode(name) << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/CMakeLists.txt b/test/test_geometry/CMakeLists.txt
index 32a503a45..be6faedcf 100644
--- a/test/test_geometry/CMakeLists.txt
+++ b/test/test_geometry/CMakeLists.txt
@@ -1,46 +1,56 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
#
# @date creation: Fri Jun 19 2015
-# @date last modification: Sat Jan 23 2016
+# @date last modification: Sat Jan 23 2016
#
# @brief configuration for solver tests
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_geometry_predicates
SOURCES test_geometry_predicates.cc
PACKAGE CGAL
)
register_test(test_geometry_intersection
SOURCES test_geometry_intersection.cc
FILES_TO_COPY test_geometry_triangle.msh
PACKAGE CGAL
)
register_test(test_segment_intersection_triangle_3
SOURCES test_segment_intersection_triangle_3.cc
FILES_TO_COPY test_geometry_triangle.msh
PACKAGE CGAL
)
register_test(test_segment_intersection_tetrahedron_4
SOURCES test_segment_intersection_tetrahedron_4.cc
FILES_TO_COPY test_geometry_tetrahedron.msh
PACKAGE CGAL
)
diff --git a/test/test_geometry/test_geometry_intersection.cc b/test/test_geometry/test_geometry_intersection.cc
index a6ae20104..6dd8020e1 100644
--- a/test/test_geometry/test_geometry_intersection.cc
+++ b/test/test_geometry/test_geometry_intersection.cc
@@ -1,130 +1,132 @@
/**
* @file test_geometry_intersection.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Jan 31 2018
*
* @brief Tests the intersection module
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "geom_helper_functions.hh"
#include "mesh_geom_factory.hh"
#include "tree_type_helper.hh"
#include "mesh_geom_common.hh"
#include <iostream>
#include <iterator>
#include <CGAL/Exact_spherical_kernel_3.h>
#include <CGAL/Spherical_kernel_intersections.h>
#include <CGAL/intersections.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef cgal::Cartesian K;
typedef IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>,
K::Segment_3>::intersection_type result_type;
typedef cgal::Spherical SK;
typedef boost::variant<std::pair<SK::Circular_arc_point_3, UInt>> sk_inter_res;
/*typedef CGAL::cpp11::result_of<SK::Intersect_3(SK::Line_arc_3,
SK::Sphere_3,
std::back_insert_iterator<
std::list<sk_inter_res> >)>::type sk_res;*/
typedef std::pair<SK::Circular_arc_point_3, UInt> pair_type;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("", argc, argv);
debug::setDebugLevel(dblWarning);
Mesh mesh(2);
mesh.read("test_geometry_triangle.msh");
MeshGeomFactory<2, _triangle_3, Triangle<K>, K> factory(mesh);
factory.constructData();
const TreeTypeHelper<Triangle<K>, K>::tree & tree = factory.getTree();
K::Point_3 a(0., 0.25, 0.), b(1., 0.25, 0.);
K::Segment_3 line(a, b);
K::Point_3 begin(a), intermediate(0.25, 0.25, 0.), end(0.75, 0.25, 0.);
K::Segment_3 result_0(begin, intermediate), result_1(intermediate, end);
std::list<result_type> list_of_intersections;
tree.all_intersections(line, std::back_inserter(list_of_intersections));
const result_type & intersection_0 = list_of_intersections.back();
const result_type & intersection_1 = list_of_intersections.front();
if (!intersection_0 || !intersection_1)
return EXIT_FAILURE;
/// *-> first is the intersection ; *->second is the primitive id
if (const K::Segment_3 * segment =
boost::get<K::Segment_3>(&(intersection_0->first))) {
if (!compareSegments(*segment, result_0)) {
return EXIT_FAILURE;
}
} else
return EXIT_FAILURE;
if (const K::Segment_3 * segment =
boost::get<K::Segment_3>(&(intersection_1->first))) {
if (!compareSegments(*segment, result_1)) {
return EXIT_FAILURE;
}
} else
return EXIT_FAILURE;
SK::Sphere_3 sphere(SK::Point_3(0, 0, 0), 3.);
SK::Segment_3 seg(SK::Point_3(0, 0, 0), SK::Point_3(2., 2., 2.));
SK::Line_arc_3 arc(seg);
std::list<sk_inter_res> s_results;
CGAL::intersection(arc, sphere, std::back_inserter(s_results));
if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
std::cout << "xi = " << to_double(pair->first.x())
<< ", yi = " << to_double(pair->first.y()) << std::endl;
if (!comparePoints(pair->first, SK::Circular_arc_point_3(1.0, 1.0, 1.0)))
return EXIT_FAILURE;
} else
return EXIT_FAILURE;
MeshGeomFactory<2, _triangle_3, Line_arc<SK>, SK> Sfactory(mesh);
Sfactory.constructData();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_geometry_predicates.cc b/test/test_geometry/test_geometry_predicates.cc
index e5496f3ea..5f6044010 100644
--- a/test/test_geometry/test_geometry_predicates.cc
+++ b/test/test_geometry/test_geometry_predicates.cc
@@ -1,87 +1,89 @@
/**
* @file test_geometry_predicates.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Fri Jan 04 2013
- * @date last modification: Wed Jan 31 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jan 31 2018
*
* @brief Tests the geometry predicates
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "geom_helper_functions.hh"
#include "mesh_geom_common.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef cgal::Cartesian K;
typedef K::Point_3 Point;
typedef K::Segment_3 Segment;
int main(int argc, char * argv[]) {
initialize("", argc, argv);
debug::setDebugLevel(dblWarning);
Point a(0, 1, 0);
Point b(0, 1, 1);
Segment seg1(a, b);
Segment seg2(b, a);
if (!compareSegments(seg1, seg2))
return EXIT_FAILURE;
// Testing sort + unique on list of segments
std::vector<std::pair<K::Segment_3, UInt>> pair_list;
pair_list.push_back(std::make_pair(seg1, 1));
pair_list.push_back(std::make_pair(seg2, 2));
segmentPairsLess sorter;
std::sort(pair_list.begin(), pair_list.end(), sorter);
std::vector<std::pair<K::Segment_3, UInt>>::iterator it =
std::unique(pair_list.begin(), pair_list.end(), compareSegmentPairs);
if (it - pair_list.begin() != 1) {
std::cout << pair_list.size() << std::endl;
return EXIT_FAILURE;
}
// Testing insertion in set
std::set<std::pair<K::Segment_3, UInt>, segmentPairsLess> pair_set;
pair_set.insert(pair_set.begin(), std::make_pair(seg1, 1));
pair_set.insert(pair_set.begin(), std::make_pair(seg2, 2));
if (pair_set.size() != 1) {
std::cout << pair_set.size() << std::endl;
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_segment_intersection_tetrahedron_4.cc b/test/test_geometry/test_segment_intersection_tetrahedron_4.cc
index acdfc4977..78877d7a2 100644
--- a/test/test_geometry/test_segment_intersection_tetrahedron_4.cc
+++ b/test/test_geometry/test_segment_intersection_tetrahedron_4.cc
@@ -1,142 +1,144 @@
/**
* @file test_segment_intersection_tetrahedron_4.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Tue Mar 13 2018
*
* @brief Tests the intersection module with _tetrahedron_4 elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_segment_intersector.hh"
#include "mesh_geom_common.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef cgal::Cartesian K;
typedef K::Point_3 Point;
typedef K::Segment_3 Segment;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("", argc, argv);
debug::setDebugLevel(dblError);
Mesh mesh(3), interface_mesh(3, "interface_mesh");
mesh.read("test_geometry_tetrahedron.msh");
MeshSegmentIntersector<3, _tetrahedron_4> intersector(mesh, interface_mesh);
intersector.constructData();
// Testing a segment going through the cube
Point point(1., 1., 1.);
Segment segment(CGAL::ORIGIN, point);
intersector.computeIntersectionQuery(segment);
std::cout << "number of seg_2 : " << interface_mesh.getNbElement(_segment_2)
<< std::endl;
if (interface_mesh.getNbElement(_segment_2) != 2)
return EXIT_FAILURE;
Vector<Real> bary(2), bary1(2), bary2(2);
Element test{_segment_2, 0, _not_ghost};
interface_mesh.getBarycenter(test, bary1);
test.element = 1;
interface_mesh.getBarycenter(test, bary2);
Real first_bary[] = {1. / 6., 1. / 6., 1. / 6.};
Real second_bary[] = {2. / 3., 2. / 3., 2. / 3.};
// We don't know the order of the elements, so here we test permutations
if (!((Math::are_vector_equal(3, bary1.storage(), first_bary) &&
Math::are_vector_equal(3, bary2.storage(), second_bary)) ||
(Math::are_vector_equal(3, bary1.storage(), second_bary) &&
Math::are_vector_equal(3, bary2.storage(), first_bary))))
return EXIT_FAILURE;
// Testing a segment completely inside one element
Point a(0.05, 0.05, 0.05), b(0.06, 0.06, 0.06);
Segment inside_segment(a, b);
intersector.computeIntersectionQuery(inside_segment);
test.element = interface_mesh.getNbElement(_segment_2) - 1;
interface_mesh.getBarycenter(test, bary);
Real third_bary[] = {0.055, 0.055, 0.055};
if (!Math::are_vector_equal(3, bary.storage(), third_bary))
return EXIT_FAILURE;
// Testing a segment whose end points are inside elements
Point c(0.1, 0.1, 0.1), d(0.9, 0.9, 0.9);
Segment crossing_segment(c, d);
intersector.computeIntersectionQuery(crossing_segment);
UInt el1 = interface_mesh.getNbElement(_segment_2) - 2;
UInt el2 = el1 + 1;
test.element = el1;
interface_mesh.getBarycenter(test, bary1);
test.element = el2;
interface_mesh.getBarycenter(test, bary2);
Real fourth_bary[] = {13. / 60., 13. / 60., 13. / 60.};
Real fifth_bary[] = {37. / 60., 37. / 60., 37. / 60.};
// We don't know the order of the elements, so here we test permutations
if (!((Math::are_vector_equal(3, bary1.storage(), fourth_bary) &&
Math::are_vector_equal(3, bary2.storage(), fifth_bary)) ||
(Math::are_vector_equal(3, bary1.storage(), fifth_bary) &&
Math::are_vector_equal(3, bary2.storage(), fourth_bary))))
return EXIT_FAILURE;
// Testing a segment along the edge of elements
Point e(1, 0, 0), f(0, 1, 0);
Segment edge_segment(e, f);
UInt current_nb_elements = interface_mesh.getNbElement(_segment_2);
intersector.computeIntersectionQuery(edge_segment);
if (interface_mesh.getNbElement(_segment_2) != current_nb_elements + 1)
return EXIT_FAILURE;
test.element = interface_mesh.getNbElement(_segment_2) - 1;
interface_mesh.getBarycenter(test, bary);
Real sixth_bary[] = {0.5, 0.5, 0};
if (!Math::are_vector_equal(3, bary.storage(), sixth_bary))
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_segment_intersection_triangle_3.cc b/test/test_geometry/test_segment_intersection_triangle_3.cc
index 04a747695..c336c80e3 100644
--- a/test/test_geometry/test_segment_intersection_triangle_3.cc
+++ b/test/test_geometry/test_segment_intersection_triangle_3.cc
@@ -1,135 +1,137 @@
/**
* @file test_segment_intersection_triangle_3.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Feb 27 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Tue Mar 13 2018
*
* @brief Tests the interface mesh generation
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "geom_helper_functions.hh"
#include "mesh_geom_common.hh"
#include "mesh_segment_intersector.hh"
#include "mesh_sphere_intersector.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef cgal::Cartesian K;
typedef cgal::Spherical SK;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("", argc, argv);
debug::setDebugLevel(dblError);
Math::setTolerance(1e-10);
Mesh mesh(2), interface_mesh(2, "interface_mesh");
mesh.read("test_geometry_triangle.msh");
MeshSegmentIntersector<2, _triangle_3> intersector(mesh, interface_mesh);
intersector.constructData();
// Testing a segment going out of the mesh
K::Point_3 a(0, 0.25, 0), b(1, 0.25, 0), c(0.25, 0, 0), d(0.25, 1, 0);
K::Segment_3 h_interface(a, b), v_interface(c, d);
std::list<K::Segment_3> interface_list;
interface_list.push_back(h_interface);
interface_list.push_back(v_interface);
intersector.computeIntersectionQueryList(interface_list);
if (interface_mesh.getNbElement(_segment_2) != 4)
return EXIT_FAILURE;
Vector<Real> bary(2);
Element test{_segment_2, 0, _not_ghost};
interface_mesh.getBarycenter(test, bary);
Real first_bary[] = {0.125, 0.25};
if (!Math::are_vector_equal(2, bary.storage(), first_bary))
return EXIT_FAILURE;
// Testing a segment completely inside an element
K::Point_3 e(0.1, 0.33, 0), f(0.1, 0.67, 0);
K::Segment_3 inside_segment(e, f);
intersector.computeIntersectionQuery(inside_segment);
test.element = interface_mesh.getNbElement(_segment_2) - 1;
interface_mesh.getBarycenter(test, bary);
Real second_bary[] = {0.1, 0.5};
if (!Math::are_vector_equal(2, bary.storage(), second_bary))
return EXIT_FAILURE;
#if 0
// cgal::Spherical kernel testing the addition of nodes
std::cout << "initial mesh size = " << mesh.getNodes().size() << " nodes" << std::endl;
SK::Sphere_3 sphere(SK::Point_3(0, 1, 0), 0.2*0.2);
SK::Sphere_3 sphere2(SK::Point_3(1, 0, 0), 0.4999999999);
MeshSphereIntersector<2, _triangle_3> intersector_sphere(mesh);
intersector_sphere.constructData();
std::list<SK::Sphere_3> sphere_list;
sphere_list.push_back(sphere);
sphere_list.push_back(sphere2);
intersector_sphere.computeIntersectionQueryList(sphere_list);
std::cout << "final mesh size = " << mesh.getNodes().size() << std::endl;
const Array<UInt> new_node_triangle_3 = intersector_sphere.getNewNodePerElem();
const Array<Real> & nodes = mesh.getNodes();
std::cout << "New nodes :" << std::endl;
std::cout << "node 5, x=" << nodes(4,0) << ", y=" << nodes(4,1) << std::endl;
std::cout << "node 6, x=" << nodes(5,0) << ", y=" << nodes(5,1) << std::endl;
std::cout << "node 7, x=" << nodes(6,0) << ", y=" << nodes(6,1) << std::endl;
if ( (new_node_triangle_3(0,0) != 1) || (new_node_triangle_3(1,0) != 2)){
for(UInt k=0; k != new_node_triangle_3.size(); ++k){
std::cout << new_node_triangle_3(k,0) << " new nodes in element " << k << ", node(s): "
<< new_node_triangle_3(k,1) << ", " << new_node_triangle_3(k,3)
<< ", on segment(s):" << new_node_triangle_3(k,2) << ", "
<< new_node_triangle_3(k,4) << std::endl;
}
return EXIT_FAILURE;
}
#endif
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_gtest_main.cc b/test/test_gtest_main.cc
index 3f879c00e..7c92f45aa 100644
--- a/test/test_gtest_main.cc
+++ b/test/test_gtest_main.cc
@@ -1,82 +1,84 @@
/**
* @file test_gtest_main.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Nov 09 2017
- * @date last modification: Tue Jan 16 2018
+ * @date last modification: Tue Dec 10 2019
*
* @brief Main function for gtest tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#if defined(AKANTU_TEST_USE_PYBIND11)
#include <pybind11/embed.h>
namespace py = pybind11;
#endif
/* -------------------------------------------------------------------------- */
namespace {
class AkaEnvironment : public ::testing::Environment {
public:
AkaEnvironment(int & argc, char **& argv) : argc(argc), argv(argv) {}
// Override this to define how to set up the environment.
void SetUp() override {
::akantu::initialize(argc, argv);
#if defined(AKANTU_USE_PYBIND11)
// py::initialize_interpreter();
#endif
}
// Override this to define how to tear down the environment.
void TearDown() override {
::akantu::finalize();
#if defined(AKANTU_USE_PYBIND11)
// py::finalize_interpreter();
#endif
}
protected:
int & argc;
char **& argv;
};
} // namespace
int main(int argc, char ** argv) {
#if defined(AKANTU_TEST_USE_PYBIND11)
py::scoped_interpreter guard{};
#endif
::testing::InitGoogleTest(&argc, argv);
::testing::AddGlobalTestEnvironment(new AkaEnvironment(argc, argv));
::testing::TestEventListeners & listeners =
::testing::UnitTest::GetInstance()->listeners();
if (::akantu::Communicator::getStaticCommunicator().whoAmI() != 0) {
delete listeners.Release(listeners.default_result_printer());
}
return RUN_ALL_TESTS();
}
diff --git a/test/test_gtest_utils.hh b/test/test_gtest_utils.hh
index 6a1f51c18..0f5b6269d 100644
--- a/test/test_gtest_utils.hh
+++ b/test/test_gtest_utils.hh
@@ -1,258 +1,260 @@
/**
* @file test_gtest_utils.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Fri Jan 10 2020
*
* @brief Utils to help write tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_iterators.hh"
/* -------------------------------------------------------------------------- */
#include <boost/preprocessor.hpp>
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_GTEST_UTILS_HH_
#define AKANTU_TEST_GTEST_UTILS_HH_
#if !defined(TYPED_TEST_SUITE)
#define TYPED_TEST_SUITE(...) TYPED_TEST_CASE(__VA_ARGS__)
#endif
#if !defined(TYPED_TEST_SUITE_P)
#define TYPED_TEST_SUITE_P(...) TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
#if !defined(REGISTER_TYPED_TEST_SUITE_P)
#define REGISTER_TYPED_TEST_SUITE_P(...) REGISTER_TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
#if !defined(INSTANTIATE_TYPED_TEST_SUITE_P)
#define INSTANTIATE_TYPED_TEST_SUITE_P(...) \
INSTANTIATE_TYPED_TEST_CASE_P(__VA_ARGS__)
#endif
namespace {
/* -------------------------------------------------------------------------- */
template <::akantu::ElementType t>
using element_type_t = std::integral_constant<::akantu::ElementType, t>;
/* -------------------------------------------------------------------------- */
template <typename... T> struct gtest_list {};
template <typename... Ts> struct gtest_list<std::tuple<Ts...>> {
using type = ::testing::Types<Ts...>;
};
template <typename... T> using gtest_list_t = typename gtest_list<T...>::type;
/* -------------------------------------------------------------------------- */
//template <typename... T> struct tuple_concat {};
template <typename... Ts>
struct tuple_concat {
using type = decltype(std::tuple_cat(std::declval<Ts>()...));
};
template <typename... T>
using tuple_concat_t = typename tuple_concat<T...>::type;
/* -------------------------------------------------------------------------- */
template <template <typename> class Pred, typename... Ts>
struct tuple_filter {};
template <template <typename> class Pred, typename T>
struct tuple_filter<Pred, std::tuple<T>> {
using type = std::conditional_t<Pred<T>::value, std::tuple<T>, std::tuple<>>;
};
template <template <typename> class Pred, typename T, typename... Ts>
struct tuple_filter<Pred, std::tuple<T, Ts...>> {
using type =
tuple_concat_t<typename tuple_filter<Pred, std::tuple<T>>::type,
typename tuple_filter<Pred, std::tuple<Ts...>>::type>;
};
template <template <typename> class Pred, typename... Ts>
using tuple_filter_t = typename tuple_filter<Pred, Ts...>::type;
/* -------------------------------------------------------------------------- */
template <size_t N, typename... Ts> struct tuple_split {};
template <size_t N, typename T, typename... Ts>
struct tuple_split<N, std::tuple<T, Ts...>> {
protected:
using split = tuple_split<N - 1, std::tuple<Ts...>>;
public:
using type = tuple_concat_t<std::tuple<T>, typename split::type>;
using type_tail = typename split::type_tail;
};
template <typename T, typename... Ts>
struct tuple_split<1, std::tuple<T, Ts...>> {
using type = std::tuple<T>;
using type_tail = std::tuple<Ts...>;
};
template <size_t N, typename... T>
using tuple_split_t = typename tuple_split<N, T...>::type;
template <size_t N, typename... T>
using tuple_split_tail_t = typename tuple_split<N, T...>::type_tail;
/* -------------------------------------------------------------------------- */
template <typename... T> struct cross_product {};
template <typename... T2s>
struct cross_product<std::tuple<>, std::tuple<T2s...>> {
using type = std::tuple<>;
};
template <typename T1, typename... T1s, typename... T2s>
struct cross_product<std::tuple<T1, T1s...>, std::tuple<T2s...>> {
using type = tuple_concat_t<
std::tuple<std::tuple<T1, T2s>...>,
typename cross_product<std::tuple<T1s...>, std::tuple<T2s...>>::type>;
};
template <typename... T>
using cross_product_t = typename cross_product<T...>::type;
/* -------------------------------------------------------------------------- */
} // namespace
#define OP_CAT(s, data, elem) BOOST_PP_CAT(_element_type, elem)
// creating a type instead of a using helps to debug
#define AKANTU_DECLARE_ELEMENT_TYPE_STRUCT(r, data, elem) \
struct BOOST_PP_CAT(_element_type, elem) \
: public element_type_t<::akantu::elem> {};
BOOST_PP_SEQ_FOR_EACH(AKANTU_DECLARE_ELEMENT_TYPE_STRUCT, _,
AKANTU_ALL_ELEMENT_TYPE)
#undef AKANTU_DECLARE_ELEMENT_TYPE_STRUCT
using TestElementTypesAll = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_regular_ELEMENT_TYPE))>;
#if defined(AKANTU_COHESIVE_ELEMENT)
using TestCohesiveElementTypes = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_cohesive_ELEMENT_TYPE))>;
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
using TestElementTypesStructural = std::tuple<BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(OP_CAT, _, AKANTU_ek_structural_ELEMENT_TYPE))>;
#endif
using TestAllDimensions = std::tuple<std::integral_constant<unsigned int, 1>,
std::integral_constant<unsigned int, 2>,
std::integral_constant<unsigned int, 3>>;
template <typename T, ::akantu::ElementType type>
using is_element = aka::bool_constant<T::value == type>;
template <typename T>
using not_is_point_1 = aka::negation<is_element<T, ::akantu::_point_1>>;
using TestElementTypes = tuple_filter_t<not_is_point_1, TestElementTypesAll>;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
using StructuralTestElementTypes =
tuple_filter_t<not_is_point_1, TestElementTypesStructural>;
#endif
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <size_t degree> class Polynomial {
public:
Polynomial() = default;
Polynomial(std::initializer_list<double> && init) {
for (auto && pair : akantu::zip(init, constants))
std::get<1>(pair) = std::get<0>(pair);
}
double operator()(double x) {
double res = 0.;
for (auto && vals : akantu::enumerate(constants)) {
double a;
int k;
std::tie(k, a) = vals;
res += a * std::pow(x, k);
}
return res;
}
Polynomial extract(size_t pdegree) {
Polynomial<degree> extract(*this);
for (size_t d = pdegree + 1; d < degree + 1; ++d)
extract.constants[d] = 0;
return extract;
}
auto integral() {
Polynomial<degree + 1> integral_;
integral_.set(0, 0.);
;
for (size_t d = 0; d < degree + 1; ++d) {
integral_.set(1 + d, get(d) / double(d + 1));
}
return integral_;
}
auto integrate(double a, double b) {
auto primitive = integral();
return (primitive(b) - primitive(a));
}
double get(int i) const { return constants[i]; }
void set(int i, double a) { constants[i] = a; }
protected:
std::array<double, degree + 1> constants;
};
template <size_t degree>
std::ostream & operator<<(std::ostream & stream, const Polynomial<degree> & p) {
for (size_t d = 0; d < degree + 1; ++d) {
if (d != 0)
stream << " + ";
stream << p.get(degree - d);
if (d != degree)
stream << "x ^ " << degree - d;
}
return stream;
}
/* -------------------------------------------------------------------------- */
#endif /* AKANTU_TEST_GTEST_UTILS_HH_ */
diff --git a/test/test_io/CMakeLists.txt b/test/test_io/CMakeLists.txt
index e75d7e538..c4aac79d7 100644
--- a/test/test_io/CMakeLists.txt
+++ b/test/test_io/CMakeLists.txt
@@ -1,26 +1,36 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_akantu_test(test_parser "Test the input file parser")
add_akantu_test(test_dumper "Test the dumping of output files")
\ No newline at end of file
diff --git a/test/test_io/test_dumper/CMakeLists.txt b/test/test_io/test_dumper/CMakeLists.txt
index ca05ec0fd..506d6626f 100644
--- a/test/test_io/test_dumper/CMakeLists.txt
+++ b/test/test_io/test_dumper/CMakeLists.txt
@@ -1,30 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author David Simon Kammer <david.kammer@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_dumper
SOURCES test_dumper.cc
FILES_TO_COPY input_file.dat test_dumper.msh
DIRECTORIES_TO_CREATE paraview
PACKAGE iohelper
)
diff --git a/test/test_io/test_dumper/test_dumper.cc b/test/test_io/test_dumper/test_dumper.cc
index d42645a85..fd6a34f42 100644
--- a/test/test_io/test_dumper/test_dumper.cc
+++ b/test/test_io/test_dumper/test_dumper.cc
@@ -1,159 +1,161 @@
/**
* @file test_dumper.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
- * @date creation: Tue Sep 02 2014
- * @date last modification: Mon Jan 22 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue May 21 2019
*
* @brief test dumper
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "dumper_nodal_field.hh"
#include "dumper_text.hh"
#include "dumper_variable.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("input_file.dat", argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
mesh.read("test_dumper.msh");
SolidMechanicsModel model(mesh);
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
model.initFull();
model.assembleInternalForces();
Real time_step = 0.1;
const Array<Real> & coord = mesh.getNodes();
Array<Real> & disp = model.getDisplacement();
Array<bool> & bound = model.getBlockedDOFs();
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
Real dist = 0.;
for (UInt d = 0; d < spatial_dimension; ++d) {
dist += coord(n, d) * coord(n, d);
}
dist = sqrt(dist);
for (UInt d = 0; d < spatial_dimension; ++d) {
disp(n, d) = (d + 1) * dist;
bound(n, d) = bool((n % 2) + d);
}
}
// dump boundary bottom as reference
model.setGroupDirectory("paraview", "Bottom");
model.setGroupBaseName("paraview_bottom", "Bottom");
model.addDumpGroupField("displacement", "Bottom");
model.addDumpGroupField("blocked_dofs", "Bottom");
UInt nbp = 3;
DumperParaview prvdumper("paraview_bottom_parallel", "paraview", false);
iohelper::Dumper & prvdpr = prvdumper.getDumper();
for (UInt p = 0; p < nbp; ++p) {
prvdpr.setParallelContext(p, nbp, 0);
if (p != 0) {
prvdumper.unRegisterField("connectivities");
prvdumper.unRegisterField("element_type");
prvdumper.unRegisterField("positions");
prvdumper.unRegisterField("displacement");
}
prvdumper.registerFilteredMesh(
mesh, mesh.getElementGroup("Bottom").getElements(),
mesh.getElementGroup("Bottom").getNodeGroup().getNodes());
prvdumper.registerField(
"displacement",
std::make_shared<dumpers::NodalField<Real, true>>(
model.getDisplacement(), 0, 0,
&(mesh.getElementGroup("Bottom").getNodeGroup().getNodes())));
prvdumper.dump(0);
}
DumperText txtdumper("text_bottom", iohelper::_tdm_csv);
txtdumper.setDirectory("paraview");
txtdumper.setPrecision(8);
txtdumper.setTimeStep(time_step);
txtdumper.registerFilteredMesh(
mesh, mesh.getElementGroup("Bottom").getElements(),
mesh.getElementGroup("Bottom").getNodeGroup().getNodes());
txtdumper.registerField(
"displacement",
std::make_shared<dumpers::NodalField<Real, true>>(
model.getDisplacement(), 0, 0,
&(mesh.getElementGroup("Bottom").getNodeGroup().getNodes())));
txtdumper.registerField(
"blocked_dofs",
std::make_shared<dumpers::NodalField<bool, true>>(
model.getBlockedDOFs(), 0, 0,
&(mesh.getElementGroup("Bottom").getNodeGroup().getNodes())));
Real pot_energy = 1.2345567891;
Vector<Real> gforces(2, 1.);
txtdumper.registerVariable(
"potential_energy", std::make_shared<dumpers::Variable<Real>>(pot_energy));
txtdumper.registerVariable(
"global_forces",
std::make_shared<dumpers::Variable<Vector<Real>>>(gforces));
// dump a first time before the main loop
model.dumpGroup("Bottom");
txtdumper.dump();
Real time = 0.;
for (UInt i = 1; i < 5; ++i) {
pot_energy += 2.;
gforces(0) += 0.1;
gforces(1) += 0.2;
// pre -> cor
// increment time after all steps of integration
time += time_step;
// dump after time increment
if (i % 2 == 0) {
txtdumper.dump(time, i);
model.dumpGroup("Bottom");
// parallel test
for (UInt p = 0; p < nbp; ++p) {
prvdpr.setParallelContext(p, nbp, 0);
prvdumper.dump(i);
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_io/test_parser/CMakeLists.txt b/test/test_io/test_parser/CMakeLists.txt
index 57d291b23..62c001bc8 100644
--- a/test/test_io/test_parser/CMakeLists.txt
+++ b/test/test_io/test_parser/CMakeLists.txt
@@ -1,29 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_parser
SOURCES test_parser.cc
FILES_TO_COPY input_file.dat
PACKAGE core
)
diff --git a/test/test_io/test_parser/test_parser.cc b/test/test_io/test_parser/test_parser.cc
index 427077118..4e85c0cb3 100644
--- a/test/test_io/test_parser/test_parser.cc
+++ b/test/test_io/test_parser/test_parser.cc
@@ -1,74 +1,76 @@
/**
* @file test_parser.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Nov 13 2013
- * @date last modification: Sun Jul 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sun Jul 09 2017
*
* @brief test the input file parser
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_random_generator.hh"
#include "parser.hh"
#include <iostream>
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("input_file.dat", argc, argv);
const Parser & p = getStaticParser();
std::cout << RandomGenerator<UInt>::seed() << "==123456" << std::endl;
std::cout << p << std::endl;
Real toto = p.getParameter("toto");
std::cout << toto;
Real ref = 2 * M_PI + std::max(2., 50.);
if (std::abs(toto - ref) > std::numeric_limits<Real>::epsilon()) {
std::cout << "!=" << ref << std::endl;
return 1;
}
std::cout << "==" << ref << std::endl;
Vector<Real> vect = p.getParameter("vect");
std::cout << vect << std::endl;
Matrix<Real> mat = p.getParameter("mat");
std::cout << mat << std::endl;
RandomParameter<Real> rand1 = p.getParameter("rand1");
std::cout << rand1 << std::endl;
RandomParameter<Real> rand2 = p.getParameter("rand2");
std::cout << rand2 << std::endl;
RandomParameter<Real> rand3 = p.getParameter("rand3");
std::cout << rand3 << std::endl;
finalize();
return 0;
}
diff --git a/test/test_mesh/CMakeLists.txt b/test/test_mesh/CMakeLists.txt
index 66f1c2a69..66b9ef90b 100644
--- a/test/test_mesh/CMakeLists.txt
+++ b/test/test_mesh/CMakeLists.txt
@@ -1,8 +1,40 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Mon Feb 12 2018
+# @date last modification: Fri Nov 02 2018
+#
+# @brief CMakeList of the mesh tests
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_mesh(cube_periodic cube_periodic.geo DIM 3 ORDER 1)
add_mesh(square_periodic square_periodic.geo DIM 2 ORDER 1)
register_test(test_mesh_periodic
SOURCES test_mesh_periodic.cc
DEPENDS cube_periodic square_periodic
PACKAGE core
UNSTABLE)
diff --git a/test/test_mesh/test_mesh_periodic.cc b/test/test_mesh/test_mesh_periodic.cc
index 2b3285ea2..9c80849e0 100644
--- a/test/test_mesh/test_mesh_periodic.cc
+++ b/test/test_mesh/test_mesh_periodic.cc
@@ -1,139 +1,143 @@
/**
* @file test_mesh_periodic.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Sun Feb 11 2018
+ * @date creation: Mon Feb 12 2018
+ * @date last modification: Sun Dec 30 2018
*
- * @brief test makePeriodic
+ * @brief test makePeriodic
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
//#include "mesh_partition_scotch.hh"
#include "periodic_node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
//#include "dumper_element_partition.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char ** argv) {
initialize(argc, argv);
constexpr UInt dim = 3;
auto prank = Communicator::getStaticCommunicator().whoAmI();
// auto psize = Communicator::getStaticCommunicator().getNbProc();
Mesh mesh(dim);
if (prank == 0) {
mesh.read("cube_periodic.msh");
}
MeshAccessor mesh_accessor(mesh);
// mesh_accessor.wipePeriodicInfo();
// mesh.makePeriodic(_z);
// if (prank == 0) {
// MeshPartitionScotch partition(mesh, dim);
// partition.partitionate(psize);
// }
UInt offset = 0;
for (auto && type : mesh.elementTypes()) {
auto & g_ids = mesh.getDataPointer<UInt>("global_ids", type);
for (auto && data : enumerate(g_ids)) {
std::get<1>(data) = offset + std::get<0>(data);
}
offset += g_ids.size();
}
mesh.distribute();
mesh.makePeriodic(_x);
mesh.makePeriodic(_y);
mesh.makePeriodic(_z);
auto * dumper = new DumperParaview("periodic", "./paraview");
mesh.registerExternalDumper(*dumper, "periodic", true);
mesh.addDumpMesh(mesh);
if (mesh.isDistributed()) {
mesh.addDumpFieldExternalToDumper(
"periodic", "node_type",
const_cast<const Mesh &>(mesh).getNodesFlags());
}
mesh.dump();
Array<Int> periodic(mesh.getNbNodes(), 1, 0.);
Array<Int> masters(mesh.getNbNodes(), 1, 0.);
Array<Int> global_ids(mesh.getNbNodes(), 1, 0.);
UInt prev_node = -1;
UInt value = 0;
const auto & periodic_ms = mesh.getPeriodicMasterSlaves();
for (auto & pair : periodic_ms) {
if (prev_node != pair.first) {
++value;
}
prev_node = pair.first;
periodic(pair.first) = value;
periodic(pair.second) = value;
masters(pair.first) = 1;
global_ids(pair.first) = mesh.getNodeGlobalId(pair.second);
auto it = periodic_ms.find(pair.second);
if (it != periodic_ms.end()) {
AKANTU_EXCEPTION(pair.second << " is slave of " << pair.first
<< " and master of " << it->second);
}
}
mesh.addDumpFieldExternalToDumper("periodic", "periodic", periodic);
mesh.addDumpFieldExternalToDumper("periodic", "masters", masters);
mesh.addDumpFieldExternalToDumper("periodic", "global_ids", global_ids);
mesh.addDumpFieldExternalToDumper("periodic", "element_global_ids",
mesh.getData<UInt>("global_ids"));
mesh.dump();
Array<Int> data(mesh.getNbNodes(), 1, 0.);
mesh.addDumpFieldExternalToDumper("periodic", "data", data);
for (auto node : arange(mesh.getNbNodes())) {
if (mesh.isPeriodicMaster(node)) {
data(node) = 1 * (prank + 1);
if (mesh.isMasterNode(node) or mesh.isLocalNode(node)) {
data(node) = 10 * (prank + 1);
}
}
}
mesh.dump();
// SimpleUIntDataAccessor<Int> data_accessor(data,
// SynchronizationTag::_user_1);
// mesh.getPeriodicNodeSynchronizer().synchronizeOnce(data_accessor,
// SynchronizationTag::_user_1);
mesh.dump();
}
diff --git a/test/test_mesh_utils/CMakeLists.txt b/test/test_mesh_utils/CMakeLists.txt
index fc96d3a5e..b0232178b 100644
--- a/test/test_mesh_utils/CMakeLists.txt
+++ b/test/test_mesh_utils/CMakeLists.txt
@@ -1,46 +1,56 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Aug 09 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Aug 09 2017
#
# @brief configuration for MeshUtils tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
# List of tests
#===============================================================================
add_akantu_test(test_mesh_io "Test mesh io object")
add_akantu_test(test_pbc_tweak "Test pbc facilities")
add_akantu_test(test_buildfacets "Tests for the generation of facets")
add_akantu_test(test_segment_nodetype "segment_nodetype")
register_test(test_purify_mesh
SOURCES test_purify_mesh.cc
FILES_TO_COPY purify_mesh.msh
PACKAGE core
)
add_mesh(test_mesh_iterators_mesh iterators_mesh.geo 3 1 OUTPUT iterators_mesh.msh)
register_test(test_mesh_iterators
SOURCES test_mesh_iterators.cc
PACKAGE core
DEPENDS test_mesh_iterators_mesh
)
add_akantu_test(test_mesh_partitionate "Test mesh partition creation")
diff --git a/test/test_mesh_utils/test_buildfacets/CMakeLists.txt b/test/test_mesh_utils/test_buildfacets/CMakeLists.txt
index 25bc18aa2..5563c8a6d 100644
--- a/test/test_mesh_utils/test_buildfacets/CMakeLists.txt
+++ b/test/test_mesh_utils/test_buildfacets/CMakeLists.txt
@@ -1,102 +1,112 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mauro Corrado <mauro.corrado@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Tue Dec 07 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Mon Sep 28 2015
#
# @brief configuration for build facets test
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_buildfacets_triangle_3
SOURCES test_buildfacets_triangle_3.cc
FILES_TO_COPY triangle_3.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_triangle_6
SOURCES test_buildfacets_triangle_6.cc
FILES_TO_COPY triangle_6.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_quadrangle_4
SOURCES test_buildfacets_quadrangle_4.cc
FILES_TO_COPY quadrangle_4.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_quadrangle_8
SOURCES test_buildfacets_quadrangle_8.cc
FILES_TO_COPY quadrangle_8.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_mixed2d_linear
SOURCES test_buildfacets_mixed2d_linear.cc
FILES_TO_COPY mixed2d_linear.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_mixed2d_quadratic
SOURCES test_buildfacets_mixed2d_quadratic.cc
FILES_TO_COPY mixed2d_quadratic.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_tetrahedron_10
SOURCES test_buildfacets_tetrahedron_10.cc
FILES_TO_COPY tetrahedron_10.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_hexahedron_8
SOURCES test_buildfacets_hexahedron_8.cc
FILES_TO_COPY hexahedron_8.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_hexahedron_20
SOURCES test_buildfacets_hexahedron_20.cc
FILES_TO_COPY hexahedron_20.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_pentahedron_6
SOURCES test_buildfacets_pentahedron_6.cc
FILES_TO_COPY pentahedron_6.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_pentahedron_15
SOURCES test_buildfacets_pentahedron_15.cc
FILES_TO_COPY pentahedron_15.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_mixed3d_linear
SOURCES test_buildfacets_mixed3d_linear.cc
FILES_TO_COPY mixed3d_linear.msh
PACKAGE cohesive_element
)
register_test(test_buildfacets_mixed3d_quadratic
SOURCES test_buildfacets_mixed3d_quadratic.cc
FILES_TO_COPY mixed3d_quadratic.msh
PACKAGE cohesive_element
)
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
index 1767bc759..3aebe1106 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_20.cc
@@ -1,148 +1,150 @@
/**
* @file test_buildfacets_hexahedron_20.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Nov 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _hexahedron_20;
Mesh mesh(spatial_dimension);
mesh.read("hexahedron_20.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel3 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j) {
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
index 78e27e334..0610e7b6b 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_hexahedron_8.cc
@@ -1,148 +1,150 @@
/**
* @file test_buildfacets_hexahedron_8.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _hexahedron_8;
Mesh mesh(spatial_dimension);
mesh.read("hexahedron_8.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel3 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j) {
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
index 72a244f45..214ee1049 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_linear.cc
@@ -1,131 +1,133 @@
/**
* @file test_buildfacets_mixed2d_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Thu Nov 09 2017
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with quadrangles
* and triangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type1 = _quadrangle_4;
const ElementType type2 = _triangle_3;
Mesh mesh(spatial_dimension);
mesh.read("mixed2d_linear.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type1);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2_1 =
mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el2_2 =
mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.size(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2_1(i, j).type << " "
<< subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.size(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2_2(i, j).type << " "
<< subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
index f52d871ce..77ee43d3e 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed2d_quadratic.cc
@@ -1,131 +1,133 @@
/**
* @file test_buildfacets_mixed2d_quadratic.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Thu Nov 09 2017
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with quadrangles
* and triangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type1 = _quadrangle_8;
const ElementType type2 = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("mixed2d_quadratic.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type1);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2_1 =
mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el2_2 =
mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.size(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2_1(i, j).type << " "
<< subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.size(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2_2(i, j).type << " "
<< subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
index 455076699..cab9ed2e9 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_linear.cc
@@ -1,179 +1,181 @@
/**
* @file test_buildfacets_mixed3d_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Nov 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
* and pentahedrons
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type1 = _hexahedron_8;
const ElementType type2 = _pentahedron_6;
Mesh mesh(spatial_dimension);
mesh.read("mixed3d_linear.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet1 = mesh.getFacetType(type1);
const ElementType type_facet2 = mesh.getFacetType(type2);
const ElementType type_subfacet = mesh.getFacetType(type_facet1);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel3_1 =
mesh_facets.getElementToSubelement(type_facet1);
const Array<std::vector<Element>> & el_to_subel3_2 =
mesh_facets.getElementToSubelement(type_facet2);
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3_1.size(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3_1(i)[j].type << " "
<< el_to_subel3_1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < el_to_subel3_2.size(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3_2(i)[j].type << " "
<< el_to_subel3_2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3_1 =
mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el3_2 =
mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el2_1 =
mesh_facets.getSubelementToElement(type_facet1);
const Array<Element> & subel_to_el2_2 =
mesh_facets.getSubelementToElement(type_facet2);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3_1.size(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j) {
std::cout << subel_to_el3_1(i, j).type << " "
<< subel_to_el3_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el3_2.size(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 5; ++j) {
std::cout << subel_to_el3_2(i, j).type << " "
<< subel_to_el3_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.size(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2_1(i, j).type << " "
<< subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el2_2.size(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2_2(i, j).type << " "
<< subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
index 186656611..62e5eaa94 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_mixed3d_quadratic.cc
@@ -1,180 +1,182 @@
/**
* @file test_buildfacets_mixed3d_quadratic.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Nov 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with hexahedrons
* and pentahedrons
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type1 = _hexahedron_20;
const ElementType type2 = _pentahedron_15;
Mesh mesh(spatial_dimension);
mesh.read("mixed3d_quadratic.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet1 = mesh.getFacetType(type1);
const ElementType type_facet2 = mesh.getFacetType(type2);
const ElementType type_subfacet = mesh.getFacetType(type_facet1);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel3_1 =
mesh_facets.getElementToSubelement(type_facet1);
const Array<std::vector<Element>> & el_to_subel3_2 =
mesh_facets.getElementToSubelement(type_facet2);
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3_1.size(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3_1(i)[j].type << " "
<< el_to_subel3_1(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < el_to_subel3_2.size(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3_2(i)[j].type << " "
<< el_to_subel3_2(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3_1 =
mesh_facets.getSubelementToElement(type1);
const Array<Element> & subel_to_el3_2 =
mesh_facets.getSubelementToElement(type2);
const Array<Element> & subel_to_el2_1 =
mesh_facets.getSubelementToElement(type_facet1);
const Array<Element> & subel_to_el2_2 =
mesh_facets.getSubelementToElement(type_facet2);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3_1.size(); ++i) {
std::cout << type1 << " " << i << " connected to ";
for (UInt j = 0; j < 6; ++j) {
std::cout << subel_to_el3_1(i, j).type << " "
<< subel_to_el3_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
for (UInt i = 0; i < subel_to_el3_2.size(); ++i) {
std::cout << type2 << " " << i << " connected to ";
for (UInt j = 0; j < 5; ++j) {
std::cout << subel_to_el3_2(i, j).type << " "
<< subel_to_el3_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_1.size(); ++i) {
std::cout << type_facet1 << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2_1(i, j).type << " "
<< subel_to_el2_1(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2_2.size(); ++i) {
std::cout << type_facet2 << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2_2(i, j).type << " "
<< subel_to_el2_2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
index e22c0d8f2..671a51fbe 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_15.cc
@@ -1,152 +1,154 @@
/**
* @file test_buildfacets_pentahedron_15.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Wed Nov 29 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Sep 08 2020
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _pentahedron_15;
Mesh mesh(spatial_dimension);
mesh.read("pentahedron_15.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
Vector<const ElementType> types_facet(mesh.getAllFacetTypes(type));
const ElementType type_subfacet = mesh.getFacetType(types_facet(0));
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
auto && el_to_subel3 =
mesh_facets.getElementToSubelement(type_facet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3(i)[j].type << " "
<< el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 =
mesh_facets.getSubelementToElement(type);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el3.getNbComponent(); ++j) {
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
auto && subel_to_el2 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el2.getNbComponent(); ++j) {
std::cout << subel_to_el2(i, j).type << " "
<< subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el1.getNbComponent(); ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
index 172331a47..ad15df1a7 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_pentahedron_6.cc
@@ -1,152 +1,154 @@
/**
* @file test_buildfacets_pentahedron_6.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Wed Nov 29 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Sep 08 2020
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _pentahedron_6;
Mesh mesh(spatial_dimension);
mesh.read("pentahedron_6.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
Vector<const ElementType> types_facet(mesh.getAllFacetTypes(type));
const ElementType type_subfacet = mesh.getFacetType(types_facet(0));
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
auto && el_to_subel3 =
mesh_facets.getElementToSubelement(type_facet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3(i)[j].type << " "
<< el_to_subel3(i)[j].element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
auto && subel_to_el3 =
mesh_facets.getSubelementToElement(type);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el3.getNbComponent(); ++j) {
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
for (UInt ft = 0; ft < types_facet.size(); ++ft) {
ElementType type_facet = types_facet(ft);
auto && subel_to_el2 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el2.getNbComponent(); ++j) {
std::cout << subel_to_el2(i, j).type << " "
<< subel_to_el2(i, j).element << ", ";
}
std::cout << " " << std::endl;
}
}
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < subel_to_el1.getNbComponent(); ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
index 75be65b8d..d9836686e 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_4.cc
@@ -1,118 +1,120 @@
/**
* @file test_buildfacets_quadrangle_4.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Thu Nov 09 2017
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with quadrangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle_4.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
index 4b66ec82a..11bc1c7b0 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_quadrangle_8.cc
@@ -1,118 +1,120 @@
/**
* @file test_buildfacets_quadrangle_8.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Thu Nov 09 2017
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with quadrangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_8;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle_8.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
index 54dea1018..ce3608b50 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_tetrahedron_10.cc
@@ -1,147 +1,149 @@
/**
* @file test_buildfacets_tetrahedron_10.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Nov 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron_10.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// std::cout << mesh_facets << std::endl;
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
const ElementType type_subsubfacet = mesh.getFacetType(type_subfacet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel3 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_subfacet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subsubfacet);
std::cout << "ElementToSubelement3" << std::endl;
for (UInt i = 0; i < el_to_subel3.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel3(i)[j].type << " " << el_to_subel3(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel2(i).size(); ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subsubfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el3 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type_facet);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_subfacet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement3" << std::endl;
for (UInt i = 0; i < subel_to_el3.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 4; ++j) {
std::cout << subel_to_el3(i, j).type << " " << subel_to_el3(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
index 357715ec3..5af6b3f78 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_3.cc
@@ -1,117 +1,119 @@
/**
* @file test_buildfacets_triangle_3.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Test to check the building of the facets. Mesh with triangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _triangle_3;
Mesh mesh(spatial_dimension);
mesh.read("triangle_3.msh");
const auto & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
index 8c934d244..06613981a 100644
--- a/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
+++ b/test/test_mesh_utils/test_buildfacets/test_buildfacets_triangle_6.cc
@@ -1,118 +1,120 @@
/**
* @file test_buildfacets_triangle_6.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Thu Nov 09 2017
+ * @date last modification: Thu Nov 09 2017
*
* @brief Test to check the building of the facets. Mesh with triangles
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const ElementType type = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("triangle_6.msh");
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
const ElementType type_facet = mesh.getFacetType(type);
const ElementType type_subfacet = mesh.getFacetType(type_facet);
/* ------------------------------------------------------------------------ */
/* Element to Subelement testing */
/* ------------------------------------------------------------------------ */
const Array<std::vector<Element>> & el_to_subel2 =
mesh_facets.getElementToSubelement(type_facet);
const Array<std::vector<Element>> & el_to_subel1 =
mesh_facets.getElementToSubelement(type_subfacet);
std::cout << "ElementToSubelement2" << std::endl;
for (UInt i = 0; i < el_to_subel2.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << el_to_subel2(i)[j].type << " " << el_to_subel2(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "ElementToSubelement1" << std::endl;
for (UInt i = 0; i < el_to_subel1.size(); ++i) {
std::cout << type_subfacet << " " << i << " connected to ";
for (UInt j = 0; j < el_to_subel1(i).size(); ++j) {
std::cout << el_to_subel1(i)[j].type << " " << el_to_subel1(i)[j].element
<< ", ";
}
std::cout << " " << std::endl;
}
/* ------------------------------------------------------------------------ */
/* Subelement to Element testing */
/* ------------------------------------------------------------------------ */
const Array<Element> & subel_to_el2 =
mesh_facets.getSubelementToElement(type);
const Array<Element> & subel_to_el1 =
mesh_facets.getSubelementToElement(type_facet);
std::cout << " " << std::endl;
std::cout << "SubelementToElement2" << std::endl;
for (UInt i = 0; i < subel_to_el2.size(); ++i) {
std::cout << type << " " << i << " connected to ";
for (UInt j = 0; j < 3; ++j) {
std::cout << subel_to_el2(i, j).type << " " << subel_to_el2(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
std::cout << "SubelementToElement1" << std::endl;
for (UInt i = 0; i < subel_to_el1.size(); ++i) {
std::cout << type_facet << " " << i << " connected to ";
for (UInt j = 0; j < 2; ++j) {
std::cout << subel_to_el1(i, j).type << " " << subel_to_el1(i, j).element
<< ", ";
}
std::cout << " " << std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_mesh_io/CMakeLists.txt b/test/test_mesh_utils/test_mesh_io/CMakeLists.txt
index 1b95c1512..4c1d278ab 100644
--- a/test/test_mesh_utils/test_mesh_io/CMakeLists.txt
+++ b/test/test_mesh_utils/test_mesh_io/CMakeLists.txt
@@ -1,46 +1,56 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for MeshIO tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_msh_cube cube.geo 3 1)
add_mesh(test_msh_cube_physical_names cube_physical_names.geo 3 1)
register_test(test_mesh_io_msh
SOURCES test_mesh_io_msh.cc
DEPENDS test_msh_cube
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
register_test(test_mesh_io_msh_physical_names
SOURCES test_mesh_io_msh_physical_names.cc
DEPENDS test_msh_cube_physical_names
PACKAGE core
)
#===============================================================================
#register_test(test_mesh_io_diana test_mesh_io_diana.cc)
#copy_files(test_mesh_io_diana dam.dat)
#file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/paraview/mesh_io_diana)
diff --git a/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh.cc b/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh.cc
index 6c69ecb5f..c9cc4731c 100644
--- a/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh.cc
+++ b/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh.cc
@@ -1,52 +1,54 @@
/**
* @file test_mesh_io_msh.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
- * @date last modification: Wed Feb 03 2016
+ * @date last modification: Fri Jan 15 2016
*
* @brief unit test for the MeshIOMSH class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
akantu::MeshIOMSH mesh_io;
akantu::Mesh mesh(3);
mesh_io.read("./cube.msh", mesh);
std::cout << mesh << std::endl;
mesh_io.write("./cube.out", mesh);
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh_physical_names.cc b/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh_physical_names.cc
index fa047adad..dd08e5e41 100644
--- a/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh_physical_names.cc
+++ b/test/test_mesh_utils/test_mesh_io/test_mesh_io_msh_physical_names.cc
@@ -1,59 +1,61 @@
/**
* @file test_mesh_io_msh_physical_names.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
*
- * @date creation: Fri May 03 2013
- * @date last modification: Sun Aug 13 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Nov 02 2018
*
* @brief unit test for the MeshIOMSH physical names class
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "aka_common.hh"
#include "mesh.hh"
#include <iostream>
#include <sstream>
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
UInt spatialDimension(3);
akantu::initialize(argc, argv);
Mesh mesh(spatialDimension);
mesh.read("./cube_physical_names.msh");
std::stringstream sstr;
for (auto type : mesh.elementTypes()) {
const Array<std::string> & name_vec =
mesh.getData<std::string>("physical_names", type);
for (UInt i(0); i < name_vec.size(); i++) {
std::cout << "Element " << i << " (of type " << type
<< ") has physical name " << name_vec(i) << "." << std::endl;
}
}
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_mesh_iterators.cc b/test/test_mesh_utils/test_mesh_iterators.cc
index 0adbae1b6..a17321c8c 100644
--- a/test/test_mesh_utils/test_mesh_iterators.cc
+++ b/test/test_mesh_utils/test_mesh_iterators.cc
@@ -1,73 +1,75 @@
/**
* @file test_mesh_iterators.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Wed Aug 16 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Jun 13 2019
*
* @brief Test the mesh iterators
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_iterators.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
Mesh mesh(3);
const Mesh & cmesh = mesh;
mesh.read("iterators_mesh.msh");
std::cout << "ElementGroups" << std::endl;
for (auto && element_group : mesh.iterateElementGroups()) {
std::cout << element_group.getName() << " " << element_group.getDimension()
<< std::endl;
}
std::cout << "NodeGroups" << std::endl;
for (auto && node_group : cmesh.iterateNodeGroups()) {
std::cout << node_group.getName() << std::endl;
}
std::cout << "enumerate(ElementGroups)" << std::endl;
for (auto && element_group : enumerate(mesh.iterateElementGroups())) {
std::cout << std::get<0>(element_group) << " "
<< std::get<1>(element_group).getName() << std::endl;
}
// for (auto && node_group :
// counting(NodeGroupsIterable(cmesh))) {
// std::cout << std::get<0>(node_group) << " " <<
// std::get<1>(node_group).getName() << std::endl;
// }
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_mesh_partitionate/CMakeLists.txt b/test/test_mesh_utils/test_mesh_partitionate/CMakeLists.txt
index 2e1e32de9..ff75c56d2 100644
--- a/test/test_mesh_utils/test_mesh_partitionate/CMakeLists.txt
+++ b/test/test_mesh_utils/test_mesh_partitionate/CMakeLists.txt
@@ -1,46 +1,56 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Dana Christen <dana.christen@gmail.com>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for mesh partitioner tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_mesh_partitionate_mesh
triangle.geo 2 2)
add_mesh(test_mesh_partitionate_mesh_data_mesh
quad.geo 2 1)
register_test(test_mesh_partitionate_scotch
SOURCES test_mesh_partitionate_scotch.cc
DEPENDS test_mesh_partitionate_mesh
DIRECTORIES_TO_CREATE paraview
PACKAGE scotch
)
register_test(test_mesh_partitionate_mesh_data
SOURCES test_mesh_partitionate_mesh_data.cc
DEPENDS test_mesh_partitionate_mesh_data_mesh
DIRECTORIES_TO_CREATE paraview
PACKAGE scotch
)
diff --git a/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_mesh_data.cc b/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_mesh_data.cc
index a0e740e47..8d4697d66 100644
--- a/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_mesh_data.cc
+++ b/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_mesh_data.cc
@@ -1,114 +1,117 @@
/**
* @file test_mesh_partitionate_mesh_data.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
*
- * @date creation: Wed May 08 2013
- * @date last modification: Tue Nov 07 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Nov 02 2018
*
* @brief test of manual partitioner
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_partition_mesh_data.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_paraview.hh"
#endif // AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt dim = 2;
UInt nb_partitions = 8;
akantu::Mesh mesh(dim);
mesh.read("quad.msh");
ElementTypeMapArray<UInt> partition;
UInt nb_component = 1;
GhostType gt = _not_ghost;
for (auto & type : mesh.elementTypes(dim, gt)) {
UInt nb_element = mesh.getNbElement(type, gt);
partition.alloc(nb_element, nb_component, type, gt);
Array<UInt> & type_partition_reference = partition(type, gt);
for (UInt i(0); i < nb_element; ++i) {
Vector<Real> barycenter(dim);
Element element{type, i, gt};
mesh.getBarycenter(element, barycenter);
Real real_proc = barycenter[0] * nb_partitions;
if (std::abs(real_proc - round(real_proc)) <
10 * std::numeric_limits<Real>::epsilon()) {
type_partition_reference(i) = round(real_proc);
} else {
std::cout << "*";
type_partition_reference(i) = floor(real_proc);
}
std::cout << "Assigned proc " << type_partition_reference(i)
<< " to elem " << i << " (type " << type
<< ", barycenter x-coordinate " << barycenter[0] << ")"
<< std::endl;
}
}
akantu::MeshPartitionMeshData * partitioner =
new akantu::MeshPartitionMeshData(mesh, dim);
partitioner->setPartitionMapping(partition);
partitioner->partitionate(nb_partitions);
for (auto & type : mesh.elementTypes(dim, gt)) {
UInt nb_element = mesh.getNbElement(type, gt);
const Array<UInt> & type_partition_reference = partition(type, gt);
const Array<UInt> & type_partition = partitioner->getPartitions()(type, gt);
for (UInt i(0); i < nb_element; ++i) {
if (not(type_partition(i) == type_partition_reference(i))) {
std::cout << "Incorrect partitioning" << std::endl;
return 1;
}
}
}
#ifdef DEBUG_TEST
DumperParaview dumper("test-mesh-data-partition");
dumpers::Field * field1 =
new dumpers::ElementalField<UInt>(partitioner->getPartitions(), dim);
dumpers::Field * field2 = new dumpers::ElementalField<UInt>(partition, dim);
dumper.registerMesh(mesh, dim);
dumper.registerField("partitions", field1);
dumper.registerField("partitions_ref", field2);
dumper.dump();
#endif
delete partitioner;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc b/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc
index 57defce1b..253fa2700 100644
--- a/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc
+++ b/test/test_mesh_utils/test_mesh_partitionate/test_mesh_partitionate_scotch.cc
@@ -1,73 +1,75 @@
/**
* @file test_mesh_partitionate_scotch.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 12 2010
- * @date last modification: Mon Jan 22 2018
+ * @date last modification: Fri Nov 02 2018
*
* @brief test of internal facet extraction
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_iohelper_paraview.hh"
#endif // AKANTU_USE_IOHELPER
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
debug::setDebugLevel(akantu::dblDump);
int dim = 2;
Mesh mesh(dim);
mesh.read("triangle.msh");
MeshPartitionScotch partition(mesh, dim);
partition.partitionate(8);
#ifdef AKANTU_USE_IOHELPER
DumperParaview dumper("test-scotch-partition");
auto field = std::make_shared<dumpers::ElementalField<UInt>>(
partition.getPartitions(), dim);
dumper.registerMesh(mesh, dim);
dumper.registerField("partitions", field);
dumper.dump();
#endif // AKANTU_USE_IOHELPER
partition.reorder();
mesh.write("triangle_reorder.msh");
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_pbc_tweak/CMakeLists.txt b/test/test_mesh_utils/test_pbc_tweak/CMakeLists.txt
index b1b095125..8eb28ada0 100644
--- a/test/test_mesh_utils/test_pbc_tweak/CMakeLists.txt
+++ b/test/test_mesh_utils/test_pbc_tweak/CMakeLists.txt
@@ -1,34 +1,44 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for pcb tweal test
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
add_mesh(test_pbc_cube_mesh cube.geo 3 1)
register_test(test_pbc_tweak
SOURCES test_pbc_tweak.cc
DEPENDS test_pbc_cube_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
diff --git a/test/test_mesh_utils/test_pbc_tweak/test_pbc_tweak.cc b/test/test_mesh_utils/test_pbc_tweak/test_pbc_tweak.cc
index d680a69e3..2d8ac8555 100644
--- a/test/test_mesh_utils/test_pbc_tweak/test_pbc_tweak.cc
+++ b/test/test_mesh_utils/test_pbc_tweak/test_pbc_tweak.cc
@@ -1,69 +1,71 @@
/**
* @file test_pbc_tweak.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
- * @date creation: Fri Aug 20 2010
- * @date last modification: Wed Dec 07 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Dec 07 2016
*
* @brief test of internal facet extraction
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
int dim = 3;
initialize("material.dat", argc, argv);
debug::setDebugLevel(akantu::dblInfo);
Mesh mesh(dim);
mesh.read("cube.msh");
SolidMechanicsModel model(mesh);
/* --------------------------------------------------------------------------
*/
model.initFull();
/* --------------------------------------------------------------------------
*/
// model.setPBC(1,1,1);
// model.initPBC();
model.assembleMassLumped();
/* --------------------------------------------------------------------------
*/
model.setBaseName("test-pbc-tweak");
model.addDumpField("mass");
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_purify_mesh.cc b/test/test_mesh_utils/test_purify_mesh.cc
index 3b8f515f5..e48adc491 100644
--- a/test/test_mesh_utils/test_purify_mesh.cc
+++ b/test/test_mesh_utils/test_purify_mesh.cc
@@ -1,60 +1,62 @@
/**
* @file test_purify_mesh.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Jul 15 2010
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test the purifyMesh function from MeshUtils
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
Mesh mesh(2);
mesh.read("purify_mesh.msh");
MeshUtils::purifyMesh(mesh);
mesh.write("purify_mesh_after.msh");
if (mesh.getNbNodes() != 21)
AKANTU_ERROR(
"The purified mesh does not contain the good number of nodes.");
if (mesh.getNbElement(_quadrangle_8) != 4)
AKANTU_ERROR(
"The purified mesh does not contain the good number of element.");
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt b/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
index 2b5f714c6..b0289fb3c 100644
--- a/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
+++ b/test/test_mesh_utils/test_segment_nodetype/CMakeLists.txt
@@ -1,27 +1,37 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Aug 09 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Aug 09 2017
#
# @brief CMakeLists for segment nodetype tests
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
# register_test(test_segment_nodetype
# SOURCES test_segment_nodetype.cc
# FILES_TO_COPY mesh.msh
# PACKAGE parallel
# )
diff --git a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
index 06209d452..12c9024bf 100644
--- a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
+++ b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
@@ -1,96 +1,98 @@
/**
* @file test_segment_nodetype.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Sep 18 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test to verify that the node type is correctly associated to
* the segments in parallel
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// partition the mesh
if (prank == 0) {
mesh.read("mesh.msh");
}
mesh.distribute();
// compute the node types for each segment
Mesh & mesh_facets = mesh.initMeshFacets();
MeshUtils::buildSegmentToNodeType(mesh, mesh_facets);
// verify that the number of segments per node type makes sense
std::map<Int, UInt> nb_facets_per_nodetype;
UInt nb_segments = 0;
for (auto ghost_type : ghost_types) {
const Array<Int> & segment_to_nodetype =
mesh_facets.getData<Int>("segment_to_nodetype", _segment_2, ghost_type);
// count the number of segments per node type
for (auto & stn : segment_to_nodetype) {
if (nb_facets_per_nodetype.find(stn) == nb_facets_per_nodetype.end())
nb_facets_per_nodetype[stn] = 1;
else
++nb_facets_per_nodetype[stn];
}
nb_segments += segment_to_nodetype.size();
}
// checking the solution
if (nb_segments != 24)
AKANTU_ERROR("The number of segments is wrong");
if (prank == 0) {
if (nb_facets_per_nodetype[-1] != 3 || nb_facets_per_nodetype[-2] != 9 ||
nb_facets_per_nodetype[-3] != 12)
AKANTU_ERROR("The segments of processor 0 have the wrong node type");
if (nb_facets_per_nodetype.size() > 3)
AKANTU_ERROR("Processor 0 cannot have any slave segment");
}
if (prank == psize - 1 &&
nb_facets_per_nodetype.find(-2) != nb_facets_per_nodetype.end())
AKANTU_ERROR("The last processor must not have any master facets");
finalize();
return 0;
}
diff --git a/test/test_model/CMakeLists.txt b/test/test_model/CMakeLists.txt
index a3da36a7c..1fe7ffd50 100644
--- a/test/test_model/CMakeLists.txt
+++ b/test/test_model/CMakeLists.txt
@@ -1,31 +1,41 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Tue Jan 30 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Jan 30 2019
#
# @brief configuration for model tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_subdirectory(patch_tests)
add_akantu_test(test_common "Tests the common part of the models")
add_akantu_test(test_solid_mechanics_model "Test for the solid mechanics model")
add_akantu_test(test_structural_mechanics_model "Test for the structural mechanics model")
add_akantu_test(test_heat_transfer_model "Test heat transfer model")
add_akantu_test(test_contact_mechanics_model "Test contact mechanics model")
add_akantu_test(test_phase_field_model "Test phase field model")
diff --git a/test/test_model/patch_tests/CMakeLists.txt b/test/test_model/patch_tests/CMakeLists.txt
index 75533ca82..8c2ac228f 100644
--- a/test/test_model/patch_tests/CMakeLists.txt
+++ b/test/test_model/patch_tests/CMakeLists.txt
@@ -1,136 +1,138 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author David Simon Kammer <david.kammer@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Thu Feb 08 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Thu Oct 29 2020
#
# @brief configuration for patch tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_subdirectory(data)
register_gtest_sources(SOURCES patch_test_linear_elastic_explicit.cc
PACKAGE solid_mechanics
FILES_TO_COPY data/material_check_stress_plane_strain.dat
data/material_check_stress_plane_stress.dat
data/material_check_stress_plane_strain_finite_deformation.dat
data/material_check_stress_plane_stress_finite_deformation.dat)
register_gtest_sources(SOURCES patch_test_linear_elastic_implicit.cc
PACKAGE solid_mechanics implicit
FILES_TO_COPY data/material_check_stress_plane_strain.dat
data/material_check_stress_plane_stress.dat
data/material_check_stress_plane_strain_finite_deformation.dat
data/material_check_stress_plane_stress_finite_deformation.dat)
register_gtest_sources(SOURCES patch_test_linear_anisotropic_explicit.cc
PACKAGE solid_mechanics lapack
FILES_TO_COPY
data/material_anisotropic_1.dat
data/material_anisotropic_2.dat
data/material_anisotropic_3.dat
)
register_gtest_sources(SOURCES patch_test_linear_anisotropic_implicit.cc
PACKAGE solid_mechanics lapack implicit
FILES_TO_COPY
data/material_anisotropic_1.dat
data/material_anisotropic_2.dat
data/material_anisotropic_3.dat
)
register_gtest_sources(SOURCES test_lumped_mass.cc
PACKAGE solid_mechanics
FILES_TO_COPY data/material_lumped.dat)
register_gtest_sources(
SOURCES patch_test_linear_heat_transfer_explicit.cc
FILES_TO_COPY data/heat_transfer_input.dat
PACKAGE heat_transfer)
register_gtest_sources(
SOURCES patch_test_linear_heat_transfer_static.cc
FILES_TO_COPY data/heat_transfer_input.dat
PACKAGE heat_transfer implicit)
register_gtest_sources(
SOURCES patch_test_linear_heat_transfer_implicit.cc
FILES_TO_COPY data/heat_transfer_input.dat
PACKAGE heat_transfer implicit
)
register_gtest_test(patch_test_linear
FILES_TO_COPY ${PATCH_TEST_MESHES})
register_test(test_linear_elastic_explicit_python
SCRIPT test_patch_linear_elastic_explicit.py
PYTHON
PACKAGE python_interface
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_solid_mechanics_fixture.py
FILES_TO_COPY ${PATCH_TEST_MESHES})
register_test(test_linear_elastic_static_python
SCRIPT test_patch_linear_elastic_static.py
PYTHON
PACKAGE python_interface implicit
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_solid_mechanics_fixture.py)
register_test(test_linear_anisotropic_explicit_python
SCRIPT test_patch_linear_anisotropic_explicit.py
PYTHON
UNSTABLE
PACKAGE python_interface lapack
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_solid_mechanics_fixture.py
FILES_TO_COPY data/material_anisotropic_3.dat)
register_test(patch_test_linear_heat_transfer_explicit_python
SCRIPT test_patch_linear_heat_transfer_explicit.py
PYTHON
PACKAGE python_interface heat_transfer
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_heat_transfer_fixture.py
FILES_TO_COPY data/heat_transfer_input.dat)
register_test(patch_test_linear_heat_transfer_static_python
SCRIPT test_patch_linear_heat_transfer_static.py
PYTHON
PACKAGE python_interface heat_transfer implicit
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_heat_transfer_fixture.py
FILES_TO_COPY data/heat_transfer_input.dat)
register_test(patch_test_linear_heat_transfer_implicit_python
SCRIPT test_patch_linear_heat_transfer_implicit.py
PYTHON
PACKAGE python_interface heat_transfer implicit
FILES_TO_COPY patch_test_linear_fixture.py
FILES_TO_COPY patch_test_linear_heat_transfer_fixture.py
FILES_TO_COPY data/heat_transfer_input.dat)
diff --git a/test/test_model/patch_tests/data/CMakeLists.txt b/test/test_model/patch_tests/data/CMakeLists.txt
index 8a411a852..94dbf9a29 100644
--- a/test/test_model/patch_tests/data/CMakeLists.txt
+++ b/test/test_model/patch_tests/data/CMakeLists.txt
@@ -1,64 +1,75 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Jan 30 2018
+# @date last modification: Tue Jan 30 2018
#
-# @brief
+# @brief CMakeLists patch test data
#
-# @section LICENSE
-#
-# Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(bar_segment_2 bar_segment.geo
DIM 1 ORDER 1 OUTPUT bar_segment_2.msh)
add_mesh(bar_segment_3 bar_segment.geo
DIM 1 ORDER 2 OUTPUT bar_segment_3.msh)
add_mesh(bar_triangle_3 bar_triangle.geo
DIM 2 ORDER 1 OUTPUT bar_triangle_3.msh)
add_mesh(bar_triangle_6 bar_triangle.geo
DIM 2 ORDER 2 OUTPUT bar_triangle_6.msh)
add_mesh(bar_quadrangle_4 bar_quadrangle.geo
DIM 2 ORDER 1 OUTPUT bar_quadrangle_4.msh)
add_mesh(bar_quadrangle_8 bar_quadrangle.geo
DIM 2 ORDER 2 OUTPUT bar_quadrangle_8.msh)
add_mesh(bar_tetrahedron_4 bar_tetrahedron.geo
DIM 3 ORDER 1 OUTPUT bar_tetrahedron_4.msh)
add_mesh(bar_tetrahedron_10 bar_tetrahedron.geo
DIM 3 ORDER 2 OUTPUT bar_tetrahedron_10.msh)
add_mesh(bar_hexahedron_8 bar_hexahedron.geo
DIM 3 ORDER 1 OUTPUT bar_hexahedron_8.msh)
add_mesh(bar_hexahedron_20 bar_hexahedron.geo
DIM 3 ORDER 2 OUTPUT bar_hexahedron_20.msh)
add_mesh(bar_pentahedron_6 bar_pentahedron.geo
DIM 3 ORDER 1 OUTPUT bar_pentahedron_6.msh)
add_mesh(bar_pentahedron_15 bar_pentahedron.geo
DIM 3 ORDER 2 OUTPUT bar_pentahedron_15.msh)
#===============================================================================
# Meshes
#===============================================================================
set(_patch_tests_meshes)
set(_patch_tests_bar_meshes)
package_get_variable(ET_ELEMENT_TYPES core _element_list)
foreach(_et ${_element_list})
if(NOT _et STREQUAL _point_1)
list(APPEND _patch_tests_meshes ${CMAKE_CURRENT_SOURCE_DIR}/${_et}.msh)
list(APPEND _patch_tests_bar_meshes bar${_et})
endif()
endforeach()
set(PATCH_TEST_MESHES ${_patch_tests_meshes}
CACHE INTERNAL "List of mesh files")
set(PATCH_TEST_BAR_MESHES ${_patch_tests_bar_meshes}
CACHE INTERNAL "List of bar mesh files")
diff --git a/test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc b/test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc
index 6cf532a2a..14e981590 100644
--- a/test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_anisotropic_explicit.cc
@@ -1,136 +1,138 @@
/**
* @file patch_test_linear_anisotropic_explicit.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
- * @date creation: Tue Dec 05 2017
- * @date last modification: Tue Feb 13 2018
+ * @date creation: Tue May 14 2019
+ * @date last modification: Thu Oct 29 2020
*
* @brief patch test for elastic material in solid mechanics model
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "patch_test_linear_solid_mechanics_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
// Stiffness tensor, rotated by hand
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, AnisotropicExplicit) {
Real C[3][3][3][3] = {
{{{112.93753505, 1.85842452538e-10, -4.47654358027e-10},
{1.85847317471e-10, 54.2334345331, -3.69840984824},
{-4.4764768395e-10, -3.69840984824, 56.848605217}},
{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38797920011e-11},
{-3.69840984816, -8.38804581349e-11, -1.97875715813e-10}},
{{-4.47654358027e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374961813e-10, 9.4857455224e-12},
{28.044464917, 9.48308098714e-12, -2.1367885239e-10}}},
{{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38793479119e-11},
{-3.69840984816, -8.38795699565e-11, -1.97876381947e-10}},
{{54.2334345331, 3.31617400207e-10, 2.09372075233e-10},
{3.3161562385e-10, 115.552705733, -3.15093728886e-10},
{2.09372075233e-10, -3.15090176173e-10, 54.2334345333}},
{{-3.69840984824, -8.38795699565e-11, 9.48219280872e-12},
{-8.38795699565e-11, -3.1509195253e-10, 25.4292942335},
{9.48441325477e-12, 25.4292942335, 3.69840984851}}},
{{{-4.47653469848e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374073634e-10, 9.48752187924e-12},
{28.044464917, 9.48552347779e-12, -2.1367885239e-10}},
{{-3.69840984824, -8.3884899027e-11, 9.48219280872e-12},
{-8.3884899027e-11, -3.150972816e-10, 25.4292942335},
{9.48041645188e-12, 25.4292942335, 3.69840984851}},
{{56.848605217, -1.97875493768e-10, -2.13681516925e-10},
{-1.97877270125e-10, 54.2334345333, 3.69840984851},
{-2.13683293282e-10, 3.69840984851, 112.93753505}}}};
if (this->dim == 2) {
for (UInt i = 0; i < this->dim; ++i) {
for (UInt j = 0; j < this->dim; ++j) {
for (UInt k = 0; k < this->dim; ++k) {
for (UInt l = 0; l < this->dim; ++l) {
C[i][j][k][l] = 0;
}
}
}
}
C[0][0][0][0] = C[1][1][1][1] = 112.93753504999995;
C[0][0][1][1] = C[1][1][0][0] = 51.618263849999984;
C[0][1][0][1] = C[1][0][0][1] = C[0][1][1][0] = C[1][0][1][0] =
22.814123549999987;
}
if (this->dim == 1) {
C[0][0][0][0] = 105.092023;
}
this->initModel(_explicit_lumped_mass,
"material_anisotropic_" + std::to_string(this->dim) + ".dat");
const auto & coordinates = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
// set the position of all nodes to the static solution
for (auto && tuple : zip(make_view(coordinates, this->dim),
make_view(displacement, this->dim))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
auto ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(0, ekin, 1e-16);
auto & mat = this->model->getMaterial(0);
this->checkDOFs(displacement);
this->checkGradient(mat.getGradU(this->type), displacement);
this->result_tolerance = 1e-11;
this->checkResults(
[&](const Matrix<Real> & pstrain) {
auto strain = (pstrain + pstrain.transpose()) / 2.;
decltype(strain) stress(this->dim, this->dim);
for (UInt i = 0; i < this->dim; ++i) {
for (UInt j = 0; j < this->dim; ++j) {
stress(i, j) = 0;
for (UInt k = 0; k < this->dim; ++k) {
for (UInt l = 0; l < this->dim; ++l) {
stress(i, j) += C[i][j][k][l] * strain(k, l);
}
}
}
}
return stress;
},
mat.getStress(this->type), displacement);
}
diff --git a/test/test_model/patch_tests/patch_test_linear_anisotropic_implicit.cc b/test/test_model/patch_tests/patch_test_linear_anisotropic_implicit.cc
index a9e6e8c37..88faf78f3 100644
--- a/test/test_model/patch_tests/patch_test_linear_anisotropic_implicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_anisotropic_implicit.cc
@@ -1,129 +1,131 @@
/**
- * @file patch_test_linear_anisotropic_explicit.cc
+ * @file patch_test_linear_anisotropic_implicit.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
- * @date creation: Tue Dec 05 2017
- * @date last modification: Tue Feb 13 2018
+ * @date creation: Tue May 14 2019
+ * @date last modification: Thu Oct 29 2020
*
* @brief patch test for elastic material in solid mechanics model
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "patch_test_linear_solid_mechanics_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
// Stiffness tensor, rotated by hand
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, AnisotropicStatic) {
Real C[3][3][3][3] = {
{{{112.93753505, 1.85842452538e-10, -4.47654358027e-10},
{1.85847317471e-10, 54.2334345331, -3.69840984824},
{-4.4764768395e-10, -3.69840984824, 56.848605217}},
{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38797920011e-11},
{-3.69840984816, -8.38804581349e-11, -1.97875715813e-10}},
{{-4.47654358027e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374961813e-10, 9.4857455224e-12},
{28.044464917, 9.48308098714e-12, -2.1367885239e-10}}},
{{{1.85847781609e-10, 25.429294233, -3.69840984816},
{25.429294233, 3.31613847493e-10, -8.38793479119e-11},
{-3.69840984816, -8.38795699565e-11, -1.97876381947e-10}},
{{54.2334345331, 3.31617400207e-10, 2.09372075233e-10},
{3.3161562385e-10, 115.552705733, -3.15093728886e-10},
{2.09372075233e-10, -3.15090176173e-10, 54.2334345333}},
{{-3.69840984824, -8.38795699565e-11, 9.48219280872e-12},
{-8.38795699565e-11, -3.1509195253e-10, 25.4292942335},
{9.48441325477e-12, 25.4292942335, 3.69840984851}}},
{{{-4.47653469848e-10, -3.69840984816, 28.044464917},
{-3.69840984816, 2.09374073634e-10, 9.48752187924e-12},
{28.044464917, 9.48552347779e-12, -2.1367885239e-10}},
{{-3.69840984824, -8.3884899027e-11, 9.48219280872e-12},
{-8.3884899027e-11, -3.150972816e-10, 25.4292942335},
{9.48041645188e-12, 25.4292942335, 3.69840984851}},
{{56.848605217, -1.97875493768e-10, -2.13681516925e-10},
{-1.97877270125e-10, 54.2334345333, 3.69840984851},
{-2.13683293282e-10, 3.69840984851, 112.93753505}}}};
if (this->dim == 2) {
for (UInt i = 0; i < this->dim; ++i) {
for (UInt j = 0; j < this->dim; ++j) {
for (UInt k = 0; k < this->dim; ++k) {
for (UInt l = 0; l < this->dim; ++l) {
C[i][j][k][l] = 0;
}
}
}
}
C[0][0][0][0] = C[1][1][1][1] = 112.93753504999995;
C[0][0][1][1] = C[1][1][0][0] = 51.618263849999984;
C[0][1][0][1] = C[1][0][0][1] = C[0][1][1][0] = C[1][0][1][0] =
22.814123549999987;
}
if (this->dim == 1) {
C[0][0][0][0] = 105.092023;
}
this->initModel(_static,
"material_anisotropic_" + std::to_string(this->dim) + ".dat");
auto & solver = this->model->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
this->model->solveStep();
auto & mat = this->model->getMaterial(0);
const auto & displacement = this->model->getDisplacement();
this->checkDOFs(displacement);
this->checkGradient(mat.getGradU(this->type), displacement);
this->result_tolerance = 1e-11;
this->checkResults(
[&](const Matrix<Real> & pstrain) {
auto strain = (pstrain + pstrain.transpose()) / 2.;
decltype(strain) stress(this->dim, this->dim);
for (UInt i = 0; i < this->dim; ++i) {
for (UInt j = 0; j < this->dim; ++j) {
stress(i, j) = 0;
for (UInt k = 0; k < this->dim; ++k) {
for (UInt l = 0; l < this->dim; ++l) {
stress(i, j) += C[i][j][k][l] * strain(k, l);
}
}
}
}
return stress;
},
mat.getStress(this->type), displacement);
}
diff --git a/test/test_model/patch_tests/patch_test_linear_elastic_explicit.cc b/test/test_model/patch_tests/patch_test_linear_elastic_explicit.cc
index fb0a39e83..c0a9845b6 100644
--- a/test/test_model/patch_tests/patch_test_linear_elastic_explicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_elastic_explicit.cc
@@ -1,97 +1,100 @@
/**
* @file patch_test_linear_elastic_explicit.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
+ * @date last modification: Thu Oct 29 2020
*
* @brief patch test solid mechanics explicit
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_solid_mechanics_fixture.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, Explicit) {
std::string filename = "material_check_stress_plane_stress.dat";
if (this->plane_strain)
filename = "material_check_stress_plane_strain.dat";
this->initModel(_explicit_lumped_mass, filename);
const auto & coordinates = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
// set the position of all nodes to the static solution
for (auto && tuple : zip(make_view(coordinates, this->dim),
make_view(displacement, this->dim))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
auto ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(0, ekin, 1e-16);
this->checkAll();
#define debug 0
#if debug
this->model->setBaseName(std::to_string(this->type) + "_explicit");
this->model->addDumpField("stress");
this->model->addDumpField("grad_u");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpFieldVector("displacement");
this->model->dump();
#endif
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, ExplicitFiniteDeformation) {
std::string filename = "material_check_stress_plane_stress_finite_deformation.dat";
if (this->plane_strain) {
filename = "material_check_stress_plane_strain_finite_deformation.dat";
} else {
SUCCEED();
return;
}
this->initModel(_explicit_lumped_mass, filename);
const auto & coordinates = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
// set the position of all nodes to the static solution
for (auto && tuple : zip(make_view(coordinates, this->dim),
make_view(displacement, this->dim))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
auto ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(0, ekin, 1e-16);
this->checkAll();
}
diff --git a/test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc b/test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc
index b6a6e9874..9932bc8f6 100644
--- a/test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_elastic_implicit.cc
@@ -1,169 +1,172 @@
/**
* @file patch_test_linear_elastic_implicit.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
+ * @date last modification: Tue Mar 24 2020
*
* @brief Patch test for SolidMechanics implicit
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_solid_mechanics_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
TYPED_TEST(TestPatchTestSMMLinear, Implicit) {
std::string filename = "material_check_stress_plane_stress.dat";
if (this->plane_strain)
filename = "material_check_stress_plane_strain.dat";
this->initModel(_implicit_dynamic, filename);
const auto & coordinates = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
// set the position of all nodes to the static solution
for (auto && tuple : zip(make_view(coordinates, this->dim),
make_view(displacement, this->dim))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
auto ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(0, ekin, 1e-16);
this->checkAll();
#define debug 0
#if debug
this->model->setBaseName(std::to_string(this->type) + "_implicit");
this->model->addDumpField("stress");
this->model->addDumpField("grad_u");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpFieldVector("displacement");
this->model->dump();
#endif
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, Static) {
std::string filename = "material_check_stress_plane_stress.dat";
if (this->plane_strain)
filename = "material_check_stress_plane_strain.dat";
this->initModel(_static, filename);
auto & solver = this->model->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
this->model->solveStep();
this->checkAll();
#define debug 0
#if debug
this->model->setBaseName(std::to_string(this->type) + "_static");
this->model->addDumpField("stress");
this->model->addDumpField("grad_u");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpFieldVector("displacement");
this->model->dump();
#endif
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, ImplicitFiniteDeformation) {
std::string filename =
"material_check_stress_plane_stress_finite_deformation.dat";
if (this->plane_strain)
filename = "material_check_stress_plane_strain_finite_deformation.dat";
else {
SUCCEED();
return;
}
this->initModel(_implicit_dynamic, filename);
const auto & coordinates = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
// set the position of all nodes to the static solution
for (auto && tuple : zip(make_view(coordinates, this->dim),
make_view(displacement, this->dim))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
auto ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(0, ekin, 1e-16);
this->checkAll();
#define debug 0
#if debug
this->model->setBaseName(std::to_string(this->type) + "_implicit_finit_def");
this->model->addDumpField("stress");
this->model->addDumpField("grad_u");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpFieldVector("displacement");
this->model->dump();
#endif
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestSMMLinear, StaticFiniteDeformation) {
std::string filename =
"material_check_stress_plane_stress_finite_deformation.dat";
if (this->plane_strain) {
filename = "material_check_stress_plane_strain_finite_deformation.dat";
} else {
SUCCEED();
return;
}
this->initModel(_static, filename);
auto & solver = this->model->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
this->model->solveStep();
this->checkAll();
}
diff --git a/test/test_model/patch_tests/patch_test_linear_fixture.hh b/test/test_model/patch_tests/patch_test_linear_fixture.hh
index fbdb13a3c..d0b2ce86c 100644
--- a/test/test_model/patch_tests/patch_test_linear_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_fixture.hh
@@ -1,182 +1,185 @@
/**
* @file patch_test_linear_fixture.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Sun Jun 02 2019
*
* @brief Fixture for linear patch tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_utils.hh"
#include "model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_
#define AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_
//#define DEBUG_TEST
using namespace akantu;
template <typename type_, typename M>
class TestPatchTestLinear : public ::testing::Test {
public:
static constexpr ElementType type = type_::value;
static constexpr size_t dim = ElementClass<type>::getSpatialDimension();
virtual void SetUp() {
mesh = std::make_unique<Mesh>(dim);
mesh->read(std::to_string(type) + ".msh");
MeshUtils::buildFacets(*mesh);
mesh->createBoundaryGroupFromGeometry();
model = std::make_unique<M>(*mesh);
}
virtual void TearDown() {
model.reset(nullptr);
mesh.reset(nullptr);
}
virtual void initModel(const AnalysisMethod & method,
const std::string & material_file) {
debug::setDebugLevel(dblError);
getStaticParser().parse(material_file);
this->model->initFull(_analysis_method = method);
this->applyBC();
if (method != _static)
this->model->setTimeStep(0.8 * this->model->getStableTimeStep());
}
virtual void applyBC() {
auto & boundary = this->model->getBlockedDOFs();
for (auto & eg : mesh->iterateElementGroups()) {
for (const auto & node : eg.getNodeGroup()) {
for (UInt s = 0; s < boundary.getNbComponent(); ++s) {
boundary(node, s) = true;
}
}
}
}
virtual void applyBConDOFs(const Array<Real> & dofs) {
const auto & coordinates = this->mesh->getNodes();
for (auto & eg : this->mesh->iterateElementGroups()) {
for (const auto & node : eg.getNodeGroup()) {
this->setLinearDOF(dofs.begin(dofs.getNbComponent())[node],
coordinates.begin(this->dim)[node]);
}
}
}
template <typename V> Matrix<Real> prescribed_gradient(const V & dof) {
Matrix<Real> gradient(dof.getNbComponent(), dim);
for (UInt i = 0; i < gradient.rows(); ++i) {
for (UInt j = 0; j < gradient.cols(); ++j) {
gradient(i, j) = alpha(i, j + 1);
}
}
return gradient;
}
template <typename Gradient, typename DOFs>
void checkGradient(const Gradient & gradient, const DOFs & dofs) {
auto pgrad = prescribed_gradient(dofs);
for (auto & grad :
make_view(gradient, gradient.getNbComponent() / dim, dim)) {
auto diff = grad - pgrad;
auto gradient_error =
diff.template norm<L_inf>() / grad.template norm<L_inf>();
EXPECT_NEAR(0, gradient_error, gradient_tolerance);
}
}
template <typename presult_func_t, typename Result, typename DOFs>
void checkResults(presult_func_t && presult_func, const Result & results,
const DOFs & dofs) {
auto presult = presult_func(prescribed_gradient(dofs));
for (auto & result :
make_view(results, results.getNbComponent() / dim, dim)) {
auto diff = result - presult;
auto result_error =
diff.template norm<L_inf>() / presult.template norm<L_inf>();
EXPECT_NEAR(0, result_error, result_tolerance);
}
}
template <typename V1, typename V2>
void setLinearDOF(V1 && dof, V2 && coord) {
for (UInt i = 0; i < dof.size(); ++i) {
dof(i) = this->alpha(i, 0);
for (UInt j = 0; j < coord.size(); ++j) {
dof(i) += this->alpha(i, j + 1) * coord(j);
}
}
}
template <typename V> void checkDOFs(V && dofs) {
const auto & coordinates = mesh->getNodes();
Vector<Real> ref_dof(dofs.getNbComponent());
for (auto && tuple : zip(make_view(coordinates, dim),
make_view(dofs, dofs.getNbComponent()))) {
setLinearDOF(ref_dof, std::get<0>(tuple));
auto diff = std::get<1>(tuple) - ref_dof;
auto dofs_error = diff.template norm<L_inf>();
EXPECT_NEAR(0, dofs_error, dofs_tolerance);
}
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<M> model;
Matrix<Real> alpha{{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
Real gradient_tolerance{1e-13};
Real result_tolerance{1e-13};
Real dofs_tolerance{1e-15};
};
template <typename type_, typename M>
constexpr ElementType TestPatchTestLinear<type_, M>::type;
template <typename tuple_, typename M>
constexpr size_t TestPatchTestLinear<tuple_, M>::dim;
#endif /* AKANTU_PATCH_TEST_LINEAR_FIXTURE_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_fixture.py b/test/test_model/patch_tests/patch_test_linear_fixture.py
index 862b55f9c..2cd441a6f 100644
--- a/test/test_model/patch_tests/patch_test_linear_fixture.py
+++ b/test/test_model/patch_tests/patch_test_linear_fixture.py
@@ -1,136 +1,137 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
-__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+""" patch_test_linear_fixture.py: linear patch test in python"""
+
+__author__ = "Guillaume Anciaux and Nicolas Richart"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
-from mpi4py import MPI
-import akantu
+__license__ = "LGPLv3"
+
import unittest
import numpy as np
+import akantu
class TestPatchTestLinear(unittest.TestCase):
alpha = np.array([[0.01, 0.02, 0.03, 0.04],
[0.05, 0.06, 0.07, 0.08],
[0.09, 0.10, 0.11, 0.12]])
gradient_tolerance = 1e-13
result_tolerance = 1e-13
dofs_tolerance = 1e-15
def __init__(self, test_name, elem_type_str, functor=None):
self.test_name = test_name
self.functor = functor
self.elem_type = akantu.getElementTypes()[elem_type_str]
self.elem_type_str = elem_type_str
self.dim = akantu.Mesh.getSpatialDimension(self.elem_type)
super().__init__(test_name)
def _internal_call(self):
self.functor(self)
def __getattr__(self, key):
if key == self.test_name:
return self._internal_call
def setUp(self):
self.mesh = akantu.Mesh(self.dim, self.elem_type_str)
self.mesh.read(str(self.elem_type_str) + ".msh")
akantu.MeshUtils.buildFacets(self.mesh)
self.mesh.createBoundaryGroupFromGeometry()
self.model = self.model_type(self.mesh)
def tearDown(self):
del self.model
del self.mesh
def initModel(self, method, material_file):
akantu.parseInput(material_file)
akantu.setDebugLevel(akantu.dblError)
self.model.initFull(method)
self.applyBC()
if method != akantu._static:
self.model.setTimeStep(0.8 * self.model.getStableTimeStep())
def applyBC(self):
boundary = self.model.getBlockedDOFs()
for eg in self.mesh.iterateElementGroups():
nodes = eg.getNodeGroup().getNodes()
boundary[nodes, :] = True
def applyBConDOFs(self, dofs):
coordinates = self.mesh.getNodes()
for eg in self.mesh.iterateElementGroups():
nodes = eg.getNodeGroup().getNodes().flatten()
dofs[nodes] = self.setLinearDOF(dofs[nodes],
coordinates[nodes])
def prescribed_gradient(self, dof):
gradient = self.alpha[:dof.shape[1], 1:self.dim + 1]
return gradient
def checkGradient(self, gradient, dofs):
pgrad = self.prescribed_gradient(dofs).T
gradient = gradient.reshape(gradient.shape[0], *pgrad.shape)
diff = gradient[:] - pgrad
norm = np.abs(pgrad).max()
gradient_error = np.abs(diff).max() / norm
self.assertAlmostEqual(0, gradient_error,
delta=self.gradient_tolerance)
def checkResults(self, presult_func, results, dofs):
presult = presult_func(self.prescribed_gradient(dofs)).flatten()
remaining_size = np.prod(np.array(results.shape[1:]))
results = results.reshape((results.shape[0], remaining_size))
for result in results:
diff = result - presult
norm = np.abs(result).max()
if norm == 0:
result_error = np.abs(diff).max()
else:
result_error = np.abs(diff).max() / norm
self.assertAlmostEqual(0., result_error,
delta=self.result_tolerance)
def setLinearDOF(self, dof, coord):
nb_dofs = dof.shape[1]
dof[:] = np.einsum('ik,ak->ai',
self.alpha[:nb_dofs, 1:self.dim + 1], coord)
for i in range(0, nb_dofs):
dof[:, i] += self.alpha[i, 0]
return dof
def checkDOFs(self, dofs):
coordinates = self.mesh.getNodes()
ref_dofs = np.zeros_like(dofs)
self.setLinearDOF(ref_dofs, coordinates)
diff = dofs - ref_dofs
dofs_error = np.abs(diff).max()
self.assertAlmostEqual(0., dofs_error, delta=self.dofs_tolerance)
@classmethod
def TYPED_TEST(cls, functor, label):
for type_name, _type in akantu.getElementTypes().items():
if type_name == "_point_1":
continue
method_name = type_name + '_' + label
test_case = cls(method_name, type_name, functor)
test_case.setUp()
functor(test_case)
test_case.tearDown()
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_explicit.cc b/test/test_model/patch_tests/patch_test_linear_heat_transfer_explicit.cc
index 95b9d98be..434543f98 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_explicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_explicit.cc
@@ -1,50 +1,52 @@
/**
* @file patch_test_linear_heat_transfer_explicit.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Jan 31 2018
*
* @brief HeatTransfer patch test
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_heat_transfer_fixture.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestHTMLinear, Explicit) {
this->initModel(_explicit_lumped_mass, "heat_transfer_input.dat");
const auto & coordinates = this->mesh->getNodes();
auto & temperature = this->model->getTemperature();
// set the position of all nodes to the static solution
for (auto && tuple :
zip(make_view(coordinates, this->dim), make_view(temperature, 1))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
this->checkAll();
}
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
index f1ea709aa..04e17e7f8 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.hh
@@ -1,76 +1,79 @@
/**
* @file patch_test_linear_heat_transfer_fixture.hh
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief HeatTransfer patch tests fixture
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "heat_transfer_model.hh"
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_fixture.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_
#define AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_
/* -------------------------------------------------------------------------- */
template <typename type>
class TestPatchTestHTMLinear
: public TestPatchTestLinear<type, HeatTransferModel> {
using parent = TestPatchTestLinear<type, HeatTransferModel>;
public:
void applyBC() override {
parent::applyBC();
auto & temperature = this->model->getTemperature();
this->applyBConDOFs(temperature);
}
void initModel(const AnalysisMethod & method,
const std::string & material_file) override {
TestPatchTestLinear<type, HeatTransferModel>::initModel(method,
material_file);
if (method != _static)
this->model->setTimeStep(0.5 * this->model->getStableTimeStep());
}
void checkAll() {
auto & temperature = this->model->getTemperature();
Matrix<Real> C = this->model->get("conductivity");
this->checkDOFs(temperature);
this->checkGradient(this->model->getTemperatureGradient(this->type),
temperature);
this->checkResults(
[&](const Matrix<Real> & grad_T) { return C * grad_T.transpose(); },
this->model->getKgradT(this->type), temperature);
}
};
using htm_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestPatchTestHTMLinear, htm_types, );
#endif /* AKANTU_PATCH_TEST_LINEAR_HEAT_TRANSFER_FIXTURE_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.py b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.py
index 0ac2f0cbd..8bea9412d 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.py
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_fixture.py
@@ -1,43 +1,58 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+"""patch_test_linear_heat_transfer_fixture.py: heat transfer patch test in
+python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
import patch_test_linear_fixture
import akantu
class TestPatchTestHTMLinear(patch_test_linear_fixture.TestPatchTestLinear):
model_type = akantu.HeatTransferModel
def applyBC(self):
super().applyBC()
temperature = self.model.getTemperature()
self.applyBConDOFs(temperature)
def checkAll(self):
temperature = self.model.getTemperature()
C = self.model.getMatrix("conductivity")
self.checkDOFs(temperature)
self.checkGradient(self.model.getTemperatureGradient(self.elem_type),
temperature)
self.prescribed_gradient(temperature)
self.checkResults(lambda grad_T: C.dot(grad_T.T),
self.model.getKgradT(self.elem_type),
temperature)
def initModel(self, method, material_file):
super().initModel(method, material_file)
if method != akantu._static:
self.model.setTimeStep(0.5 * self.model.getStableTimeStep())
+
+
+def run_test_generic(self_, method):
+ self_.initModel(method, "heat_transfer_input.dat")
+
+ coordinates = self_.mesh.getNodes()
+ temperature = self_.model.getTemperature()
+ # set the position of all nodes to the static solution
+ self_.setLinearDOF(temperature, coordinates)
+
+ for s in range(0, 100):
+ self_.model.solveStep()
+
+ self_.checkAll()
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_implicit.cc b/test/test_model/patch_tests/patch_test_linear_heat_transfer_implicit.cc
index 63c265eab..db20f25aa 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_implicit.cc
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_implicit.cc
@@ -1,52 +1,54 @@
/**
* @file patch_test_linear_heat_transfer_implicit.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
- * @date last modification: Thu Feb 08 2018
+ * @date last modification: Wed Feb 28 2018
*
* @brief HeatTransfer patch test
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_heat_transfer_fixture.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestHTMLinear, Implicit) {
this->initModel(_implicit_dynamic, "heat_transfer_input.dat");
const auto & coordinates = this->mesh->getNodes();
auto & temperature = this->model->getTemperature();
// set the position of all nodes to the static solution
for (auto && tuple :
zip(make_view(coordinates, this->dim), make_view(temperature, 1))) {
this->setLinearDOF(std::get<1>(tuple), std::get<0>(tuple));
}
for (UInt s = 0; s < 100; ++s) {
this->model->solveStep();
}
this->checkAll();
}
diff --git a/test/test_model/patch_tests/patch_test_linear_heat_transfer_static.cc b/test/test_model/patch_tests/patch_test_linear_heat_transfer_static.cc
index 20596adaf..e68bade48 100644
--- a/test/test_model/patch_tests/patch_test_linear_heat_transfer_static.cc
+++ b/test/test_model/patch_tests/patch_test_linear_heat_transfer_static.cc
@@ -1,46 +1,48 @@
/**
* @file patch_test_linear_heat_transfer_static.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief HeatTransfer patch test
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_heat_transfer_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestPatchTestHTMLinear, Static) {
this->initModel(_static, "heat_transfer_input.dat");
auto & solver = this->model->getNonLinearSolver();
solver.set("max_iterations", 2);
solver.set("threshold", 2e-4);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
this->model->solveStep();
this->checkAll();
}
diff --git a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
index 2cd9e46aa..56ee38b0d 100644
--- a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
+++ b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.hh
@@ -1,153 +1,156 @@
/**
* @file patch_test_linear_solid_mechanics_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jan 30 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief SolidMechanics patch tests fixture
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "patch_test_linear_fixture.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_
#define AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_
/* -------------------------------------------------------------------------- */
template <typename tuple_>
class TestPatchTestSMMLinear
: public TestPatchTestLinear<std::tuple_element_t<0, tuple_>,
SolidMechanicsModel> {
using parent =
TestPatchTestLinear<std::tuple_element_t<0, tuple_>, SolidMechanicsModel>;
public:
static constexpr bool plane_strain = std::tuple_element_t<1, tuple_>::value;
void applyBC() override {
parent::applyBC();
auto & displacement = this->model->getDisplacement();
this->applyBConDOFs(displacement);
}
void checkForces() {
auto & mat = this->model->getMaterial(0);
auto & internal_forces = this->model->getInternalForce();
auto & external_forces = this->model->getExternalForce();
auto dim = this->dim;
Matrix<Real> sigma =
make_view(mat.getStress(this->type), dim, dim).begin()[0];
external_forces.zero();
if (dim > 1) {
for (auto & eg : this->mesh->iterateElementGroups()) {
this->model->applyBC(BC::Neumann::FromHigherDim(sigma), eg.getName());
}
} else {
external_forces(0) = -sigma(0, 0);
external_forces(1) = sigma(0, 0);
}
Real force_norm_inf = -std::numeric_limits<Real>::max();
Vector<Real> total_force(dim);
total_force.zero();
for (auto && f : make_view(internal_forces, dim)) {
total_force += f;
force_norm_inf = std::max(force_norm_inf, f.template norm<L_inf>());
}
EXPECT_NEAR(0, total_force.template norm<L_inf>() / force_norm_inf, 1e-9);
for (auto && tuple : zip(make_view(internal_forces, dim),
make_view(external_forces, dim))) {
auto && f_int = std::get<0>(tuple);
auto && f_ext = std::get<1>(tuple);
auto f = f_int + f_ext;
EXPECT_NEAR(0, f.template norm<L_inf>() / force_norm_inf, 1e-9);
}
}
void checkAll() {
auto & displacement = this->model->getDisplacement();
auto & mat = this->model->getMaterial(0);
this->checkDOFs(displacement);
this->checkGradient(mat.getGradU(this->type), displacement);
this->checkResults(
[&](const Matrix<Real> & pstrain) {
Real nu = this->model->getMaterial(0).get("nu");
Real E = this->model->getMaterial(0).get("E");
auto strain = (pstrain + pstrain.transpose()) / 2.;
auto trace = strain.trace();
auto lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
auto mu = E / (2 * (1 + nu));
if (not this->plane_strain) {
lambda = nu * E / (1 - nu * nu);
}
decltype(strain) stress(this->dim, this->dim);
if (this->dim == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
for (UInt i = 0; i < this->dim; ++i)
for (UInt j = 0; j < this->dim; ++j)
stress(i, j) =
(i == j) * lambda * trace + 2 * mu * strain(i, j);
}
return stress;
},
mat.getStress(this->type), displacement);
this->checkForces();
}
};
template <typename tuple_>
constexpr bool TestPatchTestSMMLinear<tuple_>::plane_strain;
template <typename T> struct invalid_plan_stress : std::true_type {};
template <typename type, typename bool_c>
struct invalid_plan_stress<std::tuple<type, bool_c>>
: aka::bool_constant<ElementClass<type::value>::getSpatialDimension() !=
2 and
not bool_c::value> {};
using true_false =
std::tuple<aka::bool_constant<true>, aka::bool_constant<false>>;
template <typename T> using valid_types = aka::negation<invalid_plan_stress<T>>;
using model_types = gtest_list_t<
tuple_filter_t<valid_types, cross_product_t<TestElementTypes, true_false>>>;
TYPED_TEST_SUITE(TestPatchTestSMMLinear, model_types, );
#endif /* AKANTU_PATCH_TEST_LINEAR_SOLID_MECHANICS_FIXTURE_HH_ */
diff --git a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.py b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.py
index acece65bb..078e5e1b4 100644
--- a/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.py
+++ b/test/test_model/patch_tests/patch_test_linear_solid_mechanics_fixture.py
@@ -1,146 +1,147 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+"""patch_test_linear_solid_mechanics_fixture.py: solid mechanics model patch
+test in python
+"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
import patch_test_linear_fixture
import numpy as np
import akantu
# custom material (this patch test also checks for custom material features)
class LocalElastic(akantu.Material):
-
def __init__(self, model, _id):
super().__init__(model, _id)
super().registerParamReal('E',
akantu._pat_readable | akantu._pat_parsable,
'Youngs modulus')
super().registerParamReal('nu',
akantu._pat_readable | akantu._pat_parsable,
'Poisson ratio')
# declares all the internals
def initMaterial(self, internals, params):
nu = self.getReal('nu')
E = self.getReal('E')
self.mu = E / (2 * (1 + nu))
self.lame_lambda = nu * E / (
(1. + nu) * (1. - 2. * nu))
# Second Lame coefficient (shear modulus)
self.lame_mu = E / (2. * (1. + nu))
super().initMaterial()
# declares all the parameters that are needed
def getPushWaveSpeed(self, element):
rho = self.getReal('rho')
return np.sqrt((self.lame_lambda + 2 * self.lame_mu) / rho)
# compute small deformation tensor
@staticmethod
def computeEpsilon(grad_u):
return 0.5 * (grad_u + np.einsum('aij->aji', grad_u))
# constitutive law
def computeStress(self, el_type, ghost_type):
grad_u = self.getGradU(el_type, ghost_type)
sigma = self.getStress(el_type, ghost_type)
n_quads = grad_u.shape[0]
grad_u = grad_u.reshape((n_quads, 2, 2))
epsilon = self.computeEpsilon(grad_u)
sigma = sigma.reshape((n_quads, 2, 2))
trace = np.einsum('aii->a', grad_u)
sigma[:, :, :] = (
np.einsum('a,ij->aij', trace,
self.lame_lambda * np.eye(2))
+ 2. * self.lame_mu * epsilon)
# constitutive law tangent modulii
def computeTangentModuli(self, el_type, tangent_matrix, ghost_type):
n_quads = tangent_matrix.shape[0]
tangent = tangent_matrix.reshape(n_quads, 3, 3)
Miiii = self.lame_lambda + 2 * self.lame_mu
Miijj = self.lame_lambda
Mijij = self.lame_mu
tangent[:, 0, 0] = Miiii
tangent[:, 1, 1] = Miiii
tangent[:, 0, 1] = Miijj
tangent[:, 1, 0] = Miijj
tangent[:, 2, 2] = Mijij
# computes the energy density
def computePotentialEnergy(self, el_type):
sigma = self.getStress(el_type)
grad_u = self.getGradU(el_type)
nquads = sigma.shape[0]
stress = sigma.reshape(nquads, 2, 2)
grad_u = grad_u.reshape((nquads, 2, 2))
epsilon = self.computeEpsilon(grad_u)
energy_density = self.getPotentialEnergy(el_type)
energy_density[:, 0] = 0.5 * np.einsum('aij,aij->a', stress, epsilon)
class TestPatchTestSMMLinear(patch_test_linear_fixture.TestPatchTestLinear):
plane_strain = True
model_type = akantu.SolidMechanicsModel
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
def initModel(self, method, material_file):
# mat.__dict__['dim'] = self.dim
super().initModel(method, material_file)
def applyBC(self):
super().applyBC()
displacement = self.model.getDisplacement()
self.applyBConDOFs(displacement)
def checkAll(self):
displacement = self.model.getDisplacement()
mat = self.model.getMaterial(0)
self.checkDOFs(displacement)
self.checkGradient(mat.getGradU(self.elem_type), displacement)
def foo(pstrain):
nu = self.model.getMaterial(0).getReal("nu")
E = self.model.getMaterial(0).getReal("E")
strain = (pstrain + pstrain.transpose()) / 2.
trace = strain.trace()
_lambda = nu * E / ((1 + nu) * (1 - 2 * nu))
mu = E / (2 * (1 + nu))
if (not self.plane_strain):
_lambda = nu * E / (1 - nu * nu)
stress = np.zeros((self.dim, self.dim))
if self.dim == 1:
stress[0, 0] = E * strain[0, 0]
else:
stress[:, :] = (
_lambda * trace * np.eye(self.dim) + 2 * mu * strain)
return stress
self.checkResults(foo,
mat.getStress(self.elem_type),
displacement)
diff --git a/test/test_model/patch_tests/test_lumped_mass.cc b/test/test_model/patch_tests/test_lumped_mass.cc
index f149fcaa1..b8c0aa087 100644
--- a/test/test_model/patch_tests/test_lumped_mass.cc
+++ b/test/test_model/patch_tests/test_lumped_mass.cc
@@ -1,101 +1,103 @@
/**
* @file test_lumped_mass.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Dec 05 2017
- * @date last modification: Tue Jan 30 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief test the lumping of the mass matrix
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <tuple>
/* -------------------------------------------------------------------------- */
using namespace akantu;
template <typename tuple_>
class TestLumpedMassesFixture : public ::testing::Test {
public:
static constexpr ElementType type = tuple_::value;
static constexpr size_t dim = ElementClass<type>::getSpatialDimension();
void SetUp() override {
debug::setDebugLevel(dblError);
getStaticParser().parse("material_lumped.dat");
std::stringstream element_type;
element_type << type;
mesh = std::make_unique<Mesh>(dim);
mesh->read(element_type.str() + ".msh");
SCOPED_TRACE(element_type.str().c_str());
model = std::make_unique<SolidMechanicsModel>(*mesh);
model->initFull(_analysis_method = _explicit_lumped_mass);
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModel> model;
};
template <typename T> constexpr ElementType TestLumpedMassesFixture<T>::type;
template <typename T> constexpr size_t TestLumpedMassesFixture<T>::dim;
using mass_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestLumpedMassesFixture, mass_types, );
TYPED_TEST(TestLumpedMassesFixture, TestLumpedMass) {
this->model->assembleMassLumped();
auto rho = this->model->getMaterial(0).getRho();
auto & fem = this->model->getFEEngine();
auto nb_element = this->mesh->getNbElement(this->type);
auto nb_quadrature_points =
fem.getNbIntegrationPoints(this->type) * nb_element;
Array<Real> rho_on_quad(nb_quadrature_points, 1, rho, "rho_on_quad");
auto mass = fem.integrate(rho_on_quad, this->type);
const auto & masses = this->model->getMass();
Vector<Real> sum(this->dim, 0.);
for (auto & mass : make_view(masses, this->dim)) {
sum += mass;
}
for (UInt s = 0; s < sum.size(); ++s)
EXPECT_NEAR(0., (mass - sum[s]) / mass, 2e-15);
}
diff --git a/test/test_model/patch_tests/test_patch_linear_anisotropic_explicit.py b/test/test_model/patch_tests/test_patch_linear_anisotropic_explicit.py
index 7ba974329..a18d1a992 100644
--- a/test/test_model/patch_tests/test_patch_linear_anisotropic_explicit.py
+++ b/test/test_model/patch_tests/test_patch_linear_anisotropic_explicit.py
@@ -1,85 +1,87 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+"""test_patch_linear_anisotropic_explicit.py: linear anisotropic test in
+python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
-from patch_test_linear_solid_mechanics_fixture import TestPatchTestSMMLinear
-import akantu
import unittest
import numpy as np
+from patch_test_linear_solid_mechanics_fixture import TestPatchTestSMMLinear
+import akantu
+
# Stiffness tensor, rotated by hand
C = np.array([[[[112.93753505, 1.85842452538e-10, -4.47654358027e-10],
[1.85847317471e-10, 54.2334345331, -3.69840984824],
[-4.4764768395e-10, -3.69840984824, 56.848605217]],
[[1.85847781609e-10, 25.429294233, -3.69840984816],
[25.429294233, 3.31613847493e-10, -8.38797920011e-11],
[-3.69840984816, -8.38804581349e-11, -1.97875715813e-10]],
[[-4.47654358027e-10, -3.69840984816, 28.044464917],
[-3.69840984816, 2.09374961813e-10, 9.4857455224e-12],
[28.044464917, 9.48308098714e-12, -2.1367885239e-10]]],
[[[1.85847781609e-10, 25.429294233, -3.69840984816],
[25.429294233, 3.31613847493e-10, -8.38793479119e-11],
[-3.69840984816, -8.38795699565e-11, -1.97876381947e-10]],
[[54.2334345331, 3.31617400207e-10, 2.09372075233e-10],
[3.3161562385e-10, 115.552705733, -3.15093728886e-10],
[2.09372075233e-10, -3.15090176173e-10, 54.2334345333]],
[[-3.69840984824, -8.38795699565e-11, 9.48219280872e-12],
[-8.38795699565e-11, -3.1509195253e-10, 25.4292942335],
[9.48441325477e-12, 25.4292942335, 3.69840984851]]],
[[[-4.47653469848e-10, -3.69840984816, 28.044464917],
[-3.69840984816, 2.09374073634e-10, 9.48752187924e-12],
[28.044464917, 9.48552347779e-12, -2.1367885239e-10]],
[[-3.69840984824, -8.3884899027e-11, 9.48219280872e-12],
[-8.3884899027e-11, -3.150972816e-10, 25.4292942335],
[9.48041645188e-12, 25.4292942335, 3.69840984851]],
[[56.848605217, -1.97875493768e-10, -2.13681516925e-10],
[-1.97877270125e-10, 54.2334345333, 3.69840984851],
[-2.13683293282e-10, 3.69840984851, 112.93753505]]]])
def foo(self):
self.initModel(
akantu.SolidMechanicsModelOptions(akantu._explicit_lumped_mass),
"material_anisotropic.dat")
coordinates = self.mesh.getNodes()
displacement = self.model.getDisplacement()
# set the position of all nodes to the static solution
self.setLinearDOF(displacement, coordinates)
for s in range(0, 100):
self.model.solveStep()
ekin = self.model.getEnergy("kinetic")
self.assertAlmostEqual(0, ekin, delta=1e-16)
self.checkDisplacements()
self.checkStrains()
def foo(pstrain):
strain = (pstrain + pstrain.transpose()) / 2.
stress = np.zeros((self.dim, self.dim))
for i in range(0, self.dim):
for j in range(0, self.dim):
stress[i, j] = 0
for k in range(0, self.dim):
- for l in range(0, self.dim):
+ for l in range(0, self.dim): # NOQA: E741
stress[i, j] += C[i][j][k][l] * strain(k, l)
return stress
self.checkStresses(foo)
suite = TestPatchTestSMMLinear.TYPED_TEST(foo, "AnisotropicExplicit")
unittest.TextTestRunner(verbosity=1).run(suite)
diff --git a/test/test_model/patch_tests/test_patch_linear_elastic_explicit.py b/test/test_model/patch_tests/test_patch_linear_elastic_explicit.py
index 68598ce1c..e84e0e71f 100755
--- a/test/test_model/patch_tests/test_patch_linear_elastic_explicit.py
+++ b/test/test_model/patch_tests/test_patch_linear_elastic_explicit.py
@@ -1,44 +1,45 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+"""test_patch_linear_elastic_explicit.py: linear elatic patch test in python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
+
+import sys
from patch_test_linear_solid_mechanics_fixture import TestPatchTestSMMLinear
import akantu
-import sys
def foo(self):
filename = "material_check_stress_plane_stress.dat"
if self.plane_strain:
filename = "material_check_stress_plane_strain.dat"
self.initModel(akantu._explicit_lumped_mass, filename)
coordinates = self.mesh.getNodes()
displacement = self.model.getDisplacement()
# set the position of all nodes to the static solution
self.setLinearDOF(displacement, coordinates)
for s in range(0, 100):
self.model.solveStep()
ekin = self.model.getEnergy("kinetic")
self.assertAlmostEqual(0, ekin, delta=1e-16)
self.checkAll()
def test():
TestPatchTestSMMLinear.TYPED_TEST(foo, "Explicit")
if 'pytest' not in sys.modules:
test()
diff --git a/test/test_model/patch_tests/test_patch_linear_elastic_static.py b/test/test_model/patch_tests/test_patch_linear_elastic_static.py
index c5f1dd813..e731eabbc 100755
--- a/test/test_model/patch_tests/test_patch_linear_elastic_static.py
+++ b/test/test_model/patch_tests/test_patch_linear_elastic_static.py
@@ -1,41 +1,41 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+""" test_patch_linear_elastic_static.py: static patch test in python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
+import sys
from patch_test_linear_solid_mechanics_fixture import TestPatchTestSMMLinear
import akantu
-import sys
def foo(self):
filename = "material_check_stress_plane_stress.dat"
if self.plane_strain:
filename = "material_check_stress_plane_strain.dat"
self.initModel(akantu._static, filename)
solver = self.model.getNonLinearSolver()
solver.set("max_iterations", 2)
solver.set("threshold", 2e-4)
solver.set("convergence_type", akantu.SolveConvergenceCriteria.residual)
self.model.solveStep()
self.checkAll()
def test():
TestPatchTestSMMLinear.TYPED_TEST(foo, "Static")
if 'pytest' not in sys.modules:
test()
diff --git a/test/test_model/patch_tests/test_patch_linear_heat_transfer_explicit.py b/test/test_model/patch_tests/test_patch_linear_heat_transfer_explicit.py
index 567c1ebb6..072940ae0 100644
--- a/test/test_model/patch_tests/test_patch_linear_heat_transfer_explicit.py
+++ b/test/test_model/patch_tests/test_patch_linear_heat_transfer_explicit.py
@@ -1,39 +1,30 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+""" test_patch_linear_heat_transfer_explicit.py: heat transfer patch test in
+python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
+import sys
from patch_test_linear_heat_transfer_fixture import TestPatchTestHTMLinear
+from patch_test_linear_heat_transfer_fixture import run_test_generic
import akantu
-import sys
-
-
-def foo(self):
-
- self.initModel(akantu._explicit_lumped_mass, "heat_transfer_input.dat")
-
- coordinates = self.mesh.getNodes()
- temperature = self.model.getTemperature()
- # set the position of all nodes to the static solution
- self.setLinearDOF(temperature, coordinates)
- for s in range(0, 100):
- self.model.solveStep()
- self.checkAll()
+def run_test(self_):
+ run_test_generic(self_, akantu._explicit_lumped_mass)
def test():
- TestPatchTestHTMLinear.TYPED_TEST(foo, "Explicit")
+ TestPatchTestHTMLinear.TYPED_TEST(run_test, "Explicit")
if 'pytest' not in sys.modules:
test()
diff --git a/test/test_model/patch_tests/test_patch_linear_heat_transfer_implicit.py b/test/test_model/patch_tests/test_patch_linear_heat_transfer_implicit.py
index beed8a53c..120247f79 100644
--- a/test/test_model/patch_tests/test_patch_linear_heat_transfer_implicit.py
+++ b/test/test_model/patch_tests/test_patch_linear_heat_transfer_implicit.py
@@ -1,38 +1,30 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+""" test_patch_linear_heat_transfer_implicit.py: heat transfer patch test in
+python"""
+
__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
-from patch_test_linear_heat_transfer_fixture import TestPatchTestHTMLinear
-import akantu
import sys
+import akantu
+from patch_test_linear_heat_transfer_fixture import TestPatchTestHTMLinear
+from patch_test_linear_heat_transfer_fixture import run_test_generic
-def foo(self):
- self.initModel(akantu._implicit_dynamic, "heat_transfer_input.dat")
-
- coordinates = self.mesh.getNodes()
- temperature = self.model.getTemperature()
- # set the position of all nodes to the static solution
- self.setLinearDOF(temperature, coordinates)
-
- for s in range(0, 100):
- self.model.solveStep()
-
- self.checkAll()
+def run_test(self_):
+ run_test_generic(self_, akantu._implicit_dynamic)
def test():
- TestPatchTestHTMLinear.TYPED_TEST(foo, "Explicit")
+ TestPatchTestHTMLinear.TYPED_TEST(run_test, "Explicit")
if 'pytest' not in sys.modules:
test()
diff --git a/test/test_model/patch_tests/test_patch_linear_heat_transfer_static.py b/test/test_model/patch_tests/test_patch_linear_heat_transfer_static.py
index 385e33d77..5163cc5a5 100644
--- a/test/test_model/patch_tests/test_patch_linear_heat_transfer_static.py
+++ b/test/test_model/patch_tests/test_patch_linear_heat_transfer_static.py
@@ -1,36 +1,37 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
-__author__ = "Guillaume Anciaux"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+"""test_patch_linear_heat_transfer_static.py: heat transfer patch test in
+python"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Guillaume Anciaux"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Guillaume Anciaux"
-__email__ = "guillaume.anciaux@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
+import sys
from patch_test_linear_heat_transfer_fixture import TestPatchTestHTMLinear
import akantu
-import sys
def foo(self):
self.initModel(akantu._static, "heat_transfer_input.dat")
solver = self.model.getNonLinearSolver()
solver.set("max_iterations", 2)
solver.set("threshold", 2e-4)
solver.set("convergence_type", akantu.SolveConvergenceCriteria.residual)
self.model.solveStep()
self.checkAll()
def test():
TestPatchTestHTMLinear.TYPED_TEST(foo, "Static")
if 'pytest' not in sys.modules:
test()
diff --git a/test/test_model/test_common/CMakeLists.txt b/test/test_model/test_common/CMakeLists.txt
index fcc329306..391ed3b73 100644
--- a/test/test_model/test_common/CMakeLists.txt
+++ b/test/test_model/test_common/CMakeLists.txt
@@ -1,8 +1,40 @@
+#===============================================================================
+# @file CMakeLists.txt
+#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
+#
+# @date creation: Wed Jan 30 2019
+# @date last modification: Tue Feb 26 2019
+#
+# @brief CMakeLists for common part of Models
+#
+#
+# @section LICENSE
+#
+# Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+#===============================================================================
+
+
add_akantu_test(test_model_solver "Test for the solvers")
add_akantu_test(test_non_local_toolbox "Test of the functionalities in the non-local toolbox")
add_mesh(dof_manager_mesh mesh.geo 3 1)
register_gtest_sources(
SOURCES test_dof_manager.cc
PACKAGE core)
register_gtest_test(test_dof_manager DEPENDS dof_manager_mesh)
diff --git a/test/test_model/test_common/test_dof_manager.cc b/test/test_model/test_common/test_dof_manager.cc
index 4e63fb6db..61baaadbf 100644
--- a/test/test_model/test_common/test_dof_manager.cc
+++ b/test/test_model/test_common/test_dof_manager.cc
@@ -1,298 +1,302 @@
/**
* @file test_dof_manager.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Wed Jan 30 2019
+ * @date creation: Tue Feb 26 2019
+ * @date last modification: Wed Nov 18 2020
*
- * @brief test the dof managers
+ * @brief test the dof managers
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <dof_manager.hh>
#include <mesh_partition_scotch.hh>
#include <mesh_utils.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <numeric>
#include <string>
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
enum DOFManagerType { _dmt_default, _dmt_petsc };
}
AKANTU_ENUM_HASH(DOFManagerType)
using namespace akantu;
// defined as struct to get there names in gtest outputs
struct dof_manager_default_
: public std::integral_constant<DOFManagerType, _dmt_default> {};
struct dof_manager_petsc_
: public std::integral_constant<DOFManagerType, _dmt_petsc> {};
using dof_manager_types = ::testing::Types<
#ifdef AKANTU_USE_PETSC
dof_manager_petsc_,
#endif
dof_manager_default_>;
namespace std {
std::string to_string(const DOFManagerType & type) {
std::unordered_map<DOFManagerType, std::string> map{
#ifdef AKANTU_USE_PETSC
{_dmt_petsc, "petsc"},
#endif
{_dmt_default, "default"},
};
return map.at(type);
}
} // namespace std
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerTester {
public:
DOFManagerTester(std::unique_ptr<DOFManager> dof_manager)
: dof_manager(std::move(dof_manager)) {}
DOFManager & operator*() { return *dof_manager; }
DOFManager * operator->() { return dof_manager.get(); }
void getArrayPerDOFs(const ID & id, SolverVector & vector,
Array<Real> & array) {
dof_manager->getArrayPerDOFs(id, vector, array);
}
SolverVector & residual() { return *dof_manager->residual; }
private:
std::unique_ptr<DOFManager> dof_manager;
};
} // namespace akantu
template <class T> class DOFManagerFixture : public ::testing::Test {
public:
constexpr static DOFManagerType type = T::value;
constexpr static UInt dim = 3;
void SetUp() override {
mesh = std::make_unique<Mesh>(this->dim);
auto & communicator = Communicator::getStaticCommunicator();
if (communicator.whoAmI() == 0) {
mesh->read("mesh.msh");
}
mesh->distribute();
nb_nodes = this->mesh->getNbNodes();
nb_total_nodes = this->mesh->getNbGlobalNodes();
auto && range_nodes = arange(nb_nodes);
nb_pure_local =
std::accumulate(range_nodes.begin(), range_nodes.end(), 0,
[&](auto && init, auto && val) {
return init + mesh->isLocalOrMasterNode(val);
});
}
void TearDown() override {
mesh.reset();
dof1.reset();
dof2.reset();
}
decltype(auto) alloc() {
std::unordered_map<DOFManagerType, std::string> types{
{_dmt_default, "default"}, {_dmt_petsc, "petsc"}};
return DOFManagerTester(DOFManagerFactory::getInstance().allocate(
types[T::value], *mesh, "dof_manager"));
}
decltype(auto) registerDOFs(DOFSupportType dst1, DOFSupportType dst2) {
auto dof_manager = DOFManagerTester(this->alloc());
auto n1 = dst1 == _dst_nodal ? nb_nodes : nb_pure_local;
this->dof1 = std::make_unique<Array<Real>>(n1, 3);
dof_manager->registerDOFs("dofs1", *this->dof1, dst1);
EXPECT_EQ(dof_manager.residual().size(), nb_total_nodes * 3);
auto n2 = dst2 == _dst_nodal ? nb_nodes : nb_pure_local;
this->dof2 = std::make_unique<Array<Real>>(n2, 5);
dof_manager->registerDOFs("dofs2", *this->dof2, dst2);
EXPECT_EQ(dof_manager.residual().size(), nb_total_nodes * 8);
return dof_manager;
}
protected:
Int nb_nodes{0}, nb_total_nodes{0}, nb_pure_local{0};
std::unique_ptr<Mesh> mesh;
std::unique_ptr<Array<Real>> dof1;
std::unique_ptr<Array<Real>> dof2;
};
template <class T> constexpr DOFManagerType DOFManagerFixture<T>::type;
template <class T> constexpr UInt DOFManagerFixture<T>::dim;
TYPED_TEST_SUITE(DOFManagerFixture, dof_manager_types, );
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, Construction) {
auto dof_manager = this->alloc();
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, DoubleConstruction) {
auto dof_manager = this->alloc();
dof_manager = this->alloc();
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterGenericDOF1) {
auto dof_manager = this->alloc();
Array<Real> dofs(this->nb_pure_local, 3);
dof_manager->registerDOFs("dofs1", dofs, _dst_generic);
EXPECT_GE(dof_manager.residual().size(), this->nb_total_nodes * 3);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterNodalDOF1) {
auto dof_manager = this->alloc();
Array<Real> dofs(this->nb_nodes, 3);
dof_manager->registerDOFs("dofs1", dofs, _dst_nodal);
EXPECT_GE(dof_manager.residual().size(), this->nb_total_nodes * 3);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterGenericDOF2) {
this->registerDOFs(_dst_generic, _dst_generic);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterNodalDOF2) {
this->registerDOFs(_dst_nodal, _dst_nodal);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, RegisterMixedDOF) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_generic);
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, AssembleVector) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_generic);
dof_manager.residual().zero();
for (auto && data :
enumerate(make_view(*this->dof1, this->dof1->getNbComponent()))) {
auto n = std::get<0>(data);
auto & l = std::get<1>(data);
l.set(1. * this->mesh->isLocalOrMasterNode(n));
}
this->dof2->set(2.);
dof_manager->assembleToResidual("dofs1", *this->dof1);
dof_manager->assembleToResidual("dofs2", *this->dof2);
this->dof1->set(0.);
this->dof2->set(0.);
dof_manager.getArrayPerDOFs("dofs1", dof_manager.residual(), *this->dof1);
for (auto && data :
enumerate(make_view(*this->dof1, this->dof1->getNbComponent()))) {
if (this->mesh->isLocalOrMasterNode(std::get<0>(data))) {
const auto & l = std::get<1>(data);
auto e = (l - Vector<Real>{1., 1., 1.}).norm();
ASSERT_EQ(e, 0.);
}
}
dof_manager.getArrayPerDOFs("dofs2", dof_manager.residual(), *this->dof2);
for (auto && l : make_view(*this->dof2, this->dof2->getNbComponent())) {
auto e = (l - Vector<Real>{2., 2., 2., 2., 2.}).norm();
ASSERT_EQ(e, 0.);
}
}
/* -------------------------------------------------------------------------- */
TYPED_TEST(DOFManagerFixture, AssembleMatrixNodal) {
auto dof_manager = this->registerDOFs(_dst_nodal, _dst_nodal);
auto && K = dof_manager->getNewMatrix("K", _symmetric);
K.zero();
auto && elemental_matrix = std::make_unique<Array<Real>>(
this->mesh->getNbElement(this->dim), 8 * 3 * 8 * 3);
for (auto && m : make_view(*elemental_matrix, 8 * 3, 8 * 3)) {
m.set(1.);
}
dof_manager->assembleElementalMatricesToMatrix(
"K", "dofs1", *elemental_matrix, _hexahedron_8);
elemental_matrix = std::make_unique<Array<Real>>(
this->mesh->getNbElement(this->dim), 8 * 5 * 8 * 5);
for (auto && m : make_view(*elemental_matrix, 8 * 5, 8 * 5)) {
m.set(1.);
}
dof_manager->assembleElementalMatricesToMatrix(
"K", "dofs2", *elemental_matrix, _hexahedron_8);
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(*this->mesh, node_to_elem, this->dim);
dof_manager.residual().zero();
for (auto && data :
enumerate(zip(make_view(*this->dof1, this->dof1->getNbComponent()),
make_view(*this->dof2, this->dof2->getNbComponent())))) {
auto n = std::get<0>(data);
auto & l1 = std::get<0>(std::get<1>(data));
auto & l2 = std::get<1>(std::get<1>(data));
auto v = 1. * this->mesh->isLocalOrMasterNode(n);
l1.set(v);
l2.set(v);
}
dof_manager->assembleToResidual("dofs1", *this->dof1);
dof_manager->assembleToResidual("dofs2", *this->dof2);
for (auto && n : arange(this->nb_nodes)) {
if (not this->mesh->isLocalOrMasterNode(n)) {
}
}
}
diff --git a/test/test_model/test_common/test_model_solver/CMakeLists.txt b/test/test_model/test_common/test_model_solver/CMakeLists.txt
index 24e5110d4..f377cb362 100644
--- a/test/test_model/test_common/test_model_solver/CMakeLists.txt
+++ b/test/test_model/test_common/test_model_solver/CMakeLists.txt
@@ -1,57 +1,67 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Sat Apr 01 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Tue Apr 23 2019
#
# @brief test for the common solvers interface of the models
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
register_test(test_dof_manager_default
SOURCES test_dof_manager_default.cc
PACKAGE mumps
)
register_test(test_model_solver_mumps
SOURCES test_model_solver.cc
COMPILE_OPTIONS "DOF_MANAGER_TYPE=\"mumps\""
PACKAGE mumps
)
register_test(test_model_solver_petsc
SOURCES test_model_solver.cc
COMPILE_OPTIONS "DOF_MANAGER_TYPE=\"petsc\""
PACKAGE petsc
)
register_test(test_model_solver_dynamic_explicit
SOURCES test_model_solver_dynamic.cc
PACKAGE core
COMPILE_OPTIONS "EXPLICIT=true"
)
register_test(test_model_solver_dynamic_implicit
SOURCES test_model_solver_dynamic.cc
PACKAGE mumps
COMPILE_OPTIONS "EXPLICIT=false"
)
register_test(test_model_solver_dynamic_petsc
SOURCES test_model_solver_dynamic.cc
PACKAGE petsc
COMPILE_OPTIONS "EXPLICIT=false;DOF_MANAGER_TYPE=\"petsc\""
)
diff --git a/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc b/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
index 09354c24b..da17e643e 100644
--- a/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
+++ b/test/test_model/test_common/test_model_solver/test_dof_manager_default.cc
@@ -1,129 +1,131 @@
/**
* @file test_dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 26 2016
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Wed Jan 30 2019
*
* @brief Test default dof manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "sparse_matrix_aij.hh"
#include "time_step_solver.hh"
using namespace akantu;
/**
* =\o-----o-----o-> F
* | |
* |---- L ----|
*/
class MySolverCallback : public SolverCallback {
public:
MySolverCallback(Real F, DOFManagerDefault & dof_manager, UInt nb_dofs = 3)
: dof_manager(dof_manager), dispacement(nb_dofs, 1, "disp"),
blocked(nb_dofs, 1), forces(nb_dofs, 1), nb_dofs(nb_dofs) {
dof_manager.registerDOFs("disp", dispacement, _dst_generic);
dof_manager.registerBlockedDOFs("disp", blocked);
dispacement.set(0.);
forces.set(0.);
blocked.set(false);
forces(nb_dofs - 1, _x) = F;
blocked(0, _x) = true;
}
void assembleMatrix(const ID & matrix_id) {
if (matrix_id != "K")
return;
auto & K = dynamic_cast<SparseMatrixAIJ &>(dof_manager.getMatrix("K"));
K.zero();
for (UInt i = 1; i < nb_dofs - 1; ++i)
K.add(i, i, 2.);
for (UInt i = 0; i < nb_dofs - 1; ++i)
K.add(i, i + 1, -1.);
K.add(0, 0, 1);
K.add(nb_dofs - 1, nb_dofs - 1, 1);
// K *= 1 / L_{el}
K *= nb_dofs - 1;
}
MatrixType getMatrixType(const ID & matrix_id) {
if (matrix_id == "K")
return _symmetric;
return _mt_not_defined;
}
void assembleLumpedMatrix(const ID &) {}
void assembleResidual() { dof_manager.assembleToResidual("disp", forces); }
void predictor() {}
void corrector() {}
DOFManagerDefault & dof_manager;
Array<Real> dispacement;
Array<bool> blocked;
Array<Real> forces;
UInt nb_dofs;
};
int main(int argc, char * argv[]) {
initialize(argc, argv);
DOFManagerDefault dof_manager("test_dof_manager");
MySolverCallback callback(10., dof_manager, 11);
NonLinearSolver & nls =
dof_manager.getNewNonLinearSolver("my_nls", NonLinearSolverType::_linear);
TimeStepSolver & tss = dof_manager.getNewTimeStepSolver(
"my_tss", TimeStepSolverType::_static, nls, callback);
tss.setIntegrationScheme("disp", IntegrationSchemeType::_pseudo_time);
tss.solveStep(callback);
dof_manager.getMatrix("K").saveMatrix("K_dof_manager_default.mtx");
Array<Real>::const_scalar_iterator disp_it = callback.dispacement.begin();
Array<Real>::const_scalar_iterator force_it = callback.forces.begin();
Array<bool>::const_scalar_iterator blocked_it = callback.blocked.begin();
std::cout << std::setw(8) << "disp"
<< " " << std::setw(8) << "force"
<< " " << std::setw(8) << "blocked" << std::endl;
for (; disp_it != callback.dispacement.end();
++disp_it, ++force_it, ++blocked_it) {
std::cout << std::setw(8) << *disp_it << " " << std::setw(8) << *force_it
<< " " << std::setw(8) << std::boolalpha << *blocked_it
<< std::endl;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver.cc b/test/test_model/test_common/test_model_solver/test_model_solver.cc
index 5f8e9d6df..0d8eb11bd 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver.cc
+++ b/test/test_model/test_common/test_model_solver/test_model_solver.cc
@@ -1,176 +1,178 @@
/**
* @file test_model_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Tue Apr 23 2019
*
* @brief Test default dof manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_random_generator.hh"
#include "dof_manager.hh"
#include "dof_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "model_solver.hh"
#include "non_linear_solver.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include "test_model_solver_my_model.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void genMesh(Mesh & mesh, UInt nb_nodes);
static void printResults(MyModel & model, UInt nb_nodes);
Real F = -10;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt prank = Communicator::getStaticCommunicator().whoAmI();
std::cout << std::setprecision(7);
ID dof_manager_type = "default";
#if defined(DOF_MANAGER_TYPE)
dof_manager_type = DOF_MANAGER_TYPE;
#endif
UInt global_nb_nodes = 100;
Mesh mesh(1);
RandomGenerator<UInt>::seed(1);
if (prank == 0) {
genMesh(mesh, global_nb_nodes);
}
// std::cout << prank << RandGenerator<Real>::seed() << std::endl;
mesh.distribute();
MyModel model(F, mesh, false, dof_manager_type);
model.getNewSolver("static", TimeStepSolverType::_static,
NonLinearSolverType::_newton_raphson);
model.setIntegrationScheme("static", "disp",
IntegrationSchemeType::_pseudo_time);
NonLinearSolver & solver = model.getDOFManager().getNonLinearSolver("static");
solver.set("max_iterations", 2);
model.solveStep();
printResults(model, global_nb_nodes);
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
mesh_accessor.setNbGlobalNodes(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
}
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
mesh_accessor.makeReady();
}
/* -------------------------------------------------------------------------- */
void printResults(MyModel & model, UInt /*nb_nodes*/) {
// if (model.mesh.isDistributed()) {
// UInt prank = model.mesh.getCommunicator().whoAmI();
// auto & sync = dynamic_cast<DOFManagerDefault &>(model.getDOFManager())
// .getSynchronizer();
// if (prank == 0) {
// Array<Real> global_displacement(nb_nodes);
// Array<Real> global_forces(nb_nodes);
// Array<bool> global_blocked(nb_nodes);
// sync.gather(model.forces, global_forces);
// sync.gather(model.displacement, global_displacement);
// sync.gather(model.blocked, global_blocked);
// auto force_it = global_forces.begin();
// auto disp_it = global_displacement.begin();
// auto blocked_it = global_blocked.begin();
// std::cout << "node"
// << ", " << std::setw(8) << "disp"
// << ", " << std::setw(8) << "force"
// << ", " << std::setw(8) << "blocked" << std::endl;
// UInt node = 0;
// for (; disp_it != global_displacement.end();
// ++disp_it, ++force_it, ++blocked_it, ++node) {
// std::cout << node << ", " << std::setw(8) << *disp_it << ", "
// << std::setw(8) << *force_it << ", " << std::setw(8)
// << *blocked_it << std::endl;
// std::cout << std::flush;
// }
// } else {
// sync.gather(model.forces);
// sync.gather(model.displacement);
// sync.gather(model.blocked);
// }
// } else {
auto force_it = model.forces.begin();
auto disp_it = model.displacement.begin();
auto blocked_it = model.blocked.begin();
std::cout << "node"
<< ", " << std::setw(8) << "disp"
<< ", " << std::setw(8) << "force"
<< ", " << std::setw(8) << "blocked" << std::endl;
UInt node = 0;
for (; disp_it != model.displacement.end();
++disp_it, ++force_it, ++blocked_it, ++node) {
std::cout << node << ", " << std::setw(8) << *disp_it << ", "
<< std::setw(8) << *force_it << ", " << std::setw(8)
<< *blocked_it << std::endl;
std::cout << std::flush;
}
// }
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver.py b/test/test_model/test_common/test_model_solver/test_model_solver.py
index 74799cdb1..9f6523f8d 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver.py
+++ b/test/test_model/test_common/test_model_solver/test_model_solver.py
@@ -1,38 +1,38 @@
#!/usr/bin/env python3
-# ------------------------------------------------------------------------------
+""" test_model_solver.py: Test the model solver in python"""
+
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
import numpy as np
import numpy.linalg as npl
import python_fe as pfe
sim_u = np.genfromtxt("disp.csv", delimiter=",", names=True)
Ne = int(sim_u['node'][-1])
F = sim_u['force']
blocked = sim_u['blocked']
u = sim_u['disp']
trusses = pfe.TrussFE(Ne=Ne,
F={f: [np.where(F == f)] for f in np.unique(F)},
blocked=(np.where(blocked == 1),
u[blocked == 1]))
solver = pfe.StaticSolver(trusses)
solver.solveStep()
upy = trusses.u
n = npl.norm(upy - u) / npl.norm(upy)
if n > 1e-14:
raise ValueError('Something went wrong in the simulation')
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
index 3a4247ffd..9b27bc55c 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.cc
@@ -1,245 +1,247 @@
/**
* @file test_model_solver_dynamic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Aug 14 2019
*
* @brief Test default dof manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_element_partition.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include "test_model_solver_my_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#ifndef EXPLICIT
#define EXPLICIT true
#endif
using namespace akantu;
class Sinusoidal : public BC::Dirichlet::DirichletFunctor {
public:
Sinusoidal(MyModel & model, Real amplitude, Real pulse_width, Real t)
: model(model), A(amplitude), k(2 * M_PI / pulse_width),
t(t), v{std::sqrt(model.E / model.rho)} {}
void operator()(UInt n, Vector<bool> & /*flags*/, Vector<Real> & disp,
const Vector<Real> & coord) const {
auto x = coord(_x);
model.velocity(n, _x) = k * v * A * sin(k * (x - v * t));
disp(_x) = A * cos(k * (x - v * t));
}
private:
MyModel & model;
Real A{1.};
Real k{2 * M_PI};
Real t{1.};
Real v{1.};
};
static void genMesh(Mesh & mesh, UInt nb_nodes);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt prank = Communicator::getStaticCommunicator().whoAmI();
UInt global_nb_nodes = 201;
UInt max_steps = 400;
Real time_step = 0.001;
Mesh mesh(1);
Real F = -9.81;
bool _explicit = EXPLICIT;
const Real pulse_width = 0.2;
const Real A = 0.01;
ID dof_manager_type = "default";
#if defined(DOF_MANAGER_TYPE)
dof_manager_type = DOF_MANAGER_TYPE;
#endif
if (prank == 0)
genMesh(mesh, global_nb_nodes);
mesh.distribute();
// mesh.makePeriodic(_x);
MyModel model(F, mesh, _explicit, dof_manager_type);
model.forces.zero();
model.blocked.zero();
model.applyBC(Sinusoidal(model, A, pulse_width, 0.), "all");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "border");
if (!_explicit) {
model.getNewSolver("dynamic", TimeStepSolverType::_dynamic,
NonLinearSolverType::_newton_raphson);
model.setIntegrationScheme("dynamic", "disp",
IntegrationSchemeType::_trapezoidal_rule_2,
IntegrationScheme::_displacement);
} else {
model.getNewSolver("dynamic", TimeStepSolverType::_dynamic_lumped,
NonLinearSolverType::_lumped);
model.setIntegrationScheme("dynamic", "disp",
IntegrationSchemeType::_central_difference,
IntegrationScheme::_acceleration);
}
model.setTimeStep(time_step);
if (prank == 0) {
std::cout << std::scientific;
std::cout << std::setw(14) << "time"
<< "," << std::setw(14) << "wext"
<< "," << std::setw(14) << "epot"
<< "," << std::setw(14) << "ekin"
<< "," << std::setw(14) << "total"
<< "," << std::setw(14) << "max_disp"
<< "," << std::setw(14) << "min_disp" << std::endl;
}
Real wext = 0.;
model.getDOFManager().zeroResidual();
model.assembleResidual();
Real epot = 0; // model.getPotentialEnergy();
Real ekin = 0; // model.getKineticEnergy();
Real einit = ekin + epot;
Real etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << 0. << "," << std::setw(14) << wext << ","
<< std::setw(14) << epot << "," << std::setw(14) << ekin << ","
<< std::setw(14) << etot << "," << std::setw(14) << max_disp
<< "," << std::setw(14) << min_disp << std::endl;
}
#if EXPLICIT == false
NonLinearSolver & solver =
model.getDOFManager().getNonLinearSolver("dynamic");
solver.set("max_iterations", 20);
#endif
auto && dumper = std::make_shared<DumperParaview>("dynamic", "./paraview");
mesh.registerExternalDumper(dumper, "dynamic", true);
mesh.addDumpMesh(mesh);
mesh.addDumpFieldExternalToDumper("dynamic", "displacement",
model.displacement);
mesh.addDumpFieldExternalToDumper("dynamic", "velocity", model.velocity);
mesh.addDumpFieldExternalToDumper("dynamic", "forces", model.forces);
mesh.addDumpFieldExternalToDumper("dynamic", "internal_forces",
model.internal_forces);
mesh.addDumpFieldExternalToDumper("dynamic", "acceleration",
model.acceleration);
mesh.dump();
for (UInt i = 1; i < max_steps + 1; ++i) {
model.applyBC(Sinusoidal(model, A, pulse_width, time_step * (i - 1)),
"border");
model.solveStep("dynamic");
mesh.dump();
epot = model.getPotentialEnergy();
ekin = model.getKineticEnergy();
wext += model.getExternalWorkIncrement();
etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << time_step * i << "," << std::setw(14)
<< wext << "," << std::setw(14) << epot << "," << std::setw(14)
<< ekin << "," << std::setw(14) << etot << "," << std::setw(14)
<< max_disp << "," << std::setw(14) << min_disp << std::endl;
}
}
// output.close();
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
auto & all = mesh.createNodeGroup("all_nodes");
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
all.add(n);
}
mesh.createElementGroupFromNodeGroup("all", "all_nodes");
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
Array<UInt> & conn_points = mesh_accessor.getConnectivity(_point_1);
conn_points.resize(2);
conn_points(0, 0) = 0;
conn_points(1, 0) = nb_nodes - 1;
auto & border = mesh.createElementGroup("border", 0);
border.add({_point_1, 0, _not_ghost}, true);
border.add({_point_1, 1, _not_ghost}, true);
mesh_accessor.makeReady();
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.py b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.py
index 16b064c5d..16fddb04a 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.py
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic.py
@@ -1,56 +1,56 @@
#!/usr/bin/env python3
+""" test_model_solver_dynamic.py: Test the model solver in python"""
-# ------------------------------------------------------------------------------
__author__ = "Nicolas Richart"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Nicolas Richart"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
+__license__ = "LGPLv3"
# ------------------------------------------------------------------------------
import numpy as np
import python_fe as pfe
import matplotlib.pyplot as plt
import matplotlib.animation as animation
# sim_u = np.genfromtxt("disp.csv", delimiter=",", names=True)
L = 1.
Ne = 200 # int(sim_u['node'][-1])
F = np.zeros(Ne + 1) # sim_u['force']
F[-1] = - 9.81
blocked = np.zeros(Ne + 1) # sim_u['blocked']
blocked[0] = 1
u = np.zeros(Ne + 1) # sim_u['disp']
trusses = pfe.TrussFE(Ne=Ne,
F={f: [np.where(F == f)] for f in np.unique(F)},
blocked=(np.where(blocked == 1),
u[blocked == 1]))
solver = pfe.DynamicSolver(trusses, delta_t=0.001)
# for s in range(200):
# solver.solveStep()
fig, ax = plt.subplots()
x = np.arange(Ne+1) * L / Ne # x-array
line, = ax.plot(x, trusses.u)
def animate(i):
solver.solveStep()
line.set_ydata(trusses.u) # update the data
plt.ylim(np.min(trusses.u), np.max(trusses.u))
return line,
ani = animation.FuncAnimation(fig, animate, np.arange(1, 200),
interval=25, blit=True)
plt.show()
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
index 725148a1b..d4b5b81e2 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_dynamic_petsc.cc
@@ -1,837 +1,839 @@
/**
- * @file test_model_solver_dynamic.cc
+ * @file test_model_solver_dynamic_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Apr 13 2016
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Sun Jan 06 2019
+ * @date last modification: Wed Mar 13 2019
*
* @brief Test default dof manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include "dumpable_inline_impl.hh"
#include "dumper_element_partition.hh"
#include "dumper_iohelper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
#include <petscsnes.h>
#include <petscvec.h>
/* -------------------------------------------------------------------------- */
#ifndef EXPLICIT
#define EXPLICIT true
#endif
template <typename func>
void CHECK_ERR_CXX(func && func_, PetscErrorCode ierr) {
if (PetscUnlikely(ierr != 0)) {
const char * desc;
PetscErrorMessage(ierr, &desc, nullptr);
AKANTU_EXCEPTION("Error in PETSc call to \'" << func_ << "\': " << desc);
}
}
using namespace akantu;
static void genMesh(Mesh & mesh, UInt nb_nodes);
class MyModel {
public:
MyModel(Real F, Mesh & mesh, bool lumped)
: nb_dofs(mesh.getNbNodes()), nb_elements(mesh.getNbElement(_segment_2)),
lumped(lumped), E(1.), A(1.), rho(1.), mesh(mesh),
displacement(nb_dofs, 1, "disp"), velocity(nb_dofs, 1, "velo"),
acceleration(nb_dofs, 1, "accel"), blocked(nb_dofs, 1, "blocked"),
forces(nb_dofs, 1, "force_ext"),
internal_forces(nb_dofs, 1, "force_int"),
stresses(nb_elements, 1, "stress"), strains(nb_elements, 1, "strain"),
initial_lengths(nb_elements, 1, "L0") {
auto n_global = mesh.getNbGlobalNodes();
int n_local = 0;
std::vector<PetscInt> nodes_global_ids(nb_dofs);
for (auto && data : enumerate(nodes_global_ids)) {
auto n = std::get<0>(data);
n_local += mesh.isLocalOrMasterNode(n);
std::get<1>(data) = mesh.getNodeGlobalId(n);
}
mpi_comm = dynamic_cast<MPICommunicatorData &>(
mesh.getCommunicator().getCommunicatorData())
.getMPICommunicator();
MeshAccessor mesh_accessor(mesh);
ierr = ISLocalToGlobalMappingCreate(
mpi_comm, 1, mesh.getNbNodes(), nodes_global_ids.data(),
PETSC_COPY_VALUES, &petsc_local_to_global);
CHECK_ERR_CXX("ISLocalToGlobalMappingCreate", ierr);
auto setName = [](auto && Obj, auto && name) {
PetscObjectSetName(reinterpret_cast<PetscObject>(Obj), name);
};
ierr = VecCreate(mpi_comm, &rhs);
ierr = VecSetSizes(rhs, n_local, n_global);
ierr = VecSetFromOptions(rhs);
ierr = VecSetLocalToGlobalMapping(rhs, petsc_local_to_global);
setName(rhs, "rhs");
ierr = VecDuplicate(rhs, &x);
ierr = VecDuplicate(rhs, &x_save);
ierr = VecDuplicate(rhs, &dx);
ierr = VecDuplicate(rhs, &f_int);
ierr = VecDuplicate(rhs, &f_dirichlet);
setName(x, "x");
setName(x_save, "x save");
setName(dx, "dx");
setName(f_int, "f_int");
setName(f_dirichlet, "f_dirichlet");
ierr = MatCreate(mpi_comm, &M);
ierr = MatSetSizes(M, n_local, n_local, n_global, n_global);
ierr = MatSetFromOptions(M);
ierr = MatSetOption(M, MAT_SYMMETRIC, PETSC_TRUE);
ierr = MatSetOption(M, MAT_ROW_ORIENTED, PETSC_TRUE);
ierr = MatSetUp(M);
ierr = MatSetLocalToGlobalMapping(M, petsc_local_to_global,
petsc_local_to_global);
setName(M, "M");
assembleMass();
ierr = MatDuplicate(M, MAT_DO_NOT_COPY_VALUES, &K);
setName(K, "K");
ierr = MatDuplicate(M, MAT_DO_NOT_COPY_VALUES, &J);
setName(J, "J");
ierr = SNESCreate(mpi_comm, &snes);
ierr = SNESSetFromOptions(snes);
ierr = SNESSetFunction(snes, rhs, MyModel::FormFunction, this);
ierr = SNESSetJacobian(snes, J, J, MyModel::FormJacobian, this);
PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_ASCII_INDEX);
displacement.set(0.);
velocity.set(0.);
acceleration.set(0.);
forces.set(0.);
blocked.set(false);
blocked(0, 0) = true;
blocked(nb_dofs - 1, 0) = true;
displacement(0, 0) = 0;
displacement(nb_dofs - 1, 0) = 1;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(this->initial_lengths))) {
const auto & conn = std::get<0>(data);
auto & L = std::get<1>(data);
auto p1 = this->mesh.getNodes()(conn(0), _x);
auto p2 = this->mesh.getNodes()(conn(1), _x);
L = std::abs(p2 - p1);
}
}
// static PetscErrorCode SNESMonitor(SNES snes,PetscInt its,PetscReal
// fnorm,void *ctx) {
// auto & _this = *reinterpret_cast<MyModel *>(ctx);
// //SNESMonitorDefault(snes, its, fnorm, PETSC_VIEWER_STDOUT_WORLD);
// }
static PetscErrorCode FormFunction(SNES /*snes*/, Vec /*dx*/, Vec /*f*/,
void * ctx) {
auto & _this = *reinterpret_cast<MyModel *>(ctx);
_this.assembleResidual();
return 0;
}
static PetscErrorCode FormJacobian(SNES /*snes*/, Vec /*dx*/, Mat /*J*/,
Mat /*P*/, void * ctx) {
auto & _this = *reinterpret_cast<MyModel *>(ctx);
_this.assembleJacobian();
return 0;
}
~MyModel() {
ierr = MatDestroy(&M);
ierr = MatDestroy(&K);
ierr = MatDestroy(&J);
ierr = VecDestroy(&rhs);
ierr = VecDestroy(&x);
ierr = VecDestroy(&dx);
ierr = VecDestroy(&x_save);
ierr = VecDestroy(&f_int);
PetscFinalize();
}
void solveStep() {
std::cout << "solveStep" << std::endl;
copy(x_save, displacement);
ierr = SNESSolve(snes, NULL, dx);
CHECK_ERR_CXX("SNESSolve", ierr);
setSolutionToDisplacement();
assembleResidual();
}
void applyBC() {
std::vector<PetscInt> rows;
for (auto && data : enumerate(blocked)) {
if (std::get<1>(data)) {
rows.push_back(std::get<0>(data));
}
}
copy(x, displacement);
ierr = MatZeroRowsColumnsLocal(J, rows.size(), rows.data(), 1., x,
f_dirichlet);
VecView(f_dirichlet, PETSC_VIEWER_STDOUT_WORLD);
CHECK_ERR_CXX("MatZeroRowsColumnsLocal", ierr);
}
void setSolutionToDisplacement() {
std::cout << "setSolutionToDisplacement" << std::endl;
ierr = VecWAXPY(x, 1, x_save, dx);
copy(displacement, x);
}
void assembleJacobian() {
std::cout << "assembleJacobian" << std::endl;
setSolutionToDisplacement();
assembleStiffness();
ierr = MatZeroEntries(J);
CHECK_ERR_CXX("MatZeroEntries", ierr);
ierr = MatAXPY(J, 1., K, SAME_NONZERO_PATTERN);
CHECK_ERR_CXX("MatAXPY", ierr);
MatView(J, PETSC_VIEWER_STDOUT_WORLD);
applyBC();
MatView(J, PETSC_VIEWER_STDOUT_WORLD);
}
void assembleMass() {
std::cout << "assembleMass" << std::endl;
ierr = MatZeroEntries(M);
CHECK_ERR_CXX("MatZeroEntries", ierr);
Array<Real> m_all_el(this->nb_elements, 4);
Matrix<Real> m(2, 2);
m(0, 0) = m(1, 1) = 2;
m(0, 1) = m(1, 0) = 1;
// under integrated
// m(0, 0) = m(1, 1) = 3./2.;
// m(0, 1) = m(1, 0) = 3./2.;
// lumping the mass matrix
// m(0, 0) += m(0, 1);
// m(1, 1) += m(1, 0);
// m(0, 1) = m(1, 0) = 0;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
m_el = m;
m_el *= rho * A * L / 6.;
Vector<Int> conn_int(conn.size());
for (auto && data : zip(conn_int, conn)) {
std::get<0>(data) = std::get<1>(data);
}
ierr = MatSetValuesLocal(M, conn_int.size(), conn_int.storage(),
conn_int.size(), conn_int.storage(), m.storage(),
ADD_VALUES);
}
ierr = MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY);
ierr = MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY);
ierr = MatSetOption(M, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(mpi_comm, "M.mtx", &viewer);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
ierr = MatView(M, viewer);
PetscViewerPopFormat(viewer);
ierr = PetscViewerDestroy(&viewer);
// this->getDOFManager().assembleElementalMatricesToMatrix(
// "M", "disp", m_all_el, _segment_2);
is_mass_assembled = true;
}
// MatrixType getMatrixType(const ID &) { return _symmetric; }
// void assembleMatrix(const ID & matrix_id) {
// if (matrix_id == "K") {
// if (not is_stiffness_assembled)
// this->assembleStiffness();
// } else if (matrix_id == "M") {
// if (not is_mass_assembled)
// this->assembleMass();
// } else if (matrix_id == "C") {
// // pass, no damping matrix
// } else {
// AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
// << matrix_id);
// }
// }
void assembleLumpedMatrix(const ID & matrix_id) {
std::cout << "assembleLumpedMatrix" << std::endl;
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
void assembleStiffness() {
std::cout << "assembleStiffness" << std::endl;
// SparseMatrix & K = this->getDOFManager().getMatrix("K");
// K.zero();
ierr = MatZeroEntries(K);
CHECK_ERR_CXX("MatZeroEntries", ierr);
Matrix<Real> k(2, 2);
k(0, 0) = k(1, 1) = 1;
k(0, 1) = k(1, 0) = -1;
Array<Real> k_all_el(this->nb_elements, 4);
auto k_it = k_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
for (; cit != cend; ++cit, ++k_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
auto & k_el = *k_it;
k_el = k;
k_el *= E * A / L;
Vector<Int> conn_int(conn.size());
for (auto && data : zip(conn_int, conn)) {
std::get<0>(data) = std::get<1>(data);
}
ierr = MatSetValuesLocal(K, conn_int.size(), conn_int.storage(),
conn_int.size(), conn_int.storage(),
k_el.storage(), ADD_VALUES);
}
ierr = MatAssemblyBegin(K, MAT_FINAL_ASSEMBLY);
CHECK_ERR_CXX("MatAssemblyBegin", ierr);
ierr = MatAssemblyEnd(K, MAT_FINAL_ASSEMBLY);
CHECK_ERR_CXX("MatAssemblyEnd", ierr);
ierr = MatSetOption(K, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);
CHECK_ERR_CXX("MatSetOption", ierr);
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(mpi_comm, "K.mtx", &viewer);
CHECK_ERR_CXX("PetscViewerASCIIOpen", ierr);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATRIXMARKET);
ierr = MatView(K, viewer);
CHECK_ERR_CXX("MatView", ierr);
PetscViewerPopFormat(viewer);
ierr = PetscViewerDestroy(&viewer);
CHECK_ERR_CXX("PetscViewerDestroy", ierr);
// this->getDOFManager().assembleElementalMatricesToMatrix(
// "K", "disp", k_all_el, _segment_2);
is_stiffness_assembled = true;
}
void copy(Array<Real> & y, Vec x) {
std::cout << "copy <-" << std::endl;
const PetscScalar * x_local;
ierr = VecGetArrayRead(x, &x_local);
for (auto && data : zip(y, range(x_local + 0, x_local + y.size()))) {
std::get<0>(data) = std::get<1>(data);
}
ierr = VecRestoreArrayRead(x, &x_local);
// VecView(x, PETSC_VIEWER_STDOUT_WORLD);
// std::cout << y.getID() << " " << Vector<Real>(y.storage(), y.size())
// << std::endl;
}
void print(const Array<Real> & x) const {
std::cout << x.getID() << " " << Vector<Real>(x.storage(), x.size())
<< std::endl;
}
void copy(Vec x, const Array<Real> & y) {
std::cout << "copy ->" << std::endl;
PetscScalar * x_local;
ierr = VecGetArray(x, &x_local);
for (auto && data : zip(y, range(x_local + 0, x_local + y.size()))) {
std::get<1>(data) = std::get<0>(data);
}
ierr = VecRestoreArray(x, &x_local);
// std::cout << y.getID() << " " << Vector<Real>(y.storage(), y.size())
// << std::endl;
// VecView(x, PETSC_VIEWER_STDOUT_WORLD);
}
void assembleResidual() {
std::cout << "assembleResidual" << std::endl;
// this->getDOFManager().assembleToResidual("disp", forces);
setSolutionToDisplacement();
copy(rhs, forces);
// VecAXPY(rhs, -1., f_dirichlet);
print(displacement);
this->assembleResidual(_not_ghost);
// this->synchronize(SynchronizationTag::_user_1);
// this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
VecAXPY(rhs, 1., f_int);
for (auto && data : enumerate(blocked)) {
if (std::get<1>(data)) {
VecSetValueLocal(rhs, std::get<0>(data), 0., INSERT_VALUES);
}
}
VecAssemblyBegin(rhs);
VecAssemblyEnd(rhs);
VecView(rhs, PETSC_VIEWER_STDOUT_WORLD);
}
void assembleResidual(GhostType ghost_type) {
std::cout << "assembleResidual" << std::endl;
VecZeroEntries(f_int);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++strain_it, ++stress_it, ++L_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real u1 = this->displacement(n1, _x);
Real u2 = this->displacement(n2, _x);
*strain_it = (u2 - u1) / *L_it;
*stress_it = E * *strain_it;
Real f_n = A * *stress_it;
std::cout << n1 << "[" << u1 << "]"
<< " <-> " << n2 << "[" << u2 << "]"
<< " : " << f_n << std::endl;
ierr = VecSetValueLocal(f_int, n1, -f_n, ADD_VALUES);
ierr = VecSetValueLocal(f_int, n2, f_n, ADD_VALUES);
}
ierr = VecAssemblyBegin(f_int);
ierr = VecAssemblyEnd(f_int);
// this->getDOFManager().assembleElementalArrayLocalArray(
// forces_internal_el, internal_forces, _segment_2, ghost_type);
}
Real getPotentialEnergy() {
std::cout << "getPotentialEnergy" << std::endl;
copy(x, displacement);
Vec Ax;
ierr = VecDuplicate(x, &Ax);
ierr = MatMult(K, x, Ax);
PetscScalar res;
ierr = VecDot(x, Ax, &res);
return res / 2.;
}
Real getKineticEnergy() {
std::cout << "getKineticEnergy" << std::endl;
return 0;
}
// Real getExternalWorkIncrement() {
// Real res = 0;
// auto it = velocity.begin();
// auto end = velocity.end();
// auto if_it = internal_forces.begin();
// auto ef_it = forces.begin();
// auto b_it = blocked.begin();
// for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
// if (mesh.isLocalOrMasterNode(node))
// res += (*b_it ? -*if_it : *ef_it) * *it;
// }
// mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
// return res * this->getTimeStep();
// }
// void predictor() {}
// void corrector() {}
// /* ------------------------------------------------------------------------
// */ UInt getNbData(const Array<Element> & elements,
// const SynchronizationTag &) const {
// return elements.size() * sizeof(Real);
// }
// void packData(CommunicationBuffer & buffer, const Array<Element> &
// elements,
// const SynchronizationTag & tag) const {
// if (tag == SynchronizationTag::_user_1) {
// for (const auto & el : elements) {
// buffer << this->stresses(el.element);
// }
// }
// }
// void unpackData(CommunicationBuffer & buffer, const Array<Element> &
// elements,
// const SynchronizationTag & tag) {
// if (tag == SynchronizationTag::_user_1) {
// auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);
// for (const auto & el : elements) {
// Real stress;
// buffer >> stress;
// Real f = A * stress;
// Vector<UInt> conn = cit[el.element];
// this->internal_forces(conn(0), _x) += -f;
// this->internal_forces(conn(1), _x) += f;
// }
// }
// }
Real getExternalWorkIncrement() {
std::cout << "getExternalWorkIncrement" << std::endl;
return 0.;
}
template <class Functor> void applyBC(Functor && func, const ID & group_id) {
auto & group = mesh.getElementGroup(group_id).getNodeGroup().getNodes();
auto blocked_dofs = make_view(blocked, 1).begin();
auto disps = make_view(displacement, 1).begin();
auto poss = make_view(mesh.getNodes(), 1).begin();
for (auto && node : group) {
auto disp = Vector<Real>(disps[node]);
auto pos = Vector<Real>(poss[node]);
auto flags = Vector<bool>(blocked_dofs[node]);
func(node, flags, disp, pos);
}
}
const Mesh & getMesh() const { return mesh; }
UInt getSpatialDimension() const { return 1; }
auto & getBlockedDOFs() { return blocked; }
void setTimeStep(Real dt) {
std::cout << "setTimeStep" << std::endl;
this->dt = dt;
}
private:
PetscErrorCode ierr{0};
MPI_Comm mpi_comm;
ISLocalToGlobalMapping petsc_local_to_global;
UInt nb_dofs;
UInt nb_elements;
bool lumped;
bool is_stiffness_assembled{false};
bool is_mass_assembled{false};
bool is_lumped_mass_assembled{false};
Mat K{nullptr}, J{nullptr}, M{nullptr};
Vec rhs{nullptr}, x{nullptr}, x_save{nullptr}, dx{nullptr}, f_int{nullptr},
f_dirichlet{nullptr};
SNES snes;
Real dt{0};
Array<Real> save_displacement;
public:
Real E, A, rho;
Mesh & mesh;
Array<Real> displacement;
Array<Real> velocity;
Array<Real> acceleration;
Array<bool> blocked;
Array<Real> forces;
Array<Real> internal_forces;
Array<Real> stresses;
Array<Real> strains;
Array<Real> initial_lengths;
};
/* -------------------------------------------------------------------------- */
class Sinusoidal : public BC::Dirichlet::DirichletFunctor {
public:
Sinusoidal(MyModel & model, Real amplitude, Real pulse_width, Real t)
: model(model), A(amplitude), k(2 * M_PI / pulse_width),
t(t), v{std::sqrt(model.E / model.rho)} {}
void operator()(UInt n, Vector<bool> & /*flags*/, Vector<Real> & disp,
const Vector<Real> & coord) const {
auto x = coord(_x);
model.velocity(n, _x) = k * v * A * sin(k * (x - v * t));
disp(_x) = A * cos(k * (x - v * t));
}
private:
MyModel & model;
Real A{1.};
Real k{2 * M_PI};
Real t{1.};
Real v{1.};
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
PetscInitialize(&argc, &argv, nullptr, nullptr);
UInt prank = Communicator::getStaticCommunicator().whoAmI();
UInt global_nb_nodes = 3;
UInt max_steps = 400;
Real time_step = 0.001;
Mesh mesh(1);
Real F = -9.81;
bool _explicit = EXPLICIT;
// const Real pulse_width = 0.2;
const Real A = 0.01;
if (prank == 0)
genMesh(mesh, global_nb_nodes);
mesh.distribute();
// mesh.makePeriodic(_x);
MyModel model(F, mesh, _explicit);
// model.forces.zero();
// model.blocked.zero();
// model.applyBC(Sinusoidal(model, A, pulse_width, 0.), "all");
// model.applyBC(BC::Dirichlet::FlagOnly(_x), "border");
// if (!_explicit) {
// model.getNewSolver("dynamic", TimeStepSolverType::_dynamic,
// NonLinearSolverType::_newton_raphson);
// model.setIntegrationScheme("dynamic", "disp",
// IntegrationSchemeType::_trapezoidal_rule_2,
// IntegrationScheme::_displacement);
// } else {
// model.getNewSolver("dynamic", TimeStepSolverType::_dynamic_lumped,
// NonLinearSolverType::_lumped);
// model.setIntegrationScheme("dynamic", "disp",
// IntegrationSchemeType::_central_difference,
// IntegrationScheme::_acceleration);
// }
model.setTimeStep(time_step);
if (prank == 0) {
std::cout << std::scientific;
std::cout << std::setw(14) << "time"
<< "," << std::setw(14) << "wext"
<< "," << std::setw(14) << "epot"
<< "," << std::setw(14) << "ekin"
<< "," << std::setw(14) << "total"
<< "," << std::setw(14) << "max_disp"
<< "," << std::setw(14) << "min_disp" << std::endl;
}
Real wext = 0.;
// model.getDOFManager().clearResidual();
// model.assembleResidual();
Real epot = 0; // model.getPotentialEnergy();
Real ekin = 0; // model.getKineticEnergy();
Real einit = ekin + epot;
Real etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << 0. << "," << std::setw(14) << wext << ","
<< std::setw(14) << epot << "," << std::setw(14) << ekin << ","
<< std::setw(14) << etot << "," << std::setw(14) << max_disp
<< "," << std::setw(14) << min_disp << std::endl;
}
// #if EXPLICIT == false
// NonLinearSolver & solver =
// model.getDOFManager().getNonLinearSolver("dynamic");
// solver.set("max_iterations", 20);
// #endif
auto * dumper = new DumperParaview("dynamic", "./paraview");
mesh.registerExternalDumper(*dumper, "dynamic", true);
mesh.addDumpMesh(mesh);
mesh.addDumpFieldExternalToDumper("dynamic", "displacement",
model.displacement);
mesh.addDumpFieldExternalToDumper("dynamic", "velocity", model.velocity);
mesh.addDumpFieldExternalToDumper("dynamic", "forces", model.forces);
mesh.addDumpFieldExternalToDumper("dynamic", "acceleration",
model.acceleration);
mesh.dump();
max_steps = 1;
for (UInt i = 1; i < max_steps + 1; ++i) {
// model.applyBC(Sinusoidal(model, A, pulse_width, time_step * (i - 1)),
// "border");
model.solveStep();
mesh.dump();
epot = model.getPotentialEnergy();
ekin = model.getKineticEnergy();
wext += model.getExternalWorkIncrement();
etot = ekin + epot - wext - einit;
Real max_disp = 0., min_disp = 0.;
for (auto && disp : model.displacement) {
max_disp = std::max(max_disp, disp);
min_disp = std::min(min_disp, disp);
}
if (prank == 0) {
std::cout << std::setw(14) << time_step * i << "," << std::setw(14)
<< wext << "," << std::setw(14) << epot << "," << std::setw(14)
<< ekin << "," << std::setw(14) << etot << "," << std::setw(14)
<< max_disp << "," << std::setw(14) << min_disp << std::endl;
}
}
// output.close();
// finalize();
// PetscFinalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
// auto & all = mesh.createNodeGroup("all_nodes");
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
// all.add(n);
}
// mesh.createElementGroupFromNodeGroup("all", "all_nodes");
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
// Array<UInt> & conn_points = mesh_accessor.getConnectivity(_point_1);
// conn_points.resize(2);
// conn_points(0, 0) = 0;
// conn_points(1, 0) = nb_nodes - 1;
// auto & border = mesh.createElementGroup("border", 0);
// border.add({_point_1, 0, _not_ghost}, true);
// border.add({_point_1, 1, _not_ghost}, true);
mesh_accessor.makeReady();
}
diff --git a/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh b/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
index 2b885cffc..03f3e4980 100644
--- a/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
+++ b/test/test_model/test_common/test_model_solver/test_model_solver_my_model.hh
@@ -1,451 +1,453 @@
/**
* @file test_model_solver_my_model.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 13 2016
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jun 26 2020
*
* @brief Test default dof manager
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "boundary_condition.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "model_solver.hh"
#include "periodic_node_synchronizer.hh"
#include "solver_vector_default.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
#ifndef AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_
#define AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_
/**
* =\o-----o-----o-> F
* | |
* |---- L ----|
*/
class MyModel : public ModelSolver,
public BoundaryCondition<MyModel>,
public DataAccessor<Element> {
public:
MyModel(Real F, Mesh & mesh, bool lumped,
const ID & dof_manager_type = "default")
: ModelSolver(mesh, ModelType::_model, "model_solver"),
nb_dofs(mesh.getNbNodes()), nb_elements(mesh.getNbElement(_segment_2)),
lumped(lumped), E(1.), A(1.), rho(1.), mesh(mesh),
displacement(nb_dofs, 1, "disp"), velocity(nb_dofs, 1, "velo"),
acceleration(nb_dofs, 1, "accel"), blocked(nb_dofs, 1, "blocked"),
forces(nb_dofs, 1, "force_ext"),
internal_forces(nb_dofs, 1, "force_int"),
stresses(nb_elements, 1, "stress"), strains(nb_elements, 1, "strain"),
initial_lengths(nb_elements, 1, "L0") {
this->initDOFManager(dof_manager_type);
this->initBC(*this, displacement, forces);
this->getDOFManager().registerDOFs("disp", displacement, _dst_nodal);
this->getDOFManager().registerDOFsDerivative("disp", 1, velocity);
this->getDOFManager().registerDOFsDerivative("disp", 2, acceleration);
this->getDOFManager().registerBlockedDOFs("disp", blocked);
displacement.set(0.);
velocity.set(0.);
acceleration.set(0.);
forces.set(0.);
blocked.set(false);
UInt global_nb_nodes = mesh.getNbGlobalNodes();
for (auto && n : arange(nb_dofs)) {
auto global_id = mesh.getNodeGlobalId(n);
if (global_id == (global_nb_nodes - 1))
forces(n, _x) = F;
if (global_id == 0)
blocked(n, _x) = true;
}
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++L_it) {
const Vector<UInt> & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
*L_it = std::abs(p2 - p1);
}
this->registerDataAccessor(*this);
this->registerSynchronizer(
const_cast<ElementSynchronizer &>(this->mesh.getElementSynchronizer()),
SynchronizationTag::_user_1);
}
void assembleLumpedMass() {
auto & M = this->getDOFManager().getLumpedMatrix("M");
M.zero();
this->assembleLumpedMass(_not_ghost);
if (this->mesh.getNbElement(_segment_2, _ghost) > 0)
this->assembleLumpedMass(_ghost);
is_lumped_mass_assembled = true;
}
void assembleLumpedMass(GhostType ghost_type) {
Array<Real> M(nb_dofs, 1, 0.);
Array<Real> m_all_el(this->mesh.getNbElement(_segment_2, ghost_type), 2);
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
Real M_n = rho * A * L / 2;
m_el(0) = m_el(1) = M_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
m_all_el, M, _segment_2, ghost_type);
this->getDOFManager().assembleToLumpedMatrix("disp", M, "M");
}
void assembleMass() {
SparseMatrix & M = this->getDOFManager().getMatrix("M");
M.zero();
Array<Real> m_all_el(this->nb_elements, 4);
Matrix<Real> m(2, 2);
m(0, 0) = m(1, 1) = 2;
m(0, 1) = m(1, 0) = 1;
// under integrated
// m(0, 0) = m(1, 1) = 3./2.;
// m(0, 1) = m(1, 0) = 3./2.;
// lumping the mass matrix
// m(0, 0) += m(0, 1);
// m(1, 1) += m(1, 0);
// m(0, 1) = m(1, 0) = 0;
for (auto && data :
zip(make_view(this->mesh.getConnectivity(_segment_2), 2),
make_view(m_all_el, 2, 2))) {
const auto & conn = std::get<0>(data);
auto & m_el = std::get<1>(data);
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
m_el = m;
m_el *= rho * A * L / 6.;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"M", "disp", m_all_el, _segment_2);
is_mass_assembled = true;
}
MatrixType getMatrixType(const ID &) override { return _symmetric; }
void assembleMatrix(const ID & matrix_id) override {
if (matrix_id == "K") {
if (not is_stiffness_assembled)
this->assembleStiffness();
} else if (matrix_id == "M") {
if (not is_mass_assembled)
this->assembleMass();
} else if (matrix_id == "C") {
// pass, no damping matrix
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleLumpedMatrix(const ID & matrix_id) override {
if (matrix_id == "M") {
if (not is_lumped_mass_assembled)
this->assembleLumpedMass();
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleStiffness() {
SparseMatrix & K = this->getDOFManager().getMatrix("K");
K.zero();
Matrix<Real> k(2, 2);
k(0, 0) = k(1, 1) = 1;
k(0, 1) = k(1, 0) = -1;
Array<Real> k_all_el(this->nb_elements, 4);
auto k_it = k_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
for (; cit != cend; ++cit, ++k_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
auto & k_el = *k_it;
k_el = k;
k_el *= E * A / L;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "disp", k_all_el, _segment_2);
is_stiffness_assembled = true;
}
void assembleResidual() override {
this->getDOFManager().assembleToResidual("disp", forces);
internal_forces.zero();
this->assembleResidualInternal(_not_ghost);
this->synchronize(SynchronizationTag::_user_1);
this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
}
void assembleResidualInternal(GhostType ghost_type) {
Array<Real> forces_internal_el(
this->mesh.getNbElement(_segment_2, ghost_type), 2);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
auto f_it = forces_internal_el.begin(2);
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++f_it, ++strain_it, ++stress_it, ++L_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real u1 = this->displacement(n1, _x);
Real u2 = this->displacement(n2, _x);
*strain_it = (u2 - u1) / *L_it;
*stress_it = E * *strain_it;
Real f_n = A * *stress_it;
Vector<Real> & f = *f_it;
f(0) = -f_n;
f(1) = f_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
forces_internal_el, internal_forces, _segment_2, ghost_type);
}
Real getPotentialEnergy() {
Real res = 0;
if (not lumped) {
res = this->mulVectMatVect(this->displacement, "K", this->displacement);
} else {
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto strain_end = this->strains.end();
auto L_it = this->initial_lengths.begin();
for (; strain_it != strain_end; ++strain_it, ++stress_it, ++L_it) {
res += *strain_it * *stress_it * A * *L_it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getKineticEnergy() {
Real res = 0;
if (not lumped) {
res = this->mulVectMatVect(this->velocity, "M", this->velocity);
} else {
Array<Real> & m = dynamic_cast<SolverVectorDefault &>(
this->getDOFManager().getLumpedMatrix("M"));
auto it = velocity.begin();
auto end = velocity.end();
auto m_it = m.begin();
for (UInt node = 0; it != end; ++it, ++m_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += *m_it * *it * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getExternalWorkIncrement() {
Real res = 0;
auto it = velocity.begin();
auto end = velocity.end();
auto if_it = internal_forces.begin();
auto ef_it = forces.begin();
auto b_it = blocked.begin();
for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += (*b_it ? -*if_it : *ef_it) * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res * this->getTimeStep();
}
Real mulVectMatVect(const Array<Real> & x, const ID & A_id,
const Array<Real> & y) {
Array<Real> Ay(nb_dofs);
this->getDOFManager().assembleMatMulVectToArray("disp", A_id, y, Ay);
Real res = 0.;
for (auto && data : zip(arange(nb_dofs), make_view(Ay), make_view(x))) {
res += std::get<2>(data) * std::get<1>(data) *
mesh.isLocalOrMasterNode(std::get<0>(data));
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res;
}
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag &) const override {
return elements.size() * sizeof(Real);
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override {
if (tag == SynchronizationTag::_user_1) {
for (const auto & el : elements) {
buffer << this->stresses(el.element);
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override {
if (tag == SynchronizationTag::_user_1) {
auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);
for (const auto & el : elements) {
Real stress;
buffer >> stress;
Real f = A * stress;
Vector<UInt> conn = cit[el.element];
this->internal_forces(conn(0), _x) += -f;
this->internal_forces(conn(1), _x) += f;
}
}
}
const Mesh & getMesh() const { return mesh; }
UInt getSpatialDimension() const { return 1; }
auto & getBlockedDOFs() { return blocked; }
private:
UInt nb_dofs;
UInt nb_elements;
bool lumped;
bool is_stiffness_assembled{false};
bool is_mass_assembled{false};
bool is_lumped_mass_assembled{false};
public:
Real E, A, rho;
Mesh & mesh;
Array<Real> displacement;
Array<Real> velocity;
Array<Real> acceleration;
Array<bool> blocked;
Array<Real> forces;
Array<Real> internal_forces;
Array<Real> stresses;
Array<Real> strains;
Array<Real> initial_lengths;
};
#endif /* AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH_ */
} // namespace akantu
diff --git a/test/test_model/test_common/test_non_local_toolbox/CMakeLists.txt b/test/test_model/test_common/test_non_local_toolbox/CMakeLists.txt
index 184e1d7ef..fbf03a83f 100644
--- a/test/test_model/test_common/test_non_local_toolbox/CMakeLists.txt
+++ b/test/test_model/test_common/test_non_local_toolbox/CMakeLists.txt
@@ -1,84 +1,86 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Feb 02 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Nov 27 2019
#
# @brief configuration for heat transfer model tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
package_is_activated(damage_non_local _act)
if(_act)
add_library(test_material STATIC
test_material.hh test_material.cc)
add_library(test_material_damage STATIC
test_material_damage.hh test_material_damage.cc)
target_link_libraries(test_material akantu)
target_link_libraries(test_material_damage akantu)
endif()
register_test(test_non_local_neighborhood_base
SOURCES test_non_local_neighborhood_base.cc
FILES_TO_COPY material.dat plot_neighborhoods.py plate.msh
PACKAGE damage_non_local
)
register_test(test_weight_computation
SOURCES test_weight_computation.cc
FILES_TO_COPY material_weight_computation.dat plate.msh
PACKAGE damage_non_local
)
register_test(test_non_local_averaging
SOURCES test_non_local_averaging.cc test_material.hh test_material.cc
FILES_TO_COPY material_avg.dat plate.msh
PACKAGE damage_non_local
)
register_test(test_remove_damage_weight_function
SOURCES test_remove_damage_weight_function.cc test_material_damage.hh test_material_damage.cc
FILES_TO_COPY material_remove_damage.dat plate.msh
PACKAGE damage_non_local
)
register_test(test_build_neighborhood_parallel
SOURCES test_build_neighborhood_parallel.cc test_material.hh test_material.cc
FILES_TO_COPY material_parallel_test.dat parallel_test.msh
PARALLEL
PARALLEL_LEVEL 2
PACKAGE damage_non_local
)
register_test(test_pair_computation
SOURCES test_pair_computation.cc test_material_damage.hh test_material_damage.cc
FILES_TO_COPY material_remove_damage.dat pair_test.msh
PARALLEL
PARALLEL_LEVEL 1 2
PACKAGE damage_non_local
)
diff --git a/test/test_model/test_common/test_non_local_toolbox/my_model.hh b/test/test_model/test_common/test_non_local_toolbox/my_model.hh
index 4b4e9fd80..3e78a2df5 100644
--- a/test/test_model/test_common/test_non_local_toolbox/my_model.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/my_model.hh
@@ -1,123 +1,125 @@
/**
* @file my_model.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 11 2017
- * @date last modification: Sat Feb 03 2018
+ * @date last modification: Fri Jun 26 2020
*
- * @brief A Documented file.
+ * @brief A dummy model for tests purposes
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "non_local_manager_callback.hh"
#include "non_local_neighborhood_base.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class MyModel : public Model, public NonLocalManagerCallback {
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
public:
MyModel(Mesh & mesh, UInt spatial_dimension)
: Model(mesh, ModelType::_model, spatial_dimension),
manager(*this, *this) {
registerFEEngineObject<MyFEEngineType>("FEEngine", mesh, spatial_dimension);
manager.registerNeighborhood("test_region", "test_region");
getFEEngine().initShapeFunctions();
manager.initialize();
}
void initModel() override {}
MatrixType getMatrixType(const ID &) override { return _mt_not_defined; }
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & /*method*/) override {
return std::make_tuple("test", TimeStepSolverType::_static);
}
void assembleMatrix(const ID &) override {}
void assembleLumpedMatrix(const ID &) override {}
void assembleResidual() override {}
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override {}
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override {}
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
void insertIntegrationPointsInNeighborhoods(
GhostType ghost_type) override {
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
IntegrationPoint q;
q.ghost_type = ghost_type;
q.global_num = 0;
auto & neighborhood = manager.getNeighborhood("test_region");
for (auto & type : quadrature_points_coordinates.elementTypes(
spatial_dimension, ghost_type)) {
q.type = type;
auto & quads = quadrature_points_coordinates(type, ghost_type);
this->getFEEngine().computeIntegrationPointsCoordinates(quads, type,
ghost_type);
auto quad_it = quads.begin(quads.getNbComponent());
auto quad_end = quads.end(quads.getNbComponent());
q.num_point = 0;
for (; quad_it != quad_end; ++quad_it) {
neighborhood.insertIntegrationPoint(q, *quad_it);
++q.num_point;
++q.global_num;
}
}
}
void computeNonLocalStresses(GhostType) override {}
void updateLocalInternal(ElementTypeMapReal &, GhostType,
ElementKind) override {}
void updateNonLocalInternal(ElementTypeMapReal &, GhostType,
ElementKind) override {}
const auto & getNonLocalManager() const { return manager; }
private:
NonLocalManager manager;
};
diff --git a/test/test_model/test_common/test_non_local_toolbox/plot_neighborhoods.py b/test/test_model/test_common/test_non_local_toolbox/plot_neighborhoods.py
index ddc71bd64..09d59617a 100644
--- a/test/test_model/test_common/test_non_local_toolbox/plot_neighborhoods.py
+++ b/test/test_model/test_common/test_non_local_toolbox/plot_neighborhoods.py
@@ -1,109 +1,109 @@
#!/usr/bin/env python
-# ------------------------------------------------------------------------------
+""" plot_neighborhoods.py: plot the neighborhoods in non local manager"""
+
__author__ = "Aurelia Isabel Cuba Ramos"
-__copyright__ = "Copyright (C) 2016-2018, EPFL (Ecole Polytechnique Fédérale" \
+__credits__ = [
+ "Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale" \
" de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
" en Mécanique des Solides)"
-__credits__ = ["Aurelia Isabel Cuba Ramos"]
-__license__ = "L-GPLv3"
-__maintainer__ = "Nicolas Richart"
-__email__ = "nicolas.richart@epfl.ch"
-# ------------------------------------------------------------------------------
+__license__ = "LGPLv3"
+import sys
from matplotlib import rc
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
-import sys
from matplotlib.backends.backend_pdf import PdfPages
# ------------------------------------------------------------------------------
def readFile(filename):
quad_x_coords = list()
quad_y_coords = list()
with open(filename) as fh:
for line in fh:
if line.strip().startswith("#"):
line = fh.next()
x, y = [float(s) for s in line[1:-3].split(", ")]
quad_x_coords.append(float(x))
quad_y_coords.append(float(y))
return quad_x_coords, quad_y_coords
# ------------------------------------------------------------------------------
def readNeighborhoods(filename):
neighborhoods = dict()
with open(filename) as fh:
first_line = fh.readline()
key = int(first_line[0:-1].split(" ")[-1])
current_list = list()
for line in fh:
if line.strip().startswith("#"):
neighborhoods[key] = current_list
key = int(line[0:-1].split(" ")[-1])
current_list = list()
else:
coord = [float(s) for s in line[1:-3].split(", ")]
current_list.append(coord)
neighborhoods[key] = current_list
return neighborhoods
# ------------------------------------------------------------------------------
def plotNeighborhood(quad_x_coords, quad_y_coords, neighborhood, r):
ax = plt.subplot(111)
plt.axis([-1, 1, -1, 1])
# plot all quads
ax.plot(quad_x_coords, quad_y_coords, label='free',
linestyle='None', marker="+", markeredgewidth=0.2, markersize=4)
# plot center of neighborhood and circle
x = neighborhood[0][0]
y = neighborhood[0][1]
ax.plot(x, y, label='free', marker="+", markeredgewidth=0.2,
markersize=4, color='r')
circ = plt.Circle((x, y), radius=r, color='g', fill=False)
ax.add_patch(circ)
formatter = ticker.ScalarFormatter()
formatter.set_powerlimits((-2, 2))
ax.xaxis.set_major_formatter(formatter)
# plot all the neighbors
for i in range(1, len(neighborhood)):
ax.plot(neighborhood[i][0], neighborhood[i][1], label='free',
linestyle='None', marker="x", markeredgewidth=0.2,
markersize=4, color='y')
ax.grid(b=True, which='major', color='0.75',
linestyle='-', linewidth=0.5)
ax.grid(b=True, which='minor', color='0.75',
linestyle='-', linewidth=0.5)
# ------------------------------------------------------------------------------
def main():
non_local_radius = 0.5
rc('text', usetex=True)
rc('font', family='serif', size=8, serif='Times')
neighborhood_file = sys.argv[1]
quad_x_coords, quad_y_coords = readFile(neighborhood_file)
nb_quads = len(quad_x_coords)
neighborhoods = readNeighborhoods(neighborhood_file)
with PdfPages('resulting_neighborhoods.pdf') as pdf:
for i in range(nb_quads):
plt.figure(1, figsize=(7/2.54, 7/2.54))
plotNeighborhood(quad_x_coords, quad_y_coords,
neighborhoods[i], non_local_radius)
pdf.savefig()
plt.close()
if __name__ == "__main__":
main()
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc b/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
index e401abce2..b975f7bf7 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_build_neighborhood_parallel.cc
@@ -1,188 +1,190 @@
/**
* @file test_build_neighborhood_parallel.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Jan 30 2019
*
* @brief test in parallel for the class NonLocalNeighborhood
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper_paraview.hh"
#include "non_local_neighborhood_base.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_parallel_test.dat", argc, argv);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// some configuration variables
const UInt spatial_dimension = 2;
// mesh creation and read
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("parallel_test.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// dump the ghost elements before the non-local part is intialized
DumperParaview dumper_ghost("ghost_elements");
dumper_ghost.registerMesh(mesh, spatial_dimension, _ghost);
if (psize > 1) {
dumper_ghost.dump();
}
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// dump material index in paraview
model.addDumpField("partitions");
model.dump();
/// model initialization changed to use our material
model.initFull();
/// dump the ghost elements after ghosts for non-local have been added
if (psize > 1)
dumper_ghost.dump();
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("material_index");
/// apply constant strain field everywhere in the plate
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
ElementType element_type = _triangle_3;
GhostType ghost_type = _not_ghost;
/// apply constant grad_u field in all elements
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
auto & mat = model.getMaterial(m);
auto & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(element_type, ghost_type));
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
for (; grad_u_it != grad_u_end; ++grad_u_it)
(*grad_u_it) = -1. * applied_strain;
}
/// double the strain in the center: find the closed gauss point to the center
/// compute the quadrature points
ElementTypeMapReal quad_coords("quad_coords");
quad_coords.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_with_nb_element = true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
Vector<Real> center(spatial_dimension, 0.);
Real min_distance = 2;
IntegrationPoint q_min;
for (auto type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_elements = mesh.getNbElement(type, _not_ghost);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & coords = quad_coords(type, _not_ghost);
auto coord_it = coords.begin(spatial_dimension);
for (UInt e = 0; e < nb_elements; ++e) {
for (UInt q = 0; q < nb_quads; ++q, ++coord_it) {
Real dist = center.distance(*coord_it);
if (dist < min_distance) {
min_distance = dist;
q_min.element = e;
q_min.num_point = q;
q_min.global_num = nb_elements * nb_quads + q;
q_min.type = type;
}
}
}
}
Real global_min = min_distance;
comm.allReduce(global_min, SynchronizerOperation::_min);
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(q_min.type, _not_ghost));
Array<Real>::iterator<Matrix<Real>> grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
grad_u_it += local_num;
Matrix<Real> & g_u = *grad_u_it;
g_u += applied_strain;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// damage the element with higher grad_u completely, so that it is
/// not taken into account for the averaging
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & damage = const_cast<Array<Real> &>(
mat.getInternal<Real>("damage")(q_min.type, _not_ghost));
Real * dam_ptr = damage.storage();
dam_ptr += local_num;
*dam_ptr = 0.9;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material.cc b/test/test_model/test_common/test_non_local_toolbox/test_material.cc
index 08225c0dd..654f808c3 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material.cc
@@ -1,55 +1,57 @@
/**
* @file test_material.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Tue Sep 19 2017
+ * @date last modification: Wed Jan 30 2019
*
* @brief Implementation of test material for the non-local neighborhood base
* test
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
template <UInt dim>
TestMaterial<dim>::TestMaterial(SolidMechanicsModel & model, const ID & id)
: Parent(model, id), grad_u_nl("grad_u non local", *this) {
this->is_non_local = true;
this->grad_u_nl.initialize(dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void TestMaterial<dim>::registerNonLocalVariables() {
this->model.getNonLocalManager().registerNonLocalVariable(
this->gradu.getName(), grad_u_nl.getName(), dim * dim);
this->model.getNonLocalManager()
.getNeighborhood(this->getNeighborhoodName())
.registerNonLocalVariable(grad_u_nl.getName());
}
/* -------------------------------------------------------------------------- */
// Instantiate the material for the 3 dimensions
INSTANTIATE_MATERIAL(test_material, TestMaterial);
/* -------------------------------------------------------------------------- */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material.hh b/test/test_model/test_common/test_non_local_toolbox/test_material.hh
index 1d5e79fc1..9b0130132 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material.hh
@@ -1,71 +1,73 @@
/**
* @file test_material.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jan 30 2019
*
* @brief test material for the non-local neighborhood base test
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "material_damage_non_local.hh"
#ifndef TEST_MATERIAL_HH_
#define TEST_MATERIAL_HH_
using namespace akantu;
template <UInt dim>
class TestMaterial
: public MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>> {
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
using Parent =
MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>>;
TestMaterial(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerNonLocalVariables() override final;
void computeNonLocalStress(ElementType, GhostType) override final{};
void computeNonLocalStresses(GhostType) override final{};
protected:
ID getNeighborhoodName() override { return "test_region"; }
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
#endif /* TEST_MATERIAL_HH_ */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.cc b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.cc
index e949e44a0..b64e75bfa 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.cc
@@ -1,57 +1,59 @@
/**
* @file test_material_damage.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Wed Jan 30 2019
*
* @brief Implementation of test material damage
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_material_damage.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim>
TestMaterialDamage<dim>::TestMaterialDamage(SolidMechanicsModel & model,
const ID & id)
: Parent(model, id), grad_u_nl("grad_u non local", *this) {
this->is_non_local = true;
this->grad_u_nl.initialize(dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void TestMaterialDamage<dim>::registerNonLocalVariables() {
this->model.getNonLocalManager().registerNonLocalVariable(
this->gradu.getName(), grad_u_nl.getName(), dim * dim);
this->model.getNonLocalManager()
.getNeighborhood(this->getNeighborhoodName())
.registerNonLocalVariable(grad_u_nl.getName());
}
/* -------------------------------------------------------------------------- */
// Instantiate the material for the 3 dimensions
INSTANTIATE_MATERIAL(test_material, TestMaterialDamage);
/* -------------------------------------------------------------------------- */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
index df0f12c6b..6b1c38081 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
+++ b/test/test_model/test_common/test_non_local_toolbox/test_material_damage.hh
@@ -1,73 +1,75 @@
/**
* @file test_material_damage.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Tue Sep 19 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jan 30 2019
*
* @brief test material damage for the non-local remove damage test
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_damage.hh"
#include "material_damage_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef TEST_MATERIAL_DAMAGE_HH_
#define TEST_MATERIAL_DAMAGE_HH_
using namespace akantu;
template <UInt dim>
class TestMaterialDamage
: public MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>> {
using Parent =
MaterialDamageNonLocal<dim, MaterialDamage<dim, MaterialElastic>>;
/* ------------------------------------------------------------------------ */
/* Constructor/Destructor */
/* ------------------------------------------------------------------------ */
public:
TestMaterialDamage(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerNonLocalVariables() override final;
void computeNonLocalStress(ElementType, GhostType) override final{};
void insertQuadsInNeighborhoods(GhostType ghost_type);
protected:
// ID getNeighborhoodName() override { return "test_region"; }
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> grad_u_nl;
};
#endif /* TEST_MATERIAL_DAMAGE_HH_ */
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc b/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
index 17099789a..6db9ae1fe 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_non_local_averaging.cc
@@ -1,110 +1,112 @@
/**
* @file test_non_local_averaging.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Tue Dec 05 2017
+ * @date last modification: Sun Jun 16 2019
*
* @brief test for non-local averaging of strain
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_avg.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
ElementType element_type = _quadrangle_4;
GhostType ghost_type = _not_ghost;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.dump();
/// apply constant strain field everywhere in the plate
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
/// apply constant grad_u field in all elements
for (auto & mat : model.getMaterials()) {
auto & grad_us =
mat.getInternal<Real>("eigen_grad_u")(element_type, ghost_type);
for (auto & grad_u :
make_view(grad_us, spatial_dimension, spatial_dimension)) {
grad_u = -1. * applied_strain;
}
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// verify the result: non-local averaging over constant field must
/// yield same constant field
Real test_result = 0.;
Matrix<Real> difference(spatial_dimension, spatial_dimension, 0.);
for (auto & mat : model.getMaterials()) {
auto & grad_us_nl =
mat.getInternal<Real>("grad_u non local")(element_type, ghost_type);
for (auto & grad_u_nl :
make_view(grad_us_nl, spatial_dimension, spatial_dimension)) {
difference = grad_u_nl - applied_strain;
test_result += difference.norm<L_2>();
}
}
if (test_result > 10.e-13) {
AKANTU_EXCEPTION("the total norm is: " << test_result);
}
return 0;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_non_local_neighborhood_base.cc b/test/test_model/test_common/test_non_local_toolbox/test_non_local_neighborhood_base.cc
index 0d03950fa..42c36be2a 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_non_local_neighborhood_base.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_non_local_neighborhood_base.cc
@@ -1,80 +1,82 @@
/**
* @file test_non_local_neighborhood_base.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Wed Jan 30 2019
*
* @brief test for the class NonLocalNeighborhoodBase
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "my_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
MyModel model(mesh, spatial_dimension);
const auto & manager = model.getNonLocalManager();
const auto & neighborhood = manager.getNeighborhood("test_region");
/// save the pair of quadrature points and the coords of all neighbors
std::string output_1 = "quadrature_pairs";
std::string output_2 = "neighborhoods";
neighborhood.savePairs(output_1);
neighborhood.saveNeighborCoords(output_2);
/// print results to screen for validation
std::ifstream quad_pairs;
quad_pairs.open("quadrature_pairs.0");
std::string current_line;
while (getline(quad_pairs, current_line))
std::cout << current_line << std::endl;
quad_pairs.close();
std::ifstream neighborhoods;
neighborhoods.open("neighborhoods.0");
while (getline(neighborhoods, current_line))
std::cout << current_line << std::endl;
neighborhoods.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_pair_computation.cc b/test/test_model/test_common/test_non_local_toolbox/test_pair_computation.cc
index caf408d1d..e5a4390f8 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_pair_computation.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_pair_computation.cc
@@ -1,223 +1,225 @@
/**
* @file test_pair_computation.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 25 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jul 10 2020
*
* @brief test the weight computation with and without grid
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material_damage.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef std::vector<std::pair<IntegrationPoint, IntegrationPoint>> PairList;
/* -------------------------------------------------------------------------- */
void computePairs(SolidMechanicsModel & model, PairList * pair_list);
int main(int argc, char * argv[]) {
akantu::initialize("material_remove_damage.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
// mesh creation and read
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("pair_test.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.dump();
/// compute the pairs by looping over all the quadrature points
std::array<PairList, 2> pair_list;
computePairs(model, pair_list.data());
const auto & pairs_mat_1_not_ghost =
model.getNonLocalManager().getNeighborhood("mat_1").getPairLists(_not_ghost);
const auto & pairs_mat_1_ghost =
model.getNonLocalManager().getNeighborhood("mat_1").getPairLists(_ghost);
const auto & pairs_mat_2_not_ghost =
model.getNonLocalManager().getNeighborhood("mat_2").getPairLists(_not_ghost);
const auto & pairs_mat_2_ghost =
model.getNonLocalManager().getNeighborhood("mat_2").getPairLists(_ghost);
/// compare the number of pairs
UInt nb_not_ghost_pairs_grid = pairs_mat_1_not_ghost.size() + pairs_mat_2_not_ghost.size();
UInt nb_ghost_pairs_grid = pairs_mat_1_ghost.size() + pairs_mat_2_ghost.size();
UInt nb_not_ghost_pairs_no_grid = pair_list[0].size();
UInt nb_ghost_pairs_no_grid = pair_list[1].size();
if ((nb_not_ghost_pairs_grid != nb_not_ghost_pairs_no_grid) ||
(nb_ghost_pairs_grid != nb_ghost_pairs_no_grid)) {
std::cout << "The number of pairs is not correct: TEST FAILED!!!"
<< std::endl;
finalize();
return EXIT_FAILURE;
}
for (UInt i = 0; i < pairs_mat_1_not_ghost.size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[0].begin(), pair_list[0].end(), (pairs_mat_1_not_ghost)[i]);
if (it == pair_list[0].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_2_not_ghost.size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[0].begin(), pair_list[0].end(), (pairs_mat_2_not_ghost)[i]);
if (it == pair_list[0].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_1_ghost.size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[1].begin(), pair_list[1].end(), (pairs_mat_1_ghost)[i]);
if (it == pair_list[1].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_2_ghost.size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[1].begin(), pair_list[1].end(), (pairs_mat_2_ghost)[i]);
if (it == pair_list[1].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
finalize();
return 0;
}
/* -------------------------------------------------------------------------- */
void computePairs(SolidMechanicsModel & model, PairList * pair_list) {
ElementKind kind = _ek_regular;
Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
/// compute the quadrature points
ElementTypeMapReal quad_coords("quad_coords");
quad_coords.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_with_nb_element = true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
/// loop in a n^2 way over all the quads to generate the pairs
Real neighborhood_radius = 0.5;
IntegrationPoint q1;
IntegrationPoint q2;
GhostType ghost_type_1 = _not_ghost;
q1.ghost_type = ghost_type_1;
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
for (auto type_1 : mesh.elementTypes(spatial_dimension, _not_ghost, kind)) {
q1.type = type_1;
UInt nb_elements_1 = mesh.getNbElement(type_1, ghost_type_1);
UInt nb_quads_1 = model.getFEEngine().getNbIntegrationPoints(type_1);
Array<Real> & quad_coords_1 = quad_coords(q1.type, q1.ghost_type);
auto coord_it_1 = quad_coords_1.begin(spatial_dimension);
for (UInt e_1 = 0; e_1 < nb_elements_1; ++e_1) {
q1.element = e_1;
UInt mat_index_1 = model.getMaterialByElement(q1.type, q1.ghost_type)
.begin()[q1.element];
for (UInt q_1 = 0; q_1 < nb_quads_1; ++q_1) {
q1.global_num = nb_quads_1 * e_1 + q_1;
q1.num_point = q_1;
q1_coords = coord_it_1[q1.global_num];
/// loop over all other quads and create pairs for this given quad
for (auto ghost_type_2 : ghost_types) {
q2.ghost_type = ghost_type_2;
for (auto type_2 :
mesh.elementTypes(spatial_dimension, ghost_type_2, kind)) {
q2.type = type_2;
UInt nb_elements_2 = mesh.getNbElement(type_2, ghost_type_2);
UInt nb_quads_2 =
model.getFEEngine().getNbIntegrationPoints(type_2);
Array<Real> & quad_coords_2 = quad_coords(q2.type, q2.ghost_type);
auto coord_it_2 = quad_coords_2.begin(spatial_dimension);
for (UInt e_2 = 0; e_2 < nb_elements_2; ++e_2) {
q2.element = e_2;
UInt mat_index_2 =
model.getMaterialByElement(q2.type, q2.ghost_type)
.begin()[q2.element];
for (UInt q_2 = 0; q_2 < nb_quads_2; ++q_2) {
q2.global_num = nb_quads_2 * e_2 + q_2;
q2.num_point = q_2;
q2_coords = coord_it_2[q2.global_num];
Real distance = q1_coords.distance(q2_coords);
if (mat_index_1 != mat_index_2)
continue;
else if (distance <=
neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <=
q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
}
}
}
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc b/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
index fff5be6a4..b8c2cbaab 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_remove_damage_weight_function.cc
@@ -1,190 +1,192 @@
/**
* @file test_remove_damage_weight_function.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 07 2015
- * @date last modification: Tue Dec 05 2017
+ * @date last modification: Wed Nov 27 2019
*
* @brief Test the damage weight funcion for non local computations
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_remove_damage.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
ElementType element_type = _quadrangle_4;
GhostType ghost_type = _not_ghost;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
auto && mat_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("damage");
model.dump();
/// apply constant strain field in all elements except element 3 and 15
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
applied_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
/// apply different strain in element 3 and 15
Matrix<Real> modified_strain(spatial_dimension, spatial_dimension);
modified_strain.zero();
for (UInt i = 0; i < spatial_dimension; ++i)
modified_strain(i, i) = 1.;
/// apply constant grad_u field in all elements
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
Material & mat = model.getMaterial(m);
Array<Real> & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("eigen_grad_u")(element_type, ghost_type));
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
UInt element_counter = 0;
for (; grad_u_it != grad_u_end; ++grad_u_it, ++element_counter)
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
(*grad_u_it) = -1. * modified_strain;
else
(*grad_u_it) = -1. * applied_strain;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// save the weights in a file
auto & neighborhood_1 = model.getNonLocalManager().getNeighborhood("mat_1");
auto & neighborhood_2 = model.getNonLocalManager().getNeighborhood("mat_2");
neighborhood_1.saveWeights("before_0");
neighborhood_2.saveWeights("before_1");
for (UInt n = 0; n < 2; ++n) {
/// print results to screen for validation
std::stringstream sstr;
sstr << "before_" << n << ".0";
std::ifstream weights;
weights.open(sstr.str());
std::string current_line;
while (getline(weights, current_line))
std::cout << current_line << std::endl;
weights.close();
}
/// apply damage to not have the elements with lower strain impact the
/// averaging
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
auto & mat =
dynamic_cast<MaterialDamage<spatial_dimension> &>(model.getMaterial(m));
auto & damage = const_cast<Array<Real> &>(
mat.getInternal<Real>("damage")(element_type, ghost_type));
auto dam_it = damage.begin();
auto dam_end = damage.end();
UInt element_counter = 0;
for (; dam_it != dam_end; ++dam_it, ++element_counter)
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
*dam_it = 0.9;
}
/// compute the non-local strains
model.assembleInternalForces();
neighborhood_1.saveWeights("after_0");
neighborhood_2.saveWeights("after_1");
for (UInt n = 0; n < 2; ++n) {
/// print results to screen for validation
std::stringstream sstr;
sstr << "after_" << n << ".0";
std::ifstream weights;
weights.open(sstr.str());
std::string current_line;
while (getline(weights, current_line))
std::cout << current_line << std::endl;
weights.close();
}
model.dump();
/// verify the result: non-local averaging over constant field must
/// yield same constant field
Real test_result = 0.;
Matrix<Real> difference(spatial_dimension, spatial_dimension, 0.);
Matrix<Real> difference_in_damaged_elements(spatial_dimension,
spatial_dimension, 0.);
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
difference_in_damaged_elements.zero();
auto & mat = model.getMaterial(m);
auto & grad_u_nl = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u non local")(element_type, ghost_type));
auto grad_u_nl_it = grad_u_nl.begin(spatial_dimension, spatial_dimension);
auto grad_u_nl_end = grad_u_nl.end(spatial_dimension, spatial_dimension);
UInt element_counter = 0;
for (; grad_u_nl_it != grad_u_nl_end; ++grad_u_nl_it, ++element_counter) {
if (element_counter == 12 || element_counter == 13 ||
element_counter == 14 || element_counter == 15)
difference_in_damaged_elements += (*grad_u_nl_it);
else
difference = (*grad_u_nl_it) - applied_strain;
test_result += difference.norm<L_2>();
}
difference_in_damaged_elements *= (1 / 4.);
difference_in_damaged_elements -= (1.41142 * modified_strain);
test_result += difference_in_damaged_elements.norm<L_2>();
}
if (test_result > 10.e-5) {
std::cout << "the total norm is: " << test_result << std::endl;
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_common/test_non_local_toolbox/test_weight_computation.cc b/test/test_model/test_common/test_non_local_toolbox/test_weight_computation.cc
index d7261b169..459512160 100644
--- a/test/test_model/test_common/test_non_local_toolbox/test_weight_computation.cc
+++ b/test/test_model/test_common/test_non_local_toolbox/test_weight_computation.cc
@@ -1,67 +1,69 @@
/**
* @file test_weight_computation.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Wed Jan 30 2019
*
* @brief test for the weight computation with base weight function
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "my_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_weight_computation.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
// mesh creation and read
Mesh mesh(spatial_dimension);
mesh.read("plate.msh");
/// model creation
MyModel model(mesh, spatial_dimension);
/// save the weights in a file
const auto & neighborhood =
model.getNonLocalManager().getNeighborhood("test_region");
neighborhood.saveWeights("weights");
/// print results to screen for validation
std::ifstream weights;
weights.open("weights.0");
std::string current_line;
while (getline(weights, current_line))
std::cout << current_line << std::endl;
weights.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_contact_mechanics_model/CMakeLists.txt b/test/test_model/test_contact_mechanics_model/CMakeLists.txt
index e0dee2ff9..3e6f31255 100644
--- a/test/test_model/test_contact_mechanics_model/CMakeLists.txt
+++ b/test/test_model/test_contact_mechanics_model/CMakeLists.txt
@@ -1,42 +1,52 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Tue Dec 18 2018
-# @date last modification: Tue Dec 18 2018
+# @date creation: Fri Sep 03 2010
+# @date last modification: Sun Jun 06 2021
#
# @brief configuration for ContactMechanicsModel tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_akantu_test(test_selector "selector_test")
add_mesh(flat_on_flat flat_on_flat.geo 2 1)
register_test(test_explicit_dynamic
SOURCES test_explicit_dynamic.cc
DEPENDS flat_on_flat
FILES_TO_COPY material.dat
- PACKAGE core
+ PACKAGE contact_mechanics
)
add_mesh(sliding-block-2D sliding-block-2D.geo 2 1)
register_test(test_explicit_friction
SOURCES test_explicit_friction.cc
DEPENDS sliding-block-2D
FILES_TO_COPY material-friction.dat
- PACKAGE core
+ PACKAGE contact_mechanics
)
diff --git a/test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt b/test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt
index 45f11aae3..21ae0ff5d 100644
--- a/test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt
+++ b/test/test_model/test_contact_mechanics_model/test_coupler/CMakeLists.txt
@@ -1,42 +1,52 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Tue May 07 2019
-# @date last modification: Tue May 07 2019
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri May 24 2019
#
# @brief configuration for testing coupler class for contact mechanics model
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh (coupling coupling.geo 2 1)
add_mesh (flat_on_flat flat_on_flat.geo 2 1)
register_test( test_contact_coupling
SOURCES test_contact_coupling.cc
DEPENDS coupling
FILES_TO_COPY material.dat
PACKAGE contact_mechanics model_couplers
)
register_test( test_coupled_stiffness
SOURCES test_coupled_stiffness.cc
DEPENDS flat_on_flat
FILES_TO_COPY material_stiffness.dat
PACKAGE contact_mechanics model_couplers
)
diff --git a/test/test_model/test_contact_mechanics_model/test_coupler/test_contact_coupling.cc b/test/test_model/test_contact_mechanics_model/test_coupler/test_contact_coupling.cc
index f6b5938c9..3aab210d9 100644
--- a/test/test_model/test_contact_mechanics_model/test_coupler/test_contact_coupling.cc
+++ b/test/test_model/test_contact_mechanics_model/test_coupler/test_contact_coupling.cc
@@ -1,76 +1,77 @@
/**
- * @file test_contact_coupler.cc
+ * @file test_contact_coupling.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Apr 30 2019
- * @date last modification: Tue Apr 30 2019
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Thu May 16 2019
*
* @brief Test for contact mechanics model class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_contact.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
const UInt spatial_dimension = 2;
initialize("material.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("coupling.msh");
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
solid.initFull(_analysis_method = _static);
contact.initFull(_analysis_method = _implicit_contact);
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "bot_body");
solid.applyBC(BC::Dirichlet::IncrementValue(0.001, _y), "bot_body");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "top");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "top");
coupler.initFull(_analysis_method = _implicit_contact);
coupler.setBaseName("coupling");
coupler.addDumpFieldVector("displacement");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("external_force");
coupler.addDumpField("internal_force");
coupler.addDumpField("grad_u");
coupler.addDumpField("stress");
coupler.solveStep();
contact.dump();
return 0;
}
diff --git a/test/test_model/test_contact_mechanics_model/test_coupler/test_coupled_stiffness.cc b/test/test_model/test_contact_mechanics_model/test_coupler/test_coupled_stiffness.cc
index b4e321b29..1338dbeae 100644
--- a/test/test_model/test_contact_mechanics_model/test_coupler/test_coupled_stiffness.cc
+++ b/test/test_model/test_contact_mechanics_model/test_coupler/test_coupled_stiffness.cc
@@ -1,138 +1,139 @@
/**
- * @file test_contact_mechanics_model.cc
+ * @file test_coupled_stiffness.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Tue Apr 30 2019
- * @date last modification: Tue Apr 30 2019
+ * @date creation: Fri May 24 2019
+ * @date last modification: Wed Oct 02 2019
*
* @brief Test for contact mechanics model class
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
#include "contact_mechanics_model.hh"
#include "coupler_solid_contact.hh"
#include "non_linear_solver.hh"
#include "sparse_matrix.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
Real max_displacement = 0.01;
const UInt spatial_dimension = 2;
initialize("material_stiffness.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("flat_on_flat.msh");
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
auto && selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names", solid);
solid.setMaterialSelector(selector);
solid.initFull( _analysis_method = _static);
contact.initFull(_analysis_method = _implicit_contact);
auto &&surface_selector = std::make_shared<PhysicalSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "bottom");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "bottom");
solid.applyBC(BC::Dirichlet::IncrementValue(-max_displacement, _y), "top");
coupler.initFull(_analysis_method = _implicit_contact);
auto &solver = coupler.getNonLinearSolver();
solver.set("max_iterations", 1000);
solver.set("threshold", 1e-2);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
coupler.setBaseName("test-coupled-stiffness");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("normals");
coupler.addDumpFieldVector("contact_force");
coupler.addDumpFieldVector("external_force");
coupler.addDumpFieldVector("internal_force");
coupler.addDumpField("gaps");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("grad_u");
coupler.addDumpField("stress");
auto & before_assembly =
const_cast<SparseMatrix &>(coupler.getDOFManager().getNewMatrix("K", _symmetric));
solid.assembleStiffnessMatrix();
auto & solid_assembly =
const_cast<SparseMatrix &>(coupler.getDOFManager().getMatrix("K"));
solid_assembly.saveMatrix("solid_assembly.mtx");
auto & displacement = solid.getDisplacement();
contact.search(displacement);
contact.assembleStiffnessMatrix();
auto contact_map = contact.getContactMap();
auto nb_contacts = contact_map.size();
auto & contact_assembly =
const_cast<SparseMatrix &>(coupler.getDOFManager().getMatrix("K"));
contact_assembly.saveMatrix("contact_assembly.mtx");
solid.assembleInternalForces();
contact.assembleInternalForces();
coupler.dump();
Array<Real> & contact_force = contact.getInternalForce();
for (UInt n : arange(contact_force.size())) {
std::cerr << contact_force(n, 1) << std::endl;
}
if (solid_assembly.size() == contact_assembly.size() and nb_contacts > 0) {
std::cerr << "size of stiffness matrix of solid = " << solid_assembly.size() << std::endl;
std::cerr << "size of stiffness matrix of coupled = " << contact_assembly.size() << std::endl;
std::cerr << "number of contacts = " << nb_contacts << std::endl;
for (auto & pair : contact_map) {
std::cerr << "Node " << pair.first << " in contact with " << pair.second.master <<
" of gap " << pair.second.gap << std::endl;
}
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt b/test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt
index 7e1992d17..53bbaf055 100644
--- a/test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt
+++ b/test/test_model/test_contact_mechanics_model/test_detector/CMakeLists.txt
@@ -1,58 +1,68 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Wed Dec 18 2018
-# @date last modification: Wed Apr 29 2019
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Dec 11 2020
#
# @brief configuration for contact detection tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
set(_meshes)
add_mesh(detection_seg data/cohesive_1D.geo
DIM 2 ORDER 1
OUTPUT _detection_segment_2.msh)
list(APPEND _meshes detection_seg)
add_mesh(detection_tri data/cohesive_strait_2D.geo
DIM 2 ORDER 1
OUTPUT _detection_triangle_3.msh)
list(APPEND _meshes detection_tri)
add_mesh(detection_quad data/cohesive_strait_2D_structured.geo
DIM 2 ORDER 1
OUTPUT _detection_quadrangle_4.msh)
list(APPEND _meshes detection_quad)
add_mesh(detection_tri_quad data/cohesive_strait_2D_mixte.geo
DIM 2 ORDER 1
OUTPUT _detection_triangle_3_quadrangle_4.msh)
list(APPEND _meshes detection_tri_quad)
add_mesh(detection_tet data/cohesive_strait_3D.geo
DIM 3 ORDER 1
OUTPUT _detection_tetrahedron_4.msh)
list(APPEND _meshes detection_tet)
register_gtest_sources(
SOURCES test_detection.cc
PACKAGE contact_mechanics
DEPENDS ${_meshes}
FILES_TO_COPY material_0.dat material_1.dat
)
diff --git a/test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc b/test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc
index 4e5ba3fee..351ae4aa9 100644
--- a/test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc
+++ b/test/test_model/test_contact_mechanics_model/test_detector/test_detection.cc
@@ -1,61 +1,62 @@
/**
* @file test_detection.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sat Feb 29 2020
- * @date last modification: Sat Feb 29 2020
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Fri Dec 11 2020
*
* @brief Generic test for detection between different element types
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "test_detection_fixture.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestCMMDFixture, Implicit) {
this->analysis_method = _static;
this->detection_type = _implicit_contact;
this->testImplicit();
this->checkGap();
}
TYPED_TEST(TestCMMDFixture, Explicit) {
this->analysis_method = _static;
this->detection_type = _explicit_contact;
this->testExplicit();
this->checkGap();
}
diff --git a/test/test_model/test_contact_mechanics_model/test_detector/test_detection_fixture.hh b/test/test_model/test_contact_mechanics_model/test_detector/test_detection_fixture.hh
index 779295793..72011760d 100644
--- a/test/test_model/test_contact_mechanics_model/test_detector/test_detection_fixture.hh
+++ b/test/test_model/test_contact_mechanics_model/test_detector/test_detection_fixture.hh
@@ -1,224 +1,226 @@
/**
* @file test_detection_fixture.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sat Feb 29 2020
- * @date last modification: Sat Feb 29 2020
+ * @date creation: Fri Dec 11 2020
+ * @date last modification: Fri Dec 11 2020
*
* @brief Contact detection test fixture
*
+ *
* @section LICENSE
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_mdoel.hh"
#include "solid_mechanics_model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TEST_DETECTION_FIXTURE_HH__
#define __AKANTU_TEST_DETECTION_FIXTURE_HH__
using namespace akantu;
template <::akantu::AnalysisMethod t>
using analysis_method_t std::integral_constant<::akantu::AnalysisMethod, t>;
class StrainIncrement : public BC::Functor {
public:
StrainIncrement(const Matrix<Real> & strain, BC::Axis dir)
: strain_inc(strain), dir(dir) {}
void operator()(UInt /*node*/, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
if (std::abs(coord(dir)) < 1e-8) {
return;
}
flags.set(true);
primal += strain_inc * coord;
}
static const BC::Functor::Type type = BC::Functor::_dirichlet;
private:
Matrix<Real> strain_inc;
BC::Axis dir;
};
template <typename param_> class TestCMMDFixture : public ::testing::Test {
public:
static constexpr ElementType type_1 = std::tuple_element_t<1, param_>::value;
static constexpr ElementType type_2 = std::tuple_element_t<2, param_>::value;
void Setup() override {
mesh = std::make_unique<Mesh>(this->dim);
if (Communicator::getStaticCommunicator().whoAmI() == 0) {
ASSERT_NO_THROW({ mesh->read(this->mesh_name); });
}
mesh->distribute();
}
void TearDown() override {
solid.reset(nullptr);
contact.reset(nullptr);
mesh.reset(nullptr);
}
void createModel() {
solid = std::make_unique<SolidmechanicsModel>(*mesh);
solid->initFull(_analysis_method = this->analysis_method);
contact = std::make_unique<ContactMechanicsModel>(*mesh);
contact->initFull(_analysis_method = this->detection_type);
auto && surface_selector = std::make_shared<PhysicalSurfaceSelector>(*mesh);
contact->getContactDetector().setSurfaceSelector(surface_selector);
}
void setInitialCondition(const Matrix<Real> & strain) {
for (auto && data :
zip(make_view(this->mesh->getNodes(), this->dim),
make_view(this->solid->getDisplacement(), this->dim))) {
const auto & pos = std::get<0>(data);
auto & disp = std::get<1>(data);
disp = strain * pos;
}
}
void steps(const Matrix<Real> & strain) {
StrainIncrement functor((1. / 300) * strain, this->dim == 1 ? _x : _y);
for (auto _ [[gnu::unused]] : arange(nb_steps)) {
this->solid->applyBC(functor, "loading");
this->solid->applyBC(functor, "fixed");
this->solid->solveStep();
}
}
void testImplicit() {
this->createModel();
auto & mat_el = this->solid->getMaterial("body");
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
if (this->dim > 1)
this->model->applyBC(BC::Dirichlet::FlagOnly(_y), "sides");
if (this->dim > 2)
this->model->applyBC(BC::Dirichlet::FlagOnly(_z), "sides");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{1.}};
} else if (dim == 2) {
strain = {{-nu, 0.}, {0., 1. - nu}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{-nu, 0., 0.}, {0., 1., 0.}, {0., 0., -nu}};
}
this->setInitialCondition((1 - 1e-5) * strain);
this->steps(1e-2 * strain);
this->contact->search();
}
void testExplicit() {
this->createModel();
auto & mat_el = this->solid->getMaterial("body");
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
if (this->dim > 1)
this->model->applyBC(BC::Dirichlet::FlagOnly(_y), "sides");
if (this->dim > 2)
this->model->applyBC(BC::Dirichlet::FlagOnly(_z), "sides");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{-1.}};
} else if (dim == 2) {
strain = {{-nu, 0.}, {0., 1. - nu}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{-nu, 0., 0.}, {0., 1., 0.}, {0., 0., -nu}};
}
this->setInitialCondition((1 - 1e-5) * strain);
this->steps(1e-2 * strain);
this->contact->search();
}
bool checkGap() {
}
bool checkNormal() {
}
bool checkCovariantBasis() {
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModel> solid;
std::unique_ptr<ContactMechanicsModel> contact;
std::string mesh_name{std::to_string(detection_type) + std::to_string(type_1) +
(type_1 == type_2 ? "" : std::to_string(type_2)) +
".msh"};
AnalysisMethod analysis_method;
DetectionType detection_type;
};
/* -------------------------------------------------------------------------- */
using element_types = gtest_list_t<std::tuple<
std::tuple<_element_type_segment_2, _element_type_segement_2>,
std::tuple< _element_type_triangle_3, _element_type_triangle_3>,
std::tuple<_element_type_triangle_3, _element_type_quadrangle_4>,
std::tuple<_element_type_quadrangle_4, _element_type_quadrange_4>,
std::tuple<_element_type_tetrahedron_6, _element_type_tetrahedron_6> >>;
TYPED_TEST_SUITE(TestCMMDFixture, detection_types)
#endif
diff --git a/test/test_model/test_contact_mechanics_model/test_explicit_dynamic.cc b/test/test_model/test_contact_mechanics_model/test_explicit_dynamic.cc
index a228d5832..2bfaef378 100644
--- a/test/test_model/test_contact_mechanics_model/test_explicit_dynamic.cc
+++ b/test/test_model/test_contact_mechanics_model/test_explicit_dynamic.cc
@@ -1,137 +1,168 @@
+/**
+ * @file test_explicit_dynamic.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Fri Dec 11 2020
+ * @date last modification: Sun Jun 06 2021
+ *
+ * @brief Test for dynamic explicit contact
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
#include "coupler_solid_contact.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
template<typename T>
std::vector<T> arrange(T start, T stop, T step = 1) {
std::vector<T> values;
for (T value = start; value <= stop; value += step)
values.push_back(value);
return values;
}
int main(int argc, char * argv[]) {
UInt max_steps = 2000;
Real max_displacement = 1e-2;
Real damping_ratio = 0.99;
std::string mesh_file = "flat_on_flat.msh";
std::string material_file = "material.dat";
const UInt spatial_dimension = 2;
initialize(material_file, argc, argv);
Mesh mesh(spatial_dimension);
mesh.read(mesh_file);
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
auto && material_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
solid);
solid.setMaterialSelector(material_selector);
coupler.initFull(_analysis_method = _explicit_lumped_mass);
auto && surface_selector = std::make_shared<PhysicalSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "upper");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "lower");
Real time_step = solid.getStableTimeStep();
time_step *= 0.05;
coupler.setTimeStep(time_step);
std::cout << "Stable time increment : " << time_step << " sec " << std::endl;
coupler.setBaseName("explicit-dynamic");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("normals");
coupler.addDumpFieldVector("contact_force");
coupler.addDumpFieldVector("external_force");
coupler.addDumpFieldVector("internal_force");
coupler.addDumpField("gaps");
coupler.addDumpField("areas");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("strain");
coupler.addDumpField("stress");
auto & velocity = solid.getVelocity();
auto & gaps = contact.getGaps();
auto xi = arrange<Real>(0, 1, 1./max_steps);
std::vector<Real> displacements;
std::transform(xi.begin(), xi.end(), std::back_inserter(displacements),
[&](Real & p) -> Real {
return 0. + (max_displacement)*pow(p, 3)*(10-15*p+ 6*pow(p,2)); });
for (UInt s : arange(max_steps)) {
solid.applyBC(BC::Dirichlet::FixedValue(-displacements[s], _y), "loading");
solid.applyBC(BC::Dirichlet::FixedValue(displacements[s], _y), "fixed");
coupler.solveStep();
for(auto && tuple : zip(gaps,
make_view(velocity, spatial_dimension))){
auto & gap = std::get<0>(tuple);
auto & vel = std::get<1>(tuple);
if(gap > 0) {
vel *= damping_ratio;
}
}
if (s % 100 == 0) {
coupler.dump();
}
}
coupler.dump();
const ElementType element_type = _quadrangle_4;
const Array<Real> & stress_vect = solid.getMaterial("upper").getStress(element_type);
auto stress_it = stress_vect.begin(spatial_dimension, spatial_dimension);
auto stress_end = stress_vect.end(spatial_dimension, spatial_dimension);
Real stress_tolerance = 1e-2;
Matrix<Real> presc_stress{{0, 0}, {0, 7e5}};
for (; stress_it != stress_end; ++stress_it) {
const auto & stress = *stress_it;
Real stress_error = (std::abs(stress(1, 1)) - presc_stress(1, 1))/(presc_stress(1, 1));
// if error is more than 1%
if (std::abs(stress_error) > stress_tolerance) {
std::cerr << "stress error: " << stress_error << " > " << stress_tolerance
<< std::endl;
std::cerr << "stress: " << stress << std::endl
<< "prescribed stress: " << presc_stress << std::endl;
return EXIT_FAILURE;
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_contact_mechanics_model/test_explicit_friction.cc b/test/test_model/test_contact_mechanics_model/test_explicit_friction.cc
index fd99fd5ec..ca696ce3e 100644
--- a/test/test_model/test_contact_mechanics_model/test_explicit_friction.cc
+++ b/test/test_model/test_contact_mechanics_model/test_explicit_friction.cc
@@ -1,145 +1,176 @@
+/**
+ * @file test_explicit_friction.cc
+ *
+ * @author Mohit Pundir <mohit.pundir@epfl.ch>
+ *
+ * @date creation: Sun Jun 06 2021
+ * @date last modification: Sun Jun 06 2021
+ *
+ * @brief Test contact mechanics with friction
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
#include "coupler_solid_contact.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
template<typename T>
std::vector<T> arrange(T start, T stop, T step = 1) {
std::vector<T> values;
for (T value = start; value <= stop; value += step)
values.push_back(value);
return values;
}
int main(int argc, char * argv[]) {
UInt max_normal_steps = 2500;
UInt max_shear_steps = 7500;
Real max_shear_displacement = 1e-1;
Real max_normal_displacement = 2e-2;
Real damping_ratio = 0.99;
std::string mesh_file = "sliding-block-2D.msh";
std::string material_file = "material-friction.dat";
const UInt spatial_dimension = 2;
initialize(material_file, argc, argv);
Mesh mesh(spatial_dimension);
mesh.read(mesh_file);
CouplerSolidContact coupler(mesh);
auto & solid = coupler.getSolidMechanicsModel();
auto & contact = coupler.getContactMechanicsModel();
auto && material_selector =
std::make_shared<MeshDataMaterialSelector<std::string>>("physical_names",
solid);
solid.setMaterialSelector(material_selector);
coupler.initFull(_analysis_method = _explicit_lumped_mass);
auto && surface_selector = std::make_shared<PhysicalSurfaceSelector>(mesh);
contact.getContactDetector().setSurfaceSelector(surface_selector);
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "lower");
solid.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "lower");
Real time_step = solid.getStableTimeStep();
time_step *= 0.05;
coupler.setTimeStep(time_step);
std::cout << "Stable time increment : " << time_step << " sec " << std::endl;
coupler.setBaseName("explicit-friction");
coupler.addDumpFieldVector("displacement");
coupler.addDumpFieldVector("normals");
coupler.addDumpFieldVector("contact_force");
coupler.addDumpFieldVector("tangential_force");
coupler.addDumpFieldVector("external_force");
coupler.addDumpFieldVector("internal_force");
coupler.addDumpField("gaps");
coupler.addDumpField("areas");
coupler.addDumpField("blocked_dofs");
coupler.addDumpField("strain");
coupler.addDumpField("stress");
coupler.addDumpField("contact_state");
auto & velocity = solid.getVelocity();
auto & gaps = contact.getGaps();
auto xi = arrange<Real>(0, 1, 1./max_shear_steps);
std::vector<Real> shear_displacements;
std::transform(xi.begin(), xi.end(), std::back_inserter(shear_displacements),
[&](Real & p) -> Real {
return 0. + (max_shear_displacement)*pow(p, 3)*(10-15*p+ 6*pow(p,2)); });
auto normal_xi = arrange<Real>(0, 1, 1./max_normal_steps);
std::vector<Real> normal_displacements;
std::transform(normal_xi.begin(), normal_xi.end(), std::back_inserter(normal_displacements),
[&](Real & p) -> Real {
return 0. + (max_normal_displacement)*pow(p, 3)*(10-15*p+ 6*pow(p,2)); });
auto max_steps = max_normal_steps + max_shear_steps;
auto & contact_nodes = surface_selector->getSlaveList();
auto & tangential_traction = contact.getTangentialTractions();
for (UInt s : arange(max_steps)) {
if (s < max_normal_steps){
solid.applyBC(BC::Dirichlet::FixedValue(-normal_displacements[s], _y), "loading");
}
else {
solid.applyBC(BC::Dirichlet::FixedValue(shear_displacements[s - max_normal_steps], _x), "loading");
}
coupler.solveStep();
for(auto && tuple : zip(gaps,
make_view(velocity, spatial_dimension))){
auto & gap = std::get<0>(tuple);
auto & vel = std::get<1>(tuple);
if(gap > 0) {
vel *= damping_ratio;
}
}
if (s % 100 == 0) {
coupler.dump();
}
auto sum = std::accumulate(tangential_traction.begin(), tangential_traction.end(), 0.0);
auto num_tang_traction = std::abs(sum) / contact_nodes.size();
Real exp_tang_traction = 0.3*1.4e6;
Real error = std::abs(num_tang_traction - exp_tang_traction) / exp_tang_traction;
if (error > 1e-3 and num_tang_traction > exp_tang_traction){
std::cerr << error << "----" << num_tang_traction << std::endl;
return EXIT_FAILURE;
}
}
coupler.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt b/test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt
index 3334ff98e..75442d489 100644
--- a/test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt
+++ b/test/test_model/test_contact_mechanics_model/test_resolution/CMakeLists.txt
@@ -1,32 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Mon Jan 7 2019
-# @date last modification: Mon Jan 7 2019
+# @date creation: Fri Sep 03 2010
+# @date last modification: Thu Jan 17 2019
#
# @brief configuration for contact resolution tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(explicit_2d explicit_2d.geo 2 1)
register_test(test_explicit_resolution
SOURCES test_explicit_resolution.cc
DEPENDS explicit_2d
FILES_TO_COPY options.dat
PACKAGE contact_mechanics
)
diff --git a/test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc b/test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc
index 26c9c647c..23253e289 100644
--- a/test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc
+++ b/test/test_model/test_contact_mechanics_model/test_resolution/test_explicit_resolution.cc
@@ -1,53 +1,54 @@
/**
- * @file test_resolution_explicit.cc
+ * @file test_explicit_resolution.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Jan 7 2019
- * @date last modification: Mon Jan 7 2019
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Thu Jan 17 2019
*
* @brief Test for explicit contact resolution
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "contact_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
const UInt spatial_dimension = 2;
int main(int argc, char *argv[])
{
initialize("options.dat", argc, argv);
Mesh mesh(spatial_dimension);
//mesh.read("explicit_2d.msh");
ContactMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
std::cout << model;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_contact_mechanics_model/test_resolution/test_resolution.cc b/test/test_model/test_contact_mechanics_model/test_resolution/test_resolution.cc
index 4dda3c2dc..d4ba1d080 100644
--- a/test/test_model/test_contact_mechanics_model/test_resolution/test_resolution.cc
+++ b/test/test_model/test_contact_mechanics_model/test_resolution/test_resolution.cc
@@ -1,92 +1,93 @@
/**
* @file test_resolution.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon May 06 2019
- * @date last modification: Mon May 06 2019
+ * @date creation: Wed May 08 2019
+ * @date last modification: Wed May 08 2019
*
* @brief Test the resolution class common function
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "resolution.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.hh>
#include <type_traits>
#include <tuple>
#include <random>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
class TestResolutionFixture : public::testing::Test {
public:
void SetUp() override {
mesh = std::make_unique<Mesh>(spatial_dimension);
model = std::make_unique<Model>(*mesh);
resolution = std::make_unique<Resolution>(*model, "resolution");
}
void TearDown() override {
resolution.reset(nullptr);
model.reset(nullptr);
mesh.reset(nullptr);
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<ContactMechanicsModel> model;
std::unique_ptr<Resolution> resolution;
};
TYPED_TEST(TestResolutionFixture, TestComputeN) {
Vector<Real> shapes(nb_nodes_master);
Vector<Real> projection(spatial_diemnsion - 1);
#define GET_SHAPES_NATURAL(type) \
ElementClass<type>::computeShapes(projection, shapes)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPES_NATURAL);
#undef GET_SHAPES_NATURAL
Vector<Real> n(conn.size() * spatial_dimension);
resolution->computeN(n, shapes, normal);
}
TYPED_TEST(TestResolutionFixture, TestComputeDalpha) {
}
TYPED_TEST(TestResolutionFixture, TestComputeNalpha) {
}
diff --git a/test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt b/test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt
index 530b5d7cf..f0155b65e 100644
--- a/test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt
+++ b/test/test_model/test_contact_mechanics_model/test_selector/CMakeLists.txt
@@ -1,47 +1,57 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Sat Feb 29 2020
-# @date last modification: Sat feb 29 2020
+# @date creation: Fri Sep 03 2010
+# @date last modification: Fri Dec 11 2020
#
# @brief configuration for node selection tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
set(_meshes)
add_mesh(selection_seg data/selection_1D.geo
DIM 2 ORDER 1
OUTPUT _selection_segment_2.msh)
list(APPEND _meshes selection_2D)
add_mesh(selection_tri data/selection_2D.geo
DIM 2 ORDER 1
OUTPUT _selection_triangle_3.msh)
list(APPEND _meshes selection_2D)
add_mesh(detection_tet data/selection_3D.geo
DIM 3 ORDER 1
OUTPUT _selection_tetrahedron_4.msh)
list(APPEND _meshes selection_3D)
register_gtest_sources(
SOURCES test_selection.cc
PACKAGE contact_mechanics
DEPENDS ${_meshes}
FILES_TO_COPY material.dat
)
diff --git a/test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc b/test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc
index c8cd6cf87..63590fb43 100644
--- a/test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc
+++ b/test/test_model/test_contact_mechanics_model/test_selector/test_selection.cc
@@ -1,46 +1,47 @@
/**
* @file test_selection.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sun Mar 01 2020
- * @date last modification: Sun Mar 01 2020
+ * @date creation: Thu Feb 21 2013
+ * @date last modification: Fri Dec 11 2020
*
* @brief Generic test for surface selection
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_selection_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
TYPED_TEST(TestSurfaceSelectionFixture, PhysicalSurface) {
auto & actual_slave_nodes = this->mesh.getElementgroup("slave").getNodes();
auto nb_slave_nodes = actual_slave_nodes.size();
this->checkNbSlaveNodes(nb_slave_nodes);
auto & actual_master_nodes = this->mesh.getElementgroup("master").getNodes();
auto nb_master_nodes = actual_master_nodes.size();
this->checkNbMasterNodes(nb_master_nodes);
}
diff --git a/test/test_model/test_contact_mechanics_model/test_selector/test_selection_fixture.hh b/test/test_model/test_contact_mechanics_model/test_selector/test_selection_fixture.hh
index 55c8afeab..c993e4000 100644
--- a/test/test_model/test_contact_mechanics_model/test_selector/test_selection_fixture.hh
+++ b/test/test_model/test_contact_mechanics_model/test_selector/test_selection_fixture.hh
@@ -1,85 +1,86 @@
/**
- * @file test_selection.cc
+ * @file test_selection_fixture.hh
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Sat Feb 29 2020
- * @date last modification: Sat Feb 29 2020
+ * @date creation: Wed May 08 2019
+ * @date last modification: Fri Dec 11 2020
*
* @brief Generic test for selection of nodes across different surfaces
*
+ *
* @section LICENSE
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "surface_selector.hh"
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
using namespace akantu;
template <typename dim_>
class TestSurfaceSelecionFixture : public ::testing::Test {
public:
static constexpr size_t spatial_dimension = dim_::value;
void Setup() override {
mesh = std::make_unique<Mesh>(spatial_dimension);
mesh->read("selection_" + std::string(spatial_dimension) + "D.msh");
selector = make_unique<PhysicalSurfaceSelector>(*mesh);
}
void TearDown() {
mesh.reset(nullptr);
selector.reset(nullptr);
}
bool checkNbSlaveNodes(UInt & act_slave_nodes) {
auto & slave_list = this->selectior->getSlaveList();
auto nb_slave_nodes = slave_list.size();
EXCEP_EQ(nb_slave_nodes, act_slave_nodes)
}
bool checkNbmasterNodes(UInt & act_master_nodes) {
auto & master_list = this->selectior->getMasterList();
auto nb_master_nodes = master_list.size();
EXCEP_EQ(nb_master_nodes, act_master_nodes)
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<PhysicalSurfaceSelector> selector
};
using dim_types = gtest_list_t<std::tuple<1, 2, 3>>;
TYPED_TEST_SUITE(TestSurfaceSelectionFixture, dim_types);
diff --git a/test/test_model/test_phase_field_model/CMakeLists.txt b/test/test_model/test_phase_field_model/CMakeLists.txt
index 6a2001030..5d962ac21 100644
--- a/test/test_model/test_phase_field_model/CMakeLists.txt
+++ b/test/test_model/test_phase_field_model/CMakeLists.txt
@@ -1,53 +1,55 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mohit Pundir <mohit.pundir@epfl.ch>
#
-# @date creation: Thu Dec 20 2018
-# @date last modification: Thu Dec 20 2018
+# @date creation: Fri Sep 03 2010
+# @date last modification: Tue Jun 08 2021
#
# @brief test for the phase field model
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License along
# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
register_test(test_phasefield_selector
SOURCES test_phasefield_selector.cc
FILES_TO_COPY phasefield_selector.dat phasefield_selector.msh
PACKAGE phase_field
)
register_test(test_phase_solid_coupling
SOURCES test_phase_solid_coupling.cc
FILES_TO_COPY material_coupling.dat test_one_element.msh
PACKAGE phase_field
)
register_test(test_phase_solid_explicit
SOURCES test_phase_solid_explicit.cc
FILES_TO_COPY material_coupling.dat test_one_element.msh
PACKAGE phase_field
)
register_test(test_multi_material
SOURCES test_multi_material.cc
FILES_TO_COPY material_multiple.dat test_two_element.msh
PACKAGE phase_field
)
diff --git a/test/test_model/test_phase_field_model/test_multi_material.cc b/test/test_model/test_phase_field_model/test_multi_material.cc
index 612c13114..436374dc9 100644
--- a/test/test_model/test_phase_field_model/test_multi_material.cc
+++ b/test/test_model/test_phase_field_model/test_multi_material.cc
@@ -1,130 +1,131 @@
/**
- * @file tets_phase_field_2d.cc
+ * @file test_multi_material.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Mon Oct 1 2018
+ * @date creation: Wed Feb 24 2021
+ * @date last modification: Sun Feb 28 2021
*
* @brief test of the class PhaseFieldModel on the 2d square
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "non_linear_solver.hh"
#include "coupler_solid_phasefield.hh"
#include "solid_mechanics_model.hh"
#include "phase_field_model.hh"
#include "material.hh"
#include "material_phasefield.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
const UInt spatial_dimension = 2;
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel &, Real &);
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
initialize("material_multiple.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("test_two_element.msh");
CouplerSolidPhaseField coupler(mesh);
auto & model = coupler.getSolidMechanicsModel();
auto & phase = coupler.getPhaseFieldModel();
auto && mat_selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names", model);
model.setMaterialSelector(mat_selector);
model.initFull(_analysis_method = _explicit_lumped_mass);
Real time_step = model.getStableTimeStep();
time_step *= 0.8;
model.setTimeStep(time_step);
auto && selector = std::make_shared<MeshDataPhaseFieldSelector<std::string>>(
"physical_names", phase);
phase.setPhaseFieldSelector(selector);
phase.initFull(_analysis_method = _static);
model.setBaseName("multi_material");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("damage");
model.addDumpFieldVector("displacement");
model.addDumpField("blocked_dofs");
model.dump();
UInt nbSteps = 1000;
Real increment = 1e-4;
for (UInt s = 0; s < nbSteps; ++s) {
Real axial_strain = increment * s;
applyDisplacement(model, axial_strain);
coupler.solve();
model.dump();
}
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel & model, Real & increment) {
auto & displacement = model.getDisplacement();
auto & positions = model.getMesh().getNodes();
auto & blocked_dofs = model.getBlockedDOFs();
for (UInt n = 0; n < model.getMesh().getNbNodes(); ++n) {
if (positions(n, 1) == -1) {
displacement(n, 1) = 0;
blocked_dofs(n, 1) = true;
displacement(n, 0) = 0;
blocked_dofs(n ,0) = true;
}
else if (positions(n, 1) == 1) {
displacement(n, 0) = 0;
displacement(n, 1) = increment;
blocked_dofs(n, 0) = true;
blocked_dofs(n ,1) = true;
}
else {
displacement(n, 0) = 0;
blocked_dofs(n, 0) = true;
}
}
}
diff --git a/test/test_model/test_phase_field_model/test_phase_solid_coupling.cc b/test/test_model/test_phase_field_model/test_phase_solid_coupling.cc
index dc8b0ca65..dfabfa83e 100644
--- a/test/test_model/test_phase_field_model/test_phase_solid_coupling.cc
+++ b/test/test_model/test_phase_field_model/test_phase_solid_coupling.cc
@@ -1,277 +1,278 @@
/**
- * @file test_phase_field_coupling.cc
+ * @file test_phase_solid_coupling.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Thu Feb 25 2021
+ * @date creation: Sun Jan 06 2019
+ * @date last modification: Wed Mar 03 2021
*
* @brief test of the class PhaseFieldModel on the 2d square
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
-
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "phase_field_model.hh"
#include "material.hh"
#include "material_phasefield.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
const UInt spatial_dimension = 2;
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel &, Real &);
void computeStrainOnQuadPoints(SolidMechanicsModel &, PhaseFieldModel &, const GhostType &);
void computeDamageOnQuadPoints(SolidMechanicsModel &, PhaseFieldModel &, const GhostType &);
void gradUToEpsilon(const Matrix<Real> &, Matrix<Real> &);
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
std::ofstream os("data.csv");
os << "#strain stress damage analytical_sigma analytical_damage" << std::endl;
initialize("material_coupling.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("test_one_element.msh");
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
PhaseFieldModel phase(mesh);
auto && selector = std::make_shared<MeshDataPhaseFieldSelector<std::string>>(
"physical_names", phase);
phase.setPhaseFieldSelector(selector);
phase.initFull(_analysis_method = _static);
model.setBaseName("phase_solid");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpFieldVector("displacement");
model.addDumpField("damage");
model.dump();
UInt nbSteps = 1000;
Real increment = 1e-4;
auto & stress = model.getMaterial(0).getArray<Real>("stress", _quadrangle_4);
auto & damage = model.getMaterial(0).getArray<Real>("damage", _quadrangle_4);
Real analytical_damage{0.};
Real analytical_sigma{0.};
auto & phasefield = phase.getPhaseField(0);
const Real E = phasefield.getParam("E");
const Real nu = phasefield.getParam("nu");
Real c22 = E*(1-nu)/((1+nu)*(1-2*nu));
const Real gc = phasefield.getParam("gc");
const Real l0 = phasefield.getParam("l0");
Real error_stress{0.};
Real error_damage{0.};
for (UInt s = 0; s < nbSteps; ++s) {
Real axial_strain = increment * s;
applyDisplacement(model, axial_strain);
model.solveStep();
computeStrainOnQuadPoints(model, phase, _not_ghost);
phase.solveStep();
computeDamageOnQuadPoints(model, phase, _not_ghost);
model.assembleInternalForces();
analytical_damage = axial_strain*axial_strain*c22/(gc/l0 + axial_strain*axial_strain*c22);
analytical_sigma = c22*axial_strain*(1-analytical_damage)*(1-analytical_damage);
error_stress = std::abs(analytical_sigma - stress(0, 3))/analytical_sigma;
error_damage = std::abs(analytical_damage - damage(0))/analytical_damage;
if (error_damage > 1e-8 and error_stress > 1e-8) {
return EXIT_FAILURE;
}
os << axial_strain << " " << stress(0, 3) << " " << damage(0) << " "
<< analytical_sigma << " " << analytical_damage << " " <<
error_stress << " " << error_damage << std::endl;
model.dump();
}
os.close();
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel & model, Real & increment) {
auto & displacement = model.getDisplacement();
auto & positions = model.getMesh().getNodes();
auto & blocked_dofs = model.getBlockedDOFs();
for (UInt n = 0; n < model.getMesh().getNbNodes(); ++n) {
if (positions(n, 1) == -0.5) {
displacement(n, 0) = 0;
displacement(n, 1) = 0;
blocked_dofs(n, 0) = true;
blocked_dofs(n ,1) = true;
}
else {
displacement(n, 0) = 0;
displacement(n, 1) = increment;
blocked_dofs(n, 0) = true;
blocked_dofs(n ,1) = true;
}
}
}
/* -------------------------------------------------------------------------- */
void computeStrainOnQuadPoints(SolidMechanicsModel & solid, PhaseFieldModel & phase,
const GhostType & ghost_type) {
auto & mesh = solid.getMesh();
auto nb_materials = solid.getNbMaterials();
auto nb_phasefields = phase.getNbPhaseFields();
AKANTU_DEBUG_ASSERT(nb_phasefields == nb_materials,
"The number of phasefields and materials should be equal" );
for(auto index : arange(nb_materials)) {
auto & material = solid.getMaterial(index);
for(auto index2 : arange(nb_phasefields)) {
auto & phasefield = phase.getPhaseField(index2);
if(phasefield.getName() == material.getName()){
auto & strain_on_qpoints = phasefield.getStrain();
auto & gradu_on_qpoints = material.getGradU();
for (auto & type: mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & strain_on_qpoints_vect = strain_on_qpoints(type, ghost_type);
auto & gradu_on_qpoints_vect = gradu_on_qpoints(type, ghost_type);
for (auto && values:
zip(make_view(strain_on_qpoints_vect, spatial_dimension, spatial_dimension),
make_view(gradu_on_qpoints_vect, spatial_dimension, spatial_dimension))) {
auto & strain = std::get<0>(values);
auto & grad_u = std::get<1>(values);
gradUToEpsilon(grad_u, strain);
}
}
break;
}
}
}
}
/* -------------------------------------------------------------------------- */
void computeDamageOnQuadPoints(SolidMechanicsModel & solid, PhaseFieldModel & phase,
const GhostType & ghost_type) {
auto & fem = phase.getFEEngine();
auto & mesh = phase.getMesh();
auto nb_materials = solid.getNbMaterials();
auto nb_phasefields = phase.getNbPhaseFields();
AKANTU_DEBUG_ASSERT(nb_phasefields == nb_materials,
"The number of phasefields and materials should be equal" );
for(auto index : arange(nb_materials)) {
auto & material = solid.getMaterial(index);
for(auto index2 : arange(nb_phasefields)) {
auto & phasefield = phase.getPhaseField(index2);
if(phasefield.getName() == material.getName()){
switch (spatial_dimension) {
case 1: {
auto & mat = static_cast<MaterialPhaseField<1> &>(material);
auto & solid_damage = mat.getDamage();
for (auto & type: mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & damage_on_qpoints_vect = solid_damage(type, ghost_type);
fem.interpolateOnIntegrationPoints(phase.getDamage(), damage_on_qpoints_vect,
1, type, ghost_type);
}
break;
}
case 2: {
auto & mat = static_cast<MaterialPhaseField<2> &>(material);
auto & solid_damage = mat.getDamage();
for (auto & type: mesh.elementTypes(spatial_dimension, ghost_type)) {
auto & damage_on_qpoints_vect = solid_damage(type, ghost_type);
fem.interpolateOnIntegrationPoints(phase.getDamage(), damage_on_qpoints_vect,
1, type, ghost_type);
}
break;
}
default:
break;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void gradUToEpsilon(const Matrix<Real> & grad_u, Matrix<Real> & epsilon) {
for (UInt i=0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j)
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
}
}
diff --git a/test/test_model/test_phase_field_model/test_phase_solid_explicit.cc b/test/test_model/test_phase_field_model/test_phase_solid_explicit.cc
index e25c3d04c..f5d270816 100644
--- a/test/test_model/test_phase_field_model/test_phase_solid_explicit.cc
+++ b/test/test_model/test_phase_field_model/test_phase_solid_explicit.cc
@@ -1,152 +1,154 @@
/**
- * @file test_phase_field_explicit.cc
+ * @file test_phase_solid_explicit.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Thu Feb 28 2021
+ * @date creation: Sun Feb 28 2021
+ * @date last modification: Fri Jun 25 2021
*
* @brief test of the class PhaseFieldModel on the 2d square
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory
- * (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "coupler_solid_phasefield.hh"
#include "non_linear_solver.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
const UInt spatial_dimension = 2;
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel &, Real &);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
std::ofstream os("data-explicit.csv");
os << "#strain stress damage analytical_sigma analytical_damage error_stress "
"error_damage"
<< std::endl;
initialize("material_coupling.dat", argc, argv);
Mesh mesh(spatial_dimension);
mesh.read("test_one_element.msh");
CouplerSolidPhaseField coupler(mesh);
auto & model = coupler.getSolidMechanicsModel();
auto & phase = coupler.getPhaseFieldModel();
model.initFull(_analysis_method = _explicit_lumped_mass);
Real time_factor = 0.8;
Real stable_time_step = model.getStableTimeStep() * time_factor;
model.setTimeStep(stable_time_step);
auto && selector = std::make_shared<MeshDataPhaseFieldSelector<std::string>>(
"physical_names", phase);
phase.setPhaseFieldSelector(selector);
phase.initFull(_analysis_method = _static);
model.setBaseName("phase_solid");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpFieldVector("displacement");
model.addDumpField("damage");
model.dump();
UInt nbSteps = 1000;
Real increment = 1e-4;
auto & stress = model.getMaterial(0).getArray<Real>("stress", _quadrangle_4);
auto & damage = model.getMaterial(0).getArray<Real>("damage", _quadrangle_4);
Real analytical_damage{0.};
Real analytical_sigma{0.};
auto & phasefield = phase.getPhaseField(0);
const Real E = phasefield.getParam("E");
const Real nu = phasefield.getParam("nu");
Real c22 = E * (1 - nu) / ((1 + nu) * (1 - 2 * nu));
const Real gc = phasefield.getParam("gc");
const Real l0 = phasefield.getParam("l0");
Real error_stress{0.};
Real error_damage{0.};
for (UInt s = 0; s < nbSteps; ++s) {
Real axial_strain = increment * s;
applyDisplacement(model, axial_strain);
coupler.solve("explicit_lumped", "static");
analytical_damage = axial_strain * axial_strain * c22 /
(gc / l0 + axial_strain * axial_strain * c22);
analytical_sigma =
c22 * axial_strain * (1 - analytical_damage) * (1 - analytical_damage);
error_stress = std::abs(analytical_sigma - stress(0, 3)) / analytical_sigma;
error_damage = std::abs(analytical_damage - damage(0)) / analytical_damage;
if (error_damage > 1e-8 and error_stress > 1e-8) {
return EXIT_FAILURE;
}
os << axial_strain << " " << stress(0, 3) << " " << damage(0) << " "
<< analytical_sigma << " " << analytical_damage << " " << error_stress
<< " " << error_damage << std::endl;
model.dump();
}
os.close();
finalize();
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void applyDisplacement(SolidMechanicsModel & model, Real & increment) {
auto & displacement = model.getDisplacement();
auto & positions = model.getMesh().getNodes();
auto & blocked_dofs = model.getBlockedDOFs();
for (UInt n = 0; n < model.getMesh().getNbNodes(); ++n) {
if (positions(n, 1) == -0.5) {
displacement(n, 0) = 0;
displacement(n, 1) = 0;
blocked_dofs(n, 0) = true;
blocked_dofs(n, 1) = true;
} else {
displacement(n, 0) = 0;
displacement(n, 1) = increment;
blocked_dofs(n, 0) = true;
blocked_dofs(n, 1) = true;
}
}
}
diff --git a/test/test_model/test_phase_field_model/test_phasefield_selector.cc b/test/test_model/test_phase_field_model/test_phasefield_selector.cc
index 7bd6945c5..7f62938e2 100644
--- a/test/test_model/test_phase_field_model/test_phasefield_selector.cc
+++ b/test/test_model/test_phase_field_model/test_phasefield_selector.cc
@@ -1,69 +1,70 @@
/**
* @file test_phasefield_selector.cc
*
* @author Mohit Pundir <mohit.pundir@epfl.ch>
*
- * @date creation: Thu Jun 18 2020
- * @date last modification: Thu Jun 18 2020
+ * @date creation: Fri May 01 2015
+ * @date last modification: Wed Apr 28 2021
*
* @brief Test for phasefield selector
*
+ *
* @section LICENSE
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "aka_common.hh"
#include "phase_field_model.hh"
#include "phasefield_exponential.hh"
using namespace akantu;
int main(int argc, char *argv[]){
initialize("phasefield_selector.dat", argc, argv);
Math::setTolerance(1e-8);
Mesh mesh(1);
mesh.read("phasefield_selector.msh");
PhaseFieldModel model(mesh);
auto && selector = std::make_shared<MeshDataPhaseFieldSelector<std::string>>(
"physical_names", model);
model.setPhaseFieldSelector(selector);
model.initFull();
PhaseField & chocolate = model.getPhaseField("chocolate");
PhaseField & chewing_gum = model.getPhaseField("chewing-gum");
PhaseField & candy = model.getPhaseField("candy");
UInt chocolate_element = chocolate.getElementFilter(_segment_2)(0, 0);
UInt chewing_gum_element = chewing_gum.getElementFilter(_segment_2)(0, 0);
UInt candy_element = candy.getElementFilter(_segment_2)(0, 0);
if (chocolate_element != 0 || chewing_gum_element != 1 || candy_element != 2 ) {
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/CMakeLists.txt
index 8a312f6e4..9635a9efe 100644
--- a/test/test_model/test_solid_mechanics_model/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/CMakeLists.txt
@@ -1,81 +1,96 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Tobias Brink <tobias.brink@epfl.ch>
+# @author Mauro Corrado <mauro.corrado@epfl.ch>
+# @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+# @author Lucas Frerot <lucas.frerot@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Sep 03 2010
-# @date last modification: Tue Jan 30 2018
+# @date last modification: Thu Oct 29 2020
#
# @brief configuratio for SolidMechanicsModel tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_akantu_test(test_materials "test_materials")
add_akantu_test(test_cohesive "cohesive_test")
add_akantu_test(test_embedded_interface "test_embedded_interface")
add_akantu_test(test_energies "test energies")
#===============================================================================
#===============================================================================
add_mesh(test_cube3d_two_mat_mesh cube_two_materials.geo 3 1)
register_test(test_solid_mechanics_model_reassign_material
SOURCES test_solid_mechanics_model_reassign_material.cc
DEPENDS test_cube3d_two_mat_mesh
FILES_TO_COPY two_materials.dat
PACKAGE parallel implicit
PARALLEL
)
#===============================================================================
register_test(test_solid_mechanics_model_material_eigenstrain
SOURCES test_solid_mechanics_model_material_eigenstrain.cc
FILES_TO_COPY cube_3d_tet_4.msh; material_elastic_plane_strain.dat
PACKAGE implicit
)
#===============================================================================
register_test(test_solid_mechanics_model_material_large_rotation
SOURCES test_solid_mechanics_model_material_large_rotation.cc
FILES_TO_COPY cube_3d_tet_4.msh; material_elastic.dat
PACKAGE implicit
UNSTABLE
)
#===============================================================================
register_test(test_material_selector
SOURCES test_material_selector.cc
FILES_TO_COPY material_selector.dat material_selector.msh
PACKAGE core
)
#===============================================================================
# dynamics tests
#===============================================================================
register_gtest_sources(
SOURCES test_solid_mechanics_model_dynamics.cc
FILES_TO_COPY test_solid_mechanics_model_dynamics_material.dat
PACKAGE core
)
register_gtest_test(test_solid_mechanics_model
DEPENDS ${PATCH_TEST_BAR_MESHES}
#bar_segment_2 bar_segment_3
#bar_triangle_3 bar_triangle_6
#bar_quadrangle_4 bar_quadrangle_8
#bar_tetrahedron_4 bar_tetrahedron_10
#bar_hexahedron_8 bar_hexahedron_20
#bar_pentahedron_6 bar_pentahedron_15
PARALLEL
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/CMakeLists.txt
index dcb7a243a..73d57a463 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/CMakeLists.txt
@@ -1,106 +1,117 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Feb 21 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Thu Dec 20 2018
#
# @brief configuration for cohesive elements tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#add_akantu_test(test_cohesive_intrinsic "test_cohesive_intrinsic")
#add_akantu_test(test_cohesive_extrinsic "test_cohesive_extrinsic")
#add_akantu_test(test_cohesive_intrinsic_impl "test_cohesive_intrinsic_impl")
#add_akantu_test(test_cohesive_1d_element "test_cohesive_1d_element")
#add_akantu_test(test_cohesive_extrinsic_implicit "test_cohesive_extrinsic_implicit")
add_akantu_test(test_materials "test_cohesive_materials")
add_akantu_test(test_cohesive_buildfragments "test_cohesive_buildfragments")
add_akantu_test(test_cohesive_insertion "test_cohesive_insertion")
add_akantu_test(test_cohesive_linear_friction "test_cohesive_linear_friction")
#add_akantu_test(test_parallel_cohesive "parallel_cohesive_test")
set(_meshes)
add_mesh(cohesive_1d_2_seg data/cohesive_1D.geo
DIM 2 ORDER 1
OUTPUT _cohesive_1d_2_segment_2.msh)
list(APPEND _meshes cohesive_1d_2_seg)
add_mesh(cohesive_2d_4_tri data/cohesive_strait_2D.geo
DIM 2 ORDER 1
OUTPUT _cohesive_2d_4_triangle_3.msh)
list(APPEND _meshes cohesive_2d_4_tri)
add_mesh(cohesive_2d_6_tri data/cohesive_strait_2D.geo
DIM 2 ORDER 2
OUTPUT _cohesive_2d_6_triangle_6.msh)
list(APPEND _meshes cohesive_2d_6_tri)
add_mesh(cohesive_2d_4_quad data/cohesive_strait_2D_structured.geo
DIM 2 ORDER 1
OUTPUT _cohesive_2d_4_quadrangle_4.msh)
list(APPEND _meshes cohesive_2d_4_quad)
add_mesh(cohesive_2d_6_quad data/cohesive_strait_2D_structured.geo
DIM 2 ORDER 2
OUTPUT _cohesive_2d_6_quadrangle_8.msh)
list(APPEND _meshes cohesive_2d_6_quad)
add_mesh(cohesive_2d_4_tri_quad data/cohesive_strait_2D_mixte.geo
DIM 2 ORDER 1
OUTPUT _cohesive_2d_4_triangle_3_quadrangle_4.msh)
list(APPEND _meshes cohesive_2d_4_tri_quad)
add_mesh(cohesive_2d_6_tri_quad data/cohesive_strait_2D_mixte.geo
DIM 2 ORDER 2
OUTPUT _cohesive_2d_6_triangle_6_quadrangle_8.msh)
list(APPEND _meshes cohesive_2d_6_tri_quad)
add_mesh(cohesive_3d_6_tet data/cohesive_strait_3D.geo
DIM 3 ORDER 1
OUTPUT _cohesive_3d_6_tetrahedron_4.msh)
list(APPEND _meshes cohesive_3d_6_tet)
add_mesh(cohesive_3d_12_tet data/cohesive_strait_3D.geo
DIM 3 ORDER 2
OUTPUT _cohesive_3d_12_tetrahedron_10.msh)
list(APPEND _meshes cohesive_3d_12_tet)
add_mesh(cohesive_3d_8_hex data/cohesive_strait_3D_structured.geo
DIM 3 ORDER 1
OUTPUT _cohesive_3d_8_hexahedron_8.msh)
list(APPEND _meshes cohesive_3d_8_hex)
add_mesh(cohesive_3d_16_hex data/cohesive_strait_3D_structured.geo
DIM 3 ORDER 2
OUTPUT _cohesive_3d_16_hexahedron_20.msh)
list(APPEND _meshes cohesive_3d_16_hex)
register_gtest_sources(
SOURCES test_cohesive.cc
PACKAGE cohesive_element
DEPENDS ${_meshes}
FILES_TO_COPY material_0.dat material_1.dat material_0_finite_def.dat
)
register_gtest_test(test_solid_mechanics_model_cohesive
PARALLEL
PARALLEL_LEVEL 1 2
)
# ==============================================================================
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive.cc
index 4acbca459..c0f246d38 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive.cc
@@ -1,132 +1,135 @@
/**
* @file test_cohesive.cc
*
+ * @author Tobias Brink <tobias.brink@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Mon Feb 19 2018
+ * @date creation: Wed Jan 10 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief Generic test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "test_cohesive_fixture.hh"
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestSMMCFixture, ExtrinsicModeI) {
if (this->mesh->getCommunicator().getNbProc() > 1 and this->dim == 1) {
SUCCEED();
return;
}
getStaticParser().parse("material_0.dat");
this->is_extrinsic = true;
this->analysis_method = _explicit_lumped_mass;
this->testModeI();
this->checkInsertion();
auto & mat_co = this->model->getMaterial("insertion");
Real G_c = mat_co.get("G_c");
// if (this->dim != 3)
this->checkDissipated(G_c);
}
TYPED_TEST(TestSMMCFixture, ExtrinsicModeIFiniteDef) {
if (this->dim == 1) {
SUCCEED();
return;
}
getStaticParser().parse("material_0_finite_def.dat");
this->is_extrinsic = true;
this->analysis_method = _explicit_lumped_mass;
this->testModeI();
this->checkInsertion();
auto & mat_co = this->model->getMaterial("insertion");
Real G_c = mat_co.get("G_c");
// if (this->dim != 3)
this->checkDissipated(G_c);
}
TYPED_TEST(TestSMMCFixture, ExtrinsicModeII) {
if (this->mesh->getCommunicator().getNbProc() > 1 and this->dim == 1) {
SUCCEED();
return;
}
getStaticParser().parse("material_0.dat");
this->is_extrinsic = true;
this->analysis_method = _explicit_lumped_mass;
this->testModeII();
this->checkInsertion();
auto & mat_co = this->model->getMaterial("insertion");
Real G_c = mat_co.get("G_c");
// if (this->dim != 3)
this->checkDissipated(G_c);
}
TYPED_TEST(TestSMMCFixture, IntrinsicModeI) {
if (this->mesh->getCommunicator().getNbProc() > 1 and this->dim == 1) {
SUCCEED();
return;
}
getStaticParser().parse("material_1.dat");
this->is_extrinsic = false;
this->analysis_method = _explicit_lumped_mass;
this->testModeI();
this->checkInsertion();
auto & mat_co = this->model->getMaterial("insertion");
Real G_c = mat_co.get("G_c");
// if (this->dim != 3)
this->checkDissipated(G_c);
}
TYPED_TEST(TestSMMCFixture, IntrinsicModeII) {
if (this->mesh->getCommunicator().getNbProc() > 1 and this->dim == 1) {
SUCCEED();
return;
}
getStaticParser().parse("material_1.dat");
this->is_extrinsic = false;
this->analysis_method = _explicit_lumped_mass;
this->testModeII();
this->checkInsertion();
auto & mat_co = this->model->getMaterial("insertion");
Real G_c = mat_co.get("G_c");
// if (this->dim != 3)
this->checkDissipated(G_c);
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/CMakeLists.txt
index 04fff76db..55182093e 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/CMakeLists.txt
@@ -1,34 +1,44 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for parallel test for extrinsic cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
if(AKANTU_PARALLEL)
add_mesh(test_cohesive_1d_element_mesh bar.geo 1 2)
register_test(test_cohesive_1d_element
SOURCES test_cohesive_1d_element.cc
DEPENDS test_cohesive_1d_element_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element)
endif()
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
index 03710d45d..5c226fab3 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_1d_element/test_cohesive_1d_element.cc
@@ -1,102 +1,104 @@
/**
* @file test_cohesive_1d_element.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Fri Jun 14 2013
- * @date last modification: Wed Jan 10 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jan 10 2018
*
* @brief Test for 1D cohesive elements
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 2000;
const Real strain_rate = 5;
UInt spatial_dimension = 1;
Mesh mesh(spatial_dimension, "mesh");
mesh.read("bar.msh");
Math::setTolerance(1e-7);
SolidMechanicsModelCohesive model(mesh);
model.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = true);
auto time_step = model.getStableTimeStep() * 0.01;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
auto posx_max = mesh.getUpperBounds()(_x);
auto posx_min = mesh.getLowerBounds()(_x);
/// initial conditions
const auto & position = mesh.getNodes();
auto & velocity = model.getVelocity();
auto nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n)
velocity(n) = strain_rate * (position(n) - (posx_max + posx_min) / 2.);
/// boundary conditions
model.applyBC(BC::Dirichlet::FlagOnly(_x), "left");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "right");
auto disp_increment = strain_rate * (posx_max - posx_min) / 2. * time_step;
model.assembleInternalForces();
for (UInt s = 1; s <= max_steps; ++s) {
model.checkCohesiveStress();
model.solveStep();
auto nb_cohesive_elements = mesh.getNbElement(_cohesive_1d_2);
if (s % 10 == 0) {
std::cout << "passing step " << s << "/" << max_steps
<< ", number of cohesive elemets:" << nb_cohesive_elements
<< std::endl;
}
/// update external work and boundary conditions
model.applyBC(BC::Dirichlet::IncrementValue(-disp_increment, _x), "left");
model.applyBC(BC::Dirichlet::IncrementValue(disp_increment, _x), "right");
}
auto Ed = model.getEnergy("dissipated");
auto Edt = 100. * 3.;
std::cout << Ed << " " << Edt << std::endl;
if (std::abs(Ed - Edt) > 0.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/CMakeLists.txt
index 173f6321a..532a24237 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/CMakeLists.txt
@@ -1,33 +1,43 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 22 2016
#
# @brief configuration for build fragments tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_buildfragments_mesh mesh.geo 2 1)
register_test(test_cohesive_buildfragments
SOURCES test_cohesive_buildfragments.cc
DEPENDS test_cohesive_buildfragments_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/test_cohesive_buildfragments.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/test_cohesive_buildfragments.cc
index 1dad5613b..6672010ab 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/test_cohesive_buildfragments.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_buildfragments/test_cohesive_buildfragments.cc
@@ -1,180 +1,183 @@
/**
* @file test_cohesive_buildfragments.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Tue Aug 22 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu May 09 2019
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Math::setTolerance(1e-14);
const UInt spatial_dimension = 2;
const UInt max_steps = 200;
Real strain_rate = 1.e5;
ElementType type = _quadrangle_4;
Real L = 0.03;
Real theoretical_mass = L * L / 20. * 2500;
ElementType type_facet = Mesh::getFacetType(type);
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Mesh mesh(spatial_dimension);
mesh.read("mesh.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(_analysis_method = _explicit_lumped_mass,
_is_extrinsic = true);
Real time_step = model.getStableTimeStep() * 0.05;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
Real disp_increment = strain_rate * L / 2. * time_step;
model.assembleMassLumped();
Array<Real> & velocity = model.getVelocity();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
/// initial conditions
for (UInt n = 0; n < nb_nodes; ++n)
velocity(n, 0) = strain_rate * position(n, 0);
/// boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0, _x), "Left_side");
model.applyBC(BC::Dirichlet::FixedValue(0, _x), "Right_side");
UInt cohesive_index = 1;
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
MaterialCohesive & mat_cohesive =
dynamic_cast<MaterialCohesive &>(model.getMaterial(cohesive_index));
const Array<Real> & damage = mat_cohesive.getDamage(type_cohesive);
FragmentManager fragment_manager(model, false);
const Array<Real> & fragment_mass = fragment_manager.getMass();
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.checkCohesiveStress();
model.solveStep();
/// apply boundary conditions
model.applyBC(BC::Dirichlet::IncrementValue(-disp_increment, _x),
"Left_side");
model.applyBC(BC::Dirichlet::IncrementValue(disp_increment, _x),
"Right_side");
if (s % 1 == 0) {
// model.dump();
std::cout << "passing step " << s << "/" << max_steps << std::endl;
fragment_manager.computeAllData();
/// check number of fragments
UInt nb_fragment_num = fragment_manager.getNbFragment();
UInt nb_cohesive_elements = mesh.getNbElement(type_cohesive);
UInt nb_fragment = 1;
for (UInt el = 0; el < nb_cohesive_elements; ++el) {
UInt q = 0;
while (q < nb_quad_per_facet &&
Math::are_float_equal(damage(el * nb_quad_per_facet + q), 1))
++q;
if (q == nb_quad_per_facet) {
++nb_fragment;
}
}
if (nb_fragment != nb_fragment_num) {
std::cout << "The number of fragments is wrong!" << std::endl;
return EXIT_FAILURE;
}
/// check mass computation
Real total_mass = 0.;
for (UInt frag = 0; frag < nb_fragment_num; ++frag) {
total_mass += fragment_mass(frag);
}
if (!Math::are_float_equal(theoretical_mass, total_mass)) {
std::cout << "The fragments' mass is wrong!" << std::endl;
return EXIT_FAILURE;
}
}
}
model.dump();
/// check velocities
UInt nb_fragment = fragment_manager.getNbFragment();
const Array<Real> & fragment_velocity = fragment_manager.getVelocity();
const Array<Real> & fragment_center = fragment_manager.getCenterOfMass();
Real fragment_length = L / nb_fragment;
Real initial_position = -L / 2. + fragment_length / 2.;
for (UInt frag = 0; frag < nb_fragment; ++frag) {
Real theoretical_center = initial_position + fragment_length * frag;
if (!Math::are_float_equal(fragment_center(frag, 0), theoretical_center)) {
std::cout << "The fragments' center is wrong!" << std::endl;
return EXIT_FAILURE;
}
Real initial_vel = fragment_center(frag, 0) * strain_rate;
Math::setTolerance(100);
if (!Math::are_float_equal(fragment_velocity(frag), initial_vel)) {
std::cout << "The fragments' velocity is wrong!" << std::endl;
return EXIT_FAILURE;
}
}
finalize();
std::cout << "OK: test_cohesive_buildfragments was passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/CMakeLists.txt
index 90f40c4c8..6ae488063 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/CMakeLists.txt
@@ -1,54 +1,64 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for extrinsic cohesive elements tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_extrinsic_mesh triangle.geo 2 1)
add_mesh(test_cohesive_extrinsic_quadrangle_mesh quadrangle.geo 2 2)
add_mesh(test_cohesive_extrinsic_tetrahedron_mesh tetrahedron.geo 3 2)
register_test(test_cohesive_extrinsic
SOURCES test_cohesive_extrinsic.cc
DEPENDS test_cohesive_extrinsic_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element
)
register_test(test_cohesive_extrinsic_quadrangle
SOURCES test_cohesive_extrinsic_quadrangle.cc
DEPENDS test_cohesive_extrinsic_quadrangle_mesh
PACKAGE cohesive_element
)
register_test(test_cohesive_extrinsic_tetrahedron
SOURCES test_cohesive_extrinsic_tetrahedron.cc
DEPENDS test_cohesive_extrinsic_tetrahedron_mesh
PACKAGE cohesive_element
)
register_test(test_cohesive_extrinsic_fatigue
SOURCES test_cohesive_extrinsic_fatigue.cc
FILES_TO_COPY material_fatigue.dat fatigue.msh
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic.cc
index 257d2d6e4..ee94efbb1 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic.cc
@@ -1,134 +1,136 @@
/**
* @file test_cohesive_extrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Dec 14 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Dec 14 2017
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
const UInt max_steps = 1000;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
model.getElementInserter().setLimit(_y, -0.30, -0.20);
model.updateAutomaticInsertion();
mesh.setBaseName("test_cohesive_extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("mass");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.addDumpField("grad_u");
model.dump();
Real time_step = model.getStableTimeStep() * 0.05;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
/// initial conditions
Real loading_rate = 0.5;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
displacement(n, 1) += disp_update * position(n, 1);
}
model.checkCohesiveStress();
model.solveStep();
if (s % 100 == 0) {
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
model.dump();
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 200 * std::sqrt(2);
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_extrinsic was passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
index 0b54fc97a..2722d739f 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_fatigue.cc
@@ -1,242 +1,244 @@
/**
* @file test_cohesive_extrinsic_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test for the linear fatigue cohesive law
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_fatigue.hh"
#include "solid_mechanics_model_cohesive.hh"
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
// the following class contains an implementation of the 1D linear
// fatigue cohesive law
class MaterialFatigue {
public:
MaterialFatigue(Real delta_f, Real sigma_c, Real delta_c)
: delta_f(delta_f), sigma_c(sigma_c), delta_c(delta_c), delta_prec(0),
traction(sigma_c), delta_max(0),
stiff_plus(std::numeric_limits<Real>::max()),
tolerance(Math::getTolerance()){};
Real computeTraction(Real delta) {
if (delta - delta_c > -tolerance)
traction = 0;
else if (delta_max < tolerance && delta < tolerance)
traction = sigma_c;
else {
Real delta_dot = delta - delta_prec;
if (delta_dot > -tolerance) {
stiff_plus *= 1 - delta_dot / delta_f;
traction += stiff_plus * delta_dot;
Real max_traction = sigma_c * (1 - delta / delta_c);
if (traction - max_traction > -tolerance || delta_max < tolerance) {
traction = max_traction;
stiff_plus = traction / delta;
}
} else {
Real stiff_minus = traction / delta_prec;
stiff_plus += (stiff_plus - stiff_minus) * delta_dot / delta_f;
traction += stiff_minus * delta_dot;
}
}
delta_prec = delta;
delta_max = std::max(delta, delta_max);
return traction;
}
private:
const Real delta_f;
const Real sigma_c;
const Real delta_c;
Real delta_prec;
Real traction;
Real delta_max;
Real stiff_plus;
const Real tolerance;
};
void imposeOpening(SolidMechanicsModelCohesive &, Real);
void arange(Array<Real> &, Real, Real, Real);
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_fatigue.dat", argc, argv);
Math::setTolerance(1e-13);
const UInt spatial_dimension = 2;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("fatigue.msh");
// init stuff
const ElementType type_facet = Mesh::getFacetType(type);
const ElementType type_cohesive =
FEEngine::getCohesiveElementType(type_facet);
SolidMechanicsModelCohesive model(mesh);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
MaterialCohesiveLinearFatigue<2> & numerical_material =
dynamic_cast<MaterialCohesiveLinearFatigue<2> &>(
model.getMaterial("cohesive"));
Real delta_f = numerical_material.getParam("delta_f");
Real delta_c = numerical_material.getParam("delta_c");
Real sigma_c = 1;
const Array<Real> & traction_array =
numerical_material.getTraction(type_cohesive);
MaterialFatigue theoretical_material(delta_f, sigma_c, delta_c);
// model.setBaseName("fatigue");
// model.addDumpFieldVector("displacement");
// model.addDumpField("stress");
// model.dump();
// stretch material
Real strain = 1;
Array<Real> & displacement = model.getDisplacement();
const Array<Real> & position = mesh.getNodes();
for (UInt n = 0; n < mesh.getNbNodes(); ++n)
displacement(n, 0) = position(n, 0) * strain;
model.assembleInternalForces();
// model.dump();
// insert cohesive elements
model.checkCohesiveStress();
// create the displacement sequence
Real increment = 0.01;
Array<Real> openings;
arange(openings, 0, 0.5, increment);
arange(openings, 0.5, 0.1, increment);
arange(openings, 0.1, 0.7, increment);
arange(openings, 0.7, 0.3, increment);
arange(openings, 0.3, 0.6, increment);
arange(openings, 0.6, 0.3, increment);
arange(openings, 0.3, 0.7, increment);
arange(openings, 0.7, 1.3, increment);
const Array<UInt> & switches = numerical_material.getSwitches(type_cohesive);
// std::ofstream edis("fatigue_edis.txt");
// impose openings
for (UInt i = 0; i < openings.size(); ++i) {
// compute numerical traction
imposeOpening(model, openings(i));
model.assembleInternalForces();
// model.dump();
Real numerical_traction = traction_array(0, 0);
// compute theoretical traction
Real theoretical_traction =
theoretical_material.computeTraction(openings(i));
// test traction
if (std::abs(numerical_traction - theoretical_traction) > 1e-13)
AKANTU_ERROR("The numerical traction "
<< numerical_traction << " and theoretical traction "
<< theoretical_traction << " are not coincident");
// edis << model.getEnergy("dissipated") << std::endl;
}
if (switches(0) != 7)
AKANTU_ERROR("The number of switches is wrong");
std::cout << "OK: the test_cohesive_extrinsic_fatigue passed." << std::endl;
return 0;
}
/* -------------------------------------------------------------------------- */
void imposeOpening(SolidMechanicsModelCohesive & model, Real opening) {
UInt spatial_dimension = model.getSpatialDimension();
Mesh & mesh = model.getFEEngine().getMesh();
Array<Real> & position = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> update(nb_nodes);
update.zero();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> barycenter(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, barycenter);
if (barycenter(0) > 1) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(el, n);
if (!update(node)) {
displacement(node, 0) = opening + position(node, 0);
update(node) = true;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void arange(Array<Real> & openings, Real begin, Real end, Real increment) {
if (begin < end) {
for (Real opening = begin; opening < end - increment / 2.;
opening += increment)
openings.push_back(opening);
} else {
for (Real opening = begin; opening > end + increment / 2.;
opening -= increment)
openings.push_back(opening);
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_quadrangle.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_quadrangle.cc
index 437c4c066..ac249d375 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_quadrangle.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_quadrangle.cc
@@ -1,127 +1,129 @@
/**
* @file test_cohesive_extrinsic_quadrangle.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Thu Dec 14 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Dec 14 2017
*
* @brief Test for extrinsic cohesive elements and quadrangles
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 1000;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
model.getElementInserter().setLimit(_y, -0.05, 0.05);
model.updateAutomaticInsertion();
Real time_step = model.getStableTimeStep() * 0.05;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
const Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
model.assembleInternalForces();
/// initial conditions
Real loading_rate = 0.2;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
displacement(n, 1) += disp_update * position(n, 1);
}
model.checkCohesiveStress();
model.solveStep();
if (s % 1 == 0) {
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
mesh.write("mesh_final.msh");
Real Ed = model.getEnergy("dissipated");
Real Edt = 200;
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.99 || Ed > Edt * 1.01 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_extrinsic_quadrangle was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_tetrahedron.cc
index 9ac950a19..f1f1f716f 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic/test_cohesive_extrinsic_tetrahedron.cc
@@ -1,238 +1,240 @@
/**
* @file test_cohesive_extrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Tue Aug 22 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Aug 22 2017
*
* @brief Test for serial extrinsic cohesive elements for tetrahedron
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real constant, Real x, Real y, Real z) {
return constant + 2. * x + 3. * y + 4 * z;
}
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
// const UInt max_steps = 1000;
// Real increment = 0.005;
const UInt spatial_dimension = 3;
Math::setTolerance(1.e-12);
ElementType type = _tetrahedron_10;
ElementType type_facet = Mesh::getFacetType(type);
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
const MaterialCohesiveLinear<3> & mat_cohesive =
dynamic_cast<const MaterialCohesiveLinear<3> &>(model.getMaterial(1));
std::cout << mat_cohesive << std::endl;
std::cout << model.getMaterial(2) << std::endl;
const Real sigma_c = mat_cohesive.get("sigma_c");
const Real beta = mat_cohesive.get("beta");
std::cout << sigma_c << " " << beta << std::endl;
Array<Real> & position = mesh.getNodes();
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points positions on facets
const Mesh & mesh_facets = model.getMeshFacets();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets, spatial_dimension,
type_facet);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position, quad_elements,
spatial_dimension, type);
/// assign some values to stresses
Array<Real> & stress =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(type));
Array<Real>::iterator<Matrix<Real>> stress_it =
stress.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad_el; ++q, ++stress_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_it)(i, j) =
index * function(sigma_c * 5, quad_elements(q, 0),
quad_elements(q, 1), quad_elements(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_it)(i, j) = (*stress_it)(j, i);
}
}
}
/// compute stress on facet quads
Array<Real> stress_facets(nb_tot_quad, spatial_dimension * spatial_dimension);
Array<Real>::iterator<Matrix<Real>> stress_facets_it =
stress_facets.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad; ++q, ++stress_facets_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_facets_it)(i, j) =
index * function(sigma_c * 5, quad_facets(q, 0), quad_facets(q, 1),
quad_facets(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_facets_it)(i, j) = (*stress_facets_it)(j, i);
}
}
}
/// insert cohesive elements
model.checkCohesiveStress();
/// check insertion stress
const Array<Real> & normals = model.getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
const Array<Real> & tangents = model.getTangents(type_facet);
const Array<Real> & sigma_c_eff =
mat_cohesive.getInsertionTraction(type_cohesive);
Vector<Real> normal_stress(spatial_dimension);
const Array<std::vector<Element>> & coh_element_to_facet =
mesh_facets.getElementToSubelement(type_facet);
Array<Real>::iterator<Matrix<Real>> quad_facet_stress =
stress_facets.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_iterator<Vector<Real>> quad_normal =
normals.begin(spatial_dimension);
Array<Real>::const_iterator<Vector<Real>> quad_tangents =
tangents.begin(tangents.getNbComponent());
for (UInt f = 0; f < nb_facet; ++f) {
const Element & cohesive_element = coh_element_to_facet(f)[1];
for (UInt q = 0; q < nb_quad_per_facet;
++q, ++quad_facet_stress, ++quad_normal, ++quad_tangents) {
if (cohesive_element == ElementNull)
continue;
normal_stress.mul<false>(*quad_facet_stress, *quad_normal);
Real normal_contrib = normal_stress.dot(*quad_normal);
Real first_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
first_tangent_contrib += normal_stress(dim) * (*quad_tangents)(dim);
Real second_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
second_tangent_contrib +=
normal_stress(dim) * (*quad_tangents)(dim + spatial_dimension);
Real tangent_contrib =
std::sqrt(first_tangent_contrib * first_tangent_contrib +
second_tangent_contrib * second_tangent_contrib);
normal_contrib = std::max(0., normal_contrib);
Real effective_norm =
std::sqrt(normal_contrib * normal_contrib +
tangent_contrib * tangent_contrib / beta / beta);
if (effective_norm < sigma_c)
continue;
if (!Math::are_float_equal(
effective_norm,
sigma_c_eff(cohesive_element.element * nb_quad_per_facet + q))) {
std::cout << "Insertion tractions do not match" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
}
finalize();
std::cout << "OK: test_cohesive_extrinsic was passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/CMakeLists.txt
index 069250559..1e03670a1 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/CMakeLists.txt
@@ -1,29 +1,39 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mauro Corrado <mauro.corrado@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 22 2016
#
# @brief checking correct assembling of stiffness matrix in case of cohe elems
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_assembling_K_cohe_elements
SOURCES test_assembling_K_cohe_elements.cc
FILES_TO_COPY quadrangle.msh material.dat K_matrix_verified.dat
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/test_assembling_K_cohe_elements.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/test_assembling_K_cohe_elements.cc
index d2cfbcfdc..7404e924e 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/test_assembling_K_cohe_elements.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_extrinsic_implicit/test_assembling_K_cohe_elements.cc
@@ -1,170 +1,172 @@
/**
* @file test_assembling_K_cohe_elements.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri May 15 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test to check the correct matrix assembling for cohesive elements
* with degenerated nodes
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
Real increment = 0.004;
bool passed = true;
Real tol = 1.0e-13;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(SolidMechanicsModelCohesiveOptions(_static, true));
/// CohesiveElementInserter
model.getElementInserter().setLimit(_y, -0.001, 0.001);
model.updateAutomaticInsertion();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & position = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
// SparseMatrix & K_test = model.getStiffnessMatrix();
Array<Real> K_verified(0, 3, "K_matrix_verified");
Array<Real> K_test(0, 3, "K_matrix_test");
/// load the verified stiffness matrix
Vector<Real> tmp(3);
UInt nb_lines;
std::ifstream infile("K_matrix_verified.dat");
std::string line;
if (!infile.good())
AKANTU_ERROR("Cannot open file K_matrix_verified.dat");
else {
for (UInt i = 0; i < 2; ++i) {
getline(infile, line);
std::stringstream sstr_data(line);
if (i == 1) {
sstr_data >> tmp(0) >> tmp(1) >> tmp(2);
nb_lines = tmp(2);
}
}
for (UInt i = 0; i < nb_lines; ++i) {
getline(infile, line);
std::stringstream sstr_data(line);
sstr_data >> tmp(0) >> tmp(1) >> tmp(2);
K_verified.push_back(tmp);
}
}
infile.close();
/// impose boundary conditions
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 1) < -0.99) {
boundary(n, 1) = true;
boundary(n, 0) = true;
}
if (position(n, 1) > 0.99 && position(n, 0) < -0.99)
boundary(n, 1) = true;
}
/// solve step
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 1) > 0.99 && position(n, 0) < -0.99)
displacement(n, 1) += increment;
}
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 10);
solver.set("threshold", 1e-13);
model.solveStep();
model.getDOFManager().getMatrix("K").saveMatrix("K_matrix_test.dat");
/// load the stiffness matrix to be tested
std::ifstream infile2("K_matrix_test.dat");
if (!infile2.good())
AKANTU_ERROR("Cannot open file K_matrix_test.dat");
else {
for (UInt i = 0; i < 2; ++i) {
getline(infile2, line);
std::stringstream sstr_data(line);
if (i == 1) {
sstr_data >> tmp(0) >> tmp(1) >> tmp(2);
nb_lines = tmp(2);
}
}
for (UInt i = 0; i < nb_lines; ++i) {
getline(infile2, line);
std::stringstream sstr_data(line);
sstr_data >> tmp(0) >> tmp(1) >> tmp(2);
K_test.push_back(tmp);
}
}
infile2.close();
for (UInt i = 0; i < K_verified.size(); ++i) {
for (UInt j = 0; j < K_test.size(); ++j) {
if ((K_test(j, 0) == K_verified(i, 0)) &&
(K_test(j, 1) == K_verified(i, 1))) {
if (std::abs(K_verified(i, 2)) < tol) {
if (std::abs(K_test(j, 2)) > tol)
passed = false;
} else {
Real ratio = (std::abs(K_test(j, 2) - K_verified(i, 2))) /
(std::abs(K_verified(i, 2)));
if (ratio > tol)
passed = false;
}
}
}
}
finalize();
if (passed)
return EXIT_SUCCESS;
else
return EXIT_FAILURE;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
index d91ddf669..9623e1e76 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_fixture.hh
@@ -1,347 +1,350 @@
/**
* @file test_cohesive_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jan 10 2018
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Coehsive element test fixture
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_COHESIVE_FIXTURE_HH_
#define AKANTU_TEST_COHESIVE_FIXTURE_HH_
using namespace akantu;
template <::akantu::AnalysisMethod t>
using analysis_method_t = std::integral_constant<::akantu::AnalysisMethod, t>;
class StrainIncrement : public BC::Functor {
public:
StrainIncrement(const Matrix<Real> & strain, BC::Axis dir)
: strain_inc(strain), dir(dir) {}
void operator()(UInt /*node*/, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
if (std::abs(coord(dir)) < 1e-8) {
return;
}
flags.set(true);
primal += strain_inc * coord;
}
static const BC::Functor::Type type = BC::Functor::_dirichlet;
private:
Matrix<Real> strain_inc;
BC::Axis dir;
};
template <typename param_> class TestSMMCFixture : public ::testing::Test {
public:
static constexpr ElementType cohesive_type =
std::tuple_element_t<0, param_>::value;
static constexpr ElementType type_1 = std::tuple_element_t<1, param_>::value;
static constexpr ElementType type_2 = std::tuple_element_t<2, param_>::value;
static constexpr size_t dim =
ElementClass<cohesive_type>::getSpatialDimension();
void SetUp() {
mesh = std::make_unique<Mesh>(this->dim);
if (Communicator::getStaticCommunicator().whoAmI() == 0) {
mesh->read(this->mesh_name);
}
mesh->distribute();
}
void TearDown() {
model.reset(nullptr);
mesh.reset(nullptr);
}
void createModel() {
model = std::make_unique<SolidMechanicsModelCohesive>(*mesh);
model->initFull(_analysis_method = this->analysis_method,
_is_extrinsic = this->is_extrinsic);
auto time_step = this->model->getStableTimeStep() * 0.01;
this->model->setTimeStep(time_step);
if (dim == 1) {
surface = 1;
group_size = 1;
return;
}
auto facet_type = mesh->getFacetType(this->cohesive_type);
auto & fe_engine = model->getFEEngineBoundary();
const auto & group = mesh->getElementGroup("insertion");
group_size = group.size(_ghost_type = _not_ghost);
const auto & elements = group.getElements(facet_type);
Array<Real> ones(fe_engine.getNbIntegrationPoints(facet_type) *
group_size);
ones.set(1.);
surface = fe_engine.integrate(ones, facet_type, _not_ghost, elements);
mesh->getCommunicator().allReduce(surface, SynchronizerOperation::_sum);
mesh->getCommunicator().allReduce(group_size, SynchronizerOperation::_sum);
#define debug_ 0
#if debug_
this->model->addDumpFieldVector("displacement");
this->model->addDumpFieldVector("velocity");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("external_force");
this->model->addDumpField("blocked_dofs");
this->model->addDumpField("stress");
this->model->addDumpField("strain");
this->model->assembleInternalForces();
this->model->setBaseNameToDumper("cohesive elements", "cohesive_elements");
this->model->addDumpFieldVectorToDumper("cohesive elements",
"displacement");
this->model->addDumpFieldToDumper("cohesive elements", "damage");
this->model->addDumpFieldToDumper("cohesive elements", "tractions");
this->model->addDumpFieldToDumper("cohesive elements", "opening");
this->model->dump();
this->model->dump("cohesive elements");
#endif
}
void setInitialCondition(const Matrix<Real> & strain) {
for (auto && data :
zip(make_view(this->mesh->getNodes(), this->dim),
make_view(this->model->getDisplacement(), this->dim))) {
const auto & pos = std::get<0>(data);
auto & disp = std::get<1>(data);
disp = strain * pos;
}
}
bool checkDamaged() {
UInt nb_damaged = 0;
auto & damage =
model->getMaterial("insertion").getArray<Real>("damage", cohesive_type);
for (auto d : damage) {
if (d >= .99) {
++nb_damaged;
}
}
return (nb_damaged == group_size);
}
void steps(const Matrix<Real> & strain) {
StrainIncrement functor((1. / 300) * strain, this->dim == 1 ? _x : _y);
for (auto _ [[gnu::unused]] : arange(nb_steps)) {
this->model->applyBC(functor, "loading");
this->model->applyBC(functor, "fixed");
if (this->is_extrinsic) {
this->model->checkCohesiveStress();
}
this->model->solveStep();
#if debug_
this->model->dump();
this->model->dump("cohesive elements");
#endif
}
}
void checkInsertion() {
auto nb_cohesive_element = this->mesh->getNbElement(cohesive_type);
mesh->getCommunicator().allReduce(nb_cohesive_element,
SynchronizerOperation::_sum);
EXPECT_EQ(nb_cohesive_element, group_size);
}
void checkDissipated(Real expected_density) {
Real edis = this->model->getEnergy("dissipated");
EXPECT_NEAR(this->surface * expected_density, edis, 5e-1);
}
void testModeI() {
this->createModel();
auto & mat_el = this->model->getMaterial("body");
auto speed = mat_el.getPushWaveSpeed(Element());
auto direction = _y;
if (dim == 1) {
direction = _x;
}
auto length =
mesh->getUpperBounds()(direction) - mesh->getLowerBounds()(direction);
nb_steps = length / speed / model->getTimeStep();
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
auto & mat_co = this->model->getMaterial("insertion");
Real sigma_c = mat_co.get("sigma_c");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{1.}};
} else if (dim == 2) {
strain = {{-nu, 0.}, {0., 1. - nu}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{-nu, 0., 0.}, {0., 1., 0.}, {0., 0., -nu}};
}
strain *= sigma_c / E;
this->setInitialCondition((1 - 1e-5) * strain);
this->steps(2e-2 * strain);
}
void testModeII() {
this->createModel();
auto & mat_el = this->model->getMaterial("body");
Real speed;
try {
speed =
mat_el.getShearWaveSpeed(Element()); // the slowest speed if exists
} catch (...) {
speed = mat_el.getPushWaveSpeed(Element());
}
auto direction = _y;
if (dim == 1)
direction = _x;
auto length =
mesh->getUpperBounds()(direction) - mesh->getLowerBounds()(direction);
nb_steps = 2 * length / 2. / speed / model->getTimeStep();
SCOPED_TRACE(std::to_string(this->dim) + "D - " + std::to_string(type_1) +
":" + std::to_string(type_2));
if (this->dim > 1)
this->model->applyBC(BC::Dirichlet::FlagOnly(_y), "sides");
if (this->dim > 2)
this->model->applyBC(BC::Dirichlet::FlagOnly(_z), "sides");
auto & mat_co = this->model->getMaterial("insertion");
Real sigma_c = mat_co.get("sigma_c");
Real beta = mat_co.get("beta");
// Real G_c = mat_co.get("G_c");
Real E = mat_el.get("E");
Real nu = mat_el.get("nu");
Matrix<Real> strain;
if (dim == 1) {
strain = {{1.}};
} else if (dim == 2) {
strain = {{0., 1.}, {0., 0.}};
strain *= (1. + nu);
} else if (dim == 3) {
strain = {{0., 1., 0.}, {0., 0., 0.}, {0., 0., 0.}};
strain *= (1. + nu);
}
strain *= 2 * beta * beta * sigma_c / E;
// nb_steps *= 5;
this->setInitialCondition((1. - 1e-5) * strain);
this->steps(0.005 * strain);
}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModelCohesive> model;
std::string mesh_name{std::to_string(cohesive_type) + std::to_string(type_1) +
(type_1 == type_2 ? "" : std::to_string(type_2)) +
".msh"};
bool is_extrinsic;
AnalysisMethod analysis_method;
Real surface{0};
UInt nb_steps{1000};
UInt group_size{10000};
};
/* -------------------------------------------------------------------------- */
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::cohesive_type;
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::type_1;
template <typename param_>
constexpr ElementType TestSMMCFixture<param_>::type_2;
template <typename param_> constexpr size_t TestSMMCFixture<param_>::dim;
/* -------------------------------------------------------------------------- */
using IsExtrinsicTypes = std::tuple<std::true_type, std::false_type>;
using AnalysisMethodTypes =
std::tuple<analysis_method_t<_explicit_lumped_mass>>;
using coh_types = gtest_list_t<std::tuple<
std::tuple<_element_type_cohesive_1d_2, _element_type_segment_2,
_element_type_segment_2>,
std::tuple<_element_type_cohesive_2d_4, _element_type_triangle_3,
_element_type_triangle_3>,
std::tuple<_element_type_cohesive_2d_4, _element_type_quadrangle_4,
_element_type_quadrangle_4>,
std::tuple<_element_type_cohesive_2d_4, _element_type_triangle_3,
_element_type_quadrangle_4>,
std::tuple<_element_type_cohesive_2d_6, _element_type_triangle_6,
_element_type_triangle_6>,
std::tuple<_element_type_cohesive_2d_6, _element_type_quadrangle_8,
_element_type_quadrangle_8>,
std::tuple<_element_type_cohesive_2d_6, _element_type_triangle_6,
_element_type_quadrangle_8>,
std::tuple<_element_type_cohesive_3d_6, _element_type_tetrahedron_4,
_element_type_tetrahedron_4>,
std::tuple<_element_type_cohesive_3d_12, _element_type_tetrahedron_10,
_element_type_tetrahedron_10> /*,
std::tuple<_element_type_cohesive_3d_8, _element_type_hexahedron_8,
_element_type_hexahedron_8>,
std::tuple<_element_type_cohesive_3d_16, _element_type_hexahedron_20,
_element_type_hexahedron_20>*/>>;
TYPED_TEST_SUITE(TestSMMCFixture, coh_types, );
#endif /* AKANTU_TEST_COHESIVE_FIXTURE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/CMakeLists.txt
index 6dde90331..8d03d640b 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/CMakeLists.txt
@@ -1,32 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief Tests insertion of cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(3d_spherical_inclusion 3d_spherical_inclusion.geo 3 2)
register_test(test_cohesive_insertion_along_physical_surfaces
SOURCES test_cohesive_insertion_along_physical_surfaces.cc
DEPENDS 3d_spherical_inclusion
FILES_TO_COPY input_file.dat
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/test_cohesive_insertion_along_physical_surfaces.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/test_cohesive_insertion_along_physical_surfaces.cc
index fcc009c83..91928a466 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/test_cohesive_insertion_along_physical_surfaces.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_insertion/test_cohesive_insertion_along_physical_surfaces.cc
@@ -1,91 +1,95 @@
/**
* @file test_cohesive_insertion_along_physical_surfaces.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 07 2015
- * @date last modification: Mon Dec 18 2017
+ * @date last modification: Thu Oct 29 2020
*
* @brief Test intrinsic insertion of cohesive elements along physical surfaces
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_cohesive.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("input_file.dat", argc, argv);
Math::setTolerance(1e-15);
const UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
mesh.read("3d_spherical_inclusion.msh");
SolidMechanicsModelCohesive model(mesh);
auto && material_selector =
std::make_shared<MeshDataMaterialCohesiveSelector>(model);
material_selector->setFallback(model.getMaterialSelector());
model.setMaterialSelector(material_selector);
model.initFull();
std::vector<std::string> surfaces_name = {"interface", "coh1", "coh2",
"coh3", "coh4", "coh5"};
UInt nb_surf = surfaces_name.size();
for (auto & type :
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_cohesive)) {
for (UInt i = 0; i < nb_surf; ++i) {
UInt expected_insertion = mesh.getElementGroup(surfaces_name[i])
.getElements(mesh.getFacetType(type))
.size();
UInt inserted_elements =
model.getMaterial(surfaces_name[i]).getElementFilter()(type).size();
if (not(expected_insertion == inserted_elements)) {
std::cout << "!!! Mismatch in insertion of surface named "
<< surfaces_name[i] << " --> " << inserted_elements
<< " inserted elements out of " << expected_insertion
<< std::endl;
return 1;
}
}
}
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/CMakeLists.txt
index 5ab1ba428..80b34a73f 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/CMakeLists.txt
@@ -1,55 +1,65 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief test for intrinsic cohesive element configuration
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_intrinsic_mesh triangle.geo 2 2)
add_mesh(test_cohesive_intrinsic_quadrangle_mesh quadrangle.geo 2 1)
add_mesh(test_cohesive_intrinsic_tetrahedron_mesh tetrahedron.geo 3 2)
add_mesh(test_cohesive_intrinsic_tetrahedron_fragmentation_mesh tetrahedron_full.geo 3 2)
register_test(test_cohesive_intrinsic
SOURCES test_cohesive_intrinsic.cc
DEPENDS test_cohesive_intrinsic_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element
)
register_test(test_cohesive_intrinsic_quadrangle
SOURCES test_cohesive_intrinsic_quadrangle.cc
DEPENDS test_cohesive_intrinsic_quadrangle_mesh
PACKAGE cohesive_element
)
register_test(test_cohesive_intrinsic_tetrahedron
SOURCES test_cohesive_intrinsic_tetrahedron.cc
DEPENDS test_cohesive_intrinsic_tetrahedron_mesh
FILES_TO_COPY material_tetrahedron.dat
PACKAGE cohesive_element
)
register_test(test_cohesive_intrinsic_tetrahedron_fragmentation
SOURCES test_cohesive_intrinsic_tetrahedron_fragmentation.cc
DEPENDS test_cohesive_intrinsic_tetrahedron_fragmentation_mesh
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
index b2825f0ee..26d2382fd 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic.cc
@@ -1,178 +1,180 @@
/**
* @file test_cohesive_intrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Mon Dec 18 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "dumper_paraview.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void updateDisplacement(SolidMechanicsModelCohesive &, Array<UInt> &,
ElementType, Real);
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
const UInt max_steps = 350;
const ElementType type = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
std::cout << mesh << std::endl;
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.26, -0.24);
/// model initialization
model.initFull();
mesh.write("mesh_cohesive.msh");
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<bool> & boundary = model.getBlockedDOFs();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_element = mesh.getNbElement(type);
/// boundary conditions
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
for (UInt n = 0; n < nb_nodes; ++n) {
boundary(n, dim) = true;
}
}
model.assembleInternalForces();
model.setBaseName("intrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("external_force");
model.dump();
model.setBaseNameToDumper("cohesive elements", "cohesive_elements_triangle");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// update displacement
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(0) > -0.25)
elements.push_back(el);
}
Real increment = 0.01;
updateDisplacement(model, elements, type, increment);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
updateDisplacement(model, elements, type, increment);
if (s % 1 == 0) {
model.dump();
model.dump("cohesive elements");
std::cout << "passing step " << s << "/" << max_steps
<< ", Ed = " << model.getEnergy("dissipated") << std::endl;
}
}
Real Ed = model.getEnergy("dissipated");
Real Edt = 2 * sqrt(2);
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic was passed!" << std::endl;
return EXIT_SUCCESS;
}
static void updateDisplacement(SolidMechanicsModelCohesive & model,
Array<UInt> & elements, ElementType type,
Real increment) {
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_element = elements.size();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
update.zero();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elements(el), n);
if (!update(node)) {
displacement(node, 0) += increment;
// displacement(node, 1) += increment;
update(node) = true;
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
index 4dd31e523..41f6f64ff 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_quadrangle.cc
@@ -1,205 +1,207 @@
/**
* @file test_cohesive_intrinsic_quadrangle.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue May 08 2012
- * @date last modification: Mon Dec 18 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Dec 18 2017
*
* @brief Intrinsic cohesive elements' test for quadrangles
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
static void updateDisplacement(SolidMechanicsModelCohesive &, Array<UInt> &,
ElementType, Real);
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 2;
const UInt max_steps = 350;
const ElementType type = _quadrangle_4;
Mesh mesh(spatial_dimension);
mesh.read("quadrangle.msh");
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.01, 0.01);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
model.assembleMassLumped();
Array<bool> & boundary = model.getBlockedDOFs();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_element = mesh.getNbElement(type);
/// boundary conditions
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
for (UInt n = 0; n < nb_nodes; ++n) {
boundary(n, dim) = true;
}
}
model.assembleInternalForces();
model.setBaseName("intrinsic_quadrangle");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("external_force");
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_quadrangle");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// update displacement
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(_x) > 0.)
elements.push_back(el);
}
Real increment = 0.01;
updateDisplacement(model, elements, type, increment);
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// if (position(n, 0) == 0) {
// displacement(n, 1) -= 0.25;
// }
// if (position(n, 0) == 1) {
// displacement(n, 1) += 0.25;
// }
// }
// }
// std::ofstream edis("edis.txt");
// std::ofstream erev("erev.txt");
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
updateDisplacement(model, elements, type, increment);
if (s % 1 == 0) {
model.dump();
model.dump("cohesive elements");
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 1;
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_quadrangle was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
static void updateDisplacement(SolidMechanicsModelCohesive & model,
Array<UInt> & elements, ElementType type,
Real increment) {
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_element = elements.size();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
update.zero();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elements(el), n);
if (!update(node)) {
displacement(node, 0) += increment;
// displacement(node, 1) += increment;
update(node) = true;
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
index f279a440e..8712cc70f 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron.cc
@@ -1,353 +1,355 @@
/**
* @file test_cohesive_intrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Tue Aug 27 2013
- * @date last modification: Mon Dec 18 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class Checker {
public:
Checker(const SolidMechanicsModelCohesive & model,
const Array<UInt> & elements, ElementType type);
void check(const Vector<Real> & opening, const Matrix<Real> & rotation) {
checkTractions(opening, rotation);
checkEquilibrium();
computeEnergy(opening);
}
void updateDisplacement(const Vector<Real> & increment);
protected:
void checkTractions(const Vector<Real> & opening,
const Matrix<Real> & rotation);
void checkEquilibrium();
void checkResidual(const Matrix<Real> & rotation);
void computeEnergy(const Vector<Real> & opening);
private:
std::set<UInt> nodes_to_check;
const SolidMechanicsModelCohesive & model;
ElementType type;
// const Array<UInt> & elements;
const Material & mat_cohesive;
Real sigma_c;
const Real beta;
const Real G_c;
const Real delta_0;
const Real kappa;
Real delta_c;
const UInt spatial_dimension;
const ElementType type_facet;
const ElementType type_cohesive;
const Array<Real> & traction;
const Array<Real> & damage;
const UInt nb_quad_per_el;
const UInt nb_element;
const Real beta2_kappa2;
const Real beta2_kappa;
Vector<Real> theoretical_traction;
Vector<Real> traction_old;
Vector<Real> opening_old;
Real Ed;
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_tetrahedron.dat", argc, argv);
// debug::setDebugLevel(dblDump);
const UInt spatial_dimension = 3;
const UInt max_steps = 60;
const Real increment_constant = 0.01;
Math::setTolerance(1.e-12);
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron.msh");
SolidMechanicsModelCohesive model(mesh);
model.getElementInserter().setLimit(_x, -0.01, 0.01);
/// model initialization
model.initFull();
Array<bool> & boundary = model.getBlockedDOFs();
boundary.set(true);
UInt nb_element = mesh.getNbElement(type);
model.setBaseName("intrinsic_tetrahedron");
model.addDumpFieldVector("displacement");
model.addDumpField("internal_force");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_tetrahedron");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// find elements to displace
Array<UInt> elements;
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
if (bary(_x) > 0.01)
elements.push_back(el);
}
/// rotate mesh
Real angle = 1.;
// clang-format off
Matrix<Real> rotation{
{std::cos(angle), std::sin(angle) * -1., 0.},
{std::sin(angle), std::cos(angle), 0.},
{0., 0., 1.}};
// clang-format on
Vector<Real> increment_tmp{increment_constant, 2. * increment_constant,
3. * increment_constant};
Vector<Real> increment = rotation * increment_tmp;
auto & position = mesh.getNodes();
auto position_it = position.begin(spatial_dimension);
auto position_end = position.end(spatial_dimension);
for (; position_it != position_end; ++position_it) {
auto & pos = *position_it;
pos = rotation * pos;
}
model.dump();
model.dump("cohesive elements");
/// find nodes to check
Checker checker(model, elements, type);
checker.updateDisplacement(increment);
Real theoretical_Ed = 0;
Vector<Real> opening(spatial_dimension, 0.);
Vector<Real> opening_old(spatial_dimension, 0.);
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
model.dump();
model.dump("cohesive elements");
opening += increment_tmp;
checker.check(opening, rotation);
checker.updateDisplacement(increment);
}
model.dump();
model.dump("cohesive elements");
Real Ed = model.getEnergy("dissipated");
theoretical_Ed *= 4.;
std::cout << Ed << " " << theoretical_Ed << std::endl;
if (!Math::are_float_equal(Ed, theoretical_Ed) || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_tetrahedron was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void Checker::updateDisplacement(const Vector<Real> & increment) {
Mesh & mesh = model.getFEEngine().getMesh();
const auto & connectivity = mesh.getConnectivity(type);
auto & displacement = model.getDisplacement();
Array<bool> update(displacement.size());
update.zero();
auto conn_it = connectivity.begin(connectivity.getNbComponent());
auto conn_end = connectivity.begin(connectivity.getNbComponent());
for (; conn_it != conn_end; ++conn_it) {
const auto & conn = *conn_it;
for (UInt n = 0; n < conn.size(); ++n) {
UInt node = conn(n);
if (!update(node)) {
Vector<Real> node_disp(displacement.storage() +
node * spatial_dimension,
spatial_dimension);
node_disp += increment;
update(node) = true;
}
}
}
}
/* -------------------------------------------------------------------------- */
Checker::Checker(const SolidMechanicsModelCohesive & model,
const Array<UInt> & elements, ElementType type)
: model(model), type(std::move(type)), // elements(elements),
mat_cohesive(model.getMaterial(1)), sigma_c(mat_cohesive.get("sigma_c")),
beta(mat_cohesive.get("beta")), G_c(mat_cohesive.get("G_c")),
delta_0(mat_cohesive.get("delta_0")), kappa(mat_cohesive.get("kappa")),
spatial_dimension(model.getSpatialDimension()),
type_facet(Mesh::getFacetType(type)),
type_cohesive(FEEngine::getCohesiveElementType(type_facet)),
traction(mat_cohesive.getArray<Real>("tractions", type_cohesive)),
damage(mat_cohesive.getArray<Real>("damage", type_cohesive)),
nb_quad_per_el(model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive)),
nb_element(model.getMesh().getNbElement(type_cohesive)),
beta2_kappa2(beta * beta / kappa / kappa),
beta2_kappa(beta * beta / kappa) {
const Mesh & mesh = model.getMesh();
const auto & connectivity = mesh.getConnectivity(type);
const auto & position = mesh.getNodes();
auto conn_it = connectivity.begin(connectivity.getNbComponent());
for (const auto & element : elements) {
Vector<UInt> conn_el(conn_it[element]);
for (UInt n = 0; n < conn_el.size(); ++n) {
UInt node = conn_el(n);
if (Math::are_float_equal(position(node, _x), 0.))
nodes_to_check.insert(node);
}
}
delta_c = 2 * G_c / sigma_c;
sigma_c *= delta_c / (delta_c - delta_0);
}
/* -------------------------------------------------------------------------- */
void Checker::checkTractions(const Vector<Real> & opening,
const Matrix<Real> & rotation) {
auto normal_opening = opening * Vector<Real>{1., 0., 0.};
auto tangential_opening = opening - normal_opening;
const Real normal_opening_norm = normal_opening.norm();
const Real tangential_opening_norm = tangential_opening.norm();
const Real delta =
std::max(std::sqrt(tangential_opening_norm * tangential_opening_norm *
beta2_kappa2 +
normal_opening_norm * normal_opening_norm),
0.);
Real theoretical_damage = std::min(delta / delta_c, 1.);
theoretical_traction = (tangential_opening * beta2_kappa + normal_opening) *
sigma_c / delta * (1. - theoretical_damage);
// adjust damage
theoretical_damage = std::max((delta - delta_0) / (delta_c - delta_0), 0.);
theoretical_damage = std::min(theoretical_damage, 1.);
Vector<Real> theoretical_traction_rotated = rotation * theoretical_traction;
std::for_each(
traction.begin(spatial_dimension), traction.end(spatial_dimension),
[&theoretical_traction_rotated](auto && traction) {
Real diff =
Vector<Real>(theoretical_traction_rotated - traction).norm<L_inf>();
if (diff > 1e-14)
throw std::domain_error("Tractions are incorrect");
});
std::for_each(damage.begin(), damage.end(),
[&theoretical_damage](auto && damage) {
if (not Math::are_float_equal(theoretical_damage, damage))
throw std::domain_error("Damage is incorrect");
});
}
/* -------------------------------------------------------------------------- */
void Checker::computeEnergy(const Vector<Real> & opening) {
/// compute energy
auto Do = opening - opening_old;
auto Dt = traction_old + theoretical_traction;
Ed += .5 * Do.dot(Dt);
opening_old = opening;
traction_old = theoretical_traction;
}
/* -------------------------------------------------------------------------- */
void Checker::checkEquilibrium() {
Vector<Real> residual_sum(spatial_dimension, 0.);
const auto & residual = model.getInternalForce();
auto res_it = residual.begin(spatial_dimension);
auto res_end = residual.end(spatial_dimension);
for (; res_it != res_end; ++res_it)
residual_sum += *res_it;
if (!Math::are_float_equal(residual_sum.norm<L_inf>(), 0.))
throw std::domain_error("System is not in equilibrium!");
}
/* -------------------------------------------------------------------------- */
void Checker::checkResidual(const Matrix<Real> & rotation) {
Vector<Real> total_force(spatial_dimension, 0.);
const auto & residual = model.getInternalForce();
for (auto node : nodes_to_check) {
Vector<Real> res(residual.begin(spatial_dimension)[node]);
total_force += res;
}
Vector<Real> theoretical_total_force(spatial_dimension);
theoretical_total_force.mul<false>(rotation, theoretical_traction);
theoretical_total_force *= -1 * 2 * 2;
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(total_force(s), theoretical_total_force(s))) {
std::cout << "Total force isn't correct!" << std::endl;
std::terminate();
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
index 33541f192..13d47b4fe 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic/test_cohesive_intrinsic_tetrahedron_fragmentation.cc
@@ -1,125 +1,127 @@
/**
* @file test_cohesive_intrinsic_tetrahedron_fragmentation.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Oct 09 2013
- * @date last modification: Mon Dec 18 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Dec 18 2017
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
// debug::setDebugLevel(dblDump);
ElementType type = _tetrahedron_10;
const UInt spatial_dimension = 3;
const UInt max_steps = 100;
Mesh mesh(spatial_dimension);
mesh.read("tetrahedron_full.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
model.assembleInternalForces();
model.setBaseName("intrinsic_tetrahedron_fragmentation");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_tetrahedron_fragmentation");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// update displacement
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
Vector<Real> bary(spatial_dimension);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
for (UInt s = 0; s < max_steps; ++s) {
Real increment = s / 10.;
update.zero();
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter({type, el, _not_ghost}, bary);
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(el, n);
if (!update(node)) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
displacement(node, dim) = increment * bary(dim);
update(node) = true;
}
}
}
}
if (s % 10 == 0) {
model.dump();
model.dump("cohesive elements");
}
}
if (nb_nodes != nb_element * Mesh::getNbNodesPerElement(type)) {
std::cout << "Wrong number of nodes" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
std::cout << "OK: test_cohesive_intrinsic_tetrahedron was passed!"
<< std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/CMakeLists.txt
index d676f353a..0dad5ac2a 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/CMakeLists.txt
@@ -1,31 +1,41 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for intrinsic implicit cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_cohesive_intrinsic_impl
SOURCES test_cohesive_intrinsic_impl.cc
FILES_TO_COPY material.dat implicit.msh
DIRECTORIES_TO_CREATE paraview
PACKAGE cohesive_element
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/test_cohesive_intrinsic_impl.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/test_cohesive_intrinsic_impl.cc
index cc3b35920..8bfd79172 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/test_cohesive_intrinsic_impl.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_intrinsic_impl/test_cohesive_intrinsic_impl.cc
@@ -1,173 +1,175 @@
/**
* @file test_cohesive_intrinsic_impl.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Mon Jul 09 2012
- * @date last modification: Fri Jul 07 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sun Dec 30 2018
*
* @brief Test for cohesive elements
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblError);
const UInt spatial_dimension = 2;
const ElementType type = _triangle_6;
Mesh mesh(spatial_dimension);
mesh.read("implicit.msh");
CohesiveElementInserter inserter(mesh);
inserter.setLimit(_y, 0.9, 1.1);
inserter.insertIntrinsicElements();
// mesh.write("implicit_cohesive.msh");
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initFull(SolidMechanicsModelCohesiveOptions(_static));
/// boundary conditions
Array<bool> & boundary = model.getBlockedDOFs();
UInt nb_nodes = mesh.getNbNodes();
Array<Real> & position = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
const ElementType type_facet = mesh.getFacetType(type);
for (UInt n = 0; n < nb_nodes; ++n) {
if (std::abs(position(n, 1)) < Math::getTolerance()) {
boundary(n, 1) = true;
displacement(n, 1) = 0.0;
}
if ((std::abs(position(n, 0)) < Math::getTolerance()) &&
(position(n, 1) < 1.1)) {
boundary(n, 0) = true;
displacement(n, 0) = 0.0;
}
if ((std::abs(position(n, 0) - 1) < Math::getTolerance()) &&
(std::abs(position(n, 1) - 1) < Math::getTolerance())) {
boundary(n, 0) = true;
displacement(n, 0) = 0.0;
}
if (std::abs(position(n, 1) - 2) < Math::getTolerance()) {
boundary(n, 1) = true;
}
}
model.setBaseName("intrinsic_impl");
model.addDumpField("displacement");
// model.addDumpField("mass" );
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("force");
model.addDumpField("residual");
// model.addDumpField("damage" );
model.addDumpField("stress");
model.addDumpField("strain");
model.dump();
const MaterialCohesive & mat_coh =
dynamic_cast<const MaterialCohesive &>(model.getMaterial(1));
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const Array<Real> & opening = mat_coh.getOpening(type_cohesive);
// const Array<Real> & traction = mat_coh.getTraction(type_cohesive);
model.assembleInternalForces();
const Array<Real> & residual = model.getInternalForce();
UInt max_step = 1000;
Real increment = 3. / max_step;
Real error_tol = 10e-6;
std::ofstream fout;
fout.open("output");
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 100);
solver.set("threshold", 1e-5);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
/// Main loop
for (UInt nstep = 0; nstep < max_step; ++nstep) {
for (UInt n = 0; n < nb_nodes; ++n) {
if (std::abs(position(n, 1) - 2) < Math::getTolerance()) {
displacement(n, 1) += increment;
}
}
model.solveStep();
// model.dump();
Real resid = 0;
for (UInt n = 0; n < nb_nodes; ++n) {
if (std::abs(position(n, 1) - 2.) / 2. < Math::getTolerance()) {
resid += residual(n, 1);
}
}
Real analytical = exp(1) * std::abs(opening(0, 1)) *
exp(-std::abs(opening(0, 1)) / 0.5) / 0.5;
// the residual force is comparing with the theoretical value of the
// cohesive law
error_tol = std::abs((std::abs(resid) - analytical) / analytical);
fout << nstep << " " << -resid << " " << analytical << " " << error_tol
<< std::endl;
if (error_tol > 1e-3) {
std::cout << "Relative error: " << error_tol << std::endl;
std::cout << "Test failed!" << std::endl;
return EXIT_FAILURE;
}
}
model.dump();
fout.close();
finalize();
std::cout << "Test passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/CMakeLists.txt
index 35b950aa5..d63f6953e 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/CMakeLists.txt
@@ -1,30 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Mauro Corrado <mauro.corrado@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jul 07 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jul 07 2017
#
# @brief testing the correct behavior of the friction law included in
# the cohesive linear law, in implicit
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#register_test(test_cohesive_linear_friction
#SOURCES test_cohesive_friction.cc
#FILES_TO_COPY mesh_cohesive_friction.msh material.dat
#PACKAGE cohesive_element
#)
\ No newline at end of file
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/test_cohesive_friction.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/test_cohesive_friction.cc
index 72c51bbfa..1ad4dec21 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/test_cohesive_friction.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_cohesive_linear_friction/test_cohesive_friction.cc
@@ -1,239 +1,241 @@
/**
* @file test_cohesive_friction.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Thu Jan 14 2016
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief testing the correct behavior of the friction law included in
* the cohesive linear law, in implicit
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include <cmath>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <string>
#include <time.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Math::setTolerance(1.e-15);
UInt spatial_dimension = 2;
const ElementType type = _cohesive_2d_4;
Mesh mesh(spatial_dimension);
mesh.read("mesh_cohesive_friction.msh");
// Create the model
SolidMechanicsModelCohesive model(mesh);
// Model initialization
model.initFull(SolidMechanicsModelCohesiveOptions(_static, true));
// CohesiveElementInserter inserter(mesh);
model.limitInsertion(_y, -0.001, 0.001);
model.updateAutomaticInsertion();
Real eps = 1e-10;
Array<Real> & pos = mesh.getNodes();
Array<Real> & disp = model.getDisplacement();
Array<bool> & boun = model.getBlockedDOFs();
const Array<Real> & residual = model.getInternalForce();
Array<Real> & cohe_opening = const_cast<Array<Real> &>(
model.getMaterial("interface").getInternal<Real>("opening")(type));
Array<Real> & friction_force = const_cast<Array<Real> &>(
model.getMaterial("interface").getInternal<Real>("friction_force")(type));
// Boundary conditions
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (pos(i, 1) < -0.49 || pos(i, 1) > 0.49) {
boun(i, 0) = true;
boun(i, 1) = true;
}
}
bool passed = true;
Real tolerance = 1e-13;
Real error;
bool load_reduction = false;
Real tol_increase_factor = 1e5;
Real increment = 1.0e-4;
model.synchronizeBoundaries();
model.updateResidual();
/* -------------------------------------------- */
/* LOADING PHASE to introduce cohesive elements */
/* -------------------------------------------- */
for (UInt nstep = 0; nstep < 100; ++nstep) {
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (pos(n, 1) > 0.49)
disp(n, 1) += increment;
}
model.solveStepCohesive<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
tolerance, error, 25, load_reduction, tol_increase_factor);
if (error > tolerance) {
AKANTU_ERROR("Convergence not reached in the mode I loading phase");
passed = false;
}
}
/* --------------------------------------------------------- */
/* UNLOADING PHASE to bring cohesive elements in compression */
/* --------------------------------------------------------- */
for (UInt nstep = 0; nstep < 110; ++nstep) {
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (pos(n, 1) > 0.49)
disp(n, 1) -= increment;
}
model.solveStepCohesive<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
tolerance, error, 25, load_reduction, tol_increase_factor);
if (error > tolerance) {
AKANTU_ERROR("Convergence not reached in the mode I unloading phase");
passed = false;
}
}
/* -------------------------------------------------- */
/* SHEAR PHASE - displacement towards right */
/* -------------------------------------------------- */
increment *= 2;
for (UInt nstep = 0; nstep < 30; ++nstep) {
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (pos(n, 1) > 0.49)
disp(n, 0) += increment;
}
model.solveStepCohesive<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
tolerance, error, 25, load_reduction, tol_increase_factor);
if (error > tolerance) {
AKANTU_ERROR("Convergence not reached in the shear loading phase");
passed = false;
}
}
/* ---------------------------------------------------*/
/* Check the horizontal component of the reaction */
/* ---------------------------------------------------*/
// Friction + mode II cohesive behavior
Real reac_X = 0.;
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (pos(i, 1) > 0.49)
reac_X += residual(i, 0);
}
if (std::abs(reac_X - (-13.987451183762181)) > eps)
passed = false;
// Only friction
Real friction = friction_force(0, 0) + friction_force(1, 0);
if (std::abs(friction - (-12.517967866999832)) > eps)
passed = false;
/* -------------------------------------------------- */
/* SHEAR PHASE - displacement back to zero */
/* -------------------------------------------------- */
for (UInt nstep = 0; nstep < 30; ++nstep) {
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (pos(n, 1) > 0.49)
disp(n, 0) -= increment;
}
model.solveStepCohesive<_scm_newton_raphson_tangent,
SolveConvergenceCriteria::_increment>(
tolerance, error, 25, load_reduction, tol_increase_factor);
if (error > tolerance) {
AKANTU_ERROR("Convergence not reached in the shear unloading phase");
passed = false;
}
}
/* ------------------------------------------------------- */
/* Check the horizontal component of the reaction and */
/* the residual relative sliding in the cohesive elements */
/* ------------------------------------------------------- */
// Friction + mode II cohesive behavior
reac_X = 0.;
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
if (pos(i, 1) > 0.49)
reac_X += residual(i, 0);
}
if (std::abs(reac_X - 12.400313187122208) > eps)
passed = false;
// Only friction
friction = 0.;
friction = friction_force(0, 0) + friction_force(1, 0);
if (std::abs(friction - 12.523300983293165) > eps)
passed = false;
// Residual sliding
Real sliding[2];
sliding[0] = cohe_opening(0, 0);
sliding[1] = cohe_opening(1, 0);
if (std::abs(sliding[0] - (-0.00044246686809147357)) > eps)
passed = false;
if (passed)
return EXIT_SUCCESS;
else
return EXIT_FAILURE;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/CMakeLists.txt
index 7c73c63f4..0e9d82c5c 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/CMakeLists.txt
@@ -1,27 +1,38 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Wed Feb 21 2018
+# @date last modification: Wed Feb 21 2018
#
-# @brief
+# @brief CMakeLists for cohesive material tests
#
-# @section LICENSE
-#
-# Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
register_gtest_sources(
SOURCES test_material_cohesive_linear.cc
PACKAGE cohesive_element
)
register_gtest_test(test_material_cohesive)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
index 9bc4eac07..eb61607e2 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_fixture.hh
@@ -1,311 +1,314 @@
/**
* @file test_material_cohesive_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Feb 21 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief Test the traction separations laws for cohesive elements
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
//#define debug_
/* -------------------------------------------------------------------------- */
template <template <UInt> class Mat, typename dim_>
class TestMaterialCohesiveFixture : public ::testing::Test {
public:
static constexpr UInt dim = dim_::value;
using Material = Mat<dim>;
void SetUp() override {
mesh = std::make_unique<Mesh>(dim);
model = std::make_unique<SolidMechanicsModelCohesive>(*mesh);
material = std::make_unique<Material>(*model);
material->SetUps();
openings = std::make_unique<Array<Real>>(0, dim);
tractions = std::make_unique<Array<Real>>(0, dim);
reset();
gen.seed(::testing::GTEST_FLAG(random_seed));
normal = getRandomNormal();
tangents = getRandomTangents();
}
void TearDown() override {
material.reset(nullptr);
model.reset(nullptr);
mesh.reset(nullptr);
openings.reset(nullptr);
tractions.reset(nullptr);
}
void reset() {
openings->resize(1);
tractions->resize(1);
openings->zero();
tractions->zero();
}
/* ------------------------------------------------------------------------ */
void addOpening(const Vector<Real> & direction, Real start, Real stop,
UInt nb_steps) {
for (auto s : arange(nb_steps)) {
auto opening =
direction * (start + (stop - start) / Real(nb_steps) * Real(s + 1));
openings->push_back(opening);
}
tractions->resize(openings->size());
}
/* ------------------------------------------------------------------------ */
Vector<Real> getRandomVector() {
std::uniform_real_distribution<Real> dis;
Vector<Real> vector(dim);
for (auto s : arange(dim))
vector(s) = dis(gen);
return vector;
}
Vector<Real> getRandomNormal() {
auto normal = getRandomVector();
normal.normalize();
#if defined(debug_)
normal.set(0.);
normal(0) = 1.;
#endif
return normal;
}
Matrix<Real> getRandomTangents() {
auto dim = normal.size();
Matrix<Real> tangent(dim, dim - 1);
if (dim == 2) {
Math::normal2(normal.storage(), tangent(0).storage());
}
if (dim == 3) {
auto v = getRandomVector();
tangent(0) = (v - v.dot(normal) * normal).normalize();
Math::normal3(normal.storage(), tangent(0).storage(),
tangent(1).storage());
}
#if defined(debug_)
if (dim == 2)
tangent(0) = Vector<Real>{0., 1};
if (dim == 3)
tangent = Matrix<Real>{{0., 0.}, {1., 0.}, {0., 1.}};
#endif
return tangent;
}
/* ------------------------------------------------------------------------ */
void output_csv() {
const ::testing::TestInfo * const test_info =
::testing::UnitTest::GetInstance()->current_test_info();
std::ofstream cout(std::string(test_info->name()) + ".csv");
auto print_vect_name = [&](auto name) {
for (auto s : arange(dim)) {
if (s != 0) {
cout << ", ";
}
cout << name << "_" << s;
}
};
auto print_vect = [&](const auto & vect) {
cout << vect.dot(normal);
if (dim > 1)
cout << ", " << vect.dot(tangents(0));
if (dim > 2)
cout << ", " << vect.dot(tangents(1));
};
cout << "delta, ";
print_vect_name("opening");
cout << ", ";
print_vect_name("traction");
cout << std::endl;
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
auto & traction = std::get<1>(data);
cout << this->material->delta(opening, normal) << ", ";
print_vect(opening);
cout << ", ";
print_vect(traction);
cout << std::endl;
}
}
/* ------------------------------------------------------------------------ */
Real dissipated() {
Vector<Real> prev_opening(dim, 0.);
Vector<Real> prev_traction(dim, 0.);
Real etot = 0.;
Real erev = 0.;
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
const auto & traction = std::get<1>(data);
etot += (opening - prev_opening).dot(traction + prev_traction) / 2.;
erev = traction.dot(opening) / 2.;
prev_opening = opening;
prev_traction = traction;
}
return etot - erev;
}
/* ------------------------------------------------------------------------ */
void checkModeI(Real max_opening, Real expected_dissipated) {
this->material->insertion_stress_ = this->material->sigma_c_ * normal;
addOpening(normal, 0., max_opening, 100);
this->material->computeTractions(*openings, normal, *tractions);
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
auto & traction = std::get<1>(data);
auto T = traction.dot(normal);
EXPECT_NEAR(0, (traction - T * normal).norm(), 1e-9);
auto T_expected =
this->material->tractionModeI(opening, normal).dot(normal);
EXPECT_NEAR(T_expected, T, 1e-9);
}
EXPECT_NEAR(expected_dissipated, dissipated(), 1e-5);
this->output_csv();
}
/* ------------------------------------------------------------------------ */
void checkModeII(Real max_opening) {
if (this->dim == 1) {
SUCCEED();
return;
}
std::uniform_real_distribution<Real> dis;
auto direction = Vector<Real>(tangents(0));
auto alpha = dis(gen) + 0.1;
auto beta = dis(gen) + 0.2;
#ifndef debug_
direction = alpha * Vector<Real>(tangents(0));
if (dim > 2)
direction += beta * Vector<Real>(tangents(1));
direction = direction.normalize();
#endif
beta = this->material->get("beta");
this->material->insertion_stress_ =
beta * this->material->sigma_c_ * direction;
addOpening(direction, 0., max_opening, 100);
this->material->computeTractions(*openings, normal, *tractions);
for (auto && data : zip(make_view(*this->openings, this->dim),
make_view(*this->tractions, this->dim))) {
const auto & opening = std::get<0>(data);
const auto & traction = std::get<1>(data);
// In ModeII normal traction should be 0
ASSERT_NEAR(0, traction.dot(normal), 1e-9);
// Normal opening is null
ASSERT_NEAR(0, opening.dot(normal), 1e-16);
auto T = traction.dot(direction);
auto T_expected =
this->material->tractionModeII(opening, normal).dot(direction);
EXPECT_NEAR(T_expected, T, 1e-9);
}
// EXPECT_NEAR(expected_dissipated, dissipated(), 1e-5);
this->output_csv();
}
protected:
Vector<Real> normal;
Matrix<Real> tangents;
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModelCohesive> model;
std::unique_ptr<Material> material;
std::unique_ptr<Array<Real>> openings;
std::unique_ptr<Array<Real>> tractions;
std::mt19937 gen;
};
template <template <UInt> class Mat, UInt dim>
struct TestMaterialCohesive : public Mat<dim> {
TestMaterialCohesive(SolidMechanicsModel & model)
: Mat<dim>(model, "test"), insertion_stress_(dim, 0.) {}
virtual void SetUp() {}
virtual void resetInternal() {}
void SetUps() {
this->initMaterial();
this->SetUp();
this->updateInternalParameters();
this->resetInternals();
}
void resetInternals() { this->resetInternal(); }
virtual void computeTractions(Array<Real> & /*openings*/,
const Vector<Real> & /*normal*/,
Array<Real> & /*tractions*/) {}
Vector<Real> insertion_stress_;
Real sigma_c_{0};
bool is_extrinsic{true};
};
template <template <UInt> class Mat, typename dim_>
constexpr UInt TestMaterialCohesiveFixture<Mat, dim_>::dim;
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_linear.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_linear.cc
index 54e074ff3..2225bf121 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_linear.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_materials/test_material_cohesive_linear.cc
@@ -1,192 +1,195 @@
/**
* @file test_material_cohesive_linear.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Feb 21 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Test material cohesive linear
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_material_cohesive_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
template <UInt dim>
struct TestMaterialCohesiveLinear
: public TestMaterialCohesive<MaterialCohesiveLinear, dim> {
TestMaterialCohesiveLinear(SolidMechanicsModel & model)
: TestMaterialCohesive<MaterialCohesiveLinear, dim>(model) {}
void SetUp() override {
this->is_extrinsic = true;
this->beta = 2.;
this->kappa = 2;
this->G_c = 10.;
this->sigma_c_ = 1e6;
this->penalty = 1e11;
this->delta_c_ = 2. * this->G_c / this->sigma_c_;
}
void resetInternal() override {
normal_opening = Vector<Real>(dim, 0.);
tangential_opening = Vector<Real>(dim, 0.);
contact_traction = Vector<Real>(dim, 0.);
contact_opening = Vector<Real>(dim, 0.);
}
void computeTractions(Array<Real> & openings, const Vector<Real> & normal,
Array<Real> & tractions) override {
for (auto && data :
zip(make_view(openings, dim), make_view(tractions, dim))) {
auto & opening = std::get<0>(data);
auto & traction = std::get<1>(data);
this->computeTractionOnQuad(
traction, opening, normal, delta_max, this->delta_c_,
this->insertion_stress_, this->sigma_c_, normal_opening,
tangential_opening, normal_opening_norm, tangential_opening_norm,
damage, penetration, contact_traction, contact_opening);
opening += contact_opening;
traction += contact_traction;
}
}
Real delta(const Vector<Real> & opening, const Vector<Real> & normal) {
auto beta = this->beta;
auto kappa = this->kappa;
auto normal_opening = opening.dot(normal) * normal;
auto tangential_opening = opening - normal_opening;
return std::sqrt(std::pow(normal_opening.norm(), 2) +
std::pow(tangential_opening.norm() * beta / kappa, 2));
}
Vector<Real> traction(const Vector<Real> & opening,
const Vector<Real> & normal) {
auto delta_c = this->delta_c_;
auto sigma_c = this->sigma_c_;
auto beta = this->beta;
auto kappa = this->kappa;
auto normal_opening = opening.dot(normal) * normal;
auto tangential_opening = opening - normal_opening;
auto delta_ = this->delta(opening, normal);
if (delta_ < 1e-16) {
return this->insertion_stress_;
}
if (opening.dot(normal) / delta_c < -Math::getTolerance()) {
ADD_FAILURE() << "This is contact";
return Vector<Real>(dim, 0.);
}
auto T = sigma_c * (delta_c - delta_) / delta_c / delta_ *
(normal_opening + tangential_opening * beta * beta / kappa);
return T;
}
Vector<Real> tractionModeI(const Vector<Real> & opening,
const Vector<Real> & normal) {
return traction(opening, normal);
}
Vector<Real> tractionModeII(const Vector<Real> & opening,
const Vector<Real> & normal) {
return traction(opening, normal);
}
public:
Real delta_c_{0};
Real delta_max{0.};
Real normal_opening_norm{0};
Real tangential_opening_norm{0};
Real damage{0};
bool penetration{false};
Real etot{0.};
Real edis{0.};
Vector<Real> normal_opening;
Vector<Real> tangential_opening;
Vector<Real> contact_traction;
Vector<Real> contact_opening;
};
template <typename dim_>
using TestMaterialCohesiveLinearFixture =
TestMaterialCohesiveFixture<TestMaterialCohesiveLinear, dim_>;
using coh_types = gtest_list_t<TestAllDimensions>;
TYPED_TEST_SUITE(TestMaterialCohesiveLinearFixture, coh_types, );
TYPED_TEST(TestMaterialCohesiveLinearFixture, ModeI) {
this->checkModeI(this->material->delta_c_, this->material->get("G_c"));
Real G_c = this->material->get("G_c");
EXPECT_NEAR(G_c, this->dissipated(), 1e-6);
}
TYPED_TEST(TestMaterialCohesiveLinearFixture, ModeII) {
this->checkModeII(this->material->delta_c_);
if (this->dim != 1) {
Real G_c = this->material->get("G_c");
Real beta = this->material->get("beta");
Real dis = beta * G_c;
EXPECT_NEAR(dis, this->dissipated(), 1e-6);
}
}
TYPED_TEST(TestMaterialCohesiveLinearFixture, Cycles) {
auto delta_c = this->material->delta_c_;
auto sigma_c = this->material->sigma_c_;
this->material->insertion_stress_ = this->normal * sigma_c;
this->addOpening(this->normal, 0, 0.1 * delta_c, 100);
this->addOpening(this->normal, 0.1 * delta_c, 0., 100);
this->addOpening(this->normal, 0., 0.5 * delta_c, 100);
this->addOpening(this->normal, 0.5 * delta_c, -1.e-5, 100);
this->addOpening(this->normal, -1.e-5, 0.9 * delta_c, 100);
this->addOpening(this->normal, 0.9 * delta_c, 0., 100);
this->addOpening(this->normal, 0., delta_c, 100);
this->material->computeTractions(*this->openings, this->normal,
*this->tractions);
Real G_c = this->material->get("G_c");
EXPECT_NEAR(G_c, this->dissipated(), 2e-3); // due to contact dissipation at 0
this->output_csv();
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/CMakeLists.txt
index cbe2ef2c0..036c06776 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/CMakeLists.txt
@@ -1,30 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief configuration for cohesive elements tests
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_akantu_test(test_cohesive_parallel_intrinsic "test_cohesive_parallel_intrinsic")
add_akantu_test(test_cohesive_facet_stress_synchronizer "test_cohesive_facet_stress_synchronizer")
add_akantu_test(test_cohesive_parallel_extrinsic "test_cohesive_parallel_extrinsic")
add_akantu_test(test_cohesive_parallel_extrinsic_IG_TG "test_cohesive_parallel_extrinsic_IG_TG")
add_akantu_test(test_cohesive_parallel_buildfragments "test_cohesive_parallel_buildfragments")
add_akantu_test(test_cohesive_parallel_insertion "test_cohesive_parallel_insertion")
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/CMakeLists.txt
index 3584cbff2..1334bc345 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/CMakeLists.txt
@@ -1,31 +1,41 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief configuration for parallel test of facet stress synchronizer
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_facet_stress_synchronizer_mesh tetrahedron.geo 3 2)
register_test(test_cohesive_facet_stress_synchronizer
SOURCES test_cohesive_facet_stress_synchronizer.cc
DEPENDS test_cohesive_facet_stress_synchronizer_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
index 417d68a6e..cef8f089e 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
@@ -1,212 +1,214 @@
/**
* @file test_cohesive_facet_stress_synchronizer.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Test for facet stress synchronizer
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real constant, Real x, Real y, Real z) {
return constant + 2. * x + 3. * y + 4 * z;
}
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 3;
ElementType type = _tetrahedron_10;
ElementType type_facet = Mesh::getFacetType(type);
Math::setTolerance(1.e-11);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
Array<Real> & position = mesh.getNodes();
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points positions on facets
const Mesh & mesh_facets = model.getMeshFacets();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets, spatial_dimension,
type_facet);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position, quad_elements,
spatial_dimension, type);
/// assign some values to stresses
Array<Real> & stress =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(type));
Array<Real>::iterator<Matrix<Real>> stress_it =
stress.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad_el; ++q, ++stress_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_it)(i, j) = function(index, quad_elements(q, 0),
quad_elements(q, 1), quad_elements(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_it)(i, j) = (*stress_it)(j, i);
}
}
// stress_it->clear();
// for (UInt i = 0; i < spatial_dimension; ++i)
// (*stress_it)(i, i) = sigma_c * 5;
}
/// compute and communicate stress on facets
model.checkCohesiveStress();
/* ------------------------------------------------------------------------ */
/* Check facet stress */
/* ------------------------------------------------------------------------ */
const Array<Real> & facet_stress = model.getStressOnFacets(type_facet);
const Array<bool> & facet_check =
model.getElementInserter().getCheckFacets(type_facet);
const Array<std::vector<Element>> & elements_to_facet =
model.getMeshFacets().getElementToSubelement(type_facet);
Array<Real>::iterator<Vector<Real>> quad_facet_it =
quad_facets.begin(spatial_dimension);
Array<Real>::const_iterator<Matrix<Real>> facet_stress_it =
facet_stress.begin(spatial_dimension, spatial_dimension * 2);
Matrix<Real> current_stress(spatial_dimension, spatial_dimension);
for (UInt f = 0; f < nb_facet; ++f) {
if (!facet_check(f) || (elements_to_facet(f)[0].ghost_type == _not_ghost &&
elements_to_facet(f)[1].ghost_type == _not_ghost)) {
quad_facet_it += nb_quad_per_facet;
facet_stress_it += nb_quad_per_facet;
continue;
}
for (UInt q = 0; q < nb_quad_per_facet;
++q, ++quad_facet_it, ++facet_stress_it) {
/// compute current_stress
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
current_stress(i, j) =
function(index, (*quad_facet_it)(0), (*quad_facet_it)(1),
(*quad_facet_it)(2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
current_stress(i, j) = current_stress(j, i);
}
}
/// compare it to interpolated one
for (UInt s = 0; s < 2; ++s) {
Matrix<Real> stress_to_check(facet_stress_it->storage() +
s * spatial_dimension *
spatial_dimension,
spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
if (!Math::are_float_equal(stress_to_check(i, j),
current_stress(i, j))) {
std::cout << "Stress doesn't match" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
}
}
}
}
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_facet_stress_synchronizer passed!"
<< std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/CMakeLists.txt
index beaeeb6e6..05565b26d 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/CMakeLists.txt
@@ -1,32 +1,42 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief configuration for build fragments tests
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_parallel_buildfragments_mesh mesh.geo 3 2)
register_test(test_cohesive_parallel_buildfragments
SOURCES test_cohesive_parallel_buildfragments.cc
DEPENDS test_cohesive_parallel_buildfragments_mesh
FILES_TO_COPY material.dat
PACKAGE parallel_cohesive_element
DIRECTORIES_TO_CREATE paraview)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
index 01e6f6ade..4d4fd89a8 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
@@ -1,455 +1,457 @@
/**
* @file test_cohesive_parallel_buildfragments.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test to build fragments in parallel
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <fstream>
#include <functional>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "fragment_manager.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void verticalInsertionLimit(SolidMechanicsModelCohesive &);
void displaceElements(SolidMechanicsModelCohesive &, const Real, const Real);
bool isInertiaEqual(const Vector<Real> &, const Vector<Real> &);
void rotateArray(Array<Real> & array, Real angle);
UInt getNbBigFragments(FragmentManager &, UInt);
const UInt spatial_dimension = 3;
const UInt total_nb_fragment = 4;
const Real rotation_angle = M_PI / 4.;
const Real global_tolerance = 1.e-9;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
Math::setTolerance(global_tolerance);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
/// partition the mesh
MeshUtils::purifyMesh(mesh);
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
delete partition;
/// model initialization
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
mesh.computeBoundingBox();
Real L = mesh.getUpperBounds()(0) - mesh.getLowerBounds()(0);
Real h = mesh.getUpperBounds()(1) - mesh.getLowerBounds()(1);
Real rho = model.getMaterial("bulk").getParam<Real>("rho");
Real theoretical_mass = L * h * h * rho;
Real frag_theo_mass = theoretical_mass / total_nb_fragment;
UInt nb_element =
mesh.getNbElement(spatial_dimension, _not_ghost, _ek_regular);
comm.allReduce(&nb_element, 1, _so_sum);
UInt nb_element_per_fragment = nb_element / total_nb_fragment;
FragmentManager fragment_manager(model);
fragment_manager.computeAllData();
getNbBigFragments(fragment_manager, nb_element_per_fragment + 1);
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("stress");
model.addDumpField("partitions");
model.addDumpField("fragments");
model.addDumpField("fragments mass");
model.addDumpField("moments of inertia");
model.addDumpField("elements per fragment");
model.dump();
model.setBaseNameToDumper("cohesive elements", "cohesive_elements_test");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// set check facets
verticalInsertionLimit(model);
model.assembleMassLumped();
model.synchronizeBoundaries();
/// impose initial displacement
Array<Real> & displacement = model.getDisplacement();
Array<Real> & velocity = model.getVelocity();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
displacement(n, 0) = position(n, 0) * 0.1;
velocity(n, 0) = position(n, 0);
}
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
// rotateArray(velocity, rotation_angle);
model.updateResidual();
model.checkCohesiveStress();
model.dump();
model.dump("cohesive elements");
const Array<Real> & fragment_mass = fragment_manager.getMass();
const Array<Real> & fragment_center = fragment_manager.getCenterOfMass();
Real el_size = L / total_nb_fragment;
Real lim = -L / 2 + el_size * 0.99;
/// define theoretical inertia moments
Vector<Real> small_frag_inertia(spatial_dimension);
small_frag_inertia(0) = frag_theo_mass * (h * h + h * h) / 12.;
small_frag_inertia(1) = frag_theo_mass * (el_size * el_size + h * h) / 12.;
small_frag_inertia(2) = frag_theo_mass * (el_size * el_size + h * h) / 12.;
std::sort(small_frag_inertia.storage(),
small_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
const Array<Real> & inertia_moments = fragment_manager.getMomentsOfInertia();
Array<Real>::const_iterator<Vector<Real>> inertia_moments_begin =
inertia_moments.begin(spatial_dimension);
/// displace one fragment each time
for (UInt frag = 1; frag <= total_nb_fragment; ++frag) {
if (prank == 0)
std::cout << "Generating fragment: " << frag << std::endl;
fragment_manager.computeAllData();
/// check number of big fragments
UInt nb_big_fragment =
getNbBigFragments(fragment_manager, nb_element_per_fragment + 1);
model.dump();
model.dump("cohesive elements");
if (frag < total_nb_fragment) {
if (nb_big_fragment != 1) {
AKANTU_ERROR(
"The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
} else {
if (nb_big_fragment != 0) {
AKANTU_ERROR(
"The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
}
/// check number of fragments
UInt nb_fragment_num = fragment_manager.getNbFragment();
if (nb_fragment_num != frag) {
AKANTU_ERROR("The number of fragments is wrong! Numerical: "
<< nb_fragment_num << " Theoretical: " << frag);
return EXIT_FAILURE;
}
/// check mass computation
if (frag < total_nb_fragment) {
Real total_mass = 0.;
UInt small_fragments = 0;
for (UInt f = 0; f < nb_fragment_num; ++f) {
const Vector<Real> & current_inertia = inertia_moments_begin[f];
if (Math::are_float_equal(fragment_mass(f, 0), frag_theo_mass)) {
/// check center of mass
if (fragment_center(f, 0) > (L * frag / total_nb_fragment - L / 2)) {
AKANTU_ERROR("Fragment center is wrong!");
return EXIT_FAILURE;
}
/// check moment of inertia
if (!isInertiaEqual(current_inertia, small_frag_inertia)) {
AKANTU_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
++small_fragments;
total_mass += frag_theo_mass;
} else {
/// check the moment of inertia for the biggest fragment
Real big_frag_mass = frag_theo_mass * (total_nb_fragment - frag + 1);
Real big_frag_size = el_size * (total_nb_fragment - frag + 1);
Vector<Real> big_frag_inertia(spatial_dimension);
big_frag_inertia(0) = big_frag_mass * (h * h + h * h) / 12.;
big_frag_inertia(1) =
big_frag_mass * (big_frag_size * big_frag_size + h * h) / 12.;
big_frag_inertia(2) =
big_frag_mass * (big_frag_size * big_frag_size + h * h) / 12.;
std::sort(big_frag_inertia.storage(),
big_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
if (!isInertiaEqual(current_inertia, big_frag_inertia)) {
AKANTU_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
}
}
if (small_fragments != nb_fragment_num - 1) {
AKANTU_ERROR("The number of small fragments is wrong!");
return EXIT_FAILURE;
}
if (!Math::are_float_equal(total_mass,
small_fragments * frag_theo_mass)) {
AKANTU_ERROR("The mass of small fragments is wrong!");
return EXIT_FAILURE;
}
}
/// displace fragments
rotateArray(mesh.getNodes(), -rotation_angle);
// rotateArray(displacement, -rotation_angle);
displaceElements(model, lim, el_size * 2);
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
model.updateResidual();
lim += el_size;
}
model.dump();
model.dump("cohesive elements");
/// check centers
const Array<Real> & fragment_velocity = fragment_manager.getVelocity();
Real initial_position = -L / 2. + el_size / 2.;
for (UInt frag = 0; frag < total_nb_fragment; ++frag) {
Real theoretical_center = initial_position + el_size * frag;
UInt f_index = 0;
while (
f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_center(f_index, 0), theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_ERROR("The fragments' center is wrong!");
return EXIT_FAILURE;
}
f_index = 0;
while (f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_velocity(f_index, 0),
theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_ERROR("The fragments' velocity is wrong!");
return EXIT_FAILURE;
}
}
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_buildfragments was passed!" << std::endl;
return EXIT_SUCCESS;
}
void verticalInsertionLimit(SolidMechanicsModelCohesive & model) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh_facets = model.getMeshFacets();
const Array<Real> & position = mesh_facets.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<bool> & check_facets =
model.getElementInserter().getCheckFacets(type, ghost_type);
const Array<UInt> & connectivity =
mesh_facets.getConnectivity(type, ghost_type);
UInt nb_nodes_per_facet = connectivity.getNbComponent();
for (UInt f = 0; f < check_facets.getSize(); ++f) {
if (!check_facets(f))
continue;
UInt nb_aligned_nodes = 1;
Real first_node_pos = position(connectivity(f, 0), 0);
for (; nb_aligned_nodes < nb_nodes_per_facet; ++nb_aligned_nodes) {
Real other_node_pos = position(connectivity(f, nb_aligned_nodes), 0);
if (!Math::are_float_equal(first_node_pos, other_node_pos))
break;
}
if (nb_aligned_nodes != nb_nodes_per_facet) {
check_facets(f) = false;
}
}
}
}
}
void displaceElements(SolidMechanicsModelCohesive & model, const Real lim,
const Real amount) {
UInt spatial_dimension = model.getSpatialDimension();
Array<Real> & displacement = model.getDisplacement();
Mesh & mesh = model.getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> displaced(nb_nodes);
displaced.zero();
Vector<Real> barycenter(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element = connectivity.getSize();
UInt nb_nodes_per_element = connectivity.getNbComponent();
Array<UInt>::const_vector_iterator conn_el =
connectivity.begin(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, barycenter.storage(), ghost_type);
if (barycenter(0) < lim) {
const Vector<UInt> & conn = conn_el[el];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = conn(n);
if (!displaced(node)) {
displacement(node, 0) -= amount;
displaced(node) = true;
}
}
}
}
}
}
}
bool isInertiaEqual(const Vector<Real> & a, const Vector<Real> & b) {
UInt nb_terms = a.size();
UInt equal_terms = 0;
while (equal_terms < nb_terms &&
std::abs(a(equal_terms) - b(equal_terms)) / a(equal_terms) <
Math::getTolerance())
++equal_terms;
return equal_terms == nb_terms;
}
void rotateArray(Array<Real> & array, Real angle) {
UInt spatial_dimension = array.getNbComponent();
Real rotation_values[] = {std::cos(angle),
std::sin(angle),
0,
-std::sin(angle),
std::cos(angle),
0,
0,
0,
1};
Matrix<Real> rotation(rotation_values, spatial_dimension, spatial_dimension);
RVector displaced_node(spatial_dimension);
auto node_it = array.begin(spatial_dimension);
auto node_end = array.end(spatial_dimension);
for (; node_it != node_end; ++node_it) {
displaced_node.mul<false>(rotation, *node_it);
*node_it = displaced_node;
}
}
UInt getNbBigFragments(FragmentManager & fragment_manager,
UInt minimum_nb_elements) {
fragment_manager.computeNbElementsPerFragment();
const Array<UInt> & nb_elements_per_fragment =
fragment_manager.getNbElementsPerFragment();
UInt nb_fragment = fragment_manager.getNbFragment();
UInt nb_big_fragment = 0;
for (UInt frag = 0; frag < nb_fragment; ++frag) {
if (nb_elements_per_fragment(frag) >= minimum_nb_elements) {
++nb_big_fragment;
}
}
return nb_big_fragment;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/CMakeLists.txt
index f1674c690..be74e8f25 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/CMakeLists.txt
@@ -1,47 +1,57 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief configuration for parallel test for extrinsic cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_parallel_extrinsic_mesh mesh.geo 2 2)
add_mesh(test_cohesive_parallel_extrinsic_tetrahedron_mesh tetrahedron.geo 3 2)
register_test(test_cohesive_parallel_extrinsic
SOURCES test_cohesive_parallel_extrinsic.cc
DEPENDS test_cohesive_parallel_extrinsic_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview)
register_test(test_cohesive_parallel_extrinsic_tetrahedron
SOURCES test_cohesive_parallel_extrinsic_tetrahedron.cc
DEPENDS test_cohesive_parallel_extrinsic_tetrahedron_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview)
register_test(test_cohesive_parallel_extrinsic_tetrahedron_displacement
SOURCES test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
DEPENDS test_cohesive_parallel_extrinsic_tetrahedron_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview displacement)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
index 46b75defa..43fa07e70 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
@@ -1,186 +1,188 @@
/**
* @file test_cohesive_parallel_extrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief parallel test for cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 500;
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
model.limitInsertion(_y, -0.30, -0.20);
model.updateAutomaticInsertion();
// debug::setDebugLevel(dblDump);
// std::cout << mesh_facets << std::endl;
// debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep() * 0.1;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
/// initial conditions
Real loading_rate = 0.5;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("extrinsic_parallel");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("residual");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("partitions");
// model.getDumper().getDumper().setMode(iohelper::BASE64);
model.dump();
model.setBaseNameToDumper("cohesive elements",
"extrinsic_parallel_cohesive_elements");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
displacement(n, 1) += disp_update * position(n, 1);
}
model.checkCohesiveStress();
model.solveStep();
// model.dump();
if (s % 10 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
model.dump();
model.dump("cohesive elements");
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 200 * sqrt(2);
if (prank == 0) {
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
index 9c57ea605..de3c6a1d3 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
@@ -1,243 +1,245 @@
/**
* @file test_cohesive_parallel_extrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Tue May 08 2012
+ * @date last modification: Thu Mar 22 2018
*
* @brief 3D extrinsic cohesive elements test
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real constant, Real x, Real y, Real z) {
return constant + 2. * x + 3. * y + 4 * z;
}
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
// const UInt max_steps = 1000;
// Real increment = 0.005;
const UInt spatial_dimension = 3;
Math::setTolerance(1.e-12);
ElementType type = _tetrahedron_10;
ElementType type_facet = Mesh::getFacetType(type);
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initParallel(partition, NULL, true);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
const MaterialCohesiveLinear<3> & mat_cohesive =
dynamic_cast<const MaterialCohesiveLinear<3> &>(model.getMaterial(1));
const Real sigma_c =
mat_cohesive.getParam<RandomInternalField<Real, FacetInternalField>>(
"sigma_c");
const Real beta = mat_cohesive.getParam<Real>("beta");
// const Real G_cI = mat_cohesive.getParam<Real>("G_cI");
Array<Real> & position = mesh.getNodes();
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points positions on facets
const Mesh & mesh_facets = model.getMeshFacets();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets, spatial_dimension,
type_facet);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position, quad_elements,
spatial_dimension, type);
/// assign some values to stresses
Array<Real> & stress =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(type));
Array<Real>::iterator<Matrix<Real>> stress_it =
stress.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad_el; ++q, ++stress_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_it)(i, j) =
index * function(sigma_c * 5, quad_elements(q, 0),
quad_elements(q, 1), quad_elements(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_it)(i, j) = (*stress_it)(j, i);
}
}
}
/// compute stress on facet quads
Array<Real> stress_facets(nb_tot_quad, spatial_dimension * spatial_dimension);
Array<Real>::iterator<Matrix<Real>> stress_facets_it =
stress_facets.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad; ++q, ++stress_facets_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_facets_it)(i, j) =
index * function(sigma_c * 5, quad_facets(q, 0), quad_facets(q, 1),
quad_facets(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_facets_it)(i, j) = (*stress_facets_it)(j, i);
}
}
}
/// insert cohesive elements
model.checkCohesiveStress();
/// check insertion stress
const Array<Real> & normals = model.getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
const Array<Real> & tangents = model.getTangents(type_facet);
const Array<Real> & sigma_c_eff =
mat_cohesive.getInsertionTraction(type_cohesive);
Vector<Real> normal_stress(spatial_dimension);
const Array<std::vector<Element>> & coh_element_to_facet =
mesh_facets.getElementToSubelement(type_facet);
Array<Real>::iterator<Matrix<Real>> quad_facet_stress =
stress_facets.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_iterator<Vector<Real>> quad_normal =
normals.begin(spatial_dimension);
Array<Real>::const_iterator<Vector<Real>> quad_tangents =
tangents.begin(tangents.getNbComponent());
for (UInt f = 0; f < nb_facet; ++f) {
const Element & cohesive_element = coh_element_to_facet(f)[1];
for (UInt q = 0; q < nb_quad_per_facet;
++q, ++quad_facet_stress, ++quad_normal, ++quad_tangents) {
if (cohesive_element == ElementNull)
continue;
normal_stress.mul<false>(*quad_facet_stress, *quad_normal);
Real normal_contrib = normal_stress.dot(*quad_normal);
Real first_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
first_tangent_contrib += normal_stress(dim) * (*quad_tangents)(dim);
Real second_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
second_tangent_contrib +=
normal_stress(dim) * (*quad_tangents)(dim + spatial_dimension);
Real tangent_contrib =
std::sqrt(first_tangent_contrib * first_tangent_contrib +
second_tangent_contrib * second_tangent_contrib);
normal_contrib = std::max(0., normal_contrib);
Real effective_norm =
std::sqrt(normal_contrib * normal_contrib +
tangent_contrib * tangent_contrib / beta / beta);
if (effective_norm < sigma_c)
continue;
if (!Math::are_float_equal(
effective_norm,
sigma_c_eff(cohesive_element.element * nb_quad_per_facet + q))) {
std::cout << "Insertion tractions do not match" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
index d81f98650..92e8e2f14 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
@@ -1,403 +1,405 @@
/**
* @file test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Displacement test for 3D cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
using namespace akantu;
bool checkDisplacement(SolidMechanicsModelCohesive & model, ElementType type,
std::ofstream & error_output, UInt step,
bool barycenters);
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt max_steps = 500;
Math::setTolerance(1.e-12);
UInt spatial_dimension = 3;
ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
// Array<Real> limits(spatial_dimension, 2);
// limits(0, 0) = -0.01;
// limits(0, 1) = 0.01;
// limits(1, 0) = -100;
// limits(1, 1) = 100;
// limits(2, 0) = -100;
// limits(2, 1) = 100;
// model.enableFacetsCheckOnArea(limits);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
// debug::setDebugLevel(dblDump);
// std::cout << mesh_facets << std::endl;
// debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep() * 0.1;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
boundary(n, dim) = true;
}
}
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
boundary(n, dim) = true;
}
}
}
// #if defined (AKANTU_DEBUG_TOOLS)
// Vector<Real> facet_center(spatial_dimension);
// facet_center(0) = 0;
// facet_center(1) = -0.16666667;
// facet_center(2) = 0.5;
// debug::element_manager.setMesh(mesh);
// debug::element_manager.addModule(debug::_dm_material_cohesive);
// debug::element_manager.addModule(debug::_dm_debug_tools);
// //debug::element_manager.addModule(debug::_dm_integrator);
// #endif
/// initial conditions
Real loading_rate = 1;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 0) = loading_rate * position(n, 0);
velocity(n, 1) = loading_rate * position(n, 0);
}
model.synchronizeBoundaries();
model.updateResidual();
std::stringstream paraview_output;
paraview_output << "extrinsic_parallel_tetrahedron_" << psize;
model.setBaseName(paraview_output.str());
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("velocity");
model.addDumpFieldVector("acceleration");
model.addDumpFieldVector("residual");
model.addDumpFieldTensor("stress");
model.addDumpFieldTensor("grad_u");
model.addDumpField("partitions");
// model.getDumper().getDumper().setMode(iohelper::BASE64);
model.dump();
model.setBaseNameToDumper("cohesive elements",
paraview_output.str() + "_cohesive_elements");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
std::stringstream error_stream;
error_stream << "error"
<< ".csv";
std::ofstream error_output;
error_output.open(error_stream.str().c_str());
error_output << "# Step, Average, Max, Min" << std::endl;
if (checkDisplacement(model, type, error_output, 0, true)) {
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
displacement(n, 0) += disp_update * position(n, 0);
displacement(n, 1) += disp_update * position(n, 0);
}
}
model.checkCohesiveStress();
model.solveStep();
if (s % 100 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
model.dump();
model.dump("cohesive elements");
if (!checkDisplacement(model, type, error_output, max_steps, false)) {
finalize();
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
bool checkDisplacement(SolidMechanicsModelCohesive & model, ElementType type,
std::ofstream & error_output, UInt step,
bool barycenters) {
Mesh & mesh = model.getMesh();
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<UInt> & connectivity = mesh.getConnectivity(type);
const Array<Real> & displacement = model.getDisplacement();
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_elem = Mesh::getNbNodesPerElement(type);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
if (psize == 1) {
std::stringstream displacement_file;
displacement_file << "displacement/displacement_" << std::setfill('0')
<< std::setw(6) << step;
std::ofstream displacement_output;
displacement_output.open(displacement_file.str().c_str());
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = connectivity(el, n);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
displacement_output << std::setprecision(15)
<< displacement(node, dim) << " ";
}
displacement_output << std::endl;
}
}
displacement_output.close();
if (barycenters) {
std::stringstream barycenter_file;
barycenter_file << "displacement/barycenters";
std::ofstream barycenter_output;
barycenter_output.open(barycenter_file.str().c_str());
Element element(type, 0);
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
mesh.getBarycenter(element, bary);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
barycenter_output << std::setprecision(15) << bary(dim) << " ";
}
barycenter_output << std::endl;
}
barycenter_output.close();
}
} else {
if (barycenters)
return true;
/// read data
std::stringstream displacement_file;
displacement_file << "displacement/displacement_" << std::setfill('0')
<< std::setw(6) << step;
std::ifstream displacement_input;
displacement_input.open(displacement_file.str().c_str());
Array<Real> displacement_serial(0, spatial_dimension);
Vector<Real> disp_tmp(spatial_dimension);
while (displacement_input.good()) {
for (UInt i = 0; i < spatial_dimension; ++i)
displacement_input >> disp_tmp(i);
displacement_serial.push_back(disp_tmp);
}
std::stringstream barycenter_file;
barycenter_file << "displacement/barycenters";
std::ifstream barycenter_input;
barycenter_input.open(barycenter_file.str().c_str());
Array<Real> barycenter_serial(0, spatial_dimension);
while (barycenter_input.good()) {
for (UInt dim = 0; dim < spatial_dimension; ++dim)
barycenter_input >> disp_tmp(dim);
barycenter_serial.push_back(disp_tmp);
}
Element element(type, 0);
Vector<Real> bary(spatial_dimension);
Array<Real>::iterator<Vector<Real>> it;
Array<Real>::iterator<Vector<Real>> begin =
barycenter_serial.begin(spatial_dimension);
Array<Real>::iterator<Vector<Real>> end =
barycenter_serial.end(spatial_dimension);
Array<Real>::const_iterator<Vector<Real>> disp_it;
Array<Real>::iterator<Vector<Real>> disp_serial_it;
Vector<Real> difference(spatial_dimension);
Array<Real> error;
/// compute error
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
mesh.getBarycenter(element, bary);
/// find element
for (it = begin; it != end; ++it) {
UInt matched_dim = 0;
while (matched_dim < spatial_dimension &&
Math::are_float_equal(bary(matched_dim), (*it)(matched_dim)))
++matched_dim;
if (matched_dim == spatial_dimension)
break;
}
if (it == end) {
std::cout << "Element barycenter not found!" << std::endl;
return false;
}
UInt matched_el = it - begin;
disp_serial_it = displacement_serial.begin(spatial_dimension) +
matched_el * nb_nodes_per_elem;
for (UInt n = 0; n < nb_nodes_per_elem; ++n, ++disp_serial_it) {
UInt node = connectivity(el, n);
if (!mesh.isLocalOrMasterNode(node))
continue;
disp_it = displacement.begin(spatial_dimension) + node;
difference = *disp_it;
difference -= *disp_serial_it;
error.push_back(difference.norm());
}
}
/// compute average error
Real average_error = std::accumulate(error.begin(), error.end(), 0.);
comm.allReduce(&average_error, 1, _so_sum);
UInt error_size = error.getSize();
comm.allReduce(&error_size, 1, _so_sum);
average_error /= error_size;
/// compute maximum and minimum
Real max_error = *std::max_element(error.begin(), error.end());
comm.allReduce(&max_error, 1, _so_max);
Real min_error = *std::min_element(error.begin(), error.end());
comm.allReduce(&min_error, 1, _so_min);
/// output data
if (prank == 0) {
error_output << step << ", " << average_error << ", " << max_error << ", "
<< min_error << std::endl;
}
if (max_error > 1.e-9) {
std::cout << "Displacement error is too big!" << std::endl;
return false;
}
}
return true;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/CMakeLists.txt
index b276f6457..be0f67800 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/CMakeLists.txt
@@ -1,30 +1,40 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief Configuration for test_cohesive_parallel_extrinsic_IG_TG
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_cohesive_parallel_extrinsic_IG_TG
SOURCES test_cohesive_parallel_extrinsic_IG_TG.cc
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat square.msh
DIRECTORIES_TO_CREATE paraview)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
index 7a3b1aa67..63459ad60 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
@@ -1,315 +1,317 @@
/**
* @file test_cohesive_parallel_extrinsic_IG_TG.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Jul 24 2020
*
* @brief Test for considering different cohesive properties for
* intergranular (IG) and transgranular (TG) fractures in extrinsic
* cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class MultiGrainMaterialSelector : public DefaultMaterialCohesiveSelector {
public:
MultiGrainMaterialSelector(const SolidMechanicsModelCohesive & model,
const ID & transgranular_id,
const ID & intergranular_id)
: DefaultMaterialCohesiveSelector(model),
transgranular_id(transgranular_id), intergranular_id(intergranular_id),
model(model), mesh(model.getMesh()), mesh_facets(model.getMeshFacets()),
spatial_dimension(model.getSpatialDimension()), nb_IG(0), nb_TG(0) {}
UInt operator()(const Element & element) {
if (mesh_facets.getSpatialDimension(element.type) ==
(spatial_dimension - 1)) {
const std::vector<Element> & element_to_subelement =
mesh_facets.getElementToSubelement(element.type, element.ghost_type)(
element.element);
const Element & el1 = element_to_subelement[0];
const Element & el2 = element_to_subelement[1];
UInt grain_id1 =
mesh.getData<UInt>("tag_0", el1.type, el1.ghost_type)(el1.element);
if (el2 != ElementNull) {
UInt grain_id2 =
mesh.getData<UInt>("tag_0", el2.type, el2.ghost_type)(el2.element);
if (grain_id1 == grain_id2) {
// transgranular = 0 indicator
nb_TG++;
return model.getMaterialIndex(transgranular_id);
} else {
// intergranular = 1 indicator
nb_IG++;
return model.getMaterialIndex(intergranular_id);
}
} else {
// transgranular = 0 indicator
nb_TG++;
return model.getMaterialIndex(transgranular_id);
}
} else {
return DefaultMaterialCohesiveSelector::operator()(element);
}
}
private:
ID transgranular_id, intergranular_id;
const SolidMechanicsModelCohesive & model;
const Mesh & mesh;
const Mesh & mesh_facets;
UInt spatial_dimension;
UInt nb_IG;
UInt nb_TG;
};
/* -------------------------------------------------------------------------- */
void limitInsertion(SolidMechanicsModelCohesive & model) {
Real tolerance = 0.1;
const Mesh & mesh = model.getMesh();
const Mesh & mesh_facets = model.getMeshFacets();
CohesiveElementInserter & inserter = model.getElementInserter();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<bool> & f_check = inserter.getCheckFacets(type, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (f_check(f)) {
mesh_facets.getBarycenter(f, type, bary_facet.storage(), ghost_type);
if (!(bary_facet(0) > -tolerance && bary_facet(0) < tolerance) &&
!(bary_facet(1) > -tolerance && bary_facet(1) < tolerance))
f_check(f) = false;
}
}
}
}
model.updateAutomaticInsertion();
}
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
const UInt max_steps = 600;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
mesh.read("square.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initParallel(partition, NULL, true);
delete partition;
MultiGrainMaterialSelector material_selector(model, "TG_cohesive",
"IG_cohesive");
model.setMaterialSelector(material_selector);
model.initFull(
SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true, false));
Real time_step = model.getStableTimeStep() * 0.1;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
limitInsertion(model);
// std::cout << mesh << std::endl;
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("residual");
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("partitions");
model.setBaseNameToDumper("cohesive elements", "extrinsic_cohesive");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// initial conditions
Real loading_rate = 0.1;
// bar_height = 2
Real VI = loading_rate * 2 * 0.5;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
velocity(n, 0) = loading_rate * position(n, 0);
}
// std::ofstream edis("edis.txt");
// std::ofstream erev("erev.txt");
// Array<Real> & residual = model.getResidual();
// model.dump();
// const Array<Real> & stress = model.getMaterial(0).getStress(type);
Real dispy = 0;
// UInt nb_coh_elem = 0;
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
dispy += VI * time_step;
/// update displacement on extreme nodes
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 1) > 0.99) {
displacement(n, 1) = dispy;
velocity(n, 1) = VI;
}
if (position(n, 1) < -0.99) {
displacement(n, 1) = -dispy;
velocity(n, 1) = -VI;
}
if (position(n, 0) > 0.99) {
displacement(n, 0) = dispy;
velocity(n, 0) = VI;
}
if (position(n, 0) < -0.99) {
displacement(n, 0) = -dispy;
velocity(n, 0) = -VI;
}
}
model.checkCohesiveStress();
model.solveStep();
if (s % 10 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
// model.dump();
// model.dump("cohesive elements");
}
// Real Ed = model.getEnergy("dissipated");
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
model.dump();
model.dump("cohesive elements");
// edis.close();
// erev.close();
// mesh.write("mesh_final.msh");
Real Ed = model.getEnergy("dissipated");
Real Edt = 40;
if (prank == 0)
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.99 || Ed > Edt * 1.01 || std::isnan(Ed)) {
if (prank == 0)
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
// for (UInt n = 0; n < position.getSize(); ++n) {
// for (UInt s = 0; s < spatial_dimension; ++s) {
// position(n, s) += displacement(n, s);
// }
// }
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_extrinsic_IG_TG was passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/CMakeLists.txt
index c9040c786..cf800689c 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/CMakeLists.txt
@@ -1,47 +1,57 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
# @author Mauro Corrado <mauro.corrado@epfl.ch>
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief Tests parallel insertion of cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(3d_spherical_inclusion_parallel 3d_spherical_inclusion.geo 3 2)
register_test(test_cohesive_parallel_insertion_along_physical_surfaces
SOURCES test_cohesive_parallel_insertion_along_physical_surfaces.cc
DEPENDS 3d_spherical_inclusion_parallel
FILES_TO_COPY input_file.dat
PACKAGE parallel_cohesive_element
)
register_test(test_cohesive_parallel_intrinsic_implicit_insertion
PARALLEL
POSTPROCESS verify_insertion.sh
PARALLEL_LEVEL "2 4"
SOURCES test_cohesive_parallel_intrinsic_implicit_insertion.cc
FILES_TO_COPY input_file_iii.dat
2d_basic_interface.msh
output_dir_verified
PACKAGE parallel_cohesive_element
DIRECTORIES_TO_CREATE output_dir
)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
index 83bc66b7d..0f949b872 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
@@ -1,132 +1,134 @@
/**
* @file test_cohesive_parallel_insertion_along_physical_surfaces.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Test parallel intrinsic insertion of cohesive elements along physical
* surfaces
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_cohesive.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("input_file.dat", argc, argv);
Math::setTolerance(1e-15);
const UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
mesh.read("3d_spherical_inclusion.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
mesh.createGroupsFromMeshData<std::string>("physical_names");
model.initFull(SolidMechanicsModelCohesiveOptions(_static));
std::vector<std::string> surfaces_name = {"interface", "coh1", "coh2",
"coh3", "coh4", "coh5"};
UInt nb_surf = surfaces_name.size();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
std::string ghost_str;
if (*gt == 1)
ghost_str = "ghost";
else
ghost_str = "not ghost";
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, *gt, _ek_cohesive);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, *gt, _ek_cohesive);
for (; it != end; ++it) {
Array<UInt> & material_id = mesh.getMeshFacets().getData<UInt>(
"physical_names")(mesh.getFacetType(*it), *gt);
for (UInt i = 0; i < nb_surf; ++i) {
UInt expected_insertion = 0;
for (UInt m = 0; m < material_id.getSize(); ++m) {
if (material_id(m) ==
model.SolidMechanicsModel::getMaterialIndex(surfaces_name[i]))
++expected_insertion;
}
UInt inserted_elements;
inserted_elements = model.getMaterial(surfaces_name[i])
.getElementFilter()(*it, *gt)
.getSize();
if (expected_insertion != inserted_elements) {
std::cerr << std::endl
<< "!!! Mismatch in insertion of surface named "
<< surfaces_name[i] << " in proc n° " << prank << " --> "
<< inserted_elements << " inserted elements of type "
<< ghost_str << " out of " << expected_insertion
<< std::endl;
return EXIT_FAILURE;
}
}
}
}
model.assembleStiffnessMatrix();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
index d75a934a1..c5af557f5 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
@@ -1,306 +1,308 @@
/**
* @file test_cohesive_parallel_intrinsic_implicit_insertion.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Verifying the proper insertion and synchronization of intrinsic
* cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "material_cohesive.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
std::ofstream output;
/* -------------------------------------------------------------------------- */
void printMeshContent(Mesh & mesh) {
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
comm.barrier();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
mesh.firstType(_all_dimensions, *gt, _ek_not_defined);
Mesh::type_iterator last =
mesh.lastType(_all_dimensions, *gt, _ek_not_defined);
for (; first != last; ++first) {
UInt nb_element = mesh.getNbElement(*first, *gt);
output << std::endl
<< "Element type: " << *first << ", " << *gt << ": " << nb_element
<< " in the mesh of processor " << prank << std::endl;
Array<UInt> & conn = mesh.getConnectivity(*first, *gt);
for (UInt i = 0; i < conn.getSize(); ++i) {
output << "Element no " << i << " ";
for (UInt j = 0; j < conn.getNbComponent(); ++j) {
output << conn(i, j) << " ";
}
output << std::endl;
}
}
}
}
/* -------------------------------------------------------------------------- */
void printNodeList(Mesh & mesh) {
Array<double> & nodes = mesh.getNodes();
output << "Number of nodes: " << mesh.getNbNodes() << std::endl;
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
output << "Node # " << i << ", x-coord: " << nodes(i, 0)
<< ", y-coord: " << nodes(i, 1)
<< ", of type: " << mesh.getNodeType(i) << std::endl;
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void getGlobalIDs(Mesh & mesh) {
const Array<UInt> & glob_id = mesh.getGlobalNodesIds();
if (&glob_id) {
output << "Global nodes ID: " << std::endl;
for (UInt i = 0; i < glob_id.getSize(); ++i) {
output << i << " " << glob_id(i) << std::endl;
}
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void printSynchroinfo(Mesh & mesh, const DistributedSynchronizer & synch) {
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
Int psize = comm.getNbProc();
if (comm.getNbProc() == 1)
return;
for (Int p = 0; p < psize; ++p) {
if (p == prank)
continue;
output << "From processor " << prank << " to processor " << p << std::endl;
const Array<Element> & sele = *(synch.getSendElement() + p);
output << " Sending element(s): " << std::endl;
for (UInt i = 0; i < sele.getSize(); ++i) {
output << sele(i) << std::endl;
}
const Array<Element> & rele = *(synch.getReceiveElement() + p);
output << " Receiving element(s): " << std::endl;
for (UInt i = 0; i < rele.getSize(); ++i) {
output << rele(i) << std::endl;
}
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void printDOF(SolidMechanicsModelCohesive & model) {
const auto & comm = Communicator::getStaticCommunicator();
if (comm.getNbProc() == 1)
return;
Int prank = comm.whoAmI();
const DOFSynchronizer & dof = model.getDOFSynchronizer();
output << "Number of global dofs " << dof.getNbGlobalDOFs()
<< " for processor " << prank << std::endl;
const Array<UInt> & dof_global_ids = dof.getDOFGlobalIDs();
for (UInt i = 0; i < dof_global_ids.getSize(); ++i) {
output << "Local dof " << i << ", global id: " << dof_global_ids(i)
<< std::endl;
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
std::string input_file = "input_file_iii.dat";
std::string mesh_file = "2d_basic_interface.msh";
std::string dir = "output_dir/";
initialize(input_file, argc, argv);
debug::setDebugLevel(dbl0);
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
std::stringstream filename;
filename << dir.c_str() << "output_from_proc_" << prank << "_out_of_" << psize
<< ".out";
output.open(filename.str());
if (prank == 0) {
mesh.read(mesh_file);
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
const ElementTypeMapArray<UInt> & partitions = partition->getPartitions();
output << "The root processor read the mesh." << std::endl
<< "Only GMSH physical objects are created in the mesh."
<< std::endl;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(_all_dimensions, *gt);
Mesh::type_iterator last = mesh.lastType(_all_dimensions, *gt);
for (; first != last; ++first) {
output << "Element type: " << *first << " ghost type: " << *gt
<< std::endl;
UInt nb_element = mesh.getNbElement(*first, *gt);
output << nb_element << " to partitionate between " << psize
<< " processsors" << std::endl;
Array<UInt> part = partitions(*first, *gt);
for (UInt i = 0; i < part.getSize(); ++i) {
output << i << " " << part(i) << std::endl;
}
}
}
output << "Nodes are also read and set with type -1 (normal node)"
<< std::endl;
printNodeList(mesh);
}
SolidMechanicsModelCohesive model(mesh);
output << "Before initParallel(), non-root processors have empty Mesh object"
<< std::endl;
printMeshContent(mesh);
model.initParallel(partition);
output << "After initParallel(), Mesh object on each processor is a local "
"partionated mesh containing ghost elements"
<< std::endl;
printMeshContent(mesh);
output << "Nodes are also partionated and new node types are defined:"
<< std::endl;
printNodeList(mesh);
output << "-3: pure ghost node -> not a local node" << std::endl
<< "-2: master node -> node shared with other processor(s) -> local "
"and global node"
<< std::endl
<< ">0: slave node -> -> node shared with other processor(s) -> only "
"local node (its id is the rank of the processor owning the master "
"node)"
<< std::endl;
output
<< "Each local node has a corresponding global id used during assembly: "
<< std::endl;
getGlobalIDs(mesh);
Mesh & mesh_facets = mesh.getMeshFacets();
output << "Within cohesive element model, initParallel() creates a second "
"Mesh object usually called mesh_facet"
<< std::endl
<< "This Mesh object contains all sub-dimensional elements where "
"potential cohesive element can be inserted"
<< std::endl;
printMeshContent(mesh_facets);
const DistributedSynchronizer & synch_model = model.getSynchronizer();
output << "The distributed synchronizer of solid mechanics model is used to "
"synchronize fields with ghost element:"
<< std::endl;
printSynchroinfo(mesh, synch_model);
mesh.createGroupsFromMeshData<std::string>("physical_names");
model.initFull(SolidMechanicsModelCohesiveOptions(_static));
output << "In case of insertion along physical objects, cohesive elements "
"are created during initFull()"
<< std::endl;
output << "Elements list after insertion" << std::endl;
printMeshContent(mesh);
output << "Node list after insertion: (Total number of nodes "
<< mesh.getNbNodes() << ")" << std::endl;
printNodeList(mesh);
output << "Node global ids after insertion: (Total number of nodes "
<< mesh.getNbGlobalNodes() << ")" << std::endl;
getGlobalIDs(mesh);
const DistributedSynchronizer & coh_synch_model =
*(model.getCohesiveSynchronizer());
output << "Solid mechanics model cohesive has its own distributed "
"synchronizer to handle ghost cohesive element:"
<< std::endl;
printSynchroinfo(mesh, coh_synch_model);
output << "A synchronizer dedicated to degrees of freedom (DOFs) is used by "
"the solver to build matrices in parallel:"
<< std::endl
<< "This DOFSynchronizer is built based on nodes global id "
<< std::endl;
printDOF(model);
output.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/CMakeLists.txt
index a82df5570..08e50c0db 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/CMakeLists.txt
@@ -1,40 +1,50 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
#
-# @date creation: Wed Nov 05 2014
-# @date last modification: Fri Oct 13 2017
+# @date creation: Fri Oct 13 2017
+# @date last modification: Fri Oct 13 2017
#
# @brief configuration for parallel test for intrinsic cohesive elements
#
-# @section LICENSE
-#
-# Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_cohesive_parallel_intrinsic_mesh mesh.geo 2 2)
add_mesh(test_cohesive_parallel_intrinsic_tetrahedron_mesh tetrahedron.geo 3 2)
register_test(test_cohesive_parallel_intrinsic
SOURCES test_cohesive_parallel_intrinsic.cc
DEPENDS test_cohesive_parallel_intrinsic_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview)
register_test(test_cohesive_parallel_intrinsic_tetrahedron
SOURCES test_cohesive_parallel_intrinsic_tetrahedron.cc
DEPENDS test_cohesive_parallel_intrinsic_tetrahedron_mesh
PACKAGE parallel_cohesive_element
FILES_TO_COPY material_tetrahedron.dat
DIRECTORIES_TO_CREATE paraview)
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
index 0525d8ac2..e60e1dd73 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
@@ -1,174 +1,176 @@
/**
* @file test_cohesive_parallel_intrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief parallel test for intrinsic cohesive elements
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 350;
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
// /// insert cohesive elements
// CohesiveElementInserter inserter(mesh);
// inserter.setLimit('x', -0.26, -0.24);
// inserter.insertIntrinsicElements();
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
model.initFull();
model.limitInsertion(_x, -0.26, -0.24);
model.insertIntrinsicElements();
debug::setDebugLevel(dblDump);
std::cout << mesh << std::endl;
debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
// Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
Real epsilon = std::numeric_limits<Real>::epsilon();
for (UInt n = 0; n < nb_nodes; ++n) {
if (std::abs(position(n, 0) - 1.) < epsilon)
boundary(n, 0) = true;
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("intrinsic_parallel");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("residual");
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("partitions");
model.addDumpField("force");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_parallel_intrinsic");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.dump("cohesive elements");
/// initial conditions
Real loading_rate = .2;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 0) = loading_rate * position(n, 0);
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
if (s % 20 == 0) {
model.dump();
model.dump("cohesive elements");
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&>
// (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 2 * sqrt(2);
if (prank == 0) {
std::cout << Ed << " " << Edt << std::endl;
if (std::abs((Ed - Edt) / Edt) > 0.01 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
}
finalize();
if (prank == 0)
std::cout << "OK: Test passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
index 4c2647916..25cea47a5 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
@@ -1,712 +1,714 @@
/**
* @file test_cohesive_parallel_intrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Wed Nov 08 2017
*
* @brief Test for 3D intrinsic cohesive elements simulation in parallel
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dumper_paraview.hh"
#include "material_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment);
bool checkTractions(SolidMechanicsModelCohesive & model, Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation);
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check, Int psize);
bool checkEquilibrium(const Mesh & mesh, const Array<Real> & residual);
bool checkResidual(const Array<Real> & residual, const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation);
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements);
int main(int argc, char * argv[]) {
initialize("material_tetrahedron.dat", argc, argv);
const UInt spatial_dimension = 3;
const UInt max_steps = 60;
const Real increment_constant = 0.01;
ElementType type = _tetrahedron_10;
Math::setTolerance(1.e-10);
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
UInt nb_nodes_to_check_serial = 0;
UInt total_nb_nodes = 0;
UInt nb_elements_check_serial = 0;
akantu::MeshPartition * partition = NULL;
if (prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// count nodes with zero position
const Array<Real> & position = mesh.getNodes();
for (UInt n = 0; n < position.getSize(); ++n) {
if (std::abs(position(n, 0) - 0.) < 1e-6)
++nb_nodes_to_check_serial;
}
// /// insert cohesive elements
// CohesiveElementInserter inserter(mesh);
// inserter.setLimit(0, -0.01, 0.01);
// inserter.insertIntrinsicElements();
/// find nodes to check in serial
ElementTypeMapArray<UInt> elements_serial("elements_serial", "");
findElementsToDisplace(mesh, elements_serial);
nb_elements_check_serial = elements_serial(type).getSize();
total_nb_nodes = mesh.getNbNodes() + nb_nodes_to_check_serial;
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
debug::setDebugLevel(dblDump);
partition->partitionate(psize);
debug::setDebugLevel(dblInfo);
}
comm.broadcast(&nb_nodes_to_check_serial, 1, 0);
comm.broadcast(&nb_elements_check_serial, 1, 0);
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
model.initFull();
model.limitInsertion(_x, -0.01, 0.01);
model.insertIntrinsicElements();
{
comm.broadcast(&total_nb_nodes, 1, 0);
Array<Int> nb_local_nodes(psize);
nb_local_nodes.zero();
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n))
++nb_local_nodes(prank);
}
comm.allGather(nb_local_nodes.storage(), 1);
UInt total_nb_nodes_parallel =
std::accumulate(nb_local_nodes.begin(), nb_local_nodes.end(), 0);
Array<UInt> global_nodes_list(total_nb_nodes_parallel);
UInt first_global_node = std::accumulate(nb_local_nodes.begin(),
nb_local_nodes.begin() + prank, 0);
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
global_nodes_list(first_global_node) = mesh.getNodeGlobalId(n);
++first_global_node;
}
}
comm.allGatherV(global_nodes_list.storage(), nb_local_nodes.storage());
if (prank == 0)
std::cout << "Maximum node index: "
<< *(std::max_element(global_nodes_list.begin(),
global_nodes_list.end()))
<< std::endl;
Array<UInt> repeated_nodes;
repeated_nodes.resize(0);
for (UInt n = 0; n < total_nb_nodes_parallel; ++n) {
UInt appearances =
std::count(global_nodes_list.begin() + n, global_nodes_list.end(),
global_nodes_list(n));
if (appearances > 1) {
std::cout << "Node " << global_nodes_list(n) << " appears "
<< appearances << " times" << std::endl;
std::cout << " in position: " << n;
repeated_nodes.push_back(global_nodes_list(n));
UInt * node_position = global_nodes_list.storage() + n;
for (UInt i = 1; i < appearances; ++i) {
node_position =
std::find(node_position + 1,
global_nodes_list.storage() + total_nb_nodes_parallel,
global_nodes_list(n));
UInt current_index = node_position - global_nodes_list.storage();
std::cout << ", " << current_index;
}
std::cout << std::endl << std::endl;
}
}
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
UInt global_node = mesh.getNodeGlobalId(n);
if (std::find(repeated_nodes.begin(), repeated_nodes.end(),
global_node) != repeated_nodes.end()) {
std::cout << "Repeated global node " << global_node
<< " corresponds to local node " << n << std::endl;
}
}
if (total_nb_nodes != total_nb_nodes_parallel) {
if (prank == 0) {
std::cout << "Error: total number of nodes is wrong in parallel"
<< std::endl;
std::cout << "Serial: " << total_nb_nodes
<< " Parallel: " << total_nb_nodes_parallel << std::endl;
}
finalize();
return EXIT_FAILURE;
}
}
model.updateResidual();
model.setBaseName("intrinsic_parallel_tetrahedron");
model.addDumpFieldVector("displacement");
model.addDumpField("residual");
model.addDumpField("partitions");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_parallel_tetrahedron");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.dump("cohesive elements");
/// find elements to displace
ElementTypeMapArray<UInt> elements("elements", "");
findElementsToDisplace(mesh, elements);
UInt nb_elements_check = elements(type).getSize();
comm.allReduce(&nb_elements_check, 1, _so_sum);
if (nb_elements_check != nb_elements_check_serial) {
if (prank == 0) {
std::cout << "Error: number of elements to check is wrong" << std::endl;
std::cout << "Serial: " << nb_elements_check_serial
<< " Parallel: " << nb_elements_check << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// find nodes to check
Array<UInt> nodes_to_check;
findNodesToCheck(mesh, elements, nodes_to_check, psize);
Vector<Int> nodes_to_check_size(psize);
nodes_to_check_size(prank) = nodes_to_check.getSize();
comm.allGather(nodes_to_check_size.storage(), 1);
UInt nodes_to_check_global_size = std::accumulate(
nodes_to_check_size.storage(), nodes_to_check_size.storage() + psize, 0);
if (nodes_to_check_global_size != nb_nodes_to_check_serial) {
if (prank == 0) {
std::cout << "Error: number of nodes to check is wrong in parallel"
<< std::endl;
std::cout << "Serial: " << nb_nodes_to_check_serial
<< " Parallel: " << nodes_to_check_global_size << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// rotate mesh
Real angle = 1.;
Matrix<Real> rotation(spatial_dimension, spatial_dimension);
rotation.zero();
rotation(0, 0) = std::cos(angle);
rotation(0, 1) = std::sin(angle) * -1.;
rotation(1, 0) = std::sin(angle);
rotation(1, 1) = std::cos(angle);
rotation(2, 2) = 1.;
Vector<Real> increment_tmp(spatial_dimension);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
increment_tmp(dim) = (dim + 1) * increment_constant;
}
Vector<Real> increment(spatial_dimension);
increment.mul<false>(rotation, increment_tmp);
Array<Real> & position = mesh.getNodes();
Array<Real> position_tmp(position);
Array<Real>::iterator<Vector<Real>> position_it =
position.begin(spatial_dimension);
Array<Real>::iterator<Vector<Real>> position_end =
position.end(spatial_dimension);
Array<Real>::iterator<Vector<Real>> position_tmp_it =
position_tmp.begin(spatial_dimension);
for (; position_it != position_end; ++position_it, ++position_tmp_it)
position_it->mul<false>(rotation, *position_tmp_it);
model.dump();
model.dump("cohesive elements");
updateDisplacement(model, elements, increment);
Real theoretical_Ed = 0;
Vector<Real> opening(spatial_dimension);
Vector<Real> traction(spatial_dimension);
Vector<Real> opening_old(spatial_dimension);
Vector<Real> traction_old(spatial_dimension);
opening.zero();
traction.zero();
opening_old.zero();
traction_old.zero();
Vector<Real> Dt(spatial_dimension);
Vector<Real> Do(spatial_dimension);
const Array<Real> & residual = model.getResidual();
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.updateResidual();
opening += increment_tmp;
if (checkTractions(model, opening, traction, rotation) ||
checkEquilibrium(mesh, residual) ||
checkResidual(residual, traction, nodes_to_check, rotation)) {
finalize();
return EXIT_FAILURE;
}
/// compute energy
Do = opening;
Do -= opening_old;
Dt = traction_old;
Dt += traction;
theoretical_Ed += .5 * Do.dot(Dt);
opening_old = opening;
traction_old = traction;
updateDisplacement(model, elements, increment);
if (s % 10 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
model.dump();
model.dump("cohesive elements");
}
}
model.dump();
model.dump("cohesive elements");
Real Ed = model.getEnergy("dissipated");
theoretical_Ed *= 4.;
if (prank == 0)
std::cout << "Dissipated energy: " << Ed
<< ", theoretical value: " << theoretical_Ed << std::endl;
if (!Math::are_float_equal(Ed, theoretical_Ed) || std::isnan(Ed)) {
if (prank == 0)
std::cout << "Error: the dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
if (prank == 0)
std::cout << "OK: Test passed!" << std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment) {
UInt spatial_dimension = model.getSpatialDimension();
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
update.zero();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type, ghost_type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_nodes_per_element = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elem(el), n);
if (!update(node)) {
Vector<Real> node_disp(displacement.storage() +
node * spatial_dimension,
spatial_dimension);
node_disp += increment;
update(node) = true;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
bool checkTractions(SolidMechanicsModelCohesive & model, Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh = model.getMesh();
const MaterialCohesive & mat_cohesive =
dynamic_cast<const MaterialCohesive &>(model.getMaterial(1));
Real sigma_c =
mat_cohesive.getParam<RandomInternalField<Real, FacetInternalField>>(
"sigma_c");
const Real beta = mat_cohesive.getParam<Real>("beta");
const Real G_cI = mat_cohesive.getParam<Real>("G_c");
// Real G_cII = mat_cohesive.getParam<Real>("G_cII");
const Real delta_0 = mat_cohesive.getParam<Real>("delta_0");
const Real kappa = mat_cohesive.getParam<Real>("kappa");
Real delta_c = 2 * G_cI / sigma_c;
sigma_c *= delta_c / (delta_c - delta_0);
Vector<Real> normal_opening(spatial_dimension);
normal_opening.zero();
normal_opening(0) = opening(0);
Real normal_opening_norm = normal_opening.norm();
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening.zero();
for (UInt dim = 1; dim < spatial_dimension; ++dim)
tangential_opening(dim) = opening(dim);
Real tangential_opening_norm = tangential_opening.norm();
Real beta2_kappa2 = beta * beta / kappa / kappa;
Real beta2_kappa = beta * beta / kappa;
Real delta = std::sqrt(tangential_opening_norm * tangential_opening_norm *
beta2_kappa2 +
normal_opening_norm * normal_opening_norm);
delta = std::max(delta, delta_0);
Real theoretical_damage = std::min(delta / delta_c, 1.);
if (Math::are_float_equal(theoretical_damage, 1.))
theoretical_traction.zero();
else {
theoretical_traction = tangential_opening;
theoretical_traction *= beta2_kappa;
theoretical_traction += normal_opening;
theoretical_traction *= sigma_c / delta * (1. - theoretical_damage);
}
Vector<Real> theoretical_traction_rotated(spatial_dimension);
theoretical_traction_rotated.mul<false>(rotation, theoretical_traction);
// adjust damage
theoretical_damage = std::max((delta - delta_0) / (delta_c - delta_0), 0.);
theoretical_damage = std::min(theoretical_damage, 1.);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last; ++it) {
ElementType type = *it;
const Array<Real> & traction = mat_cohesive.getTraction(type, ghost_type);
const Array<Real> & damage = mat_cohesive.getDamage(type, ghost_type);
UInt nb_quad_per_el =
model.getFEEngine("CohesiveFEEngine").getNbIntegrationPoints(type);
UInt nb_element = model.getMesh().getNbElement(type, ghost_type);
UInt tot_nb_quad = nb_element * nb_quad_per_el;
for (UInt q = 0; q < tot_nb_quad; ++q) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
if (!Math::are_float_equal(
std::abs(theoretical_traction_rotated(dim)),
std::abs(traction(q, dim)))) {
std::cout << "Error: tractions are incorrect" << std::endl;
return 1;
}
}
if (ghost_type == _not_ghost)
if (!Math::are_float_equal(theoretical_damage, damage(q))) {
std::cout << "Error: damage is incorrect" << std::endl;
return 1;
}
}
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check, Int psize) {
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
nodes_to_check.resize(0);
Array<UInt> global_nodes_to_check;
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = position.getSize();
Array<bool> checked_nodes(nb_nodes);
checked_nodes.zero();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator last = mesh.lastType(spatial_dimension);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt nb_nodes_per_elem = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
UInt element = elem(el);
Vector<UInt> conn_el(connectivity.storage() + nb_nodes_per_elem * element,
nb_nodes_per_elem);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn_el(n);
if (std::abs(position(node, 0) - 0.) < 1.e-6 && !checked_nodes(node)) {
checked_nodes(node) = true;
nodes_to_check.push_back(node);
global_nodes_to_check.push_back(mesh.getNodeGlobalId(node));
}
}
}
}
std::vector<CommunicationRequest *> requests;
for (Int p = prank + 1; p < psize; ++p) {
requests.push_back(comm.asyncSend(global_nodes_to_check.storage(),
global_nodes_to_check.getSize(), p,
prank));
}
Array<UInt> recv_nodes;
for (Int p = 0; p < prank; ++p) {
CommunicationStatus status;
comm.probe<UInt>(p, p, status);
UInt recv_nodes_size = recv_nodes.getSize();
recv_nodes.resize(recv_nodes_size + status.getSize());
comm.receive(recv_nodes.storage() + recv_nodes_size, status.getSize(), p,
p);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
for (UInt i = 0; i < recv_nodes.getSize(); ++i) {
Array<UInt>::iterator<UInt> node_position =
std::find(global_nodes_to_check.begin(), global_nodes_to_check.end(),
recv_nodes(i));
if (node_position != global_nodes_to_check.end()) {
UInt index = node_position - global_nodes_to_check.begin();
nodes_to_check.erase(index);
global_nodes_to_check.erase(index);
}
}
}
/* -------------------------------------------------------------------------- */
bool checkEquilibrium(const Mesh & mesh, const Array<Real> & residual) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> residual_sum(spatial_dimension);
residual_sum.zero();
Array<Real>::const_iterator<Vector<Real>> res_it =
residual.begin(spatial_dimension);
for (UInt n = 0; n < residual.getSize(); ++n, ++res_it) {
if (mesh.isLocalOrMasterNode(n))
residual_sum += *res_it;
}
const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(residual_sum.storage(), spatial_dimension, _so_sum);
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(residual_sum(s), 0.)) {
if (comm.whoAmI() == 0)
std::cout << "Error: system is not in equilibrium!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
bool checkResidual(const Array<Real> & residual, const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> total_force(spatial_dimension);
total_force.zero();
for (UInt n = 0; n < nodes_to_check.getSize(); ++n) {
UInt node = nodes_to_check(n);
Vector<Real> res(residual.storage() + node * spatial_dimension,
spatial_dimension);
total_force += res;
}
const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(total_force.storage(), spatial_dimension, _so_sum);
Vector<Real> theoretical_total_force(spatial_dimension);
theoretical_total_force.mul<false>(rotation, traction);
theoretical_total_force *= -1 * 2 * 2;
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(total_force(s), theoretical_total_force(s))) {
if (comm.whoAmI() == 0)
std::cout << "Error: total force isn't correct!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements) {
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(elements, 1, spatial_dimension);
Vector<Real> bary(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
Array<UInt> & elem = elements(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, bary.storage(), ghost_type);
if (bary(0) > 0.0001)
elem.push_back(el);
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_embedded_interface/CMakeLists.txt
index 3c7507828..7502e962c 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/CMakeLists.txt
@@ -1,42 +1,52 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri May 15 2015
#
# @brief configuration for embedded interface tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
register_test(test_embedded_element_matrix
SOURCES test_embedded_element_matrix.cc
FILES_TO_COPY triangle.msh embedded_element.dat
PACKAGE embedded implicit
)
register_test(test_embedded_interface_model
SOURCES test_embedded_interface_model.cc
FILES_TO_COPY embedded_mesh.msh material.dat matrix
DIRECTORIES_TO_CREATE paraview
PACKAGE embedded implicit
)
register_test(test_embedded_interface_model_prestress
SOURCES test_embedded_interface_model_prestress.cc
FILES_TO_COPY embedded_mesh_prestress.msh embedded_mesh_prestress_reinforcement.msh prestress.dat
PACKAGE embedded implicit
)
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_element_matrix.cc b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_element_matrix.cc
index 2ba94bbdc..262ad1a44 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_element_matrix.cc
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_element_matrix.cc
@@ -1,98 +1,100 @@
/**
* @file test_embedded_element_matrix.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
- * @date last modification: Fri Feb 09 2018
+ * @date last modification: Wed Sep 12 2018
*
* @brief test of the class EmbeddedInterfaceModel
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "embedded_interface_model.hh"
#include "sparse_matrix_aij.hh"
#include "sparse_solver.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("embedded_element.dat", argc, argv);
constexpr UInt dim = 2;
constexpr ElementType type = _segment_2;
const Real height = 0.4;
Mesh mesh(dim);
mesh.read("triangle.msh");
Mesh reinforcement_mesh(dim, "reinforcement_mesh");
auto & nodes = reinforcement_mesh.getNodes();
nodes.push_back(Vector<Real>({0, height}));
nodes.push_back(Vector<Real>({1, height}));
reinforcement_mesh.addConnectivityType(type);
auto & connectivity = reinforcement_mesh.getConnectivity(type);
connectivity.push_back(Vector<UInt>({0, 1}));
Array<std::string> names_vec(1, 1, "reinforcement", "reinforcement_names");
reinforcement_mesh.getElementalData<std::string>("physical_names")
.alloc(1, 1, type);
reinforcement_mesh.getData<std::string>("physical_names")(type).copy(
names_vec);
EmbeddedInterfaceModel model(mesh, reinforcement_mesh, dim);
model.initFull(_analysis_method = _static);
if (model.getInterfaceMesh().getNbElement(type) != 1)
return EXIT_FAILURE;
if (model.getInterfaceMesh().getSpatialDimension() != 2)
return EXIT_FAILURE;
try { // matrix should be singular
model.solveStep();
} catch (debug::SingularMatrixException & e) {
std::cerr << "Matrix is singular, relax, everything is fine :)"
<< std::endl;
} catch (debug::Exception & e) {
std::cerr << "Unexpceted error: " << e.what() << std::endl;
throw e;
}
SparseMatrixAIJ & K =
dynamic_cast<SparseMatrixAIJ &>(model.getDOFManager().getMatrix("K"));
K.saveMatrix("stiffness.mtx");
Math::setTolerance(1e-8);
// Testing the assembled stiffness matrix
if (!Math::are_float_equal(K(0, 0), 1. - height) ||
!Math::are_float_equal(K(0, 2), height - 1.) ||
!Math::are_float_equal(K(2, 0), height - 1.) ||
!Math::are_float_equal(K(2, 2), 1. - height))
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc
index 605dffd56..d09ed6a04 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model.cc
@@ -1,107 +1,109 @@
/**
* @file test_embedded_interface_model.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
- * @date last modification: Wed Jan 31 2018
+ * @date last modification: Wed Feb 06 2019
*
* @brief Embedded model test based on potential energy
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <iostream>
#include "aka_common.hh"
#include "embedded_interface_model.hh"
#include "sparse_matrix.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("material.dat", argc, argv);
UInt dim = 2;
Math::setTolerance(1e-7);
// Mesh here is a 1x1 patch
Mesh mesh(dim);
mesh.read("embedded_mesh.msh");
Array<Real> nodes_vec(2, dim, "reinforcement_nodes");
nodes_vec.storage()[0] = 0;
nodes_vec.storage()[1] = 0.5;
nodes_vec.storage()[2] = 1;
nodes_vec.storage()[3] = 0.5;
Array<UInt> conn_vec(1, 2, "reinforcement_connectivity");
conn_vec.storage()[0] = 0;
conn_vec.storage()[1] = 1;
Array<std::string> names_vec(1, 1, "reinforcement", "reinforcement_names");
Mesh reinforcement_mesh(dim, "reinforcement_mesh");
reinforcement_mesh.getNodes().copy(nodes_vec);
reinforcement_mesh.addConnectivityType(_segment_2);
reinforcement_mesh.getConnectivity(_segment_2).copy(conn_vec);
reinforcement_mesh.getElementalData<std::string>("physical_names")
.alloc(1, 1, _segment_2);
reinforcement_mesh.getData<std::string>("physical_names")(_segment_2)
.copy(names_vec);
EmbeddedInterfaceModel model(mesh, reinforcement_mesh, dim);
model.initFull(_analysis_method = _static);
Array<Real> & nodes = mesh.getNodes();
Array<Real> & forces = model.getExternalForce();
Array<bool> & bound = model.getBlockedDOFs();
forces(2, 0) = -250;
forces(5, 0) = -500;
forces(8, 0) = -250;
for (UInt i = 0; i < mesh.getNbNodes(); i++) {
if (Math::are_float_equal(nodes(i, 0), 0.))
bound(i, 0) = true;
if (Math::are_float_equal(nodes(i, 1), 0.))
bound(i, 1) = true;
}
model.addDumpFieldVector("displacement");
model.addDumpFieldTensor("stress");
model.setBaseNameToDumper("reinforcement", "reinforcement");
model.addDumpFieldTensorToDumper("reinforcement", "stress_embedded");
model.solveStep();
model.getDOFManager().getMatrix("K").saveMatrix("matrix_test");
model.dump();
Real pot_energy = model.getEnergy("potential");
if (std::abs(pot_energy - 7.37343e-06) > 1e-5)
return EXIT_FAILURE;
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
index 689743600..157677a5b 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
@@ -1,233 +1,236 @@
/**
* @file test_embedded_interface_model_prestress.cc
*
+ * @author Zineb Fouad <zineb.fouad@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Apr 28 2015
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Jun 14 2019
*
* @brief Embedded model test for prestressing (bases on stress norm)
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "aka_common.hh"
#include "embedded_interface_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
#define YG 0.483644859
#define I_eq 0.012488874
#define A_eq (1e-2 + 1. / 7. * 1.)
/* -------------------------------------------------------------------------- */
struct StressSolution : public BC::Neumann::FromHigherDim {
Real M;
Real I;
Real yg;
Real pre_stress;
StressSolution(UInt dim, Real M, Real I, Real yg = 0, Real pre_stress = 0)
: BC::Neumann::FromHigherDim(Matrix<Real>(dim, dim)), M(M), I(I), yg(yg),
pre_stress(pre_stress) {}
virtual ~StressSolution() {}
void operator()(const IntegrationPoint & /*quad_point*/, Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const {
UInt dim = coord.size();
if (dim < 2)
AKANTU_ERROR("Solution not valid for 1D");
Matrix<Real> stress(dim, dim);
stress.zero();
stress(0, 0) = this->stress(coord(1));
dual.mul<false>(stress, normals);
}
inline Real stress(Real height) const {
return -M / I * (height - yg) + pre_stress;
}
inline Real neutral_axis() const { return -I * pre_stress / M + yg; }
};
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("prestress.dat", argc, argv);
debug::setDebugLevel(dblError);
Math::setTolerance(1e-6);
const UInt dim = 2;
/* --------------------------------------------------------------------------
*/
Mesh mesh(dim);
mesh.read("embedded_mesh_prestress.msh");
// mesh.createGroupsFromMeshData<std::string>("physical_names");
Mesh reinforcement_mesh(dim, "reinforcement_mesh");
try {
reinforcement_mesh.read("embedded_mesh_prestress_reinforcement.msh");
} catch (debug::Exception & e) {
}
// reinforcement_mesh.createGroupsFromMeshData<std::string>("physical_names");
EmbeddedInterfaceModel model(mesh, reinforcement_mesh, dim);
model.initFull(EmbeddedInterfaceModelOptions(_static));
/* --------------------------------------------------------------------------
*/
/* Computation of analytical residual */
/* --------------------------------------------------------------------------
*/
/*
* q = 1000 N/m
* L = 20 m
* a = 1 m
*/
Real steel_area = model.getMaterial("reinforcement").get("area");
Real pre_stress = model.getMaterial("reinforcement").get("pre_stress");
Real stress_norm = 0.;
StressSolution *concrete_stress = nullptr, *steel_stress = nullptr;
Real pre_force = pre_stress * steel_area;
Real pre_moment = -pre_force * (YG - 0.25);
Real neutral_axis = YG - I_eq / A_eq * pre_force / pre_moment;
concrete_stress = new StressSolution(dim, pre_moment, 7. * I_eq, YG,
-pre_force / (7. * A_eq));
steel_stress = new StressSolution(dim, pre_moment, I_eq, YG,
pre_stress - pre_force / A_eq);
stress_norm =
std::abs(concrete_stress->stress(1)) * (1 - neutral_axis) * 0.5 +
std::abs(concrete_stress->stress(0)) * neutral_axis * 0.5 +
std::abs(steel_stress->stress(0.25)) * steel_area;
model.applyBC(*concrete_stress, "XBlocked");
auto end_node = *mesh.getElementGroup("EndNode").getNodeGroup().begin();
Vector<Real> end_node_force = model.getExternalForce().begin(dim)[end_node];
end_node_force(0) += steel_stress->stress(0.25) * steel_area;
Array<Real> analytical_residual(mesh.getNbNodes(), dim,
"analytical_residual");
analytical_residual.copy(model.getExternalForce());
model.getExternalForce().zero();
delete concrete_stress;
delete steel_stress;
/* --------------------------------------------------------------------------
*/
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "XBlocked");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "YBlocked");
try {
model.solveStep();
} catch (debug::Exception & e) {
std::cerr << e.what() << std::endl;
return EXIT_FAILURE;
}
/* --------------------------------------------------------------------------
*/
/* Computation of FEM residual norm */
/* --------------------------------------------------------------------------
*/
ElementGroup & xblocked = mesh.getElementGroup("XBlocked");
NodeGroup & boundary_nodes = xblocked.getNodeGroup();
NodeGroup::const_node_iterator nodes_it = boundary_nodes.begin(),
nodes_end = boundary_nodes.end();
model.assembleInternalForces();
Array<Real> residual(mesh.getNbNodes(), dim, "my_residual");
residual.copy(model.getInternalForce());
residual -= model.getExternalForce();
auto com_res = residual.begin(dim);
auto position = mesh.getNodes().begin(dim);
Real res_sum = 0.;
UInt lower_node = -1;
UInt upper_node = -1;
Real lower_dist = 1;
Real upper_dist = 1;
for (; nodes_it != nodes_end; ++nodes_it) {
UInt node_number = *nodes_it;
const Vector<Real> res = com_res[node_number];
const Vector<Real> pos = position[node_number];
if (!Math::are_float_equal(pos(1), 0.25)) {
if ((std::abs(pos(1) - 0.25) < lower_dist) && (pos(1) < 0.25)) {
lower_dist = std::abs(pos(1) - 0.25);
lower_node = node_number;
}
if ((std::abs(pos(1) - 0.25) < upper_dist) && (pos(1) > 0.25)) {
upper_dist = std::abs(pos(1) - 0.25);
upper_node = node_number;
}
}
for (UInt i = 0; i < dim; i++) {
if (!Math::are_float_equal(pos(1), 0.25)) {
res_sum += std::abs(res(i));
}
}
}
const Vector<Real> upper_res = com_res[upper_node],
lower_res = com_res[lower_node];
const Vector<Real> end_node_res = com_res[end_node];
Vector<Real> delta = upper_res - lower_res;
delta *= lower_dist / (upper_dist + lower_dist);
Vector<Real> concrete_residual = lower_res + delta;
Vector<Real> steel_residual = end_node_res - concrete_residual;
for (UInt i = 0; i < dim; i++) {
res_sum += std::abs(concrete_residual(i));
res_sum += std::abs(steel_residual(i));
}
Real relative_error = std::abs(res_sum - stress_norm) / stress_norm;
if (relative_error > 1e-3) {
std::cerr << "Relative error = " << relative_error << std::endl;
return EXIT_FAILURE;
}
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_energies/CMakeLists.txt
index 3bd5ccdb5..05aefbc6d 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_energies/CMakeLists.txt
@@ -1,55 +1,66 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Tobias Brink <tobias.brink@epfl.ch>
+# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Fri Jan 26 2018
-# @date last modification: Tue Jan 30 2018
+# @date last modification: Mon Feb 26 2018
#
-# @brief
+# @brief CMakeLists for energie tests
#
-# @section LICENSE
-#
-# Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
#===============================================================================
# Energy tests
#===============================================================================
register_gtest_sources(
SOURCES test_solid_mechanics_model_linear_elastic_potential_energy.cc
FILES_TO_COPY test_solid_mechanics_model_linear_elastic_potential_energy_material.dat
PACKAGE implicit
)
register_gtest_sources(
SOURCES test_solid_mechanics_model_kinetic_energy.cc
FILES_TO_COPY test_solid_mechanics_model_kinetic_energy_material.dat
PACKAGE implicit
)
register_gtest_sources(
SOURCES test_solid_mechanics_model_work_quasistatic.cc
FILES_TO_COPY test_solid_mechanics_model_work_material.dat
PACKAGE implicit
)
register_gtest_sources(
SOURCES test_solid_mechanics_model_work_dynamics.cc
FILES_TO_COPY test_solid_mechanics_model_work_material.dat
PACKAGE core
)
register_gtest_test(test_solid_mechanics_model_energies
FILES_TO_COPY ${PATCH_TEST_MESHES}
DEPENDS ${PATCH_TEST_BAR_MESHES}
PARALLEL
PARALLEL_LEVEL 1 2 # some meshes are too small for more
)
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_kinetic_energy.cc b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_kinetic_energy.cc
index e9c789e85..392f65c60 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_kinetic_energy.cc
+++ b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_kinetic_energy.cc
@@ -1,88 +1,91 @@
/**
* @file test_solid_mechanics_model_kinetic_energy.cc
*
* @author Tobias Brink <tobias.brink@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Mon Feb 26 2018
*
* @brief test kinetic energy
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section description
*
* This test uses a linear elastic material with density = 1, Young's modulus =
* 1, and Poisson's ratio = 0 and imposes a uniform velocity of 1. The volume of
* the mesh is 1 and thus we have a mass of 1 and therefore a kinetic energy of
* 0.5*m*v² = 0.5. The kind of constitutive law should not matter for this test,
* so we use linear elastic. We perform 5 timesteps and check the solution every
* time.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "../test_solid_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
void test_body(SolidMechanicsModel & model, AnalysisMethod analysis_method) {
const auto spatial_dimension = model.getSpatialDimension();
getStaticParser().parse("test_solid_mechanics_model_"
"kinetic_energy_material.dat");
model.initFull(_analysis_method = analysis_method);
model.assembleMassLumped();
/// impose initial velocity of 1, it should remain constant
auto & velo = model.getVelocity();
for (auto && velov : make_view(velo, spatial_dimension)) {
velov(_x) = 1;
}
/// set up timestep
auto time_step = model.getStableTimeStep() * 0.8;
model.setTimeStep(time_step);
/// run five times and look at the kinetic energy
for (uint i = 0; i < 5; ++i) {
/// make a step
model.solveStep();
/// compare energy to analytical solution
const Real E_ref = 0.5;
auto E_kin = model.getEnergy("kinetic");
EXPECT_NEAR(E_ref, E_kin, 1e-8);
}
}
TYPED_TEST(TestSMMFixture, KineticEnergyImplicit) {
test_body(*(this->model), _implicit_dynamic);
}
TYPED_TEST(TestSMMFixture, KineticEnergyExplicit) {
test_body(*(this->model), _explicit_lumped_mass);
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_linear_elastic_potential_energy.cc b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_linear_elastic_potential_energy.cc
index 5972dfac6..f838eae4b 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_linear_elastic_potential_energy.cc
+++ b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_linear_elastic_potential_energy.cc
@@ -1,114 +1,118 @@
/**
* @file test_solid_mechanics_model_linear_elastic_potential_energy.cc
*
* @author Tobias Brink <tobias.brink@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Sun Mar 11 2018
*
* @brief test potential energy of the linear elasticity model
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section description
*
* This test uses a linear elastic material with density = 1, Young's
* modulus = 1, and Poisson's ratio = 0 and applies a linear
* displacement from 0 to ε in x direction. The resulting potential
* energy density should be 0.5*Y*ε² = ε²/2. Since the mesh always has
* a volume of 1, the energy density equals the total energy. We test
* 3 different strains.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "../test_solid_mechanics_model_fixture.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
TYPED_TEST(TestSMMFixture, LinearElasticPotentialEnergy) {
const auto spatial_dimension = this->spatial_dimension;
this->initModel("test_solid_mechanics_model_linear_elastic_"
"potential_energy_material.dat",
_static);
const auto & lower = this->mesh->getLowerBounds();
const auto & upper = this->mesh->getUpperBounds();
auto length = upper(_x) - lower(_x);
const auto & pos = this->mesh->getNodes();
auto & disp = this->model->getDisplacement();
auto & boun = this->model->getBlockedDOFs();
std::vector<Real> strains{0.0, 0.1, 0.2, 0.3};
for (auto && eps : strains) {
/// boundary conditions
for (auto && pair : zip(make_view(pos, spatial_dimension),
make_view(disp, spatial_dimension),
make_view(boun, spatial_dimension))) {
const auto & posv = std::get<0>(pair);
auto & dispv = std::get<1>(pair);
auto & bounv = std::get<2>(pair);
auto reduced_x = (posv(_x) - lower(_x)) / length;
dispv(_x) = reduced_x * eps;
bounv(_x) = true;
if (posv(_x) < (lower(_x) + 1e-6)) {
if ((spatial_dimension > 1) and (posv(_y) < (lower(_y) + 1e-6))) {
bounv(_y) = true;
if ((spatial_dimension > 2) and (posv(_z) < (lower(_z) + 1e-6))) {
bounv(_z) = true;
}
}
}
}
if (this->dump_paraview) {
this->model->dump();
}
/// "solve" a step (solution is imposed)
try {
this->model->solveStep();
} catch (...) {
const auto & A = this->model->getDOFManager().getMatrix("J");
auto prank = this->mesh->getCommunicator().whoAmI();
A.saveMatrix("solver_mumps" + std::to_string(prank) + ".mtx");
throw;
}
if (this->dump_paraview) {
const auto & A = this->model->getDOFManager().getMatrix("J");
auto prank = this->mesh->getCommunicator().whoAmI();
A.saveMatrix("solver_mumps" + std::to_string(prank) + ".mtx");
}
/// compare energy to analytical solution
auto E_ref = 0.5 * eps * eps;
auto E_pot = this->model->getEnergy("potential");
EXPECT_NEAR(E_ref, E_pot, 1e-8);
}
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc
index 95bb94ec0..b20aa2d68 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc
+++ b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_dynamics.cc
@@ -1,157 +1,159 @@
/**
* @file test_solid_mechanics_model_work_dynamics.cc
*
* @author Tobias Brink <tobias.brink@epfl.ch>
*
* @date creation: Fri Dec 15 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief test work in dynamic simulations
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section description
*
* Assuming that the kinetic energy and the potential energy of the
* linear elastic material are bug free, the work in a dynamic
* simulation must equal the change in internal energy (first law of
* thermodynamics). Work in dynamics is an infinitesimal work Fds,
* thus we need to integrate it and compare at the end. In this test,
* we use one Dirichlet boundary condition (with u = 0.0, 0.01, and
* -0.01) and one Neumann boundary condition for F on the opposite
* side. Then we do a few steps to get reference energies for work and
* internal energy. After more steps, the change in both work and
* internal energy must be equal.
*
*/
/* -------------------------------------------------------------------------- */
#include "../test_solid_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
template <typename type_>
class TestSMMFixtureWorkDynamic : public TestSMMFixture<type_> {
public:
void SetUp() override {
this->mesh_file =
"../../patch_tests/data/bar" + std::to_string(this->type) + ".msh";
TestSMMFixture<type_>::SetUp();
getStaticParser().parse("test_solid_mechanics_model_"
"work_material.dat");
/// model initialization
this->model->initFull();
/// Create a node group for Neumann BCs.
auto & apply_force_grp = this->mesh->createNodeGroup("apply_force");
auto & fixed_grp = this->mesh->createNodeGroup("fixed");
const auto & pos = this->mesh->getNodes();
const auto & lower = this->mesh->getLowerBounds();
const auto & upper = this->mesh->getUpperBounds();
UInt i = 0;
for (auto && posv : make_view(pos, this->spatial_dimension)) {
if (posv(_x) > upper(_x) - 1e-6) {
apply_force_grp.add(i);
} else if (posv(_x) < lower(_x) + 1e-6) {
fixed_grp.add(i);
}
++i;
}
this->mesh->createElementGroupFromNodeGroup("el_apply_force", "apply_force",
this->spatial_dimension - 1);
this->mesh->createElementGroupFromNodeGroup("el_fixed", "fixed",
this->spatial_dimension - 1);
Vector<Real> surface_traction(this->spatial_dimension);
surface_traction(_x) = 0.5;
if (this->spatial_dimension == 1) {
// TODO: this is a hack to work
// around non-implemented
// BC::Neumann::FromTraction for 1D
auto & force = this->model->getExternalForce();
for (auto && pair : zip(make_view(pos, this->spatial_dimension),
make_view(force, this->spatial_dimension))) {
auto & posv = std::get<0>(pair);
auto & forcev = std::get<1>(pair);
if (posv(_x) > upper(_x) - 1e-6) {
forcev(_x) = surface_traction(_x);
}
}
} else {
this->model->applyBC(BC::Neumann::FromTraction(surface_traction),
"el_apply_force");
}
/// set up timestep
auto time_step = this->model->getStableTimeStep() * 0.1;
this->model->setTimeStep(time_step);
}
};
TYPED_TEST_SUITE(TestSMMFixtureWorkDynamic, gtest_element_types, );
/* TODO: this is currently disabled for terrible results and performance
TYPED_TEST(TestSMMFixtureBar, WorkImplicit) {
test_body(*(this->model), *(this->mesh), _implicit_dynamic, 500);
}
*/
// model.assembleMassLumped();
TYPED_TEST(TestSMMFixtureWorkDynamic, WorkExplicit) {
/// Do the sim
std::vector<Real> displacements{0.00, 0.01, -0.01};
for (auto && u : displacements) {
this->model->applyBC(BC::Dirichlet::FixedValue(u, _x), "el_fixed");
// First, "equilibrate" a bit to get a reference state of total
// energy and work. This is needed when we have a Dirichlet with
// finite displacement on one side.
for (UInt i = 0; i < 25; ++i) {
this->model->solveStep();
}
// Again, work reported by Akantu is infinitesimal (dW) and we
// need to integrate a while to get a decent value.
double Etot0 =
this->model->getEnergy("potential") + this->model->getEnergy("kinetic");
double W = 0.0;
for (UInt i = 0; i < 200; ++i) {
/// Solve.
this->model->solveStep();
const auto dW = this->model->getEnergy("external work");
W += dW;
}
// Finally check.
const auto Epot = this->model->getEnergy("potential");
const auto Ekin = this->model->getEnergy("kinetic");
EXPECT_NEAR(W, Ekin + Epot - Etot0, 5e-2);
// Sadly not very exact for such a coarse mesh.
}
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
index 912029411..968309099 100644
--- a/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_energies/test_solid_mechanics_model_work_quasistatic.cc
@@ -1,145 +1,147 @@
/**
* @file test_solid_mechanics_model_work_quasistatic.cc
*
* @author Tobias Brink <tobias.brink@epfl.ch>
*
* @date creation: Wed Nov 29 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Wed Dec 04 2019
*
* @brief test work in quasistatic
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
* @section description
*
* Assuming that the potential energy of a linear elastic material
* works correctly, the work in a static simulation must equal the
* potential energy of the material. Since the work in static is an
* infinitesimal work Fds, we need to integrate by increasing F from 0
* to F_final in steps. This test uses one Dirichlet boundary
* condition (with u = 0.0, 0.1, and -0.1) and one Neumann boundary
* condition for F on the opposite side. The final work must be the
* same for all u.
*
*/
/* -------------------------------------------------------------------------- */
#include "../test_solid_mechanics_model_fixture.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
TYPED_TEST(TestSMMFixture, WorkQuasistatic) {
const auto spatial_dimension = this->spatial_dimension;
getStaticParser().parse("test_solid_mechanics_model_"
"work_material.dat");
/// model initialization
this->model->initFull(_analysis_method = _static);
/// Create a node group for Neumann BCs.
auto & apply_force_grp = this->mesh->createNodeGroup("apply_force");
auto & fixed_grp = this->mesh->createNodeGroup("fixed");
const auto & pos = this->mesh->getNodes();
auto & flags = this->model->getBlockedDOFs();
auto & lower = this->mesh->getLowerBounds();
auto & upper = this->mesh->getUpperBounds();
UInt i = 0;
for (auto && data : zip(make_view(pos, spatial_dimension),
make_view(flags, spatial_dimension))) {
const auto & posv = std::get<0>(data);
auto & flag = std::get<1>(data);
if (posv(_x) > upper(_x) - 1e-6) {
apply_force_grp.add(i);
} else if (posv(_x) < lower(_x) + 1e-6) {
fixed_grp.add(i);
if ((spatial_dimension > 1) and (posv(_y) < lower(_y) + 1e-6)) {
flag(_y) = true;
if ((spatial_dimension > 2) and (posv(_z) < lower(_z) + 1e-6)) {
flag(_z) = true;
}
}
}
++i;
}
this->mesh->createElementGroupFromNodeGroup("el_apply_force", "apply_force",
spatial_dimension - 1);
this->mesh->createElementGroupFromNodeGroup("el_fixed", "fixed",
spatial_dimension - 1);
std::vector<Real> displacements{0.0, 0.1, -0.1};
for (auto && u : displacements) {
this->model->applyBC(BC::Dirichlet::FixedValue(u, _x), "el_fixed");
Vector<Real> surface_traction(spatial_dimension);
Real work = 0.0;
Real Epot;
static const UInt N = 100;
for (UInt i = 0; i <= N; ++i) {
this->model->getExternalForce().zero(); // reset external forces to zero
surface_traction(_x) = (1.0 * i) / N;
if (spatial_dimension == 1) {
// \TODO: this is a hack to work
// around non-implemented
// BC::Neumann::FromTraction for 1D
auto & force = this->model->getExternalForce();
for (auto && pair : zip(make_view(pos, spatial_dimension),
make_view(force, spatial_dimension))) {
auto & posv = std::get<0>(pair);
auto & forcev = std::get<1>(pair);
if (posv(_x) > upper(_x) - 1e-6) {
forcev(_x) = surface_traction(_x);
}
}
} else {
this->model->applyBC(BC::Neumann::FromTraction(surface_traction),
"el_apply_force");
}
/// Solve.
this->model->solveStep();
Epot = this->model->getEnergy("potential");
// In static, this is infinitesimal work!
auto Fds = this->model->getEnergy("external work");
work += Fds; // integrate
/// Check that no work was done for zero force.
if (i == 0) {
EXPECT_NEAR(work, 0.0, 1e-12);
}
}
// Due to the finite integration steps, we make a rather large error
// in our work integration, thus the allowed delta is 1e-2.
EXPECT_NEAR(work, Epot, 1e-2);
}
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_material_selector.cc b/test/test_model/test_solid_mechanics_model/test_material_selector.cc
index 2073b787d..2a452b25b 100644
--- a/test/test_model/test_solid_mechanics_model/test_material_selector.cc
+++ b/test/test_model/test_solid_mechanics_model/test_material_selector.cc
@@ -1,62 +1,64 @@
/**
* @file test_material_selector.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
- * @date last modification: Tue Dec 05 2017
+ * @date last modification: Tue Dec 05 2017
*
* @brief Test for material selector
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "aka_common.hh"
#include "solid_mechanics_model.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material_selector.dat", argc, argv);
Math::setTolerance(1e-8);
Mesh mesh(1);
mesh.read("material_selector.msh");
SolidMechanicsModel model(mesh);
auto && selector = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names", model);
model.setMaterialSelector(selector);
model.initFull();
Material & chocolate = model.getMaterial("chocolate");
Material & chewing_gum = model.getMaterial("chewing-gum");
Material & candy = model.getMaterial("candy");
UInt chocolate_element = chocolate.getElementFilter(_segment_2)(0, 0);
UInt chewing_gum_element = chewing_gum.getElementFilter(_segment_2)(0, 0);
UInt candy_element = candy.getElementFilter(_segment_2)(0, 0);
if (chocolate_element != 0 || chewing_gum_element != 1 || candy_element != 2)
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
index f4067c3e7..6531617b1 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_materials/CMakeLists.txt
@@ -1,107 +1,110 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+# @author Mauro Corrado <mauro.corrado@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Mon Jan 29 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Tue Jun 30 2020
#
# @brief configuration for materials tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License along
# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#add_mesh(test_local_material_barre_trou_mesh barre_trou.geo 2 2)
add_mesh(test_local_material_barre_trou_mesh mesh_section_gap.geo 2 2)
register_test(test_local_material
SOURCES test_local_material.cc local_material_damage.cc
EXTRA_FILES local_material_damage.hh local_material_damage_inline_impl.hh
DEPENDS test_local_material_barre_trou_mesh
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
# ==============================================================================
add_mesh(test_interpolate_stress_mesh interpolation.geo 3 2)
register_test(test_interpolate_stress test_interpolate_stress.cc
FILES_TO_COPY material_interpolate.dat
DEPENDS test_interpolate_stress_mesh
DIRECTORIES_TO_CREATE paraview
PACKAGE lapack core
)
#===============================================================================
add_mesh(test_material_orthotropic_square_mesh square.geo 2 1)
register_test(test_material_orthotropic
SOURCES test_material_orthotropic.cc
DEPENDS test_material_orthotropic_square_mesh
FILES_TO_COPY orthotropic.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core lapack
)
#===============================================================================
register_test(test_material_mazars
SOURCES test_material_mazars.cc
FILES_TO_COPY material_mazars.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core lapack
UNSTABLE
)
# ==============================================================================
add_akantu_test(test_material_viscoelastic "test the visco elastic materials")
add_akantu_test(test_material_non_local "test the non-local materials")
add_akantu_test(test_material_elasto_plastic_linear_isotropic_hardening
"test the elasto plastic with linear isotropic hardening materials")
add_akantu_test(test_material_viscoelastic_maxwell
"test the viscoelastic maxwell material")
# ==============================================================================
add_mesh(test_multi_material_elastic_mesh test_multi_material_elastic.geo 2 1)
register_test(test_multi_material_elastic
SOURCES test_multi_material_elastic.cc
FILES_TO_COPY test_multi_material_elastic.dat
DEPENDS test_multi_material_elastic_mesh
PACKAGE implicit)
# ==============================================================================
# Material unit tests
# ==============================================================================
add_mesh(test_finite_deformation_mesh cube.geo 3 1)
register_gtest_sources(SOURCES test_finite_deformation.cc
FILES_TO_COPY material_finite_deformation.dat 1_tetrahedron.msh
DEPENDS test_finite_deformation_mesh
PACKAGE implicit)
register_gtest_sources(SOURCES test_elastic_materials.cc PACKAGE core)
register_gtest_sources(SOURCES test_finite_def_materials.cc PACKAGE core)
register_gtest_sources(SOURCES test_damage_materials.cc PACKAGE core python_interface
INCLUDE_DIRECTORIES ${PROJECT_SOURCE_DIR}/python
FILES_TO_COPY py_mazars.py)
register_gtest_sources(SOURCES test_plastic_materials.cc PACKAGE core)
register_gtest_sources(SOURCES test_material_thermal.cc PACKAGE core)
register_gtest_test(test_material)
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.cc b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.cc
index cf6ea1572..178c7fe7c 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.cc
@@ -1,105 +1,107 @@
/**
* @file local_material_damage.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri May 03 2019
*
* @brief Specialization of the material class for the damage material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
LocalMaterialDamage::LocalMaterialDamage(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), damage("damage", *this) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, 0., _pat_parsable, "Young's modulus");
this->registerParam("nu", nu, 0.5, _pat_parsable, "Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->registerParam("Yd", Yd, 50., _pat_parsmod);
this->registerParam("Sd", Sd, 5000., _pat_parsmod);
damage.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto dam = damage(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *dam);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void LocalMaterialDamage::computePotentialEnergy(ElementType el_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type);
Real * epot = potential_energy(el_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, _not_ghost);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
epot++;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
index e995b6601..f2be79e3a 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage.hh
@@ -1,125 +1,127 @@
/**
* @file local_material_damage.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 18 2010
- * @date last modification: Mon Sep 11 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri May 03 2019
*
* @brief Material isotropic elastic
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
#define AKANTU_LOCAL_MATERIAL_DAMAGE_HH_
namespace akantu {
class LocalMaterialDamage : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~LocalMaterialDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & damage);
/// compute tangent stiffness
virtual void computeTangentStiffness(__attribute__((unused))
ElementType el_type,
__attribute__((unused))
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/// compute the potential energy for all elements
void computePotentialEnergy(ElementType el_type);
/// compute the potential energy for on element
inline void computePotentialEnergyOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma, Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute the celerity of wave in the material
inline Real getCelerity(const Element & element) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "local_material_damage_inline_impl.hh"
} // namespace akantu
#endif /* AKANTU_LOCAL_MATERIAL_DAMAGE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage_inline_impl.hh b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage_inline_impl.hh
index abf910320..62bee5ea5 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage_inline_impl.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/local_material_damage_inline_impl.hh
@@ -1,78 +1,80 @@
/**
* @file local_material_damage_inline_impl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Aug 04 2010
- * @date last modification: Mon Sep 11 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Sep 11 2017
*
* @brief Implementation of the inline functions of the material damage
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real & dam) {
Real trace = grad_u.trace();
/// \sigma_{ij} = \lambda * (\nabla u)_{kk} * \delta_{ij} + \mu * (\nabla
/// u_{ij} + \nabla u_{ji})
auto && epsilon = (grad_u + grad_u.transpose()) / 2.;
sigma = Matrix<Real>::eye(spatial_dimension) * trace * lambda + mu * epsilon;
Real Y = 0;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
Y += sigma(i, j) * epsilon(i, j);
}
}
Y *= 0.5;
Real Fd = Y - Yd - Sd * dam;
if (Fd > 0)
dam = (Y - Yd) / Sd;
dam = std::min(dam, 1.);
sigma *= 1 - dam;
}
/* -------------------------------------------------------------------------- */
inline void LocalMaterialDamage::computePotentialEnergyOnQuad(
Matrix<Real> & grad_u, Matrix<Real> & sigma, Real & epot) {
epot = 0.;
for (UInt i = 0, t = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j, ++t)
epot += sigma(i, j) * (grad_u(i, j) - (i == j));
epot *= .5;
}
/* -------------------------------------------------------------------------- */
inline Real LocalMaterialDamage::getCelerity(__attribute__((unused))
const Element & element) const {
return (std::sqrt(E / rho));
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py b/test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py
index 977880e03..846c4cad2 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py
+++ b/test/test_model/test_solid_mechanics_model/test_materials/py_mazars.py
@@ -1,60 +1,70 @@
#!/usr/bin/env python3
+""" py_mazars.py: Implementation of Mazars damage law in python"""
+
+__author__ = "Nicolas Richart"
+__credits__ = [
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
import numpy as np
class Mazars:
def __init__(self, **kwargs):
self.K0 = kwargs.pop("K0", 1e-4)
self.At = kwargs.pop("At", 1.0)
self.Bt = kwargs.pop("Bt", 5e3)
self.Ac = kwargs.pop("Ac", 0.8)
self.Bc = kwargs.pop("Bc", 1391.3)
self.E = kwargs.pop("E", 25e9)
self.nu = kwargs.pop("nu", 0.2)
self.dam = 0
self.Gf = 0
self.ε_p = 0
self.σ_p = 0
def compute_step(self, ε, σ, dam, trace):
dam_t = 0
# dam_c = 0
if trace:
import pdb
pdb.set_trace()
σ = self.E * ε
if ε > self.K0:
dam_t = 1 - self.K0*(1 - self.At)/ε - \
self.At * np.exp(-self.Bt*(ε - self.K0))
# dam_c = 1 - self.K0*(1 - self.Ac)/ε - \
# self.Ac * np.exp(-self.Bc*(ε - self.K0))
dam = max(dam, dam_t)
dam = min(dam, 1)
σ = (1 - dam) * σ
return σ, dam
# def compute(self, **kwargs):
# epsilons = np.array(kwargs['epsilons'], copy=False)
# sigmas = np.array(kwargs['sigmas'], copy=False)
# damages = np.array(kwargs['damages'], copy=False)
# for t, ε in enumerate(epsilons):
# σ = 0.
# dam = 0.
# self.compute_step(ε, σ, dam)
# self.Gf = self.Gf + (σ + σ_p) * (ε - ε_p) / 2.
# self.σ_p = σ
# self.ε_p = ε
# sigmas[t] = σ
# damages[t] = self.dam
# return self.Gf
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_damage_materials.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_damage_materials.cc
index 7e3e9c4ac..b7720ea07 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_damage_materials.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_damage_materials.cc
@@ -1,243 +1,246 @@
/**
* @file test_damage_materials.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Tests for damage materials
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_material_fixtures.hh"
/* -------------------------------------------------------------------------- */
#include <material_marigo.hh>
#include <material_mazars.hh>
#include <py_aka_array.hh>
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <gtest/gtest.h>
#include <pybind11/embed.h>
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace py = pybind11;
using namespace py::literals;
using mat_types = ::testing::Types<
// Traits<MaterialMarigo, 1>, Traits<MaterialMarigo, 2>,
// Traits<MaterialMarigo, 3>,
Traits<MaterialMazars, 1>, Traits<MaterialMazars, 2>,
Traits<MaterialMazars, 3>>;
/*****************************************************************/
template <> void FriendMaterial<MaterialMazars<1>>::setParams() {
K0.setDefaultValue(1e-4);
At = 1.0;
Bt = 5e3;
Ac = 0.8;
Bc = 1391.3;
beta = 1.;
E = 25e9;
nu = 0.2;
updateInternalParameters();
}
template <> void FriendMaterial<MaterialMazars<2>>::setParams() {
K0.setDefaultValue(1e-4);
At = 1.0;
Bt = 5e3;
Ac = 0.8;
Bc = 1391.3;
beta = 1.;
E = 25e9;
nu = 0.2;
plane_stress = true;
updateInternalParameters();
}
template <> void FriendMaterial<MaterialMazars<3>>::setParams() {
K0.setDefaultValue(1e-4);
At = 1.0;
Bt = 5e3;
Ac = 0.8;
Bc = 1391.3;
beta = 1.;
E = 25e9;
nu = 0.2;
updateInternalParameters();
}
template <> void FriendMaterial<MaterialMazars<1>>::testComputeStress() {
Array<Real> epsilons(1001, 1);
Array<Real> sigmas(1001, 1);
Array<Real> damages(1001, 1);
for (auto && data : enumerate(epsilons)) {
std::get<1>(data) = 2e-6 * std::get<0>(data);
}
Real _K0 = K0;
py::module py_engine = py::module::import("py_mazars");
auto kwargs_mat_params =
py::dict("K0"_a = _K0, "At"_a = At, "Bt"_a = Bt, "Ac"_a = Ac, "Bc"_a = Bc,
"E"_a = E, "nu"_a = nu);
auto kwargs = py::dict("epsilons"_a = epsilons, "sigmas"_a = sigmas,
"damages"_a = damages);
auto py_mazars = py_engine.attr("Mazars")(**kwargs_mat_params);
// auto Gf_py = py_mazars.attr("compute")(**kwargs);
Real dam = 0.;
Real dam_ref = 0.;
Real ehat = 0.;
for (auto && epsilon : epsilons) {
Matrix<Real> strain(this->spatial_dimension, this->spatial_dimension, 0.);
Matrix<Real> sigma(this->spatial_dimension, this->spatial_dimension, 0.);
strain(0, 0) = epsilon;
computeStressOnQuad(strain, sigma, dam, ehat);
Real sigma_ref;
auto py_data =
py_mazars.attr("compute_step")(epsilon, sigma_ref, dam_ref, false);
std::tie(sigma_ref, dam_ref) = py::cast<std::pair<double, double>>(py_data);
EXPECT_NEAR(sigma(0, 0), sigma_ref, 1e-5);
EXPECT_NEAR(dam, dam_ref, 1e-10);
}
}
template <> void FriendMaterial<MaterialMazars<2>>::testComputeStress() {
Array<Real> epsilons(1001, 1);
Array<Real> sigmas(1001, 1);
Array<Real> damages(1001, 1);
for (auto && data : enumerate(epsilons)) {
std::get<1>(data) = 2e-6 * std::get<0>(data);
}
Real _K0 = K0;
py::module py_engine = py::module::import("py_mazars");
auto kwargs_mat_params =
py::dict("K0"_a = _K0, "At"_a = At, "Bt"_a = Bt, "Ac"_a = Ac, "Bc"_a = Bc,
"E"_a = E, "nu"_a = nu);
auto kwargs = py::dict("epsilons"_a = epsilons, "sigmas"_a = sigmas,
"damages"_a = damages);
auto py_mazars = py_engine.attr("Mazars")(**kwargs_mat_params);
// auto Gf_py = py_mazars.attr("compute")(**kwargs);
Real dam = 0.;
Real dam_ref = 0.;
Real ehat = 0.;
for (auto && epsilon : epsilons) {
Matrix<Real> strain(this->spatial_dimension, this->spatial_dimension, 0.);
Matrix<Real> sigma(this->spatial_dimension, this->spatial_dimension, 0.);
strain(0, 0) = epsilon;
strain(1, 1) = -this->nu * epsilon;
computeStressOnQuad(strain, sigma, dam, ehat);
Real sigma_ref;
auto py_data =
py_mazars.attr("compute_step")(epsilon, sigma_ref, dam_ref, false);
std::tie(sigma_ref, dam_ref) = py::cast<std::pair<double, double>>(py_data);
EXPECT_NEAR(sigma(0, 0), sigma_ref, 1e-5);
EXPECT_NEAR(dam, dam_ref, 1e-10);
}
}
template <> void FriendMaterial<MaterialMazars<3>>::testComputeStress() {
Array<Real> epsilons(1001, 1);
Array<Real> sigmas(1001, 1);
Array<Real> damages(1001, 1);
for (auto && data : enumerate(epsilons)) {
std::get<1>(data) = 2e-6 * std::get<0>(data);
}
Real _K0 = K0;
py::module py_engine = py::module::import("py_mazars");
auto kwargs_mat_params =
py::dict("K0"_a = _K0, "At"_a = At, "Bt"_a = Bt, "Ac"_a = Ac, "Bc"_a = Bc,
"E"_a = E, "nu"_a = nu);
auto kwargs = py::dict("epsilons"_a = epsilons, "sigmas"_a = sigmas,
"damages"_a = damages);
auto py_mazars = py_engine.attr("Mazars")(**kwargs_mat_params);
// auto Gf_py = py_mazars.attr("compute")(**kwargs);
Real dam = 0.;
Real dam_ref = 0.;
Real ehat = 0.;
for (auto && epsilon : epsilons) {
Matrix<Real> strain(this->spatial_dimension, this->spatial_dimension, 0.);
Matrix<Real> sigma(this->spatial_dimension, this->spatial_dimension, 0.);
strain(0, 0) = epsilon;
strain(1, 1) = strain(2, 2) = -this->nu * epsilon;
computeStressOnQuad(strain, sigma, dam, ehat);
Real sigma_ref;
auto py_data =
py_mazars.attr("compute_step")(epsilon, sigma_ref, dam_ref, false);
std::tie(sigma_ref, dam_ref) = py::cast<std::pair<double, double>>(py_data);
EXPECT_NEAR(sigma(0, 0), sigma_ref, 1e-5);
EXPECT_NEAR(dam, dam_ref, 1e-10);
}
}
namespace {
template <typename T>
class TestDamageMaterialFixture : public ::TestMaterialFixture<T> {};
TYPED_TEST_SUITE(TestDamageMaterialFixture, mat_types, );
TYPED_TEST(TestDamageMaterialFixture, ComputeStress) {
this->material->testComputeStress();
}
TYPED_TEST(TestDamageMaterialFixture, DISABLED_EnergyDensity) {
this->material->testEnergyDensity();
}
TYPED_TEST(TestDamageMaterialFixture, DISABLED_ComputeTangentModuli) {
this->material->testComputeTangentModuli();
}
TYPED_TEST(TestDamageMaterialFixture, DISABLED_ComputeCelerity) {
this->material->testCelerity();
}
} // namespace
/*****************************************************************/
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_elastic_materials.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_elastic_materials.cc
index 9e4d05a61..33dd2f615 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_elastic_materials.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_elastic_materials.cc
@@ -1,884 +1,887 @@
/**
* @file test_elastic_materials.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Enrico Milanese <enrico.milanese@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Tests the Elastic materials
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
#include "test_material_fixtures.hh"
/* -------------------------------------------------------------------------- */
#include <material_elastic.hh>
#include <material_elastic_orthotropic.hh>
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using mat_types =
::testing::Types<Traits<MaterialElastic, 1>, Traits<MaterialElastic, 2>,
Traits<MaterialElastic, 3>,
Traits<MaterialElasticOrthotropic, 2>,
Traits<MaterialElasticOrthotropic, 3>,
Traits<MaterialElasticLinearAnisotropic, 2>,
Traits<MaterialElasticLinearAnisotropic, 3>>;
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<1>>::setParams() {
Real E = 3.;
Real rho = 2;
setParam("E", E);
setParam("rho", rho);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<1>>::testComputeStress() {
Matrix<Real> eps = {{2}};
Matrix<Real> sigma(1, 1);
Real sigma_th = 2;
this->computeStressOnQuad(eps, sigma, sigma_th);
auto solution = E * eps(0, 0) + sigma_th;
EXPECT_NEAR(sigma(0, 0), solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<1>>::testEnergyDensity() {
Real eps = 2, sigma = 2;
Real epot = 0;
this->computePotentialEnergyOnQuad({{eps}}, {{sigma}}, epot);
Real solution = 2;
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElastic<1>>::testComputeTangentModuli() {
Matrix<Real> tangent(1, 1);
this->computeTangentModuliOnQuad(tangent);
EXPECT_NEAR(tangent(0, 0), E, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<1>>::testCelerity() {
auto wave_speed = this->getCelerity(Element());
auto solution = std::sqrt(E / rho);
EXPECT_NEAR(wave_speed, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<2>>::setParams() {
Real E = 1.;
Real nu = .3;
Real rho = 2;
setParam("E", E);
setParam("nu", nu);
setParam("rho", rho);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<2>>::testComputeStress() {
Real bulk_modulus_K = E / (3 * (1 - 2 * nu));
Real shear_modulus_mu = E / (2 * (1 + nu));
auto rotation_matrix = getRandomRotation();
auto grad_u = this->getComposedStrain(1.).block(0, 0, 2, 2);
auto grad_u_rot = this->applyRotation(grad_u, rotation_matrix);
Matrix<Real> sigma_rot(2, 2);
this->computeStressOnQuad(grad_u_rot, sigma_rot, sigma_th);
auto sigma = this->reverseRotation(sigma_rot, rotation_matrix);
auto identity = Matrix<Real>::eye(2, 1.);
auto strain = 0.5 * (grad_u + grad_u.transpose());
auto deviatoric_strain = strain - 1. / 3. * strain.trace() * identity;
auto sigma_expected = 2 * shear_modulus_mu * deviatoric_strain +
(sigma_th + 2. * bulk_modulus_K) * identity;
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>() / sigma_expected.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-13);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<2>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2}, {2, 4}};
Matrix<Real> eps = {{1, 0}, {0, 1}};
Real epot = 0;
Real solution = 2.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElastic<2>>::testComputeTangentModuli() {
Matrix<Real> tangent(3, 3);
/* Plane Strain */
// clang-format off
Matrix<Real> solution = {
{1 - nu, nu, 0},
{nu, 1 - nu, 0},
{0, 0, (1 - 2 * nu) / 2},
};
// clang-format on
solution *= E / ((1 + nu) * (1 - 2 * nu));
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - solution).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
/* Plane Stress */
this->plane_stress = true;
this->updateInternalParameters();
// clang-format off
solution = {
{1, nu, 0},
{nu, 1, 0},
{0, 0, (1 - nu) / 2},
};
// clang-format on
solution *= E / (1 - nu * nu);
this->computeTangentModuliOnQuad(tangent);
tangent_error = (tangent - solution).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<2>>::testCelerity() {
auto push_wave_speed = this->getPushWaveSpeed(Element());
auto celerity = this->getCelerity(Element());
Real K = E / (3 * (1 - 2 * nu));
Real mu = E / (2 * (1 + nu));
Real sol = std::sqrt((K + 4. / 3 * mu) / rho);
EXPECT_NEAR(push_wave_speed, sol, 1e-14);
EXPECT_NEAR(celerity, sol, 1e-14);
auto shear_wave_speed = this->getShearWaveSpeed(Element());
sol = std::sqrt(mu / rho);
EXPECT_NEAR(shear_wave_speed, sol, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<3>>::setParams() {
Real E = 1.;
Real nu = .3;
Real rho = 2;
setParam("E", E);
setParam("nu", nu);
setParam("rho", rho);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<3>>::testComputeStress() {
Real bulk_modulus_K = E / 3. / (1 - 2. * nu);
Real shear_modulus_mu = 0.5 * E / (1 + nu);
Matrix<Real> rotation_matrix = getRandomRotation();
auto grad_u = this->getComposedStrain(1.);
auto grad_u_rot = this->applyRotation(grad_u, rotation_matrix);
Matrix<Real> sigma_rot(3, 3);
this->computeStressOnQuad(grad_u_rot, sigma_rot, sigma_th);
auto sigma = this->reverseRotation(sigma_rot, rotation_matrix);
Matrix<Real> identity(3, 3);
identity.eye();
Matrix<Real> strain = 0.5 * (grad_u + grad_u.transpose());
Matrix<Real> deviatoric_strain = strain - 1. / 3. * strain.trace() * identity;
Matrix<Real> sigma_expected = 2 * shear_modulus_mu * deviatoric_strain +
(sigma_th + 3. * bulk_modulus_K) * identity;
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<3>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2, 3}, {2, 4, 5}, {3, 5, 6}};
Matrix<Real> eps = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}};
Real epot = 0;
Real solution = 5.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElastic<3>>::testComputeTangentModuli() {
Matrix<Real> tangent(6, 6);
// clang-format off
Matrix<Real> solution = {
{1 - nu, nu, nu, 0, 0, 0},
{nu, 1 - nu, nu, 0, 0, 0},
{nu, nu, 1 - nu, 0, 0, 0},
{0, 0, 0, (1 - 2 * nu) / 2, 0, 0},
{0, 0, 0, 0, (1 - 2 * nu) / 2, 0},
{0, 0, 0, 0, 0, (1 - 2 * nu) / 2},
};
// clang-format on
solution *= E / ((1 + nu) * (1 - 2 * nu));
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - solution).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElastic<3>>::testCelerity() {
auto push_wave_speed = this->getPushWaveSpeed(Element());
auto celerity = this->getCelerity(Element());
Real K = E / (3 * (1 - 2 * nu));
Real mu = E / (2 * (1 + nu));
Real sol = std::sqrt((K + 4. / 3 * mu) / rho);
EXPECT_NEAR(push_wave_speed, sol, 1e-14);
EXPECT_NEAR(celerity, sol, 1e-14);
auto shear_wave_speed = this->getShearWaveSpeed(Element());
sol = std::sqrt(mu / rho);
EXPECT_NEAR(shear_wave_speed, sol, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElasticOrthotropic<2>>::setParams() {
// Note: for this test material and canonical basis coincide
Vector<Real> n1 = {1, 0};
Vector<Real> n2 = {0, 1};
Real E1 = 1.;
Real E2 = 2.;
Real nu12 = 0.1;
Real G12 = 2.;
Real rho = 2.5;
*this->dir_vecs[0] = n1;
*this->dir_vecs[1] = n2;
this->E1 = E1;
this->E2 = E2;
this->nu12 = nu12;
this->G12 = G12;
this->rho = rho;
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<2>>::testComputeStress() {
UInt Dim = 2;
// material frame of reference is rotate by rotation_matrix starting from
// canonical basis
Matrix<Real> rotation_matrix = getRandomRotation();
// canonical basis as expressed in the material frame of reference, as
// required by MaterialElasticOrthotropic class (it is simply given by the
// columns of the rotation_matrix; the lines give the material basis expressed
// in the canonical frame of reference)
*this->dir_vecs[0] = rotation_matrix(0);
*this->dir_vecs[1] = rotation_matrix(1);
// set internal Cijkl matrix expressed in the canonical frame of reference
this->updateInternalParameters();
// gradient in material frame of reference
auto grad_u = this->getComposedStrain(2.).block(0, 0, 2, 2);
// gradient in canonical basis (we need to rotate *back* to the canonical
// basis)
auto grad_u_rot = this->reverseRotation(grad_u, rotation_matrix);
// stress in the canonical basis
Matrix<Real> sigma_rot(2, 2);
this->computeStressOnQuad(grad_u_rot, sigma_rot);
// stress in the material reference (we need to apply the rotation)
auto sigma = this->applyRotation(sigma_rot, rotation_matrix);
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real gamma = 1 / (1 - nu12 * nu21);
Matrix<Real> C_expected(2 * Dim, 2 * Dim, 0);
C_expected(0, 0) = gamma * E1;
C_expected(1, 1) = gamma * E2;
C_expected(2, 2) = G12;
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * nu21;
// epsilon is computed directly in the *material* frame of reference
Matrix<Real> epsilon = 0.5 * (grad_u + grad_u.transpose());
// sigma_expected is computed directly in the *material* frame of reference
Matrix<Real> sigma_expected(Dim, Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
sigma_expected(i, i) += C_expected(i, j) * epsilon(j, j);
}
}
sigma_expected(0, 1) = sigma_expected(1, 0) =
C_expected(2, 2) * 2 * epsilon(0, 1);
// sigmas are checked in the *material* frame of reference
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-13);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<2>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2}, {2, 4}};
Matrix<Real> eps = {{1, 0}, {0, 1}};
Real epot = 0;
Real solution = 2.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<2>>::testComputeTangentModuli() {
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real gamma = 1 / (1 - nu12 * nu21);
Matrix<Real> C_expected(3, 3);
C_expected(0, 0) = gamma * E1;
C_expected(1, 1) = gamma * E2;
C_expected(2, 2) = G12;
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * nu21;
Matrix<Real> tangent(3, 3);
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - C_expected).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElasticOrthotropic<2>>::testCelerity() {
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real gamma = 1 / (1 - nu12 * nu21);
Matrix<Real> C_expected(3, 3);
C_expected(0, 0) = gamma * E1;
C_expected(1, 1) = gamma * E2;
C_expected(2, 2) = G12;
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * nu21;
Vector<Real> eig_expected(3);
C_expected.eig(eig_expected);
auto celerity_expected = std::sqrt(eig_expected(0) / rho);
auto celerity = this->getCelerity(Element());
EXPECT_NEAR(celerity_expected, celerity, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElasticOrthotropic<3>>::setParams() {
Vector<Real> n1 = {1, 0, 0};
Vector<Real> n2 = {0, 1, 0};
Vector<Real> n3 = {0, 0, 1};
Real E1 = 1.;
Real E2 = 2.;
Real E3 = 3.;
Real nu12 = 0.1;
Real nu13 = 0.2;
Real nu23 = 0.3;
Real G12 = 2.;
Real G13 = 3.;
Real G23 = 1.;
Real rho = 2.3;
*this->dir_vecs[0] = n1;
*this->dir_vecs[1] = n2;
*this->dir_vecs[2] = n3;
this->E1 = E1;
this->E2 = E2;
this->E3 = E3;
this->nu12 = nu12;
this->nu13 = nu13;
this->nu23 = nu23;
this->G12 = G12;
this->G13 = G13;
this->G23 = G23;
this->rho = rho;
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<3>>::testComputeStress() {
UInt Dim = 3;
// material frame of reference is rotate by rotation_matrix starting from
// canonical basis
Matrix<Real> rotation_matrix = getRandomRotation();
// canonical basis as expressed in the material frame of reference, as
// required by MaterialElasticOrthotropic class (it is simply given by the
// columns of the rotation_matrix; the lines give the material basis expressed
// in the canonical frame of reference)
*this->dir_vecs[0] = rotation_matrix(0);
*this->dir_vecs[1] = rotation_matrix(1);
*this->dir_vecs[2] = rotation_matrix(2);
// set internal Cijkl matrix expressed in the canonical frame of reference
this->updateInternalParameters();
// gradient in material frame of reference
auto grad_u = this->getComposedStrain(2.);
// gradient in canonical basis (we need to rotate *back* to the canonical
// basis)
auto grad_u_rot = this->reverseRotation(grad_u, rotation_matrix);
// stress in the canonical basis
Matrix<Real> sigma_rot(3, 3);
this->computeStressOnQuad(grad_u_rot, sigma_rot);
// stress in the material reference (we need to apply the rotation)
auto sigma = this->applyRotation(sigma_rot, rotation_matrix);
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
Real gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
Matrix<Real> C_expected(6, 6);
C_expected(0, 0) = gamma * E1 * (1 - nu23 * nu32);
C_expected(1, 1) = gamma * E2 * (1 - nu13 * nu31);
C_expected(2, 2) = gamma * E3 * (1 - nu12 * nu21);
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * (nu21 + nu31 * nu23);
C_expected(2, 0) = C_expected(0, 2) = gamma * E1 * (nu31 + nu21 * nu32);
C_expected(2, 1) = C_expected(1, 2) = gamma * E2 * (nu32 + nu12 * nu31);
C_expected(3, 3) = G23;
C_expected(4, 4) = G13;
C_expected(5, 5) = G12;
// epsilon is computed directly in the *material* frame of reference
Matrix<Real> epsilon = 0.5 * (grad_u + grad_u.transpose());
// sigma_expected is computed directly in the *material* frame of reference
Matrix<Real> sigma_expected(Dim, Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
sigma_expected(i, i) += C_expected(i, j) * epsilon(j, j);
}
}
sigma_expected(0, 1) = C_expected(5, 5) * 2 * epsilon(0, 1);
sigma_expected(0, 2) = C_expected(4, 4) * 2 * epsilon(0, 2);
sigma_expected(1, 2) = C_expected(3, 3) * 2 * epsilon(1, 2);
sigma_expected(1, 0) = sigma_expected(0, 1);
sigma_expected(2, 0) = sigma_expected(0, 2);
sigma_expected(2, 1) = sigma_expected(1, 2);
// sigmas are checked in the *material* frame of reference
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-13);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<3>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2, 3}, {2, 4, 5}, {3, 5, 6}};
Matrix<Real> eps = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}};
Real epot = 0;
Real solution = 5.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticOrthotropic<3>>::testComputeTangentModuli() {
// Note: for this test material and canonical basis coincide
UInt Dim = 3;
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
Real gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
Matrix<Real> C_expected(2 * Dim, 2 * Dim, 0);
C_expected(0, 0) = gamma * E1 * (1 - nu23 * nu32);
C_expected(1, 1) = gamma * E2 * (1 - nu13 * nu31);
C_expected(2, 2) = gamma * E3 * (1 - nu12 * nu21);
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * (nu21 + nu31 * nu23);
C_expected(2, 0) = C_expected(0, 2) = gamma * E1 * (nu31 + nu21 * nu32);
C_expected(2, 1) = C_expected(1, 2) = gamma * E2 * (nu32 + nu12 * nu31);
C_expected(3, 3) = G23;
C_expected(4, 4) = G13;
C_expected(5, 5) = G12;
Matrix<Real> tangent(6, 6);
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - C_expected).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialElasticOrthotropic<3>>::testCelerity() {
// Note: for this test material and canonical basis coincide
UInt Dim = 3;
// construction of Cijkl engineering tensor in the *material* frame of
// reference
// ref: http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
Real gamma = 1 / (1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 -
2 * nu21 * nu32 * nu13);
Matrix<Real> C_expected(2 * Dim, 2 * Dim, 0);
C_expected(0, 0) = gamma * E1 * (1 - nu23 * nu32);
C_expected(1, 1) = gamma * E2 * (1 - nu13 * nu31);
C_expected(2, 2) = gamma * E3 * (1 - nu12 * nu21);
C_expected(1, 0) = C_expected(0, 1) = gamma * E1 * (nu21 + nu31 * nu23);
C_expected(2, 0) = C_expected(0, 2) = gamma * E1 * (nu31 + nu21 * nu32);
C_expected(2, 1) = C_expected(1, 2) = gamma * E2 * (nu32 + nu12 * nu31);
C_expected(3, 3) = G23;
C_expected(4, 4) = G13;
C_expected(5, 5) = G12;
Vector<Real> eig_expected(6);
C_expected.eig(eig_expected);
auto celerity_expected = std::sqrt(eig_expected(0) / rho);
auto celerity = this->getCelerity(Element());
EXPECT_NEAR(celerity_expected, celerity, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<2>>::setParams() {
Matrix<Real> C = {
{1.0, 0.3, 0.4},
{0.3, 2.0, 0.1},
{0.4, 0.1, 1.5},
};
for (auto i = 0u; i < C.rows(); ++i)
for (auto j = 0u; j < C.cols(); ++j)
this->Cprime(i, j) = C(i, j);
this->rho = 2.7;
// material frame of reference is rotate by rotation_matrix starting from
// canonical basis
Matrix<Real> rotation_matrix = getRandomRotation();
// canonical basis as expressed in the material frame of reference, as
// required by MaterialElasticLinearAnisotropic class (it is simply given by
// the columns of the rotation_matrix; the lines give the material basis
// expressed in the canonical frame of reference)
*this->dir_vecs[0] = rotation_matrix(0);
*this->dir_vecs[1] = rotation_matrix(1);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<2>>::testComputeStress() {
Matrix<Real> C = {
{1.0, 0.3, 0.4},
{0.3, 2.0, 0.1},
{0.4, 0.1, 1.5},
};
Matrix<Real> rotation_matrix(2, 2);
rotation_matrix(0) = *this->dir_vecs[0];
rotation_matrix(1) = *this->dir_vecs[1];
// gradient in material frame of reference
auto grad_u = this->getComposedStrain(1.).block(0, 0, 2, 2);
// gradient in canonical basis (we need to rotate *back* to the canonical
// basis)
auto grad_u_rot = this->reverseRotation(grad_u, rotation_matrix);
// stress in the canonical basis
Matrix<Real> sigma_rot(2, 2);
this->computeStressOnQuad(grad_u_rot, sigma_rot);
// stress in the material reference (we need to apply the rotation)
auto sigma = this->applyRotation(sigma_rot, rotation_matrix);
// epsilon is computed directly in the *material* frame of reference
Matrix<Real> epsilon = 0.5 * (grad_u + grad_u.transpose());
Vector<Real> epsilon_voigt(3);
epsilon_voigt(0) = epsilon(0, 0);
epsilon_voigt(1) = epsilon(1, 1);
epsilon_voigt(2) = 2 * epsilon(0, 1);
// sigma_expected is computed directly in the *material* frame of reference
Vector<Real> sigma_voigt = C * epsilon_voigt;
Matrix<Real> sigma_expected(2, 2);
sigma_expected(0, 0) = sigma_voigt(0);
sigma_expected(1, 1) = sigma_voigt(1);
sigma_expected(0, 1) = sigma_expected(1, 0) = sigma_voigt(2);
// sigmas are checked in the *material* frame of reference
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-13);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<2>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2}, {2, 4}};
Matrix<Real> eps = {{1, 0}, {0, 1}};
Real epot = 0;
Real solution = 2.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<
MaterialElasticLinearAnisotropic<2>>::testComputeTangentModuli() {
Matrix<Real> tangent(3, 3);
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - C).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<2>>::testCelerity() {
Vector<Real> eig_expected(3);
C.eig(eig_expected);
auto celerity_expected = std::sqrt(eig_expected(0) / this->rho);
auto celerity = this->getCelerity(Element());
EXPECT_NEAR(celerity_expected, celerity, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<3>>::setParams() {
// Note: for this test material and canonical basis coincide
Matrix<Real> C = {
{1.0, 0.3, 0.4, 0.3, 0.2, 0.1}, {0.3, 2.0, 0.1, 0.2, 0.3, 0.2},
{0.4, 0.1, 1.5, 0.1, 0.4, 0.3}, {0.3, 0.2, 0.1, 2.4, 0.1, 0.4},
{0.2, 0.3, 0.4, 0.1, 0.9, 0.1}, {0.1, 0.2, 0.3, 0.4, 0.1, 1.2},
};
for (auto i = 0u; i < C.rows(); ++i)
for (auto j = 0u; j < C.cols(); ++j)
this->Cprime(i, j) = C(i, j);
this->rho = 2.9;
// material frame of reference is rotate by rotation_matrix starting from
// canonical basis
Matrix<Real> rotation_matrix = getRandomRotation();
// canonical basis as expressed in the material frame of reference, as
// required by MaterialElasticLinearAnisotropic class (it is simply given by
// the columns of the rotation_matrix; the lines give the material basis
// expressed in the canonical frame of reference)
*this->dir_vecs[0] = rotation_matrix(0);
*this->dir_vecs[1] = rotation_matrix(1);
*this->dir_vecs[2] = rotation_matrix(2);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<3>>::testComputeStress() {
Matrix<Real> C = {
{1.0, 0.3, 0.4, 0.3, 0.2, 0.1}, {0.3, 2.0, 0.1, 0.2, 0.3, 0.2},
{0.4, 0.1, 1.5, 0.1, 0.4, 0.3}, {0.3, 0.2, 0.1, 2.4, 0.1, 0.4},
{0.2, 0.3, 0.4, 0.1, 0.9, 0.1}, {0.1, 0.2, 0.3, 0.4, 0.1, 1.2},
};
Matrix<Real> rotation_matrix(3, 3);
rotation_matrix(0) = *this->dir_vecs[0];
rotation_matrix(1) = *this->dir_vecs[1];
rotation_matrix(2) = *this->dir_vecs[2];
// gradient in material frame of reference
auto grad_u = this->getComposedStrain(2.);
// gradient in canonical basis (we need to rotate *back* to the canonical
// basis)
auto grad_u_rot = this->reverseRotation(grad_u, rotation_matrix);
// stress in the canonical basis
Matrix<Real> sigma_rot(3, 3);
this->computeStressOnQuad(grad_u_rot, sigma_rot);
// stress in the material reference (we need to apply the rotation)
auto sigma = this->applyRotation(sigma_rot, rotation_matrix);
// epsilon is computed directly in the *material* frame of reference
Matrix<Real> epsilon = 0.5 * (grad_u + grad_u.transpose());
Vector<Real> epsilon_voigt(6);
epsilon_voigt(0) = epsilon(0, 0);
epsilon_voigt(1) = epsilon(1, 1);
epsilon_voigt(2) = epsilon(2, 2);
epsilon_voigt(3) = 2 * epsilon(1, 2);
epsilon_voigt(4) = 2 * epsilon(0, 2);
epsilon_voigt(5) = 2 * epsilon(0, 1);
// sigma_expected is computed directly in the *material* frame of reference
Vector<Real> sigma_voigt = C * epsilon_voigt;
Matrix<Real> sigma_expected(3, 3);
sigma_expected(0, 0) = sigma_voigt(0);
sigma_expected(1, 1) = sigma_voigt(1);
sigma_expected(2, 2) = sigma_voigt(2);
sigma_expected(1, 2) = sigma_expected(2, 1) = sigma_voigt(3);
sigma_expected(0, 2) = sigma_expected(2, 0) = sigma_voigt(4);
sigma_expected(0, 1) = sigma_expected(1, 0) = sigma_voigt(5);
// sigmas are checked in the *material* frame of reference
auto diff = sigma - sigma_expected;
Real stress_error = diff.norm<L_inf>();
EXPECT_NEAR(stress_error, 0., 1e-13);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<3>>::testEnergyDensity() {
Matrix<Real> sigma = {{1, 2, 3}, {2, 4, 5}, {3, 5, 6}};
Matrix<Real> eps = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}};
Real epot = 0;
Real solution = 5.5;
this->computePotentialEnergyOnQuad(eps, sigma, epot);
EXPECT_NEAR(epot, solution, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<
MaterialElasticLinearAnisotropic<3>>::testComputeTangentModuli() {
Matrix<Real> tangent(6, 6);
this->computeTangentModuliOnQuad(tangent);
Real tangent_error = (tangent - C).norm<L_2>();
EXPECT_NEAR(tangent_error, 0, 1e-14);
}
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialElasticLinearAnisotropic<3>>::testCelerity() {
Vector<Real> eig_expected(6);
C.eig(eig_expected);
auto celerity_expected = std::sqrt(eig_expected(0) / this->rho);
auto celerity = this->getCelerity(Element());
EXPECT_NEAR(celerity_expected, celerity, 1e-14);
}
/* -------------------------------------------------------------------------- */
namespace {
template <typename T>
class TestElasticMaterialFixture : public ::TestMaterialFixture<T> {};
TYPED_TEST_SUITE(TestElasticMaterialFixture, mat_types, );
TYPED_TEST(TestElasticMaterialFixture, ComputeStress) {
this->material->testComputeStress();
}
TYPED_TEST(TestElasticMaterialFixture, EnergyDensity) {
this->material->testEnergyDensity();
}
TYPED_TEST(TestElasticMaterialFixture, ComputeTangentModuli) {
this->material->testComputeTangentModuli();
}
TYPED_TEST(TestElasticMaterialFixture, ComputeCelerity) {
this->material->testCelerity();
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_def_materials.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_def_materials.cc
index a93c6a31c..f8be98d4a 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_def_materials.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_def_materials.cc
@@ -1,86 +1,89 @@
/**
* @file test_finite_def_materials.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Nov 18 2020
*
- * @brief
+ * @brief Test finite deformation materials
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
#include "test_material_fixtures.hh"
/* -------------------------------------------------------------------------- */
#include <material_neohookean.hh>
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using mat_types = ::testing::Types<Traits<MaterialNeohookean, 1>,
Traits<MaterialNeohookean, 2>,
Traits<MaterialNeohookean, 3>>;
/*****************************************************************/
template <> void FriendMaterial<MaterialNeohookean<3>>::testComputeStress() {
AKANTU_TO_IMPLEMENT();
}
/*****************************************************************/
template <>
void FriendMaterial<MaterialNeohookean<3>>::testComputeTangentModuli() {
AKANTU_TO_IMPLEMENT();
}
/*****************************************************************/
template <> void FriendMaterial<MaterialNeohookean<3>>::testEnergyDensity() {
AKANTU_TO_IMPLEMENT();
}
/*****************************************************************/
namespace {
template <typename T>
class TestFiniteDefMaterialFixture : public ::TestMaterialFixture<T> {};
TYPED_TEST_SUITE(TestFiniteDefMaterialFixture, mat_types, );
TYPED_TEST(TestFiniteDefMaterialFixture, DISABLED_ComputeStress) {
this->material->testComputeStress();
}
TYPED_TEST(TestFiniteDefMaterialFixture, DISABLED_EnergyDensity) {
this->material->testEnergyDensity();
}
TYPED_TEST(TestFiniteDefMaterialFixture, DISABLED_ComputeTangentModuli) {
this->material->testComputeTangentModuli();
}
TYPED_TEST(TestFiniteDefMaterialFixture, DISABLED_DefComputeCelerity) {
this->material->testCelerity();
}
} // namespace
/*****************************************************************/
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
index 71be02ea2..1739a1071 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_finite_deformation.cc
@@ -1,110 +1,141 @@
+/**
+ * @file test_finite_deformation.cc
+ *
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Mon Nov 11 2019
+ * @date last modification: Wed May 27 2020
+ *
+ * @brief Test for dinite deformation
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
TEST(TestFiniteDeformation, NotUnit) {
getStaticParser().parse("material_finite_deformation.dat");
const double pi = std::atan(1) * 4;
constexpr int dim = 3;
Mesh mesh(dim);
mesh.read("1_tetrahedron.msh");
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
#if DEBUG_TEST
model.addDumpField("displacement");
model.addDumpField("internal_force");
model.addDumpField("stress");
model.addDumpField("strain");
model.dump();
#endif
Matrix<Real> alpha{{0.00, 0.02, 0.03, 0.04},
{0.00, 0.06, 0.07, 0.08},
{0.00, 0.10, 0.11, 0.12}};
auto impose_disp = [&] {
model.getDisplacement().zero();
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim),
make_view(model.getBlockedDOFs(), dim))) {
auto & pos = std::get<0>(data);
auto & dis = std::get<1>(data);
auto & blocked = std::get<2>(data);
blocked.set(true);
dis += Vector<Real>(alpha(0));
for (auto p : arange(dim)) {
dis += Vector<Real>(alpha(1+p)) * pos(p);
}
}
};
impose_disp();
model.solveStep();
#if DEBUG_TEST
model.dump();
#endif
auto stesses0 = model.getMaterial(0).getStress();
auto displacement0 = model.getDisplacement();
auto internal_force0 = model.getInternalForce();
auto theta = pi / 4;
Matrix<Real> R{{1., 0., 0.},
{0., std::cos(theta), -std::sin(theta)},
{0., std::sin(theta), std::cos(theta)}};
impose_disp();
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim))) {
auto & X = std::get<0>(data);
auto & u = std::get<1>(data);
u = R * (X + u) - X;
}
model.solveStep();
#if DEBUG_TEST
model.dump();
#endif
for (auto data : zip(make_view(mesh.getNodes(), dim),
make_view(model.getDisplacement(), dim),
make_view(displacement0, dim),
make_view(model.getInternalForce(), dim),
make_view(internal_force0, dim))) {
auto pos = std::get<0>(data);
Vector<Real> refdis(dim, 0.);
refdis += Vector<Real>(alpha(0));
for (auto p : arange(dim)) {
refdis += Vector<Real>(alpha(1+p)) * pos(p);
}
auto dis = std::get<1>(data);
auto dis0 = std::get<2>(data);
auto err = refdis.distance(dis0);
EXPECT_NEAR(err, 0, 1e-14);
auto err1 = dis.distance(R * (pos + dis0) - pos);
EXPECT_NEAR(err1, 0, 1e-14);
auto f = std::get<3>(data);
auto f0 = std::get<4>(data);
auto err3 = f.distance(R * f0);
EXPECT_NEAR(err3, 0, 1e-5);
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
index e997cfe06..7548dc0cd 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_interpolate_stress.cc
@@ -1,181 +1,183 @@
/**
* @file test_interpolate_stress.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Thu Jun 07 2012
- * @date last modification: Tue Nov 07 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Sep 08 2020
*
* @brief Test for the stress interpolation function
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "integrator_gauss.hh"
#include "mesh_utils.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real x, Real y, Real z) { return 100. + 2. * x + 3. * y + 4 * z; }
int main(int argc, char * argv[]) {
initialize("material_interpolate.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 3;
const ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
mesh.read("interpolation.msh");
const ElementType type_facet = mesh.getFacetType(type);
Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
MeshUtils::buildAllFacets(mesh, mesh_facets);
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
Array<Real> & position = mesh.getNodes();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_element = mesh.getNbElement(type);
/// compute quadrature points positions on facets
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange> MyFEEngineType;
model.registerFEEngineObject<MyFEEngineType>("FacetsFEEngine", mesh_facets,
spatial_dimension - 1);
model.getFEEngine("FacetsFEEngine").initShapeFunctions();
UInt nb_quad_per_facet =
model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets, spatial_dimension,
type_facet);
auto && facet_to_element = mesh_facets.getSubelementToElement(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
ElementTypeMapArray<Real> element_quad_facet;
element_quad_facet.alloc(nb_element * nb_facet_per_elem * nb_quad_per_facet,
spatial_dimension, type);
ElementTypeMapArray<Real> interpolated_stress("interpolated_stress", "");
interpolated_stress.initialize(
mesh, _nb_component = spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension);
Array<Real> & interp_stress = interpolated_stress(type);
interp_stress.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet);
Array<Real> & el_q_facet = element_quad_facet(type);
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
UInt global_facet = facet_to_element(el, f).element;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
for (UInt s = 0; s < spatial_dimension; ++s) {
el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
s) = quad_facets(global_facet * nb_quad_per_facet + q, s);
}
}
}
}
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position, quad_elements,
spatial_dimension, type);
/// assign some values to stresses
Array<Real> & stress =
const_cast<Array<Real> &>(model.getMaterial(0).getStress(type));
for (UInt q = 0; q < nb_tot_quad_el; ++q) {
for (UInt s = 0; s < spatial_dimension * spatial_dimension; ++s) {
stress(q, s) = s * function(quad_elements(q, 0), quad_elements(q, 1),
quad_elements(q, 2));
}
}
/// interpolate stresses on facets' quadrature points
model.getMaterial(0).initElementalFieldInterpolation(element_quad_facet);
model.getMaterial(0).interpolateStress(interpolated_stress);
Real tolerance = 1.e-10;
/// check results
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
for (UInt s = 0; s < spatial_dimension * spatial_dimension; ++s) {
Real x = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
0);
Real y = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
1);
Real z = el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
2);
Real theoretical = s * function(x, y, z);
Real numerical =
interp_stress(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
s);
if (std::abs(theoretical - numerical) > tolerance) {
std::cout << "Theoretical and numerical values aren't coincident!"
<< std::endl;
return EXIT_FAILURE;
}
}
}
}
}
std::cout << "OK: Stress interpolation test passed." << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_local_material.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_local_material.cc
index 0b5c43444..186129640 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_local_material.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_local_material.cc
@@ -1,132 +1,134 @@
/**
* @file test_local_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
- * @date creation: Wed Aug 04 2010
- * @date last modification: Thu Dec 14 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jun 05 2019
*
* @brief test of the class SolidMechanicsModel with custom local damage on a
* notched plate
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
akantu::initialize("material.dat", argc, argv);
UInt max_steps = 1100;
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("mesh_section_gap.msh");
/// model initialization
MaterialFactory::getInstance().registerAllocator(
"local_damage",
[](UInt, const ID &, SolidMechanicsModel & model,
const ID & id) -> std::unique_ptr<Material> {
return std::make_unique<LocalMaterialDamage>(model, id);
});
SolidMechanicsModel model(mesh);
model.initFull();
std::cout << model.getMaterial(0) << std::endl;
model.addDumpField("damage");
model.addDumpField("strain");
model.addDumpField("stress");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.dump();
Real time_step = model.getStableTimeStep();
model.setTimeStep(time_step / 2.5);
/// Dirichlet boundary conditions
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "Fixed");
// model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "Fixed");
Matrix<Real> stress(2, 2);
stress.eye(5e7);
model.applyBC(BC::Neumann::FromHigherDim(stress), "Traction");
for (UInt s = 0; s < max_steps; ++s)
model.solveStep();
model.dump();
// This should throw a bad_cast if not the proper material
auto & mat =
dynamic_cast<LocalMaterialDamage &>(model.getMaterial("concrete"));
const auto & filter = mat.getElementFilter();
for (auto & type : filter.elementTypes(spatial_dimension)) {
std::cout << mat.getDamage(type) << std::endl;
}
// This part of the test is to mesh dependent and as nothing to do with the
// fact that we can create a user defined material or not
// const auto & lower_bounds = mesh.getLowerBounds();
// const auto & upper_bounds = mesh.getUpperBounds();
// Real L = upper_bounds(_x) - lower_bounds(_x);
// Real H = upper_bounds(_y) - lower_bounds(_y);
// const auto & filter = model.getMaterial("concrete").getElementFilter();
// Vector<Real> barycenter(spatial_dimension);
// for (auto & type : filter.elementTypes(spatial_dimension)) {
// UInt nb_elem = mesh.getNbElement(type);
// const UInt nb_gp = model.getFEEngine().getNbIntegrationPoints(type);
// const auto & material_damage_array =
// model.getMaterial(0).getArray<Real>("damage", type);
// UInt cpt = 0;
// for (auto nel : arange(nb_elem)) {
// mesh.getBarycenter({type, nel, _not_ghost}, barycenter);
// if ((std::abs(barycenter(_x) - (L / 2) + 0.025) < 0.025) &&
// (std::abs(barycenter(_y) - (H / 2) + 0.045) < 0.045)) {
// if (material_damage_array(cpt, 0) < 0.9) {
// std::terminate();
// } else {
// std::cout << "element " << nel << " is correctly broken" <<
// std::endl;
// }
// }
// cpt += nb_gp;
// }
// }
akantu::finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/CMakeLists.txt
index 3b10d8256..4c6bda27b 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/CMakeLists.txt
@@ -1,38 +1,48 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Jaehyun Cho <jaehyun.cho@epfl.ch>
#
-# @date creation: Fri Oct 22 2010
-# @date last modification: Wed Mar 09 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Thu Oct 29 2020
#
# @brief test for material type elasto plastic linear isotropic hardening using
# tension-compression test
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
#===============================================================================
add_mesh(test_material_standard_linear_isotropic_hardening_mesh
test_material_elasto_plastic_linear_isotropic_hardening.geo 2 1)
register_test(test_material_standard_linear_isotropic_hardening
SOURCES test_material_elasto_plastic_linear_isotropic_hardening.cc
DEPENDS test_material_standard_linear_isotropic_hardening_mesh
FILES_TO_COPY test_material_elasto_plastic_linear_isotropic_hardening.dat
PACKAGE core implicit
)
#===============================================================================
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc
index dbcb0285a..400bbaebc 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_elasto_plastic_linear_isotropic_hardening/test_material_elasto_plastic_linear_isotropic_hardening.cc
@@ -1,91 +1,93 @@
/**
* @file test_material_elasto_plastic_linear_isotropic_hardening.cc
*
* @author Jaehyun Cho <jaehyun.cho@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Sun Oct 19 2014
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Tue May 21 2019
*
* @brief test for material type elasto plastic linear isotropic hardening
* using tension-compression test
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("test_material_elasto_plastic_linear_isotropic_hardening.dat",
argc, argv);
const UInt spatial_dimension = 2;
const Real u_increment = 0.1;
const UInt steps = 20;
Mesh mesh(spatial_dimension);
mesh.read("test_material_elasto_plastic_linear_isotropic_hardening.msh");
SolidMechanicsModel model(mesh);
model.initFull(_analysis_method = _static);
auto & solver = model.getNonLinearSolver("static");
solver.set("max_iterations", 300);
solver.set("threshold", 1e-5);
model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "left");
model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "bottom");
std::cout.precision(4);
for (UInt i = 0; i < steps; ++i) {
model.applyBC(BC::Dirichlet::FixedValue(i * u_increment, _x), "right");
try {
model.solveStep();
} catch (debug::NLSNotConvergedException & e) {
std::cout << e.niter << " " << e.error << std::endl;
throw;
}
Real strainxx = i * u_increment / 10.;
const Array<UInt> & edge_nodes =
mesh.getElementGroup("right").getNodeGroup().getNodes();
Array<Real> & residual = model.getInternalForce();
Real reaction = 0;
for (UInt n = 0; n < edge_nodes.size(); n++) {
reaction -= residual(edge_nodes(n), 0);
}
std::cout << strainxx << "," << reaction << std::endl;
}
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_fixtures.hh b/test/test_model/test_solid_mechanics_model/test_materials/test_material_fixtures.hh
index 0f727ffa7..a32953d27 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_fixtures.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_fixtures.hh
@@ -1,211 +1,215 @@
/**
* @file test_material_fixtures.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Fri Dec 13 2019
*
* @brief Fixture for material tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <material_elastic.hh>
#include <solid_mechanics_model.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <random>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
template <typename T> class FriendMaterial : public T {
public:
~FriendMaterial() = default;
FriendMaterial(SolidMechanicsModel & model, const ID & id = "material")
: T(model, id) {
gen.seed(::testing::GTEST_FLAG(random_seed));
}
virtual void testComputeStress() { AKANTU_TO_IMPLEMENT(); };
virtual void testComputeTangentModuli() { AKANTU_TO_IMPLEMENT(); };
virtual void testEnergyDensity() { AKANTU_TO_IMPLEMENT(); };
virtual void testCelerity() { AKANTU_TO_IMPLEMENT(); }
virtual void setParams() {}
virtual void SetUp() {
this->setParams();
this->initMaterial();
}
virtual void TearDown() {}
inline Matrix<Real> getDeviatoricStrain(Real intensity);
inline Matrix<Real> getHydrostaticStrain(Real intensity);
inline Matrix<Real> getComposedStrain(Real intensity);
inline const Matrix<Real> reverseRotation(Matrix<Real> mat,
Matrix<Real> rotation_matrix) {
Matrix<Real> R = rotation_matrix;
Matrix<Real> m2 = mat * R;
Matrix<Real> m1 = R.transpose();
return m1 * m2;
};
inline const Matrix<Real> applyRotation(Matrix<Real> mat,
const Matrix<Real> rotation_matrix) {
Matrix<Real> R = rotation_matrix;
Matrix<Real> m2 = mat * R.transpose();
Matrix<Real> m1 = R;
return m1 * m2;
};
inline Vector<Real> getRandomVector();
inline Matrix<Real> getRandomRotation();
protected:
std::mt19937 gen;
};
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<Real> FriendMaterial<T>::getDeviatoricStrain(Real intensity) {
Matrix<Real> dev = {{0., 1., 2.}, {1., 0., 3.}, {2., 3., 0.}};
dev *= intensity;
return dev;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<Real> FriendMaterial<T>::getHydrostaticStrain(Real intensity) {
Matrix<Real> dev = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}};
dev *= intensity;
return dev;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<Real> FriendMaterial<T>::getComposedStrain(Real intensity) {
Matrix<Real> s = FriendMaterial<T>::getHydrostaticStrain(intensity) +
FriendMaterial<T>::getDeviatoricStrain(intensity);
s *= intensity;
return s;
}
/* -------------------------------------------------------------------------- */
template <typename T> Vector<Real> FriendMaterial<T>::getRandomVector() {
auto dim = this->spatial_dimension;
std::uniform_real_distribution<Real> dis;
Vector<Real> vector(dim, 0.);
while (vector.norm() < 1e-9) {
for (auto s : arange(dim))
vector(s) = dis(gen);
}
return vector;
}
/* -------------------------------------------------------------------------- */
template <typename T> Matrix<Real> FriendMaterial<T>::getRandomRotation() {
auto dim = this->spatial_dimension;
Matrix<Real> rotation(dim, dim);
Vector<Real> v1 = rotation(0);
v1 = getRandomVector().normalize();
if (dim == 2) {
Vector<Real> v1_ = {v1(0), v1(1), 0};
Vector<Real> v2_(3);
Vector<Real> v3_ = {0, 0, 1};
v2_.crossProduct(v3_, v1_);
Vector<Real> v2 = rotation(1);
v2(0) = v2_(0);
v2(1) = v2_(1);
}
if (dim == 3) {
auto v2 = getRandomVector();
v2 = (v2 - v2.dot(v1) * v1).normalize();
Vector<Real> v3(3);
v3.crossProduct(v1, v2);
rotation(1) = v2;
rotation(2) = v3;
}
//#define debug_
#if defined(debug_)
if (dim == 2)
rotation = Matrix<Real>{{1., 0.}, {0., 1.}};
if (dim == 3)
rotation = Matrix<Real>{{1., 0., 0.}, {0., 1., 0.}, {0., 0., 1.}};
#endif
rotation = rotation.transpose();
return rotation;
}
/* -------------------------------------------------------------------------- */
template <typename T, class Model>
class TestMaterialBaseFixture : public ::testing::Test {
public:
using mat_class = typename T::mat_class;
void SetUp() override {
constexpr auto spatial_dimension = T::Dim;
mesh = std::make_unique<Mesh>(spatial_dimension);
model = std::make_unique<Model>(*mesh);
material = std::make_unique<friend_class>(*model);
material->SetUp();
}
void TearDown() override {
material->TearDown();
material.reset(nullptr);
model.reset(nullptr);
mesh.reset(nullptr);
}
using friend_class = FriendMaterial<mat_class>;
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<Model> model;
std::unique_ptr<friend_class> material;
};
/* -------------------------------------------------------------------------- */
template <template <UInt> class T, UInt _Dim> struct Traits {
using mat_class = T<_Dim>;
static constexpr UInt Dim = _Dim;
};
/* -------------------------------------------------------------------------- */
template <typename T>
using TestMaterialFixture = TestMaterialBaseFixture<T, SolidMechanicsModel>;
/* -------------------------------------------------------------------------- */
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc
index 4fc698e38..e7532cd3c 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_mazars.cc
@@ -1,288 +1,290 @@
/**
* @file test_material_mazars.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Thu Oct 08 2015
- * @date last modification: Sun Jul 09 2017
+ * @date last modification: Wed Jun 05 2019
*
* @brief test for material mazars, dissymmetric
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_accessor.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
debug::setDebugLevel(akantu::dblWarning);
akantu::initialize("material_mazars.dat", argc, argv);
const UInt spatial_dimension = 3;
// ElementType type = _quadrangle_4;
ElementType type = _hexahedron_8;
Mesh mesh(spatial_dimension);
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & connectivity = mesh_accessor.getConnectivity(type);
const Real width = 1;
UInt nb_dof = 0;
connectivity.resize(1);
if (type == _hexahedron_8) {
nb_dof = 8;
nodes.resize(nb_dof);
nodes(0, 0) = 0.;
nodes(0, 1) = 0.;
nodes(0, 2) = 0.;
nodes(1, 0) = width;
nodes(1, 1) = 0.;
nodes(1, 2) = 0.;
nodes(2, 0) = width;
nodes(2, 1) = width;
nodes(2, 2) = 0;
nodes(3, 0) = 0;
nodes(3, 1) = width;
nodes(3, 2) = 0;
nodes(4, 0) = 0.;
nodes(4, 1) = 0.;
nodes(4, 2) = width;
nodes(5, 0) = width;
nodes(5, 1) = 0.;
nodes(5, 2) = width;
nodes(6, 0) = width;
nodes(6, 1) = width;
nodes(6, 2) = width;
nodes(7, 0) = 0;
nodes(7, 1) = width;
nodes(7, 2) = width;
connectivity(0, 0) = 0;
connectivity(0, 1) = 1;
connectivity(0, 2) = 2;
connectivity(0, 3) = 3;
connectivity(0, 4) = 4;
connectivity(0, 5) = 5;
connectivity(0, 6) = 6;
connectivity(0, 7) = 7;
} else if (type == _quadrangle_4) {
nb_dof = 4;
nodes.resize(nb_dof);
nodes(0, 0) = 0.;
nodes(0, 1) = 0.;
nodes(1, 0) = width;
nodes(1, 1) = 0;
nodes(2, 0) = width;
nodes(2, 1) = width;
nodes(3, 0) = 0.;
nodes(3, 1) = width;
connectivity(0, 0) = 0;
connectivity(0, 1) = 1;
connectivity(0, 2) = 2;
connectivity(0, 3) = 3;
}
mesh_accessor.makeReady();
SolidMechanicsModel model(mesh);
model.initFull();
Material & mat = model.getMaterial(0);
std::cout << mat << std::endl;
/// boundary conditions
Array<Real> & disp = model.getDisplacement();
Array<Real> & velo = model.getVelocity();
Array<bool> & boun = model.getBlockedDOFs();
for (UInt i = 0; i < nb_dof; ++i) {
boun(i, 0) = true;
}
Real time_step = model.getStableTimeStep() * .5;
// Real time_step = 1e-5;
std::cout << "Time Step = " << time_step
<< "s - nb elements : " << mesh.getNbElement(type) << std::endl;
model.setTimeStep(time_step);
std::ofstream energy;
energy.open("energies_and_scalar_mazars.csv");
energy << "id,rtime,epot,ekin,u,wext,kin+pot,D,strain_xx,strain_yy,stress_xx,"
"stress_yy,edis,tot"
<< std::endl;
/// Set dumper
model.setBaseName("uniaxial_comp-trac_mazars");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpField("damage");
model.addDumpField("strain");
model.addDumpField("stress");
model.addDumpField("partitions");
model.dump();
const Array<Real> & strain = mat.getGradU(type);
const Array<Real> & stress = mat.getStress(type);
const Array<Real> & damage = mat.getArray<Real>("damage", type);
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
Real wext = 0.;
Real sigma_max = 0, sigma_min = 0;
Real max_disp;
Real stress_xx_compression_1;
UInt nb_steps = 7e5 / 150;
Real adisp = 0;
for (UInt s = 0; s < nb_steps; ++s) {
if (s == 0) {
max_disp = 0.003;
adisp = -(max_disp * 8. / nb_steps) / 2.;
std::cout << "Step " << s << " compression: " << max_disp << std::endl;
}
if (s == (2 * nb_steps / 8)) {
stress_xx_compression_1 = stress(0, 0);
max_disp = 0 + max_disp;
adisp = max_disp * 8. / nb_steps;
std::cout << "Step " << s << " discharge" << std::endl;
}
if (s == (3 * nb_steps / 8)) {
max_disp = 0.004;
adisp = -max_disp * 8. / nb_steps;
std::cout << "Step " << s << " compression: " << max_disp << std::endl;
}
if (s == (4 * nb_steps / 8)) {
if (stress(0, 0) < stress_xx_compression_1) {
std::cout << "after this second compression step softening should have "
"started"
<< std::endl;
return EXIT_FAILURE;
}
max_disp = 0.0015 + max_disp;
adisp = max_disp * 8. / nb_steps;
std::cout << "Step " << s << " discharge tension: " << max_disp
<< std::endl;
}
if (s == (5 * nb_steps / 8)) {
max_disp = 0. + 0.0005;
adisp = -max_disp * 8. / nb_steps;
std::cout << "Step " << s << " discharge" << std::endl;
}
if (s == (6 * nb_steps / 8)) {
max_disp = 0.0035 - 0.001;
adisp = max_disp * 8. / nb_steps;
std::cout << "Step " << s << " tension: " << max_disp << std::endl;
}
if (s == (7 * nb_steps / 8)) {
// max_disp = max_disp;
adisp = -max_disp * 8. / nb_steps;
std::cout << "Step " << s << " discharge" << std::endl;
}
for (UInt i = 0; i < nb_dof; ++i) {
if (std::abs(nodes(i, 0) - width) <
std::numeric_limits<Real>::epsilon()) {
disp(i, 0) += adisp;
velo(i, 0) = adisp / time_step;
}
}
std::cout << "S: " << s << "/" << nb_steps << " inc disp: " << adisp
<< " disp: " << std::setw(5) << disp(2, 0) << "\r" << std::flush;
model.solveStep();
Real epot = model.getEnergy("potential");
Real ekin = model.getEnergy("kinetic");
Real edis = model.getEnergy("dissipated");
wext += model.getEnergy("external work");
sigma_max = std::max(sigma_max, stress(0, 0));
sigma_min = std::min(sigma_min, stress(0, 0));
if (s % 10 == 0)
energy << s << "," // 1
<< s * time_step << "," // 2
<< epot << "," // 3
<< ekin << "," // 4
<< disp(2, 0) << "," // 5
<< wext << "," // 6
<< epot + ekin << "," // 7
<< damage(0) << "," // 8
<< strain(0, 0) << "," // 9
<< strain(0, 3) << "," // 11
<< stress(0, 0) << "," // 10
<< stress(0, 3) << "," // 10
<< edis << "," // 12
<< epot + ekin + edis // 13
<< std::endl;
if (s % 100 == 0)
model.dump();
}
std::cout << std::endl
<< "sigma_max = " << sigma_max << ", sigma_min = " << sigma_min
<< std::endl;
/// Verif the maximal/minimal stress values
if ((std::abs(sigma_max) > std::abs(sigma_min)) or
(std::abs(sigma_max - 6.24e6) > 1e5) or
(std::abs(sigma_min + 2.943e7) > 1e6))
return EXIT_FAILURE;
energy.close();
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/CMakeLists.txt
index ed6444810..db6066c97 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/CMakeLists.txt
@@ -1,43 +1,53 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Clement Roux <clement.roux@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 22 2016
#
# @brief configuration for materials tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_material_non_local_mesh mesh.geo 2 1 OUTPUT mesh.msh)
add_mesh(test_material_damage_non_local_mesh mesh_section_gap.geo 2 1 OUTPUT mesh_section_gap.msh)
register_test(test_material_damage_non_local
SOURCES test_material_damage_non_local.cc
DEPENDS test_material_damage_non_local_mesh
FILES_TO_COPY material_damage_non_local.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE damage_non_local
)
register_test(test_material_non_local
SOURCES test_material_non_local.cc custom_non_local_test_material.cc custom_non_local_test_material.hh
DEPENDS test_material_non_local_mesh
FILES_TO_COPY material.dat
PACKAGE damage_non_local
)
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.cc
index e8a70a59e..79846b81a 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.cc
@@ -1,94 +1,96 @@
/**
* @file custom_non_local_test_material.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Mar 01 2015
- * @date last modification: Mon Sep 11 2017
+ * @date last modification: Mon Sep 11 2017
*
* @brief Custom material to test the non local implementation
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "custom_non_local_test_material.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
CustomNonLocalTestMaterial<dim>::CustomNonLocalTestMaterial(
SolidMechanicsModel & model, const ID & id)
: MyNonLocalParent(model, id), local_damage("local_damage", *this),
damage("damage", *this) {
// Initialize the internal field by specifying the number of components
this->local_damage.initialize(1);
this->damage.initialize(1);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void CustomNonLocalTestMaterial<dim>::registerNonLocalVariables() {
/// register the non-local variable in the manager
this->model.getNonLocalManager().registerNonLocalVariable(
this->local_damage.getName(), this->damage.getName(), 1);
this->model.getNonLocalManager()
.getNeighborhood(this->name)
.registerNonLocalVariable(damage.getName());
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void CustomNonLocalTestMaterial<dim>::initMaterial() {
MyNonLocalParent::initMaterial();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void CustomNonLocalTestMaterial<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
MyNonLocalParent::computeStress(el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void CustomNonLocalTestMaterial<dim>::computeNonLocalStress(
ElementType el_type, GhostType ghost_type) {
Array<Real>::const_scalar_iterator dam =
this->damage(el_type, ghost_type).begin();
Array<Real>::matrix_iterator stress =
this->stress(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator stress_end =
this->stress(el_type, ghost_type).end(dim, dim);
// compute the damage and update the stresses
for (; stress != stress_end; ++stress, ++dam) {
*stress *= (1. - *dam);
}
}
/* -------------------------------------------------------------------------- */
// Instantiate the material for the 3 dimensions
INSTANTIATE_MATERIAL(custom_non_local_test_material,
CustomNonLocalTestMaterial);
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
index 7308f5ef4..75d2e4f7c 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/custom_non_local_test_material.hh
@@ -1,79 +1,81 @@
/**
* @file custom_non_local_test_material.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Thu Aug 23 2012
- * @date last modification: Mon Sep 11 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Jun 26 2020
*
* @brief Custom material to test the non local implementation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_elastic.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_
#define CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_
namespace akantu {
template <UInt dim>
class CustomNonLocalTestMaterial
: public MaterialNonLocal<dim, MaterialElastic<dim>> {
public:
using MyNonLocalParent = MaterialNonLocal<dim, MaterialElastic<dim>>;
CustomNonLocalTestMaterial(SolidMechanicsModel & model, const ID & id);
/* ------------------------------------------------------------------------ */
void initMaterial() override;
void computeNonLocalStress(ElementType el_type, GhostType ghost_type);
void computeStress(ElementType el_type, GhostType ghost_type) override;
protected:
void registerNonLocalVariables() override;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) override {
AKANTU_DEBUG_IN();
for (auto & type : this->element_filter.elementTypes(dim, ghost_type)) {
computeNonLocalStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
public:
void setDamage(Real dam) { this->local_damage.setDefaultValue(dam); }
protected:
InternalField<Real> local_damage;
InternalField<Real> damage;
};
} // namespace akantu
#endif /* CUSTOM_NON_LOCAL_TEST_MATERIAL_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_damage_non_local.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_damage_non_local.cc
index ff4e77517..b37abae23 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_damage_non_local.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_damage_non_local.cc
@@ -1,115 +1,117 @@
/**
* @file test_material_damage_non_local.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Thu Dec 14 2017
*
* @brief test for non-local damage materials on a 2D plate with a section gap
* the sample should break at the notch
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
akantu::initialize("material_damage_non_local.dat", argc, argv);
UInt max_steps = 1100;
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("mesh_section_gap.msh");
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep();
model.setTimeStep(time_step / 2.5);
std::cout << model << std::endl;
model.applyBC(BC::Dirichlet::FixedValue(0.0), "Fixed");
// Boundary condition (Neumann)
Matrix<Real> stress(2, 2);
stress.eye(5e8);
model.applyBC(BC::Neumann::FromHigherDim(stress), "Traction");
model.setBaseName("damage_non_local");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.addDumpField("damage");
model.addDumpField("stress");
model.addDumpField("strain");
model.dump();
for (UInt s = 0; s < max_steps; ++s) {
model.solveStep();
// if(s % 100 == 0) std::cout << "Step " << s+1 << "/" << max_steps
// <<std::endl; if(s % 100 == 0) model.dump();
}
model.dump();
const auto & lower_bounds = mesh.getLowerBounds();
const auto & upper_bounds = mesh.getUpperBounds();
Real L = upper_bounds(0) - lower_bounds(0);
Real H = upper_bounds(1) - lower_bounds(1);
const auto & mat = model.getMaterial(0);
const auto & filter = mat.getElementFilter();
Vector<Real> barycenter(spatial_dimension);
for (auto & type : filter.elementTypes(spatial_dimension)) {
UInt nb_elem = mesh.getNbElement(type);
const UInt nb_gp = model.getFEEngine().getNbIntegrationPoints(type);
auto & material_damage_array = mat.getArray<Real>("damage", type);
UInt cpt = 0;
for (UInt nel = 0; nel < nb_elem; ++nel) {
mesh.getBarycenter({type, nel, _not_ghost}, barycenter);
if ((std::abs(barycenter(0) - (L / 2) + 0.025) < 0.025) &&
(std::abs(barycenter(1) - (H / 2) + 0.025) < 0.025)) {
if (material_damage_array(cpt, 0) < 0.9) {
std::terminate();
}
}
cpt += nb_gp;
}
}
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_non_local.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_non_local.cc
index a7d9e4374..2e0622964 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_non_local.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_non_local/test_material_non_local.cc
@@ -1,102 +1,104 @@
/**
* @file test_material_non_local.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
- * @date last modification: Tue Nov 07 2017
+ * @date last modification: Thu Mar 22 2018
*
* @brief test of the main part of the non local materials
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "custom_non_local_test_material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
// mesh creation and read
if (prank == 0) {
mesh.read("mesh.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// model initialization changed to use our material
model.initFull();
CustomNonLocalTestMaterial<spatial_dimension> & mat =
dynamic_cast<CustomNonLocalTestMaterial<spatial_dimension> &>(
model.getMaterial("test"));
if (prank == 0)
std::cout << mat << std::endl;
// Setting up the dumpers + first dump
model.setBaseName("non_local_material");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.addDumpField("partitions");
model.addDumpField("stress");
model.addDumpField("stress");
model.addDumpField("local_damage");
model.addDumpField("damage");
model.assembleInternalForces();
model.dump();
// Array<Real> & damage = mat.getArray("local_damage", _quadrangle_4);
Array<Real> & damage = mat.getArray<Real>("local_damage", _triangle_3);
RandomGenerator<UInt> gen;
for (UInt i = 0; i < 1; ++i) {
UInt g = (gen() / Real(RandomGenerator<UInt>::max() -
RandomGenerator<UInt>::min())) *
damage.size();
std::cout << prank << " -> " << g << std::endl;
damage(g) = 1.;
}
model.assembleInternalForces();
model.dump();
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_orthotropic.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_orthotropic.cc
index 863371e3d..2eb53d280 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_orthotropic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_orthotropic.cc
@@ -1,99 +1,101 @@
/**
* @file test_material_orthotropic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Aug 04 2010
- * @date last modification: Sun Jul 09 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu May 09 2019
*
* @brief test of the class SolidMechanicsModel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
// akantu::initialize("orthotropic.dat", argc, argv);
akantu::initialize("orthotropic.dat", argc, argv);
UInt max_steps = 1000;
Real epot, ekin;
Mesh mesh(2);
mesh.read("square.msh");
mesh.createBoundaryGroupFromGeometry();
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull();
Real time_step = model.getStableTimeStep();
model.setTimeStep(time_step / 10.);
model.assembleMassLumped();
std::cout << model << std::endl;
// Boundary condition (Neumann)
Matrix<Real> stress(2, 2);
stress.eye(Real(1e3));
model.applyBC(BC::Neumann::FromHigherDim(stress), "boundary_0");
model.setBaseName("square-orthotrope");
model.addDumpFieldVector("displacement");
model.addDumpField("mass");
model.addDumpField("velocity");
model.addDumpField("acceleration");
model.addDumpFieldVector("external_force");
model.addDumpFieldVector("internal_force");
model.addDumpField("stress");
model.addDumpField("grad_u");
model.dump();
std::ofstream energy;
energy.open("energy.csv");
energy << "id,epot,ekin,tot" << std::endl;
for (UInt s = 0; s < max_steps; ++s) {
model.solveStep();
epot = model.getEnergy("potential");
ekin = model.getEnergy("kinetic");
std::cerr << "passing step " << s << "/" << max_steps << std::endl;
energy << s << "," << epot << "," << ekin << "," << epot + ekin
<< std::endl;
if (s % 100 == 0)
model.dump();
}
energy.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
index c84d43d8a..670d4e6f1 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_thermal.cc
@@ -1,104 +1,106 @@
/**
* @file test_material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Wed Aug 04 2010
- * @date last modification: Mon Jan 29 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 18 2020
*
* @brief Test the thermal material
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_thermal.hh"
#include "solid_mechanics_model.hh"
#include "test_material_fixtures.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using mat_types =
::testing::Types<Traits<MaterialThermal, 1>, Traits<MaterialThermal, 2>,
Traits<MaterialThermal, 3>>;
/* -------------------------------------------------------------------------- */
template <> void FriendMaterial<MaterialThermal<3>>::testComputeStress() {
Real E = 1.;
Real nu = .3;
Real alpha = 2;
setParam("E", E);
setParam("nu", nu);
setParam("alpha", alpha);
Real deltaT = 1;
Real sigma = 0;
this->computeStressOnQuad(sigma, deltaT);
Real solution = -E / (1 - 2 * nu) * alpha * deltaT;
auto error = std::abs(sigma - solution);
ASSERT_NEAR(error, 0, 1e-14);
}
template <> void FriendMaterial<MaterialThermal<2>>::testComputeStress() {
Real E = 1.;
Real nu = .3;
Real alpha = 2;
setParam("E", E);
setParam("nu", nu);
setParam("alpha", alpha);
Real deltaT = 1;
Real sigma = 0;
this->computeStressOnQuad(sigma, deltaT);
Real solution = -E / (1 - 2 * nu) * alpha * deltaT;
auto error = std::abs(sigma - solution);
ASSERT_NEAR(error, 0, 1e-14);
}
template <> void FriendMaterial<MaterialThermal<1>>::testComputeStress() {
Real E = 1.;
Real nu = .3;
Real alpha = 2;
setParam("E", E);
setParam("nu", nu);
setParam("alpha", alpha);
Real deltaT = 1;
Real sigma = 0;
this->computeStressOnQuad(sigma, deltaT);
Real solution = -E * alpha * deltaT;
auto error = std::abs(sigma - solution);
ASSERT_NEAR(error, 0, 1e-14);
}
namespace {
template <typename T>
class TestMaterialThermalFixture : public ::TestMaterialFixture<T> {};
TYPED_TEST_SUITE(TestMaterialThermalFixture, mat_types, );
TYPED_TEST(TestMaterialThermalFixture, ThermalComputeStress) {
this->material->testComputeStress();
}
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/CMakeLists.txt
index 524eac0cc..f91e08242 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/CMakeLists.txt
@@ -1,38 +1,48 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Thu Aug 09 2012
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Fri Jan 15 2016
#
# @brief configuration for viscoelastic materials tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(test_material_standard_linear_solid_deviatoric_relaxation_mesh
test_material_standard_linear_solid_deviatoric_relaxation.geo 2 1)
register_test(test_material_standard_linear_solid_deviatoric_relaxation
SOURCES test_material_standard_linear_solid_deviatoric_relaxation.cc
DEPENDS test_material_standard_linear_solid_deviatoric_relaxation_mesh
FILES_TO_COPY material_standard_linear_solid_deviatoric_relaxation.dat
PACKAGE core
)
register_test(test_material_standard_linear_solid_deviatoric_relaxation_tension
SOURCES test_material_standard_linear_solid_deviatoric_relaxation_tension.cc
DEPENDS test_material_standard_linear_solid_deviatoric_relaxation_mesh
FILES_TO_COPY material_standard_linear_solid_deviatoric_relaxation.dat
PACKAGE core
)
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation.cc
index f9cd18b61..f7235b84a 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation.cc
@@ -1,169 +1,171 @@
/**
* @file test_material_standard_linear_solid_deviatoric_relaxation.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Mon Aug 09 2010
- * @date last modification: Mon Jun 12 2017
+ * @date last modification: Sat Dec 19 2020
*
* @brief test of the viscoelastic material: relaxation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
akantu::initialize("material_standard_linear_solid_deviatoric_relaxation.dat",
argc, argv);
akantu::debug::setDebugLevel(akantu::dblWarning);
// sim data
Real T = 10.;
Real eps = 0.001;
const UInt dim = 2;
Real sim_time = 25.;
Real time_factor = 0.1;
Real tolerance = 1e-7;
Mesh mesh(dim);
mesh.read("test_material_standard_linear_solid_deviatoric_relaxation.msh");
const ElementType element_type = _quadrangle_4;
SolidMechanicsModel model(mesh);
/* ------------------------------------------------------------------------ */
/* Initialization */
/* ------------------------------------------------------------------------ */
model.initFull();
std::cout << model.getMaterial(0) << std::endl;
model.assembleMassLumped();
std::stringstream filename_sstr;
filename_sstr
<< "test_material_standard_linear_solid_deviatoric_relaxation.out";
std::ofstream output_data;
output_data.open(filename_sstr.str().c_str());
output_data << "#[1]-time [2]-sigma_analytic [3+]-sigma_measurements"
<< std::endl;
Material & mat = model.getMaterial(0);
const Array<Real> & stress = mat.getStress(element_type);
Real Eta = mat.get("Eta");
Real EV = mat.get("Ev");
Real Einf = mat.get("Einf");
Real nu = mat.get("nu");
Real Ginf = Einf / (2 * (1 + nu));
Real G = EV / (2 * (1 + nu));
Real G0 = G + Ginf;
Real gamma = G / G0;
Real tau = Eta / EV;
Real gammainf = Ginf / G0;
UInt nb_nodes = mesh.getNbNodes();
const Array<Real> & coordinate = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
/// Setting time step
Real time_step = model.getStableTimeStep() * time_factor;
std::cout << "Time Step = " << time_step << "s" << std::endl;
model.setTimeStep(time_step);
UInt max_steps = sim_time / time_step;
UInt out_interval = 1;
Real time = 0.;
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
for (UInt s = 0; s <= max_steps; ++s) {
if (s % 1000 == 0)
std::cerr << "passing step " << s << "/" << max_steps << std::endl;
time = s * time_step;
// impose displacement
Real epsilon = 0.;
if (time < T) {
epsilon = eps * time / T;
} else {
epsilon = eps;
}
for (UInt n = 0; n < nb_nodes; ++n) {
displacement(n, 0) = epsilon * coordinate(n, 1);
displacement(n, 1) = epsilon * coordinate(n, 0);
}
// compute stress
model.assembleInternalForces();
// print output
if (s % out_interval == 0) {
// analytical solution
Real solution = 0.;
if (time < T) {
solution = 2 * G0 * eps / T *
(gammainf * time + gamma * tau * (1 - exp(-time / tau)));
} else {
solution = 2 * G0 * eps *
(gammainf + gamma * tau / T *
(exp((T - time) / tau) - exp(-time / tau)));
}
output_data << s * time_step << " " << solution;
// data output
Array<Real>::const_matrix_iterator stress_it = stress.begin(dim, dim);
Array<Real>::const_matrix_iterator stress_end = stress.end(dim, dim);
for (; stress_it != stress_end; ++stress_it) {
output_data << " " << (*stress_it)(0, 1) << " " << (*stress_it)(1, 0);
// test error
Real rel_error_1 = std::abs(((*stress_it)(0, 1) - solution) / solution);
Real rel_error_2 = std::abs(((*stress_it)(1, 0) - solution) / solution);
if (rel_error_1 > tolerance || rel_error_2 > tolerance) {
std::cerr << "Relative error: " << rel_error_1 << " " << rel_error_2
<< std::endl;
return EXIT_FAILURE;
}
}
output_data << std::endl;
}
}
finalize();
std::cout << "Test successful!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation_tension.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation_tension.cc
index 685f130d9..38e3e9470 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation_tension.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic/test_material_standard_linear_solid_deviatoric_relaxation_tension.cc
@@ -1,179 +1,181 @@
/**
* @file test_material_standard_linear_solid_deviatoric_relaxation_tension.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 09 2010
- * @date last modification: Mon Jun 12 2017
+ * @date last modification: Sat Dec 19 2020
*
* @brief test of the viscoelastic material: relaxation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
akantu::initialize("material_standard_linear_solid_deviatoric_relaxation.dat",
argc, argv);
// sim data
Real T = 10.;
Real eps = 0.001;
// const UInt dim = 3;
const UInt dim = 2;
Real sim_time = 25.;
// Real sim_time = 250.;
Real time_factor = 0.1;
Real tolerance = 1e-5;
Mesh mesh(dim);
mesh.read("test_material_standard_linear_solid_deviatoric_relaxation.msh");
// mesh_io.read("hexa_structured.msh",mesh);
// const ElementType element_type = _hexahedron_8;
const ElementType element_type = _quadrangle_4;
SolidMechanicsModel model(mesh);
/* ------------------------------------------------------------------------ */
/* Initialization */
/* ------------------------------------------------------------------------ */
model.initFull();
std::cout << model.getMaterial(0) << std::endl;
model.assembleMassLumped();
model.assembleInternalForces();
model.getMaterial(0).setToSteadyState();
std::stringstream filename_sstr;
filename_sstr << "test_material_standard_linear_solid_deviatoric_relaxation_"
"tension.out";
std::ofstream output_data;
output_data.open(filename_sstr.str().c_str());
output_data << "#[1]-time [2]-sigma_analytic [3+]-sigma_measurements"
<< std::endl;
Material & mat = model.getMaterial(0);
const Array<Real> & stress = mat.getStress(element_type);
Real Eta = mat.get("Eta");
Real EV = mat.get("Ev");
Real Einf = mat.get("Einf");
Real E0 = mat.get("E");
Real kpa = mat.get("kapa");
Real mu = mat.get("mu");
Real gamma = EV / E0;
Real gammainf = Einf / E0;
Real tau = Eta / EV;
std::cout << "relaxation time = " << tau << std::endl;
UInt nb_nodes = mesh.getNbNodes();
const Array<Real> & coordinate = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
/// Setting time step
Real time_step = model.getStableTimeStep() * time_factor;
std::cout << "Time Step = " << time_step << "s" << std::endl;
model.setTimeStep(time_step);
UInt max_steps = sim_time / time_step;
UInt out_interval = 1;
Real time = 0.;
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
for (UInt s = 0; s <= max_steps; ++s) {
if (s % 1000 == 0)
std::cerr << "passing step " << s << "/" << max_steps << std::endl;
time = s * time_step;
// impose displacement
Real epsilon = 0.;
if (time < T) {
epsilon = eps * time / T;
} else {
epsilon = eps;
}
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt d = 0; d < dim; ++d)
displacement(n, d) = epsilon * coordinate(n, d);
}
// compute stress
model.assembleInternalForces();
// print output
if (s % out_interval == 0) {
// analytical solution
Real epskk = dim * eps;
Real solution = 0.;
if (time < T) {
solution =
2 * mu * (eps - epskk / 3.) / T *
(gammainf * time + gamma * tau * (1 - exp(-time / tau))) +
gammainf * kpa * epskk * time / T;
} else {
solution =
2 * mu * (eps - epskk / 3.) *
(gammainf +
gamma * tau / T * (exp((T - time) / tau) - exp(-time / tau))) +
gammainf * kpa * epskk;
}
output_data << s * time_step << " " << solution;
// data output
Array<Real>::const_matrix_iterator stress_it = stress.begin(dim, dim);
Array<Real>::const_matrix_iterator stress_end = stress.end(dim, dim);
for (; stress_it != stress_end; ++stress_it) {
output_data << " " << (*stress_it)(1, 1);
// test error
Real rel_error_1 = std::abs(((*stress_it)(1, 1) - solution) / solution);
if (rel_error_1 > tolerance) {
std::cerr << "Relative error: " << rel_error_1 << std::endl;
return EXIT_FAILURE;
}
}
output_data << std::endl;
}
}
finalize();
std::cout << "Test successful!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
index c9ffce608..6ed433886 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/CMakeLists.txt
@@ -1,32 +1,43 @@
#===============================================================================
# @file CMakeLists.txt
#
+# @author Emil Gallyamov <emil.gallyamov@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Thu Aug 09 2012
-# @date last modification: Wed Feb 03 2016
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Dec 04 2019
#
# @brief configuration for viscoelastic materials tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
-#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# @section LICENSE
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+#
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
add_mesh(test_material_viscoelastic_maxwell_mesh
test_material_viscoelastic_maxwell.geo 2 1)
register_test(test_material_viscoelasti_maxwell_relaxation
SOURCES test_material_viscoelastic_maxwell_relaxation.cc
DEPENDS test_material_viscoelastic_maxwell_mesh
FILES_TO_COPY material_viscoelastic_maxwell.dat
PACKAGE core
UNSTABLE
)
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc
index a88404333..c144a964d 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_material_viscoelastic_maxwell/test_material_viscoelastic_maxwell_relaxation.cc
@@ -1,194 +1,196 @@
/**
* @file test_material_viscoelastic_maxwell_relaxation.cc
*
* @author Emil Gallyamov <emil.gallyamov@epfl.ch>
*
- * @date creation: Thu May 17 2018
- * @date last modification:
+ * @date creation: Tue Nov 20 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief test of the viscoelastic material: relaxation
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
#include <sstream>
/* -------------------------------------------------------------------------- */
#include "material_viscoelastic_maxwell.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_viscoelastic_maxwell.dat", argc, argv);
// sim data
Real eps = 0.1;
const UInt dim = 2;
Real sim_time = 100.;
Real T = 10.;
Real tolerance = 1e-6;
Mesh mesh(dim);
mesh.read("test_material_viscoelastic_maxwell.msh");
const ElementType element_type = _quadrangle_4;
SolidMechanicsModel model(mesh);
/* ------------------------------------------------------------------------ */
/* Initialization */
/* ------------------------------------------------------------------------ */
model.initFull(_analysis_method = _static);
std::cout << model.getMaterial(0) << std::endl;
std::stringstream filename_sstr;
filename_sstr << "test_material_viscoelastic_maxwell.out";
std::ofstream output_data;
output_data.open(filename_sstr.str().c_str());
Material & mat = model.getMaterial(0);
const Array<Real> & stress = mat.getStress(element_type);
Vector<Real> Eta = mat.get("Eta");
Vector<Real> Ev = mat.get("Ev");
Real Einf = mat.get("Einf");
Real nu = mat.get("nu");
Real lambda = Eta(0) / Ev(0);
Real pre_mult = 1 / (1 + nu) / (1 - 2 * nu);
Real time_step = 0.1;
UInt nb_nodes = mesh.getNbNodes();
const Array<Real> & coordinate = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & blocked = model.getBlockedDOFs();
/// Setting time step
model.setTimeStep(time_step);
UInt max_steps = sim_time / time_step + 1;
Real time = 0.;
auto & solver = model.getNonLinearSolver();
solver.set("max_iterations", 200);
solver.set("threshold", 1e-7);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
/* ------------------------------------------------------------------------ */
/* Main loop */
/* ------------------------------------------------------------------------ */
for (UInt s = 0; s <= max_steps; ++s) {
std::cout << "Time Step = " << time_step << "s" << std::endl;
std::cout << "Time = " << time << std::endl;
// impose displacement
Real epsilon = 0;
if (time < T) {
epsilon = eps * time / T;
} else {
epsilon = eps;
}
for (UInt n = 0; n < nb_nodes; ++n) {
if (Math::are_float_equal(coordinate(n, 0), 0.0)) {
displacement(n, 0) = 0;
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 1), 0.0)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = 0;
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 0), 0.001)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
} else if (Math::are_float_equal(coordinate(n, 1), 0.001)) {
displacement(n, 0) = epsilon * coordinate(n, 0);
blocked(n, 0) = true;
displacement(n, 1) = epsilon * coordinate(n, 1);
blocked(n, 1) = true;
}
}
try {
model.solveStep();
} catch (debug::Exception & e) {
}
Int nb_iter = solver.get("nb_iterations");
Real error = solver.get("error");
bool converged = solver.get("converged");
if (converged) {
std::cout << "Converged in " << nb_iter << " iterations" << std::endl;
} else {
std::cout << "Didn't converge after " << nb_iter
<< " iterations. Error is " << error << std::endl;
return EXIT_FAILURE;
}
// analytical solution
Real solution_11 = 0.;
if (time < T) {
solution_11 = pre_mult * eps / T *
(Einf * time + lambda * Ev(0) * (1 - exp(-time / lambda)));
} else {
solution_11 =
pre_mult * eps *
(Einf + lambda * Ev(0) / T *
(exp((T - time) / lambda) - exp(-time / lambda)));
}
// data output
output_data << s * time_step << " " << epsilon << " " << solution_11;
Array<Real>::const_matrix_iterator stress_it = stress.begin(dim, dim);
Array<Real>::const_matrix_iterator stress_end = stress.end(dim, dim);
for (; stress_it != stress_end; ++stress_it) {
output_data << " " << (*stress_it)(0, 0);
// test error
Real rel_error_11 =
std::abs(((*stress_it)(0, 0) - solution_11) / solution_11);
if (rel_error_11 > tolerance) {
std::cerr << "Relative error: " << rel_error_11 << std::endl;
return EXIT_FAILURE;
}
}
output_data << std::endl;
time += time_step;
}
output_data.close();
finalize();
std::cout << "Test successful!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
index 1328252cd..6229906a0 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_multi_material_elastic.cc
@@ -1,122 +1,124 @@
/**
* @file test_multi_material_elastic.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Mar 03 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Thu May 09 2019
*
* @brief Test with 2 elastic materials
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "non_linear_solver.hh"
#include <solid_mechanics_model.hh>
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("test_multi_material_elastic.dat", argc, argv);
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("test_multi_material_elastic.msh");
SolidMechanicsModel model(mesh);
auto && mat_sel = std::make_shared<MeshDataMaterialSelector<std::string>>(
"physical_names", model);
model.setMaterialSelector(mat_sel);
model.initFull(_analysis_method = _static);
model.applyBC(BC::Dirichlet::FlagOnly(_y), "ground");
model.applyBC(BC::Dirichlet::FlagOnly(_x), "corner");
Vector<Real> trac(spatial_dimension, 0.);
trac(_y) = 1.;
model.applyBC(BC::Neumann::FromTraction(trac), "air");
model.addDumpField("external_force");
model.addDumpField("internal_force");
model.addDumpField("blocked_dofs");
model.addDumpField("displacement");
model.addDumpField("stress");
model.addDumpField("grad_u");
// model.dump();
auto & solver = model.getNonLinearSolver("static");
solver.set("max_iterations", 1);
solver.set("threshold", 1e-8);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
model.solveStep();
// model.dump();
std::map<std::string, Matrix<Real>> ref_strain;
ref_strain["strong"] = Matrix<Real>(spatial_dimension, spatial_dimension, 0.);
ref_strain["strong"](_y, _y) = .5;
ref_strain["weak"] = Matrix<Real>(spatial_dimension, spatial_dimension, 0.);
ref_strain["weak"](_y, _y) = 1;
Matrix<Real> ref_stress(spatial_dimension, spatial_dimension, 0.);
ref_stress(_y, _y) = 1.;
std::vector<std::string> mats = {"strong", "weak"};
typedef Array<Real>::const_matrix_iterator mat_it;
auto check = [](mat_it it, mat_it end, const Matrix<Real> & ref) -> bool {
for (; it != end; ++it) {
Real dist = (*it - ref).norm<L_2>();
// std::cout << *it << " " << dist << " " << (dist < 1e-10 ? "OK" : "Not
// OK") << std::endl;
if (dist > 1e-10)
return false;
}
return true;
};
for (auto & type : mesh.elementTypes(spatial_dimension)) {
for (auto mat_id : mats) {
auto & stress = model.getMaterial(mat_id).getStress(type);
auto & grad_u = model.getMaterial(mat_id).getGradU(type);
auto sit = stress.begin(spatial_dimension, spatial_dimension);
auto send = stress.end(spatial_dimension, spatial_dimension);
auto git = grad_u.begin(spatial_dimension, spatial_dimension);
auto gend = grad_u.end(spatial_dimension, spatial_dimension);
if (!check(sit, send, ref_stress))
AKANTU_ERROR("The stresses are not correct");
if (!check(git, gend, ref_strain[mat_id]))
AKANTU_ERROR("The grad_u are not correct");
}
}
finalize();
return 0;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_materials/test_plastic_materials.cc b/test/test_model/test_solid_mechanics_model/test_materials/test_plastic_materials.cc
index 400e57c94..fa993c305 100644
--- a/test/test_model/test_solid_mechanics_model/test_materials/test_plastic_materials.cc
+++ b/test/test_model/test_solid_mechanics_model/test_materials/test_plastic_materials.cc
@@ -1,192 +1,194 @@
/**
* @file test_plastic_materials.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 17 2017
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Tue Jan 19 2021
*
* @brief Tests the plastic material
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_linear_isotropic_hardening.hh"
#include "solid_mechanics_model.hh"
#include "test_material_fixtures.hh"
#include <gtest/gtest.h>
#include <type_traits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
using mat_types = ::testing::Types<
// Traits<MaterialLinearIsotropicHardening, 1>,
// Traits<MaterialLinearIsotropicHardening, 2>,
Traits<MaterialLinearIsotropicHardening, 3>>;
/* -------------------------------------------------------------------------- */
template <>
void FriendMaterial<MaterialLinearIsotropicHardening<3>>::testComputeStress() {
Real E = 1.;
// Real nu = .3;
Real nu = 0.;
Real rho = 1.;
Real sigma_0 = 1.;
Real h = 0.;
Real bulk_modulus_K = E / 3. / (1 - 2. * nu);
Real shear_modulus_mu = 0.5 * E / (1 + nu);
setParam("E", E);
setParam("nu", nu);
setParam("rho", rho);
setParam("sigma_y", sigma_0);
setParam("h", h);
auto rotation_matrix = getRandomRotation();
Real max_strain = 10.;
Real strain_steps = 100;
Real dt = max_strain / strain_steps;
std::vector<double> steps(strain_steps);
std::iota(steps.begin(), steps.end(), 0.);
Matrix<Real> previous_grad_u_rot(3, 3, 0.);
Matrix<Real> previous_sigma(3, 3, 0.);
Matrix<Real> previous_sigma_rot(3, 3, 0.);
Matrix<Real> inelastic_strain_rot(3, 3, 0.);
Matrix<Real> inelastic_strain(3, 3, 0.);
Matrix<Real> previous_inelastic_strain(3, 3, 0.);
Matrix<Real> previous_inelastic_strain_rot(3, 3, 0.);
Matrix<Real> sigma_rot(3, 3, 0.);
Real iso_hardening = 0.;
Real previous_iso_hardening = 0.;
// hydrostatic loading (should not plastify)
for (auto && i : steps) {
auto t = i * dt;
auto grad_u = this->getHydrostaticStrain(t);
auto grad_u_rot = this->applyRotation(grad_u, rotation_matrix);
this->computeStressOnQuad(grad_u_rot, previous_grad_u_rot, sigma_rot,
previous_sigma_rot, inelastic_strain_rot,
previous_inelastic_strain_rot, iso_hardening,
previous_iso_hardening, 0., 0.);
auto sigma = this->reverseRotation(sigma_rot, rotation_matrix);
Matrix<Real> sigma_expected =
t * 3. * bulk_modulus_K * Matrix<Real>::eye(3, 1.);
Real stress_error = (sigma - sigma_expected).norm<L_inf>();
ASSERT_NEAR(stress_error, 0., 1e-13);
ASSERT_NEAR(inelastic_strain_rot.norm<L_inf>(), 0., 1e-13);
previous_grad_u_rot = grad_u_rot;
previous_sigma_rot = sigma_rot;
previous_inelastic_strain_rot = inelastic_strain_rot;
previous_iso_hardening = iso_hardening;
}
// deviatoric loading (should plastify)
// stress at onset of plastication
Real beta = sqrt(42);
Real t_P = sigma_0 / 2. / shear_modulus_mu / beta;
Matrix<Real> sigma_P = sigma_0 / beta * this->getDeviatoricStrain(1.);
for (auto && i : steps) {
auto t = i * dt;
auto grad_u = this->getDeviatoricStrain(t);
auto grad_u_rot = this->applyRotation(grad_u, rotation_matrix);
Real iso_hardening{0.};
Real previous_iso_hardening{0.};
this->computeStressOnQuad(grad_u_rot, previous_grad_u_rot, sigma_rot,
previous_sigma_rot, inelastic_strain_rot,
previous_inelastic_strain_rot, iso_hardening,
previous_iso_hardening, 0., 0.);
auto sigma = this->reverseRotation(sigma_rot, rotation_matrix);
auto inelastic_strain =
this->reverseRotation(inelastic_strain_rot, rotation_matrix);
if (t < t_P) {
Matrix<Real> sigma_expected =
shear_modulus_mu * (grad_u + grad_u.transpose());
Real stress_error = (sigma - sigma_expected).norm<L_inf>();
ASSERT_NEAR(stress_error, 0., 1e-13);
ASSERT_NEAR(inelastic_strain_rot.norm<L_inf>(), 0., 1e-13);
} else if (t > t_P + dt) {
// skip the transition from non plastic to plastic
auto delta_lambda_expected =
dt / t * previous_sigma.doubleDot(grad_u + grad_u.transpose()) / 2.;
auto delta_inelastic_strain_expected =
delta_lambda_expected * 3. / 2. / sigma_0 * previous_sigma;
auto inelastic_strain_expected =
delta_inelastic_strain_expected + previous_inelastic_strain;
ASSERT_NEAR((inelastic_strain - inelastic_strain_expected).norm<L_inf>(),
0., 1e-13);
auto delta_sigma_expected =
2. * shear_modulus_mu *
(0.5 * dt / t * (grad_u + grad_u.transpose()) -
delta_inelastic_strain_expected);
auto delta_sigma = sigma - previous_sigma;
ASSERT_NEAR((delta_sigma_expected - delta_sigma).norm<L_inf>(), 0.,
1e-13);
}
previous_sigma = sigma;
previous_sigma_rot = sigma_rot;
previous_grad_u_rot = grad_u_rot;
previous_inelastic_strain = inelastic_strain;
previous_inelastic_strain_rot = inelastic_strain_rot;
}
}
namespace {
template <typename T>
class TestPlasticMaterialFixture : public ::TestMaterialFixture<T> {};
TYPED_TEST_SUITE(TestPlasticMaterialFixture, mat_types, );
TYPED_TEST(TestPlasticMaterialFixture, ComputeStress) {
this->material->testComputeStress();
}
TYPED_TEST(TestPlasticMaterialFixture, DISABLED_EnergyDensity) {
this->material->testEnergyDensity();
}
TYPED_TEST(TestPlasticMaterialFixture, DISABLED_ComputeTangentModuli) {
this->material->testComputeTangentModuli();
}
TYPED_TEST(TestPlasticMaterialFixture, DISABLED_ComputeCelerity) {
this->material->testCelerity();
}
} // namespace
/*****************************************************************/
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_dynamics.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_dynamics.cc
index 441dbdc00..1c6dec0ea 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_dynamics.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_dynamics.cc
@@ -1,320 +1,323 @@
/**
* @file test_solid_mechanics_model_dynamics.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 29 2017
- * @date last modification: Wed Feb 21 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief test of the class SolidMechanicsModel on the 3d cube
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
#include "test_solid_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
namespace {
const Real A = 1e-1;
const Real E = 1.;
const Real poisson = 3. / 10;
const Real lambda = E * poisson / (1 + poisson) / (1 - 2 * poisson);
const Real mu = E / 2 / (1. + poisson);
const Real rho = 1.;
const Real cp = std::sqrt((lambda + 2 * mu) / rho);
const Real cs = std::sqrt(mu / rho);
const Real c = std::sqrt(E / rho);
const Vector<Real> k = {.5, 0., 0.};
const Vector<Real> psi1 = {0., 0., 1.};
const Vector<Real> psi2 = {0., 1., 0.};
const Real knorm = k.norm();
/* -------------------------------------------------------------------------- */
template <UInt dim> struct Verification {};
/* -------------------------------------------------------------------------- */
template <> struct Verification<1> {
void displacement(Vector<Real> & disp, const Vector<Real> & coord,
Real current_time) {
const auto & x = coord(_x);
const Real omega = c * k[0];
disp(_x) = A * cos(k[0] * x - omega * current_time);
}
void velocity(Vector<Real> & vel, const Vector<Real> & coord,
Real current_time) {
const auto & x = coord(_x);
const Real omega = c * k[0];
vel(_x) = omega * A * sin(k[0] * x - omega * current_time);
}
};
/* -------------------------------------------------------------------------- */
template <> struct Verification<2> {
void displacement(Vector<Real> & disp, const Vector<Real> & X,
Real current_time) {
Vector<Real> kshear = {k[1], k[0]};
Vector<Real> kpush = {k[0], k[1]};
const Real omega_p = knorm * cp;
const Real omega_s = knorm * cs;
Real phase_p = X.dot(kpush) - omega_p * current_time;
Real phase_s = X.dot(kpush) - omega_s * current_time;
disp = A * (kpush * cos(phase_p) + kshear * cos(phase_s));
}
void velocity(Vector<Real> & vel, const Vector<Real> & X, Real current_time) {
Vector<Real> kshear = {k[1], k[0]};
Vector<Real> kpush = {k[0], k[1]};
const Real omega_p = knorm * cp;
const Real omega_s = knorm * cs;
Real phase_p = X.dot(kpush) - omega_p * current_time;
Real phase_s = X.dot(kpush) - omega_s * current_time;
vel =
A * (kpush * omega_p * cos(phase_p) + kshear * omega_s * cos(phase_s));
}
};
/* -------------------------------------------------------------------------- */
template <> struct Verification<3> {
void displacement(Vector<Real> & disp, const Vector<Real> & coord,
Real current_time) {
const auto & X = coord;
Vector<Real> kpush = k;
Vector<Real> kshear1(3);
Vector<Real> kshear2(3);
kshear1.crossProduct(k, psi1);
kshear2.crossProduct(k, psi2);
const Real omega_p = knorm * cp;
const Real omega_s = knorm * cs;
Real phase_p = X.dot(kpush) - omega_p * current_time;
Real phase_s = X.dot(kpush) - omega_s * current_time;
disp = A * (kpush * cos(phase_p) + kshear1 * cos(phase_s) +
kshear2 * cos(phase_s));
}
void velocity(Vector<Real> & vel, const Vector<Real> & coord,
Real current_time) {
const auto & X = coord;
Vector<Real> kpush = k;
Vector<Real> kshear1(3);
Vector<Real> kshear2(3);
kshear1.crossProduct(k, psi1);
kshear2.crossProduct(k, psi2);
const Real omega_p = knorm * cp;
const Real omega_s = knorm * cs;
Real phase_p = X.dot(kpush) - omega_p * current_time;
Real phase_s = X.dot(kpush) - omega_s * current_time;
vel =
A * (kpush * omega_p * cos(phase_p) + kshear1 * omega_s * cos(phase_s) +
kshear2 * omega_s * cos(phase_s));
}
};
/* -------------------------------------------------------------------------- */
template <ElementType _type>
class SolutionFunctor : public BC::Dirichlet::DirichletFunctor {
public:
SolutionFunctor(Real current_time, SolidMechanicsModel & model)
: current_time(current_time), model(model) {}
public:
static constexpr UInt dim = ElementClass<_type>::getSpatialDimension();
inline void operator()(UInt node, Vector<bool> & flags, Vector<Real> & primal,
const Vector<Real> & coord) const {
flags(0) = true;
auto & vel = model.getVelocity();
auto it = vel.begin(model.getSpatialDimension());
Vector<Real> v = it[node];
Verification<dim> verif;
verif.displacement(primal, coord, current_time);
verif.velocity(v, coord, current_time);
}
private:
Real current_time;
SolidMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
// This fixture uses somewhat finer meshes representing bars.
template <typename type_, typename analysis_method_>
class TestSMMFixtureBar : public TestSMMFixture<type_> {
using parent = TestSMMFixture<type_>;
public:
void SetUp() override {
this->mesh_file =
"../patch_tests/data/bar" + std::to_string(this->type) + ".msh";
parent::SetUp();
auto analysis_method = analysis_method_::value;
this->initModel("test_solid_mechanics_model_"
"dynamics_material.dat",
analysis_method);
const auto & position = this->mesh->getNodes();
auto & displacement = this->model->getDisplacement();
auto & velocity = this->model->getVelocity();
constexpr auto dim = parent::spatial_dimension;
Verification<dim> verif;
for (auto && tuple :
zip(make_view(position, dim), make_view(displacement, dim),
make_view(velocity, dim))) {
verif.displacement(std::get<1>(tuple), std::get<0>(tuple), 0.);
verif.velocity(std::get<2>(tuple), std::get<0>(tuple), 0.);
}
if (this->dump_paraview)
this->model->dump();
/// boundary conditions
this->model->applyBC(SolutionFunctor<parent::type>(0., *this->model), "BC");
wave_velocity = 1.; // sqrt(E/rho) = sqrt(1/1) = 1
simulation_time = 5 / wave_velocity;
time_step = this->model->getTimeStep();
max_steps = simulation_time / time_step; // 100
}
void solveStep() {
constexpr auto dim = parent::spatial_dimension;
Real current_time = 0.;
const auto & position = this->mesh->getNodes();
const auto & displacement = this->model->getDisplacement();
UInt nb_nodes = this->mesh->getNbNodes();
UInt nb_global_nodes = this->mesh->getNbGlobalNodes();
max_error = -1.;
Array<Real> displacement_solution(nb_nodes, dim);
Verification<dim> verif;
auto ndump = 50;
auto dump_freq = max_steps / ndump;
for (UInt s = 0; s < this->max_steps;
++s, current_time += this->time_step) {
if (s % dump_freq == 0 && this->dump_paraview)
this->model->dump();
/// boundary conditions
this->model->applyBC(
SolutionFunctor<parent::type>(current_time, *this->model), "BC");
// compute the disp solution
for (auto && tuple : zip(make_view(position, dim),
make_view(displacement_solution, dim))) {
verif.displacement(std::get<1>(tuple), std::get<0>(tuple),
current_time);
}
// compute the error solution
Real disp_error = 0.;
auto n = 0;
for (auto && tuple : zip(make_view(displacement, dim),
make_view(displacement_solution, dim))) {
if (this->mesh->isLocalOrMasterNode(n)) {
auto diff = std::get<1>(tuple) - std::get<0>(tuple);
disp_error += diff.dot(diff);
}
++n;
}
this->mesh->getCommunicator().allReduce(disp_error,
SynchronizerOperation::_sum);
disp_error = sqrt(disp_error) / nb_global_nodes;
max_error = std::max(disp_error, max_error);
this->model->solveStep();
}
}
protected:
Real time_step;
Real wave_velocity;
Real simulation_time;
UInt max_steps;
Real max_error{-1};
};
template <AnalysisMethod t>
using analysis_method_t = std::integral_constant<AnalysisMethod, t>;
using TestTypes = gtest_list_t<TestElementTypes>;
template <typename type_>
using TestSMMFixtureBarExplicit =
TestSMMFixtureBar<type_, analysis_method_t<_explicit_lumped_mass>>;
TYPED_TEST_SUITE(TestSMMFixtureBarExplicit, TestTypes, );
/* -------------------------------------------------------------------------- */
TYPED_TEST(TestSMMFixtureBarExplicit, Dynamics) {
this->solveStep();
EXPECT_NEAR(this->max_error, 0., 2e-3);
// std::cout << "max error: " << max_error << std::endl;
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IMPLICIT)
template <typename type_>
using TestSMMFixtureBarImplicit =
TestSMMFixtureBar<type_, analysis_method_t<_implicit_dynamic>>;
TYPED_TEST_SUITE(TestSMMFixtureBarImplicit, TestTypes, );
TYPED_TEST(TestSMMFixtureBarImplicit, Dynamics) {
if (this->type == _segment_2 and
(this->mesh->getCommunicator().getNbProc() > 2)) {
// The error are just to high after (hopefully because of the two small test
// case)
SUCCEED();
return;
}
this->solveStep();
EXPECT_NEAR(this->max_error, 0., 2e-3);
}
#endif
} // namespace
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
index 3b6e5e232..e76f956e1 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_fixture.hh
@@ -1,129 +1,131 @@
/**
* @file test_solid_mechanics_model_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Wed Nov 18 2020
*
* @brief Main solif mechanics test file
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "solid_mechanics_model.hh"
#include "test_gtest_utils.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_
#define AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_
using namespace akantu;
// This fixture uses very small meshes with a volume of 1.
template <typename type_> class TestSMMFixture : public ::testing::Test {
public:
static constexpr ElementType type = type_::value;
static constexpr size_t spatial_dimension =
ElementClass<type>::getSpatialDimension();
void SetUp() override {
this->mesh = std::make_unique<Mesh>(this->spatial_dimension);
auto prank = Communicator::getStaticCommunicator().whoAmI();
if (prank == 0) {
this->mesh->read(this->mesh_file);
if(spatial_dimension > 1 and mesh->getNbElement(spatial_dimension - 1) == 0) {
MeshUtils::buildFacets(*this->mesh);
}
}
mesh->distribute();
SCOPED_TRACE(std::to_string(this->type).c_str());
model = std::make_unique<SolidMechanicsModel>(*mesh, _all_dimensions,
std::to_string(this->type));
}
void initModel(const ID & input, const AnalysisMethod & analysis_method) {
getStaticParser().parse(input);
this->model->initFull(_analysis_method = analysis_method);
if (analysis_method != _static) {
auto time_step = this->model->getStableTimeStep() / 10.;
this->model->setTimeStep(time_step);
}
// std::cout << "timestep: " << time_step << std::endl;
if (this->dump_paraview) {
std::stringstream base_name;
base_name << "bar" << analysis_method << this->type;
this->model->setBaseName(base_name.str());
this->model->addDumpFieldVector("displacement");
this->model->addDumpFieldVector("blocked_dofs");
if (analysis_method != _static) {
this->model->addDumpField("velocity");
this->model->addDumpField("acceleration");
}
if (this->mesh->isDistributed()) {
this->model->addDumpField("partitions");
}
this->model->addDumpFieldVector("external_force");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpField("stress");
this->model->addDumpField("strain");
}
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
protected:
std::string mesh_file{std::to_string(this->type) + ".msh"};
std::unique_ptr<Mesh> mesh;
std::unique_ptr<SolidMechanicsModel> model;
bool dump_paraview{false};
};
template <typename type_> constexpr ElementType TestSMMFixture<type_>::type;
template <typename type_>
constexpr size_t TestSMMFixture<type_>::spatial_dimension;
template <typename T>
using is_not_pentahedron =
aka::negation<aka::disjunction<is_element<T, _pentahedron_6>,
is_element<T, _pentahedron_15>>>;
using TestElementTypesFiltered =
tuple_filter_t<is_not_pentahedron, TestElementTypes>;
// using gtest_element_types = gtest_list_t<TestElementTypesFiltered>;
using gtest_element_types = gtest_list_t<TestElementTypes>;
TYPED_TEST_SUITE(TestSMMFixture, gtest_element_types, );
#endif /* AKANTU_TEST_SOLID_MECHANICS_MODEL_FIXTURE_HH_ */
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
index 2399256bb..99eb66964 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_eigenstrain.cc
@@ -1,200 +1,202 @@
/**
* @file test_solid_mechanics_model_material_eigenstrain.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Apr 16 2011
- * @date last modification: Thu Feb 01 2018
+ * @date last modification: Sat Dec 19 2020
*
* @brief test the internal field prestrain
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real alpha[3][4] = {{0.01, 0.02, 0.03, 0.04},
{0.05, 0.06, 0.07, 0.08},
{0.09, 0.10, 0.11, 0.12}};
/* -------------------------------------------------------------------------- */
template <ElementType type> static Matrix<Real> prescribed_strain() {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> strain(spatial_dimension, spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
strain(i, j) = alpha[i][j + 1];
}
}
return strain;
}
template <ElementType type>
static Matrix<Real> prescribed_stress(Matrix<Real> prescribed_eigengradu) {
UInt spatial_dimension = ElementClass<type>::getSpatialDimension();
Matrix<Real> stress(spatial_dimension, spatial_dimension);
// plane strain in 2d
Matrix<Real> strain(spatial_dimension, spatial_dimension);
Matrix<Real> pstrain;
pstrain = prescribed_strain<type>();
Real nu = 0.3;
Real E = 2.1e11;
Real trace = 0;
/// symetric part of the strain tensor
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
strain(i, j) = 0.5 * (pstrain(i, j) + pstrain(j, i));
// elastic strain is equal to elastic strain minus the eigenstrain
strain -= prescribed_eigengradu;
for (UInt i = 0; i < spatial_dimension; ++i)
trace += strain(i, i);
Real lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
Real mu = E / (2 * (1 + nu));
if (spatial_dimension == 1) {
stress(0, 0) = E * strain(0, 0);
} else {
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
stress(i, j) = (i == j) * lambda * trace + 2 * mu * strain(i, j);
}
}
return stress;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize("material_elastic_plane_strain.dat", argc, argv);
UInt dim = 3;
const ElementType element_type = _tetrahedron_4;
Matrix<Real> prescribed_eigengradu(dim, dim);
prescribed_eigengradu.set(0.1);
/// load mesh
Mesh mesh(dim);
mesh.read("cube_3d_tet_4.msh");
/// declaration of model
SolidMechanicsModel model(mesh);
/// model initialization
model.initFull(_analysis_method = _static);
// model.getNewSolver("static", TimeStepSolverType::_static,
// NonLinearSolverType::_newton_raphson_modified);
auto & solver = model.getNonLinearSolver("static");
solver.set("threshold", 2e-4);
solver.set("max_iterations", 2);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
const Array<Real> & coordinates = mesh.getNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
MeshUtils::buildFacets(mesh);
mesh.createBoundaryGroupFromGeometry();
// Loop over (Sub)Boundar(ies)
for (auto & group : mesh.iterateElementGroups()) {
for (const auto & n : group.getNodeGroup()) {
std::cout << "Node " << n << std::endl;
for (UInt i = 0; i < dim; ++i) {
displacement(n, i) = alpha[i][0];
for (UInt j = 0; j < dim; ++j) {
displacement(n, i) += alpha[i][j + 1] * coordinates(n, j);
}
boundary(n, i) = true;
}
}
}
/* ------------------------------------------------------------------------ */
/* Apply eigenstrain in each element */
/* ------------------------------------------------------------------------ */
Array<Real> & eigengradu_vect =
model.getMaterial(0).getInternal<Real>("eigen_grad_u")(element_type);
auto eigengradu_it = eigengradu_vect.begin(dim, dim);
auto eigengradu_end = eigengradu_vect.end(dim, dim);
for (; eigengradu_it != eigengradu_end; ++eigengradu_it) {
*eigengradu_it = prescribed_eigengradu;
}
/* ------------------------------------------------------------------------ */
/* Static solve */
/* ------------------------------------------------------------------------ */
model.solveStep();
std::cout << "Converged in " << Int(solver.get("nb_iterations")) << " ("
<< Real(solver.get("error")) << ")" << std::endl;
/* ------------------------------------------------------------------------ */
/* Checks */
/* ------------------------------------------------------------------------ */
const Array<Real> & stress_vect =
model.getMaterial(0).getStress(element_type);
auto stress_it = stress_vect.begin(dim, dim);
auto stress_end = stress_vect.end(dim, dim);
Matrix<Real> presc_stress;
presc_stress = prescribed_stress<element_type>(prescribed_eigengradu);
Real stress_tolerance = 1e-13;
for (; stress_it != stress_end; ++stress_it) {
const auto & stress = *stress_it;
Matrix<Real> diff(dim, dim);
diff = stress;
diff -= presc_stress;
Real stress_error = diff.norm<L_inf>() / stress.norm<L_inf>();
if (stress_error > stress_tolerance) {
std::cerr << "stress error: " << stress_error << " > " << stress_tolerance
<< std::endl;
std::cerr << "stress: " << stress << std::endl
<< "prescribed stress: " << presc_stress << std::endl;
return EXIT_FAILURE;
} // else {
// std::cerr << "stress error: " << stress_error
// << " < " << stress_tolerance << std::endl;
// }
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
index 5db4f541a..278fe0227 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_material_large_rotation.cc
@@ -1,119 +1,122 @@
/**
- * @file test_solid_mechanics_model_material_eigenstrain.cc
+ * @file test_solid_mechanics_model_material_large_rotation.cc
*
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Sat Apr 16 2011
- * @date last modification: Thu Feb 01 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 27 2019
*
* @brief test the internal field prestrain
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_utils.hh"
#include "non_linear_solver.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize("material_elastic.dat", argc, argv);
UInt dim = 3;
/// load mesh
Mesh mesh(dim);
mesh.read("cube_3d_tet_4.msh");
/// declaration of model
SolidMechanicsModel model(mesh);
/// model initialization
// model.initFull(_analysis_method=akantu._explicit_lumped_mass)
model.initFull(_analysis_method = _implicit_dynamic);
// model.initFull(_analysis_method = akantu._implicit_dynamic)
auto & solver = model.getNonLinearSolver();
solver.set("threshold", 1e-4);
solver.set("max_iterations", 100);
solver.set("convergence_type", SolveConvergenceCriteria::_residual);
model.setBaseName("waves");
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("acceleration");
model.addDumpFieldVector("velocity");
model.addDumpFieldVector("internal_force");
model.addDumpFieldVector("external_force");
model.addDumpField("strain");
model.addDumpField("stress");
model.addDumpField("blocked_dofs");
/* ------------------------------------------------------------------------ */
// get mass center
/* ------------------------------------------------------------------------ */
model.assembleMass();
auto & M = model.getDOFManager().getMatrix("M");
Array<Real> _mass(M.size(), 1);
_mass.zero();
std::cout << "AAAA " << M.size() << std::endl;
std::cout << "AAAA " << _mass.size() << std::endl;
for (UInt i = 0; i < M.size(); ++i) {
for (UInt j = 0; j < M.size(); ++j) {
std::cout << i << ", " << j <<std::endl;
_mass[i] += M(i, j);
}
}
std::array<Real, 3> mass_center{0., 0., 0.};
std::cout << "AAAA " << _mass.size() << std::endl;
Real total_mass = 0.;
for (UInt i = 0; i < _mass.size(); ++i) {
for (UInt j = 0; j < 3; ++j) {
mass_center[j] += _mass(i * 3 + j);
total_mass += _mass(i * 3 + j);
}
}
mass_center[0] /= total_mass / 3.;
mass_center[1] /= total_mass / 3.;
mass_center[2] /= total_mass / 3.;
std::cout << "total mass" << total_mass << std::endl;
std::cout << mass_center[0] << " " << mass_center[1] << " " << mass_center[2]
<< std::endl;
/* ---------------------------------------------------------------------- */
/* Dynamic evolution */
/* ---------------------------------------------------------------------- */
model.dump();
model.solveStep();
model.dump();
std::cout << "Converged in " << Int(solver.get("nb_iterations")) << " ("
<< Real(solver.get("error")) << ")" << std::endl;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc
index f6db99626..0d0b467c6 100644
--- a/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc
+++ b/test/test_model/test_solid_mechanics_model/test_solid_mechanics_model_reassign_material.cc
@@ -1,194 +1,196 @@
/**
* @file test_solid_mechanics_model_reassign_material.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Mon Feb 10 2014
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Mar 11 2021
*
* @brief test the function reassign material
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_grid_dynamic.hh"
#include "mesh_iterators.hh"
#include "communicator.hh"
#include "material.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class StraightInterfaceMaterialSelector : public MaterialSelector {
public:
StraightInterfaceMaterialSelector(SolidMechanicsModel & model,
UInt horizontal, Real & pos_interface,
const std::string & mat_1_material,
const std::string & mat_2_material)
: model(model), horizontal(horizontal), pos_interface(pos_interface),
mat_1_material(mat_1_material), mat_2_material(mat_2_material) {
Mesh & mesh = model.getMesh();
UInt spatial_dimension = mesh.getSpatialDimension();
/// store barycenters of all elements
barycenters.initialize(mesh, _spatial_dimension = spatial_dimension,
_nb_component = spatial_dimension,
_with_nb_element = true);
for_each_element(mesh, [&](auto && el) {
Vector<Real> bary(barycenters.get(el));
mesh.getBarycenter(el, bary);
});
}
void setMaterials() {
mat_ids[0] = model.getMaterialIndex(mat_1_material);
mat_ids[1] = model.getMaterialIndex(mat_2_material);
}
UInt operator()(const Element & elem) override {
if (not materials_set) {
setMaterials();
}
const Vector<Real> bary = barycenters.get(elem);
/// check for a given element on which side of the material interface plane
/// the bary center lies and assign corresponding material
if (bary(horizontal) < pos_interface) {
return mat_ids[0];
}
return mat_ids[1];
}
bool isConditonVerified() {
/// check if material has been (re)-assigned correctly
auto & mesh = model.getMesh();
auto spatial_dimension = mesh.getSpatialDimension();
for (const auto & type : mesh.elementTypes(spatial_dimension)) {
auto & mat_indexes = model.getMaterialByElement(type);
for (auto && data :
enumerate(make_view(barycenters(type), spatial_dimension))) {
auto elem = std::get<0>(data);
auto & bary = std::get<1>(data);
/// compare element_index_by material to material index that should be
/// assigned due to the geometry of the interface
UInt mat_index;
if (bary(horizontal) < pos_interface) {
mat_index = mat_ids[0];
} else {
mat_index = mat_ids[1];
}
if (mat_indexes(elem) != mat_index) {
/// wrong material index, make test fail
return false;
}
}
}
return true;
}
void moveInterface(Real & pos_new, UInt horizontal_new) {
/// update position and orientation of material interface plane
pos_interface = pos_new;
horizontal = horizontal_new;
model.reassignMaterial();
}
protected:
SolidMechanicsModel & model;
ElementTypeMapArray<Real> barycenters;
std::array<UInt, 2> mat_ids;
UInt horizontal;
Real pos_interface;
bool materials_set{false};
std::string mat_1_material;
std::string mat_2_material;
};
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
bool test_passed;
debug::setDebugLevel(dblWarning);
initialize("two_materials.dat", argc, argv);
/// specify position and orientation of material interface plane
Real pos_interface = 0.;
UInt spatial_dimension = 3;
const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("cube_two_materials.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// assign the two different materials using the
/// StraightInterfaceMaterialSelector
auto && mat_selector = std::make_shared<StraightInterfaceMaterialSelector>(
model, _x, pos_interface, "mat_1", "mat_2");
model.setMaterialSelector(mat_selector);
model.initFull(_analysis_method = _static);
MeshUtils::buildFacets(mesh);
/// check if different materials have been assigned correctly
test_passed = mat_selector->isConditonVerified();
if (not test_passed) {
AKANTU_ERROR("materials not correctly assigned");
return EXIT_FAILURE;
}
model.addDumpField("material_index");
/// change orientation of material interface plane
model.dump();
mat_selector->moveInterface(pos_interface, _y);
model.dump();
/// test if material has been reassigned correctly
test_passed = mat_selector->isConditonVerified();
if (not test_passed) {
AKANTU_ERROR("materials not correctly reassigned");
return EXIT_FAILURE;
}
finalize();
if (prank == 0)
std::cout << "OK: test passed!" << std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
diff --git a/test/test_model/test_structural_mechanics_model/CMakeLists.txt b/test/test_model/test_structural_mechanics_model/CMakeLists.txt
index 81dff85c7..6dd0090b5 100644
--- a/test/test_model/test_structural_mechanics_model/CMakeLists.txt
+++ b/test/test_model/test_structural_mechanics_model/CMakeLists.txt
@@ -1,72 +1,74 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Feb 09 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Mon Mar 15 2021
#
# @brief Structural Mechanics Model Tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
+#
# You should have received a copy of the GNU Lesser General Public License along
# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
# Adding sources
register_gtest_sources(
SOURCES test_structural_mechanics_model_bernoulli_beam_2.cc
PACKAGE implicit structural_mechanics
)
register_gtest_sources(
SOURCES test_structural_mechanics_model_bernoulli_beam_3.cc
PACKAGE implicit structural_mechanics
)
register_gtest_sources(
SOURCES test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
PACKAGE implicit structural_mechanics
)
register_gtest_sources(
SOURCES test_structural_mechanics_model_bernoulli_beam_dynamics.cc
PACKAGE implicit structural_mechanics
)
#===============================================================================
# Adding meshes for element types
package_get_element_types(structural_mechanics _types)
foreach(_type ${_types})
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${_type}.msh)
list(APPEND _meshes ${_type}.msh)
#register_fem_test(fe_engine_precomputation ${_type })
else()
if(NOT ${_type} STREQUAL _point_1)
message("The mesh ${_type}.msh is missing, the fe_engine test cannot be activated without it")
endif()
endif()
endforeach()
#===============================================================================
# Registering google test
register_gtest_test(test_structural_mechanics
FILES_TO_COPY ${_meshes}
)
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_2.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_2.cc
index 65c9f4dd6..00b3acd6f 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_2.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_2.cc
@@ -1,112 +1,115 @@
/**
* @file test_structural_mechanics_model_bernoulli_beam_2.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Fri Feb 09 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Feb 25 2021
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
using namespace akantu;
/* -------------------------------------------------------------------------- */
class TestStructBernoulli2
: public TestStructuralFixture<element_type_t<_bernoulli_beam_2>> {
using parent = TestStructuralFixture<element_type_t<_bernoulli_beam_2>>;
public:
void addMaterials() override {
mat.E = 3e10;
mat.I = 0.0025;
mat.A = 0.01;
this->model->addMaterial(mat);
mat.E = 3e10;
mat.I = 0.00128;
mat.A = 0.01;
this->model->addMaterial(mat);
}
void assignMaterials() override {
auto & materials = this->model->getElementMaterial(parent::type);
materials(0) = 0;
materials(1) = 1;
}
void setDirichletBCs() override {
auto boundary = this->model->getBlockedDOFs().begin(parent::ndof);
// clang-format off
*boundary = {true, true, true}; ++boundary;
*boundary = {false, true, false}; ++boundary;
*boundary = {false, true, false}; ++boundary;
// clang-format on
}
void setNeumannBCs() override {
Real M = 3600; // Nm
Real q = 6000; // kN/m
Real L = 10; // m
auto & forces = this->model->getExternalForce();
forces(2, 2) = -M; // moment on last node
#if 1 // as long as integration is not available
forces(0, 1) = -q * L / 2;
forces(0, 2) = -q * L * L / 12;
forces(1, 1) = -q * L / 2;
forces(1, 2) = q * L * L / 12;
#else
auto & group = mesh.createElementGroup("lin_force");
group.add({type, 0, _not_ghost});
Vector<Real> lin_force = {0, q, 0};
// a linear force is not actually a *boundary* condition
// it is equivalent to a volume force
model.applyBC(BC::Neumann::FromSameDim(lin_force), group);
#endif
forces(2, 0) = mat.E * mat.A / 18;
}
protected:
StructuralMaterial mat;
};
/* -------------------------------------------------------------------------- */
TEST_F(TestStructBernoulli2, TestDisplacements) {
model->solveStep();
auto d1 = model->getDisplacement()(1, 2);
auto d2 = model->getDisplacement()(2, 2);
auto d3 = model->getDisplacement()(1, 0);
Real tol = Math::getTolerance();
EXPECT_NEAR(d1, 5.6 / 4800, tol); // first rotation
EXPECT_NEAR(d2, -3.7 / 4800, tol); // second rotation
EXPECT_NEAR(d3, 10. / 18, tol); // axial deformation
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
index 4b334e128..1a0e4040b 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_3.cc
@@ -1,99 +1,101 @@
/**
* @file test_structural_mechanics_model_bernoulli_beam_3.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Fri Feb 09 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Feb 25 2021
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class TestStructBernoulli3Static
: public TestStructuralFixture<element_type_t<_bernoulli_beam_3>> {
using parent = TestStructuralFixture<element_type_t<_bernoulli_beam_3>>;
public:
void readMesh(std::string filename) override {
parent::readMesh(filename);
}
void setNormals() override {
auto &normals = this->mesh->getData<Real>("extra_normal", parent::type);
normals(0, _z) = 1;
normals(1, _z) = 1;
}
void addMaterials() override {
StructuralMaterial mat;
mat.E = 1;
mat.Iz = 1;
mat.Iy = 1;
mat.A = 1;
mat.GJ = 1;
this->model->addMaterial(mat);
}
void setDirichletBCs() override {
// Boundary conditions (blocking all DOFs of nodes 2 & 3)
auto boundary = ++this->model->getBlockedDOFs().begin(parent::ndof);
// clang-format off
*boundary = {true, true, true, true, true, true}; ++boundary;
*boundary = {true, true, true, true, true, true}; ++boundary;
// clang-format on
}
void setNeumannBCs() override {
// Forces
Real P = 1; // N
auto & forces = this->model->getExternalForce();
forces.zero();
forces(0, 2) = -P; // vertical force on first node
}
void assignMaterials() override {
model->getElementMaterial(parent::type).set(0);
}
};
/* -------------------------------------------------------------------------- */
TEST_F(TestStructBernoulli3Static, TestDisplacements) {
model->solveStep();
auto vz = model->getDisplacement()(0, 2);
auto thy = model->getDisplacement()(0, 4);
auto thx = model->getDisplacement()(0, 3);
auto thz = model->getDisplacement()(0, 5);
Real tol = Math::getTolerance();
EXPECT_NEAR(vz, -5. / 48, tol);
EXPECT_NEAR(thy, -std::sqrt(2) / 8, tol);
EXPECT_NEAR(thz, 0, tol);
EXPECT_NEAR(thx, 0, tol);
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
index 13ed7b1f3..3388a6f98 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_bernoulli_beam_dynamics.cc
@@ -1,367 +1,370 @@
/**
* @file test_structural_mechanics_model_bernoulli_beam_dynamics.cc
*
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Jul 07 2014
- * @date last modification: Wed Feb 03 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Mon Mar 15 2021
*
* @brief Test for _bernouilli_beam in dynamic
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "mesh_accessor.hh"
#include "non_linear_solver_newton_raphson.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <iostream>
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
static Real analytical_solution(Real time, Real L, Real rho, Real E,
__attribute__((unused)) Real A, Real I,
Real F) {
Real omega = M_PI * M_PI / L / L * sqrt(E * I / rho);
Real sum = 0.;
UInt i = 5;
for (UInt n = 1; n <= i; n += 2) {
sum += (1. - cos(n * n * omega * time)) / pow(n, 4);
}
return 2. * F * pow(L, 3) / pow(M_PI, 4) / E / I * sum;
}
template <class Type>
class TestStructBernoulliDynamic : public TestStructuralFixture<Type> {
using parent = TestStructuralFixture<Type>;
public:
const UInt nb_element{40};
const Real L{2};
const Real le{L / nb_element};
const UInt nb_nodes{nb_element + 1};
const Real F{1e4};
StructuralMaterial mat;
void readMesh(std::string /*filename*/) override {
MeshAccessor mesh_accessor(*this->mesh);
auto & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
nodes.set(0.);
for (auto && data : enumerate(make_view(nodes, this->spatial_dimension))) {
auto & node = std::get<1>(data);
UInt i = std::get<0>(data);
node[_x] = i * le;
}
this->mesh->addConnectivityType(parent::type);
auto & connectivities = mesh_accessor.getConnectivity(parent::type);
connectivities.resize(nb_element);
for (auto && data : enumerate(make_view(connectivities, 2))) {
UInt i = std::get<0>(data);
auto & connectivity = std::get<1>(data);
connectivity = {i, i + 1};
}
mesh_accessor.makeReady();
}
void setNormals() override {
if (this->spatial_dimension != 3) {
return;
}
auto & normals =
this->mesh->template getData<Real>("extra_normal", parent::type);
normals.resize(nb_element);
for (auto && normal : make_view(normals, this->spatial_dimension)) {
normal = {0., 0., 1.};
}
}
AnalysisMethod getAnalysisMethod() const override {
return _implicit_dynamic;
}
void addMaterials() override {
this->mat.E = 1e9;
this->mat.rho = 10;
this->mat.I = 1;
this->mat.Iz = 1;
this->mat.Iy = 1;
this->mat.A = 1;
this->mat.GJ = 1;
this->model->addMaterial(mat);
}
void setDirichletBCs() override {
auto & boundary = this->model->getBlockedDOFs();
boundary.set(false);
boundary(0, _x) = true;
boundary(0, _y) = true;
boundary(nb_nodes - 1, _y) = true;
if (this->spatial_dimension == 3) {
boundary(0, _z) = true;
boundary(nb_nodes - 1, _z) = true;
}
}
void setNeumannBCs() override {
auto node_to_print = nb_nodes / 2;
// Forces
auto & forces = this->model->getExternalForce();
forces.zero();
forces(node_to_print, _y) = F;
}
void assignMaterials() override {
this->model->getElementMaterial(parent::type).set(0);
}
};
using beam_types = gtest_list_t<std::tuple<element_type_t<_bernoulli_beam_2>,
element_type_t<_bernoulli_beam_3>>>;
TYPED_TEST_SUITE(TestStructBernoulliDynamic, beam_types, );
template <class Type>
void getElementMassMatrix(const StructuralMaterial & /*material*/, Real /*l*/,
Matrix<Real> & /*M*/) {}
template <class Type>
void getElementStifnessMatrix(const StructuralMaterial & /*material*/,
Real /*l*/, Matrix<Real> & /*M*/) {}
template <>
void getElementMassMatrix<element_type_t<_bernoulli_beam_2>>(
const StructuralMaterial & material, Real l, Matrix<Real> & M) {
auto A = material.A;
auto rho = material.rho;
// clang-format off
M = rho * A * l / 420. * Matrix<Real>({
{140, 0, 0, 70, 0, 0},
{ 0, 156, 22*l, 0, 54, -13*l},
{ 0, 22*l, 4*l*l, 0, 13*l, -3*l*l},
{ 70, 0, 0, 140, 0, 0},
{ 0, 54, 13*l, 0, 156, -22*l},
{ 0,-13*l, -3*l*l, 0, -22*l, 4*l*l}});
// clang-format on
}
template <>
void getElementStifnessMatrix<element_type_t<_bernoulli_beam_2>>(
const StructuralMaterial & material, Real l, Matrix<Real> & K) {
auto E = material.E;
auto A = material.A;
auto I = material.I;
auto l_2 = l * l;
auto l_3 = l * l * l;
// clang-format off
K = Matrix<Real>({
{ E*A/l, 0, 0, -E*A/l, 0, 0},
{ 0, 12*E*I/l_3, 6*E*I/l_2, 0, -12*E*I/l_3, 6*E*I/l_2},
{ 0, 6*E*I/l_2, 4*E*I/l, 0, -6*E*I/l_2, 2*E*I/l},
{-E*A/l, 0, 0, E*A/l, 0, 0},
{ 0, -12*E*I/l_3, -6*E*I/l_2, 0, 12*E*I/l_3, -6*E*I/l_2},
{ 0, 6*E*I/l_2, 2*E*I/l, 0, -6*E*I/l_2, 4*E*I/l}});
// clang-format on
}
template <>
void getElementMassMatrix<element_type_t<_bernoulli_beam_3>>(
const StructuralMaterial & material, Real l, Matrix<Real> & M) {
auto A = material.A;
auto rho = material.rho;
// clang-format off
M = rho * A * l / 420. * Matrix<Real>({
{140, 0, 0, 0, 0, 0, 70, 0, 0, 0, 0, 0},
{ 0, 156, 0, 0, 0, 22*l, 0, 54, 0, 0, 0, -13*l},
{ 0, 0, 156, 0, -22*l, 0, 0, 0, 54, 0, 13*l, 0},
{ 0, 0, 0, 140, 0, 0, 0, 0, 0, 70, 0, 0},
{ 0, 0, -22*l, 0, 4*l*l, 0, 0, 0, -13*l, 0, -3*l*l, 0},
{ 0, 22*l, 0, 0, 0, 4*l*l, 0, 13*l, 0, 0, 0, -3*l*l},
{ 70, 0, 0, 0, 0, 0, 140, 0, 0, 0, 0, 0},
{ 0, 54, 0, 0, 0, 13*l, 0, 156, 0, 0, 0, -22*l},
{ 0, 0, 54, 0, -13*l, 0, 0, 0, 156, 0, 22*l, 0},
{ 0, 0, 0, 70, 0, 0, 0, 0, 0, 140, 0, 0},
{ 0, 0, 13*l, 0, -3*l*l, 0, 0, 0, 22*l, 0, 4*l*l, 0},
{ 0, -13*l, 0, 0, 0, -3*l*l, 0, -22*l, 0, 0, 0, 4*l*l}});
// clang-format on
}
template <>
void getElementStifnessMatrix<element_type_t<_bernoulli_beam_3>>(
const StructuralMaterial & material, Real l, Matrix<Real> & K) {
auto E = material.E;
auto A = material.A;
auto Iy = material.Iy;
auto Iz = material.Iz;
auto GJ = material.GJ;
auto a1 = E * A / l;
auto b1 = 12 * E * Iz / l / l / l;
auto b2 = 6 * E * Iz / l / l;
auto b3 = 4 * E * Iz / l;
auto b4 = 2 * E * Iz / l;
auto c1 = 12 * E * Iy / l / l / l;
auto c2 = 6 * E * Iy / l / l;
auto c3 = 4 * E * Iy / l;
auto c4 = 2 * E * Iy / l;
auto d1 = GJ / l;
// clang-format off
K = Matrix<Real>({
{ a1, 0, 0, 0, 0, 0, -a1, 0, 0, 0, 0, 0},
{ 0, b1, 0, 0, 0, b2, 0, -b1, 0, 0, 0, b2},
{ 0, 0, c1, 0, -c2, 0, 0, 0, -c1, 0, -c2, 0},
{ 0, 0, 0, d1, 0, 0, 0, 0, 0, -d1, 0, 0},
{ 0, 0, -c2, 0, c3, 0, 0, 0, c2, 0, c4, 0},
{ 0, b2, 0, 0, 0, b3, 0, -b2, 0, 0, 0, b4},
{ -a1, 0, 0, 0, 0, 0, a1, 0, 0, 0, 0, 0},
{ 0, -b1, 0, 0, 0, -b2, 0, b1, 0, 0, 0, -b2},
{ 0, 0, -c1, 0, c2, 0, 0, 0, c1, 0, c2, 0},
{ 0, 0, 0, -d1, 0, 0, 0, 0, 0, d1, 0, 0},
{ 0, 0, -c2, 0, c4, 0, 0, 0, c2, 0, c3, 0},
{ 0, b2, 0, 0, 0, b4, 0, -b2, 0, 0, 0, b3}});
// clang-format on
}
TYPED_TEST(TestStructBernoulliDynamic, TestBeamMatrices) {
this->model->assembleMatrix("M");
this->model->assembleMatrix("K");
const auto & K = this->model->getDOFManager().getMatrix("K");
const auto & M = this->model->getDOFManager().getMatrix("M");
Matrix<Real> Ka(this->nb_nodes * this->ndof, this->nb_nodes * this->ndof, 0.);
Matrix<Real> Ma(this->nb_nodes * this->ndof, this->nb_nodes * this->ndof, 0.);
Matrix<Real> Ke(this->ndof * 2, this->ndof * 2);
Matrix<Real> Me(this->ndof * 2, this->ndof * 2);
getElementMassMatrix<TypeParam>(this->mat, this->le, Me);
getElementStifnessMatrix<TypeParam>(this->mat, this->le, Ke);
auto assemble = [&](auto && nodes, auto && M, auto && Me) {
auto n1 = nodes[0];
auto n2 = nodes[1];
for (auto i : arange(this->ndof)) {
for (auto j : arange(this->ndof)) {
M(n1 * this->ndof + i, n1 * this->ndof + j) += Me(i, j);
M(n2 * this->ndof + i, n2 * this->ndof + j) +=
Me(this->ndof + i, this->ndof + j);
M(n1 * this->ndof + i, n2 * this->ndof + j) += Me(i, this->ndof + j);
M(n2 * this->ndof + i, n1 * this->ndof + j) += Me(this->ndof + i, j);
}
}
};
auto && connectivities = this->mesh->getConnectivity(this->type);
for (auto && connectivity : make_view(connectivities, 2)) {
assemble(connectivity, Ka, Ke);
assemble(connectivity, Ma, Me);
}
auto tol = 1e-13;
auto Ka_max = Ka.template norm<L_inf>();
auto Ma_max = Ma.template norm<L_inf>();
for (auto i : arange(Ka.rows())) {
for (auto j : arange(Ka.cols())) {
EXPECT_NEAR(Ka(i, j), K(i, j), tol * Ka_max);
EXPECT_NEAR(Ma(i, j), M(i, j), tol * Ma_max);
}
}
}
TYPED_TEST(TestStructBernoulliDynamic, TestBeamOscilation) {
Real time_step = 1e-6;
this->model->setTimeStep(time_step);
auto & solver = this->model->getNonLinearSolver();
solver.set("max_iterations", 100);
solver.set("threshold", 1e-8);
solver.set("convergence_type", SolveConvergenceCriteria::_solution);
auto node_to_print = this->nb_nodes / 2;
auto & d = this->model->getDisplacement()(node_to_print, _y);
std::ofstream pos;
std::string filename = "position" + std::to_string(this->type) + ".csv";
pos.open(filename);
if (not pos.good()) {
AKANTU_ERROR("Cannot open file \"position.csv\"");
}
pos << "id,time,position,solution" << std::endl;
//#define debug
#ifdef debug
this->model->addDumpFieldVector("displacement");
this->model->addDumpField("blocked_dofs");
this->model->addDumpFieldVector("external_force");
this->model->addDumpFieldVector("internal_force");
this->model->addDumpFieldVector("acceleration");
this->model->addDumpFieldVector("velocity");
this->model->dump();
#endif
this->model->getDisplacement().set(0.);
Real tol = 1e-6;
Real time = 0.;
for (UInt s = 1; s < 300; ++s) {
EXPECT_NO_THROW(this->model->solveStep());
time = s * time_step;
auto da = analytical_solution(time, this->L, this->mat.rho, this->mat.E,
this->mat.A, this->mat.Iy, this->F);
pos << s << "," << time << "," << d << "," << da << std::endl;
#ifdef debug
this->model->dump();
#endif
EXPECT_NEAR(d, da, tol);
}
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
index adbf05c80..62124a4ef 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
@@ -1,111 +1,113 @@
/**
* @file test_structural_mechanics_model_discrete_kirchhoff_triangle_18.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
- * @date creation: Fri Jul 15 2011
- * @date last modification: Wed Feb 21 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Thu Feb 25 2021
*
* @brief Computation of the analytical exemple 1.1 in the TGC vol 6
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
#include "test_structural_mechanics_model_fixture.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
using namespace akantu;
/* -------------------------------------------------------------------------- */
class TestStructDKT18 : public TestStructuralFixture<
element_type_t<_discrete_kirchhoff_triangle_18>> {
using parent =
TestStructuralFixture<element_type_t<_discrete_kirchhoff_triangle_18>>;
public:
void addMaterials() override {
mat.E = 1;
mat.t = 1;
mat.nu = 0.3;
this->model->addMaterial(mat);
}
void assignMaterials() override {
auto & materials = this->model->getElementMaterial(parent::type);
std::fill(materials.begin(), materials.end(), 0);
}
void setDirichletBCs() override {
this->model->getBlockedDOFs().set(true);
auto center_node = this->model->getBlockedDOFs().end(parent::ndof) - 1;
*center_node = {false, false, false, false, false, true};
this->model->getDisplacement().zero();
auto disp = ++this->model->getDisplacement().begin(parent::ndof);
// Displacement field from Batoz Vol. 2 p. 392
// with theta to beta correction from discrete Kirchhoff condition
// see also the master thesis of Michael Lozano
// clang-format off
// This displacement field tests membrane and bending modes
*disp = {40, 20, -800 , -20, 40, 0}; ++disp;
*disp = {50, 40, -1400, -40, 50, 0}; ++disp;
*disp = {10, 20, -200 , -20, 10, 0}; ++disp;
// This displacement tests the bending mode
// *disp = {0, 0, -800 , -20, 40, 0}; ++disp;
// *disp = {0, 0, -1400, -40, 50, 0}; ++disp;
// *disp = {0, 0, -200 , -20, 10, 0}; ++disp;
// This displacement tests the membrane mode
// *disp = {40, 20, 0, 0, 0, 0}; ++disp;
// *disp = {50, 40, 0, 0, 0, 0}; ++disp;
// *disp = {10, 20, 0, 0, 0, 0}; ++disp;
// clang-format on
}
void setNeumannBCs() override {}
protected:
StructuralMaterial mat;
};
/* -------------------------------------------------------------------------- */
// Batoz Vol 2. patch test, ISBN 2-86601-259-3
TEST_F(TestStructDKT18, TestDisplacements) {
model->solveStep();
Vector<Real> solution = {22.5, 22.5, -337.5, -22.5, 22.5, 0};
auto nb_nodes = this->model->getDisplacement().size();
Vector<Real> center_node_disp =
model->getDisplacement().begin(solution.size())[nb_nodes - 1];
auto error = solution - center_node_disp;
EXPECT_NEAR(error.norm<L_2>(), 0., 1e-12);
}
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
index 14b48d567..427bce303 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_fixture.hh
@@ -1,115 +1,118 @@
/**
* @file test_structural_mechanics_model_fixture.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Nov 14 2017
- * @date last modification: Fri Feb 09 2018
+ * @date last modification: Thu Feb 25 2021
*
* @brief Main test for structural model
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class_structural.hh"
#include "structural_mechanics_model.hh"
#include "test_gtest_utils.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_
#define AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_
using namespace akantu;
template <typename type_> class TestStructuralFixture : public ::testing::Test {
public:
static constexpr const ElementType type = type_::value;
static constexpr const size_t spatial_dimension =
ElementClass<type>::getSpatialDimension();
static const UInt ndof = ElementClass<type>::getNbDegreeOfFreedom();
void SetUp() override {
const auto spatial_dimension = this->spatial_dimension;
mesh = std::make_unique<Mesh>(spatial_dimension);
readMesh(makeMeshName());
std::stringstream element_type;
element_type << this->type;
model = std::make_unique<StructuralMechanicsModel>(*mesh, _all_dimensions,
element_type.str());
setNormals();
initModel();
}
virtual void initModel() {
this->addMaterials();
auto method = getAnalysisMethod();
this->model->initFull(_analysis_method = method);
this->assignMaterials();
this->setDirichletBCs();
this->setNeumannBCs();
}
virtual AnalysisMethod getAnalysisMethod() const { return _static; }
virtual void readMesh(std::string filename) {
mesh->read(filename, _miot_gmsh_struct);
}
virtual std::string makeMeshName() {
std::stringstream element_type;
element_type << type;
SCOPED_TRACE(element_type.str().c_str());
return element_type.str() + ".msh";
}
void TearDown() override {
model.reset(nullptr);
mesh.reset(nullptr);
}
virtual void addMaterials() = 0;
virtual void assignMaterials() = 0;
virtual void setDirichletBCs() = 0;
virtual void setNeumannBCs() = 0;
virtual void setNormals() {}
protected:
std::unique_ptr<Mesh> mesh;
std::unique_ptr<StructuralMechanicsModel> model;
};
template <typename type_>
constexpr ElementType TestStructuralFixture<type_>::type;
template <typename type_>
constexpr size_t TestStructuralFixture<type_>::spatial_dimension;
template <typename type_> const UInt TestStructuralFixture<type_>::ndof;
using structural_types = gtest_list_t<StructuralTestElementTypes>;
#endif /* AKANTU_TEST_STRUCTURAL_MECHANICS_MODEL_FIXTURE_HH_ */
diff --git a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc
index 163faf40e..7cb3a5ae2 100644
--- a/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc
+++ b/test/test_model/test_structural_mechanics_model/test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc
@@ -1,248 +1,250 @@
/**
* @file test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc
*
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
- * @date creation: Thu Feb 21 2013
- * @date last modification: Wed Nov 22 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 22 2017
*
* @brief patch test exemple 4.5.5 c.f. modelisation des structures par
* éléments finis J.-L. Batoz/G Dhatt
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
#include <limits>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#define TYPE _discrete_kirchhoff_triangle_18
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
Mesh shell(3);
debug::setDebugLevel(dblWarning);
std::cout << "Initialisation" << std::endl;
/* --------------------------------------------------------------------------
*/
// Defining the mesh
UInt nb_nodes = 5;
UInt nb_element = 4;
Array<Real> & nodes = const_cast<Array<Real> &>(shell.getNodes());
nodes.resize(nb_nodes);
Real a = 20.;
Real b = 10.;
nodes(0, 0) = 0.;
nodes(0, 1) = 0.;
nodes(0, 2) = 0.;
nodes(1, 0) = 2 * a;
nodes(1, 1) = 0.;
nodes(1, 2) = 0.;
nodes(2, 0) = 0.;
nodes(2, 1) = 2 * b;
nodes(2, 2) = 0.;
nodes(3, 0) = 2 * a;
nodes(3, 1) = 2 * b;
nodes(3, 2) = 0.;
nodes(4, 0) = 15.;
nodes(4, 1) = 15.;
nodes(4, 2) = 0.;
shell.addConnectivityType(TYPE);
Array<UInt> & connectivity =
const_cast<Array<UInt> &>(shell.getConnectivity(TYPE));
connectivity.resize(nb_element);
connectivity(0, 0) = 1;
connectivity(0, 1) = 3;
connectivity(0, 2) = 4;
connectivity(1, 0) = 3;
connectivity(1, 1) = 2;
connectivity(1, 2) = 4;
connectivity(2, 0) = 2;
connectivity(2, 1) = 4;
connectivity(2, 2) = 0;
connectivity(3, 0) = 0;
connectivity(3, 1) = 1;
connectivity(3, 2) = 4;
akantu::MeshIOMSH mesh_io;
mesh_io.write("b_beam_3_12_10_13.msh", shell);
std::cout << "Mesh definition" << std::endl;
/* --------------------------------------------------------------------------
*/
// Defining the materials
akantu::StructuralMechanicsModel model(shell); // ä döfinir
StructuralMaterial mat1;
mat1.E = 1000;
mat1.nu = 0.3;
mat1.t = 1;
model.addMaterial(mat1);
std::cout << "Material Definition" << std::endl;
/* --------------------------------------------------------------------------
*/
// Defining the deplacement
model.initFull();
// Array<Real> & forces = model.getForce();
Array<Real> & displacement = model.getDisplacement();
Array<bool> & boundary = model.getBlockedDOFs();
displacement(0, 0) = 0;
displacement(0, 1) = 0;
displacement(0, 2) = 0;
displacement(0, 3) = 0;
displacement(0, 4) = 0;
displacement(1, 0) = 0;
displacement(1, 1) = 0;
displacement(1, 2) = -800;
displacement(1, 3) = -40;
displacement(1, 4) = -20;
displacement(2, 0) = 0;
displacement(2, 1) = 0;
displacement(2, 2) = -200;
displacement(2, 3) = -10;
displacement(2, 4) = -20;
displacement(3, 0) = 0;
displacement(3, 1) = 0;
displacement(3, 2) = -1400;
displacement(3, 3) = -50;
displacement(3, 4) = -40;
/*displacement(4,0)=0;
displacement(4,1)=0;*/
/* displacement(4,2)=;
displacement(4,3)=;
displacement(4,4)=;*/
/* --------------------------------------------------------------------------
*/
// Defining the boundary conditions
boundary(0, 0) = true;
boundary(0, 1) = true;
boundary(0, 2) = true;
boundary(0, 3) = true;
boundary(0, 4) = true;
boundary(0, 5) = true;
boundary(1, 0) = true;
boundary(1, 1) = true;
boundary(1, 2) = true;
boundary(1, 3) = true;
boundary(1, 4) = true;
boundary(1, 5) = true;
boundary(2, 0) = true;
boundary(2, 1) = true;
boundary(2, 2) = true;
boundary(2, 3) = true;
boundary(2, 4) = true;
boundary(2, 5) = true;
boundary(3, 0) = true;
boundary(3, 1) = true;
boundary(3, 2) = true;
boundary(3, 3) = true;
boundary(3, 4) = true;
boundary(3, 5) = true;
// boundary(4,0) = true;
// boundary(4,1) = true;
// boundary(4,2) = true;
// boundary(4,3) = true;
// boundary(4,4) = true;
boundary(4, 5) = true;
std::cout << "BC Definition" << std::endl;
/* --------------------------------------------------------------------------
*/
// Solve
Real error;
model.assembleStiffnessMatrix();
std::cout << "Assemble Done" << std::endl;
model.getStiffnessMatrix().saveMatrix("K_4_5_5.mtx");
UInt count = 0;
std::cout << "Matrix saved" << std::endl;
model.addDumpField("displacement");
model.addDumpField("rotation");
model.addDumpField("force");
model.addDumpField("momentum");
do {
model.updateResidual();
model.solve();
count++;
} while (!model.testConvergenceIncrement(1e-10, error) && count < 10);
/* --------------------------------------------------------------------------
*/
// Post-Processing
model.computeStresses();
// const SparseMatrix = model.getStiffnessMatrix();
std::cout << "u = " << displacement(4, 0) << std::endl;
std::cout << "v = " << displacement(4, 1) << std::endl;
std::cout << "w5 = " << displacement(4, 2) << std::endl;
std::cout << "betax = " << displacement(4, 3) << std::endl;
std::cout << "betay = " << displacement(4, 4) << std::endl;
std::cout << "betaz = " << displacement(4, 5) << std::endl;
// model.dump();
}
diff --git a/test/test_python_interface/CMakeLists.txt b/test/test_python_interface/CMakeLists.txt
index 0e3c16319..92b7680e5 100644
--- a/test/test_python_interface/CMakeLists.txt
+++ b/test/test_python_interface/CMakeLists.txt
@@ -1,41 +1,43 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
# @author Lucas Frerot <lucas.frerot@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Mon Feb 05 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Tue Jun 30 2020
#
# @brief Python Interface tests
#
+#
# @section LICENSE
#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
-#
+#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
+
akantu_pybind11_add_module(py11_akantu_test_common MODULE test_common.cc)
add_mesh(mesh_dcb_2d mesh_dcb_2d.geo 2 2)
register_test(test_python_interface
SCRIPT test_pybind.py
PYTHON
FILES_TO_COPY elastic.dat
DEPENDS mesh_dcb_2d py11_akantu_test_common
PACKAGE python_interface
)
diff --git a/test/test_python_interface/test_common.cc b/test/test_python_interface/test_common.cc
index 8f66670ed..72ab54d28 100644
--- a/test/test_python_interface/test_common.cc
+++ b/test/test_python_interface/test_common.cc
@@ -1,121 +1,153 @@
+/**
+ * @file test_common.cc
+ *
+ * @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
+ *
+ * @date creation: Wed Oct 31 2018
+ * @date last modification: Tue Jun 30 2020
+ *
+ * @brief pybind11 interface for test
+ *
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
+ *
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation, either version 3 of the License, or (at your option) any
+ * later version.
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
/* -------------------------------------------------------------------------- */
#include "py_akantu.hh"
/* -------------------------------------------------------------------------- */
#include <pybind11/pybind11.h>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
namespace py = pybind11;
namespace _aka = akantu;
std::map<long, std::shared_ptr<_aka::Array<_aka::Real>>> arrays;
std::map<long, std::shared_ptr<_aka::Vector<_aka::Real>>> vectors;
std::map<long, std::shared_ptr<_aka::Matrix<_aka::Real>>> matrices;
PYBIND11_MODULE(py11_akantu_test_common, mod) {
mod.doc() = "Akantu Test function for common ";
mod.def("createArray",
[&](_aka::UInt size, _aka::UInt nb_components) {
auto ptr =
std::make_shared<_aka::Array<_aka::Real>>(size, nb_components);
ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
arrays[addr] = ptr;
return std::tuple<long, _aka::Array<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getArray",
[&](long addr) -> _aka::Array<_aka::Real> & {
auto & array = *arrays[addr];
py::print("gotten pointer: " +
std::to_string((long)array.storage()));
return array;
},
py::return_value_policy::reference);
mod.def("copyArray",
[&](long addr) -> _aka::Array<_aka::Real> {
auto & array = *arrays[addr];
py::print("gotten pointer: " +
std::to_string((long)array.storage()));
return array;
},
py::return_value_policy::copy);
mod.def("getRawPointerArray", [](_aka::Array<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
mod.def("createVector",
[&](_aka::UInt size) {
auto ptr = std::make_shared<_aka::Vector<_aka::Real>>(size);
ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
vectors[addr] = ptr;
return std::tuple<long, _aka::Vector<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getVector",
[&](long addr) -> _aka::Vector<_aka::Real> & {
auto & vector = *vectors[addr];
py::print("gotten pointer: " +
std::to_string((long)vector.storage()));
return vector;
},
py::return_value_policy::reference);
mod.def("copyVector",
[&](long addr) -> _aka::Vector<_aka::Real> {
auto & vector = *vectors[addr];
py::print("gotten pointer: " +
std::to_string((long)vector.storage()));
return vector;
},
py::return_value_policy::copy);
mod.def("getRawPointerVector", [](_aka::Vector<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
mod.def("createMatrix",
[&](_aka::UInt size1, _aka::UInt size2) {
auto ptr = std::make_shared<_aka::Matrix<_aka::Real>>(size1, size2);
ptr->zero();
long addr = (long)ptr->storage();
py::print("initial pointer: " + std::to_string(addr));
matrices[addr] = ptr;
return std::tuple<long, _aka::Matrix<_aka::Real> &>(addr, *ptr);
},
py::return_value_policy::reference);
mod.def("getMatrix",
[&](long addr) -> _aka::Matrix<_aka::Real> & {
auto & matrix = *matrices[addr];
py::print("gotten pointer: " +
std::to_string((long)matrix.storage()));
return matrix;
},
py::return_value_policy::reference);
mod.def("copyMatrix",
[&](long addr) -> _aka::Matrix<_aka::Real> {
auto & matrix = *matrices[addr];
py::print("gotten pointer: " +
std::to_string((long)matrix.storage()));
return matrix;
},
py::return_value_policy::copy);
mod.def("getRawPointerMatrix", [](_aka::Matrix<_aka::Real> & _data) {
py::print("received proxy: " + std::to_string((long)&_data));
py::print("raw pointer: " + std::to_string((long)_data.storage()));
return (long)_data.storage();
});
} // Module akantu_test_common
diff --git a/test/test_python_interface/test_pybind.py b/test/test_python_interface/test_pybind.py
index a66291c50..c022c9267 100644
--- a/test/test_python_interface/test_pybind.py
+++ b/test/test_python_interface/test_pybind.py
@@ -1,195 +1,208 @@
#!/bin/env python
+
+""" test_pybind.py: Test the pybind interface"""
+
+__author__ = "Guillaume Anciaux and Nicolas Richart"
+__credits__ = [
+ "Guillaume Anciaux <guillaume.anciaux@epfl.ch>",
+ "Nicolas Richart <nicolas.richart@epfl.ch>",
+]
+__copyright__ = "Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale" \
+ " de Lausanne) Laboratory (LSMS - Laboratoire de Simulation" \
+ " en Mécanique des Solides)"
+__license__ = "LGPLv3"
+
import pytest
import numpy as np
import akantu as aka
import py11_akantu_test_common as aka_test
def test_array_size():
ptr, array = aka_test.createArray(1000, 3)
assert array.shape == (1000, 3)
def test_array_nocopy():
ptr, array = aka_test.createArray(1000, 3)
through_python = aka_test.getRawPointerArray(array)
assert(ptr == through_python)
def test_modify_array():
ptr, array = aka_test.createArray(3, 3)
array[0, :] = (1., 2., 3.)
array2 = aka_test.getArray(ptr)
assert(np.linalg.norm(array-array2) < 1e-15)
for i in [1, 2, 3]:
ptr, array = aka_test.createArray(10000, i)
array[:, :] = np.random.random((10000, i))
array2 = aka_test.getArray(ptr)
assert(np.linalg.norm(array-array2) < 1e-15)
def test_array_copy():
ptr, array = aka_test.createArray(1000, 3)
array2 = aka_test.copyArray(ptr)
ptr2 = aka_test.getRawPointerArray(array2)
assert(ptr != ptr2)
def test_vector_size():
ptr, vector = aka_test.createVector(3)
assert vector.shape == (3,)
def test_vector_nocopy():
ptr, vector = aka_test.createVector(3)
through_python = aka_test.getRawPointerVector(vector)
assert(ptr == through_python)
def test_modify_vector():
ptr, vector = aka_test.createVector(3)
vector[:] = (1., 2., 3.)
vector2 = aka_test.getVector(ptr)
assert(np.linalg.norm(vector-vector2) < 1e-15)
for i in np.arange(1, 10):
ptr, vector = aka_test.createVector(i)
vector[:] = np.random.random(i)
vector2 = aka_test.getVector(ptr)
assert(np.linalg.norm(vector-vector2) < 1e-15)
def test_vector_copy():
ptr, vector = aka_test.createVector(1000)
vector2 = aka_test.copyVector(ptr)
ptr2 = aka_test.getRawPointerVector(vector2)
assert(ptr != ptr2)
def test_matrix_size():
ptr, matrix = aka_test.createMatrix(3, 2)
assert matrix.shape == (3, 2)
def test_matrix_nocopy():
ptr, matrix = aka_test.createMatrix(3, 2)
through_python = aka_test.getRawPointerMatrix(matrix)
assert(ptr == through_python)
def test_modify_matrix():
ptr, matrix = aka_test.createMatrix(2, 3)
matrix[0, :] = (1., 2., 3.)
matrix2 = aka_test.getMatrix(ptr)
assert(np.linalg.norm(matrix-matrix2) < 1e-15)
for i in np.arange(1, 10):
for j in np.arange(1, 10):
ptr, matrix = aka_test.createMatrix(i, j)
matrix[:, :] = np.random.random((i, j))
matrix2 = aka_test.getMatrix(ptr)
assert(np.linalg.norm(matrix-matrix2) < 1e-15)
def test_matrix_copy():
ptr, matrix = aka_test.createMatrix(10, 3)
matrix2 = aka_test.copyMatrix(ptr)
ptr2 = aka_test.getRawPointerMatrix(matrix2)
assert(ptr != ptr2)
def test_multiple_init():
aka.parseInput("elastic.dat")
dcb_mesh = 'mesh_dcb_2d.msh'
mesh = aka.Mesh(2)
mesh.read(dcb_mesh)
model = aka.SolidMechanicsModel(mesh)
model.initFull(aka.SolidMechanicsModelOptions(aka._static))
del model
del mesh
mesh = aka.Mesh(2)
mesh.read(dcb_mesh)
model = aka.SolidMechanicsModel(mesh)
model.initFull(aka.SolidMechanicsModelOptions(aka._static))
del model
del mesh
def test_boundary_condition_functors():
class FixedValue(aka.DirichletFunctor):
def __init__(self, value, axis):
super().__init__(axis)
self.value = value
self.axis = int(axis)
def __call__(self, node, flags, primal, coord):
primal[self.axis] = self.value
flags[self.axis] = True
class FromStress(aka.NeumannFunctor):
def __init__(self, stress):
super().__init__()
self.stress = stress
def __call__(self, quad_point, dual, coord, normals):
dual[:] = np.dot(self.stress, normals)
aka.parseInput("elastic.dat")
mesh = aka.Mesh(2)
mesh.read("mesh_dcb_2d.msh")
model = aka.SolidMechanicsModel(mesh, 2)
model.initFull()
model.applyBC(FixedValue(0.0, aka._x), "edge")
stress = np.array([[1, 0],
[0, 0]])
blocked_nodes = \
mesh.getElementGroup("edge").getNodeGroup().getNodes().flatten()
boundary = model.getBlockedDOFs()
# Testing that nodes are correctly blocked
for n in blocked_nodes:
assert boundary[n, 0]
boundary.fill(False)
model.applyBC(FromStress(stress), "edge")
force = model.getExternalForce()
# Checking that nodes have a force in the correct direction
for n in blocked_nodes:
assert force[n, 0] > 0
return 0
def test_mesh_interface():
mesh = aka.Mesh(2)
mesh.read("mesh_dcb_2d.msh")
# Tests the getNbElement() function
if mesh.getNbElement(aka._quadrangle_8) != mesh.getNbElement(2):
raise Exception("Number of elements wrong: "
" {0} != {1}".format(
mesh.getNbElement(aka._quadrangle_8),
mesh.getNbElement(2)))
def test_heat_transfer():
mesh = aka.Mesh(2)
model = aka.HeatTransferModel(mesh)
print(aka._explicit_lumped_mass)
model.initFull(aka._explicit_lumped_mass)
if __name__ == '__main__':
import sys
pytest.main(sys.argv)
diff --git a/test/test_solver/CMakeLists.txt b/test/test_solver/CMakeLists.txt
index a8f77378e..d756b0267 100644
--- a/test/test_solver/CMakeLists.txt
+++ b/test/test_solver/CMakeLists.txt
@@ -1,88 +1,98 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Tue May 30 2017
+# @date creation: Sun Oct 19 2014
+# @date last modification: Tue Jan 01 2019
#
# @brief configuration for solver tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_solver_mesh triangle.geo 2 1)
add_mesh(test_matrix_mesh square.geo 2 1)
add_mesh(test_solver_petsc_mesh 1D_bar.geo 1 1)
register_test(test_sparse_matrix_profile
SOURCES test_sparse_matrix_profile.cc
DEPENDS test_solver_mesh
PACKAGE implicit
)
register_test(test_sparse_matrix_assemble
SOURCES test_sparse_matrix_assemble.cc
DEPENDS test_solver_mesh
PACKAGE implicit
)
register_test(test_sparse_matrix_product
SOURCES test_sparse_matrix_product.cc
FILES_TO_COPY bar.msh
PACKAGE implicit
)
register_test(test_sparse_solver_mumps
SOURCES test_sparse_solver_mumps.cc
PACKAGE mumps
PARALLEL
)
# register_test(test_petsc_matrix_profile
# SOURCES test_petsc_matrix_profile.cc
# DEPENDS test_matrix_mesh
# PACKAGE petsc
# )
# register_test(test_petsc_matrix_profile_parallel
# SOURCES test_petsc_matrix_profile_parallel.cc
# DEPENDS test_matrix_mesh
# PACKAGE petsc
# )
# register_test(test_petsc_matrix_diagonal
# SOURCES test_petsc_matrix_diagonal.cc
# DEPENDS test_solver_mesh
# PACKAGE petsc
# )
# register_test(test_petsc_matrix_apply_boundary
# SOURCES test_petsc_matrix_apply_boundary.cc
# DEPENDS test_solver_mesh
# PACKAGE petsc
# )
# register_test(test_solver_petsc
# SOURCES test_solver_petsc.cc
# DEPENDS test_solver_petsc_mesh
# PACKAGE petsc
# )
# register_test(test_solver_petsc_parallel
# SOURCES test_solver_petsc.cc
# DEPENDS test_solver_petsc_mesh
# PACKAGE petsc
# )
diff --git a/test/test_solver/test_petsc_matrix_apply_boundary.cc b/test/test_solver/test_petsc_matrix_apply_boundary.cc
index 2ced920f4..b5ce50cf8 100644
--- a/test/test_solver/test_petsc_matrix_apply_boundary.cc
+++ b/test/test_solver/test_petsc_matrix_apply_boundary.cc
@@ -1,148 +1,150 @@
/**
* @file test_petsc_matrix_apply_boundary.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Mon Oct 13 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief test the applyBoundary method of the PETScMatrix class
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "petsc_matrix.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// fill the matrix with
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K(nb_global_nodes * spatial_dimension, _symmetric);
K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K, spatial_dimension, element_type, ghost_type);
// create petsc matrix
PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _symmetric);
petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
// add stiffness matrix to petsc matrix
petsc_matrix.add(K, 1);
// create boundary array: block all dofs
UInt nb_nodes = mesh.getNbNodes();
Array<bool> boundary = Array<bool>(nb_nodes, spatial_dimension, true);
// apply boundary
petsc_matrix.applyBoundary(boundary);
// test if all entries except the diagonal ones have been zeroed
Real test_passed = 0;
for (UInt i = 0; i < nb_nodes * spatial_dimension; ++i) {
if (dof_synchronizer.isLocalOrMasterDOF(i)) {
for (UInt j = 0; j < nb_nodes * spatial_dimension; ++j) {
if (dof_synchronizer.isLocalOrMasterDOF(j)) {
if (i == j)
test_passed += petsc_matrix(i, j) - 1;
else
test_passed += petsc_matrix(i, j) - 0;
}
}
}
}
if (std::abs(test_passed) > Math::getTolerance()) {
finalize();
return EXIT_FAILURE;
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_diagonal.cc b/test/test_solver/test_petsc_matrix_diagonal.cc
index 4b7f8c4d2..f2cd757fb 100644
--- a/test/test_solver/test_petsc_matrix_diagonal.cc
+++ b/test/test_solver/test_petsc_matrix_diagonal.cc
@@ -1,161 +1,163 @@
/**
* @file test_petsc_matrix_diagonal.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Mon Oct 13 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief test the connectivity is correctly represented in the PETScMatrix
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "dumper_paraview.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_partition_scotch.hh"
#include "mesh_utils.hh"
#include "petsc_matrix.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix
// for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type,
ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// check to how many elements each node is connected
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
/// test the diagonal of the PETSc matrix: the diagonal entries
/// of the PETSc matrix correspond to the number of elements
/// connected to the node of the dof. Note: for an Akantu matrix this is only
/// true for the serial case
Real error = 0.;
/// loop over all diagonal values of the matrix
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
UInt dof = i * spatial_dimension + j;
/// for PETSc matrix only DOFs on the processor and be accessed
if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
std::cout << "Number of elements connected: "
<< node_to_elem.getNbCols(i) << std::endl;
std::cout << "K_petsc(" << global_dof << "," << global_dof
<< ")=" << K_petsc(dof, dof) << std::endl;
error += std::abs(K_petsc(dof, dof) - node_to_elem.getNbCols(i));
}
}
}
if (error > Math::getTolerance()) {
std::cout << "error in the stiffness matrix!!!" << std::endl;
finalize();
return EXIT_FAILURE;
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_profile.cc
index a46521e06..fc218c3bb 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_profile.cc
@@ -1,141 +1,144 @@
/**
* @file test_petsc_matrix_profile.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Oct 13 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Jan 01 2019
*
* @brief test the profile generation of the PETScMatrix class
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "sparse_matrix_petsc.hh"
/// #include "dumper_paraview.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("square.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// dump mesh in paraview
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix
// for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type,
ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// save the profile
K_petsc.saveMatrix("profile.txt");
/// print the matrix to screen
std::ifstream profile;
profile.open("profile.txt");
std::string current_line;
while (getline(profile, current_line))
std::cout << current_line << std::endl;
profile.close();
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_profile_parallel.cc b/test/test_solver/test_petsc_matrix_profile_parallel.cc
index bda109fa1..f2a0577f7 100644
--- a/test/test_solver/test_petsc_matrix_profile_parallel.cc
+++ b/test/test_solver/test_petsc_matrix_profile_parallel.cc
@@ -1,142 +1,144 @@
/**
* @file test_petsc_matrix_profile_parallel.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Mon Oct 13 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Jan 01 2019
*
* @brief test the profile generation of the PETScMatrix class in parallel
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "sparse_matrix_petsc.hh"
/// #include "dumper_paraview.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("square.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// dump mesh in paraview
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix
// for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type,
ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// save the profile
K_petsc.saveMatrix("profile_parallel.txt");
/// print the matrix to screen
if (prank == 0) {
std::ifstream profile;
profile.open("profile_parallel.txt");
std::string current_line;
while (getline(profile, current_line))
std::cout << current_line << std::endl;
profile.close();
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_solver_petsc.cc b/test/test_solver/test_solver_petsc.cc
index 60c58207d..4fc6ab5fc 100644
--- a/test/test_solver/test_solver_petsc.cc
+++ b/test/test_solver/test_solver_petsc.cc
@@ -1,171 +1,173 @@
/**
* @file test_solver_petsc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
- * @date creation: Mon Oct 13 2014
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Jan 01 2019
*
* @brief test the PETSc solver interface
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_csr.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "solver_petsc.hh"
#include "sparse_matrix_petsc.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const ElementType element_type = _segment_2;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 1;
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
/// creation mesh
mesh.read("1D_bar.msh");
MeshPartitionScotch * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
FEEngine * fem =
new FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>(
mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// fill the matrix with
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K(nb_global_nodes * spatial_dimension, _symmetric);
K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 0);
for (UInt i = 0; i < nb_dofs_per_element; ++i) {
for (UInt j = 0; j < nb_dofs_per_element; ++j) {
element_input(i, j) = ((i == j) ? 1 : -1);
}
}
Array<Real> K_e =
Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it =
K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end =
K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for (; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K, spatial_dimension, element_type, ghost_type);
// apply boundary: block first node
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> boundary = Array<bool>(nb_nodes, spatial_dimension, false);
for (UInt i = 0; i < nb_nodes; ++i) {
if (std::abs(position(i, 0)) < Math::getTolerance())
boundary(i, 0) = true;
}
K.applyBoundary(boundary);
/// create the PETSc matrix for the solve step
PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _symmetric);
petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// copy the stiffness matrix into the petsc matrix
petsc_matrix.add(K, 1);
// initialize internal forces: they are zero because imposed displacement is
// zero
Array<Real> internal_forces(nb_nodes, spatial_dimension, 0.);
// compute residual: apply nodal force on last node
Array<Real> residual(nb_nodes, spatial_dimension, 0.);
for (UInt i = 0; i < nb_nodes; ++i) {
if (std::abs(position(i, 0) - 10) < Math::getTolerance())
residual(i, 0) += 2;
}
residual -= internal_forces;
/// initialize solver and solution
Array<Real> solution(nb_nodes, spatial_dimension, 0.);
SolverPETSc solver(petsc_matrix);
solver.initialize();
solver.setOperators();
solver.setRHS(residual);
solver.solve(solution);
/// verify solution
Math::setTolerance(1e-11);
for (UInt i = 0; i < nb_nodes; ++i) {
if (!dof_synchronizer.isPureGhostDOF(i) &&
!Math::are_float_equal(2 * position(i, 0), solution(i, 0))) {
std::cout << "The solution is not correct!!!!" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_matrix_assemble.cc b/test/test_solver/test_sparse_matrix_assemble.cc
index b943e26ed..5cd429f3e 100644
--- a/test/test_solver/test_sparse_matrix_assemble.cc
+++ b/test/test_solver/test_sparse_matrix_assemble.cc
@@ -1,84 +1,86 @@
/**
* @file test_sparse_matrix_assemble.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Dec 13 2010
- * @date last modification: Fri May 19 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri May 19 2017
*
* @brief test the assembling method of the SparseMatrix class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "dof_synchronizer.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> test_synchronize(nb_nodes, spatial_dimension, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
auto & A = dof_manager.getNewMatrix("A", _symmetric);
// const akantu::Mesh::ConnectivityTypeList & type_list =
// mesh.getConnectivityTypeList();
// akantu::Mesh::ConnectivityTypeList::const_iterator it;
// for(it = type_list.begin(); it != type_list.end(); ++it) {
// if(mesh.getSpatialDimension(*it) != spatial_dimension) continue;
// akantu::UInt nb_element = mesh.getNbElement(*it);
// akantu::UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
// akantu::Element element(*it);
// akantu::UInt m = nb_nodes_per_element * spatial_dimension;
// akantu::Array<akantu::Real> local_mat(m, m, 1, "local_mat");
// for(akantu::UInt e = 0; e < nb_element; ++e) {
// element.element = e;
// sparse_matrix.addToMatrix(local_mat.storage(), element,
// nb_nodes_per_element);
// }
// }
A.saveMatrix("matrix.mtx");
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_matrix_product.cc b/test/test_solver/test_sparse_matrix_product.cc
index aaef07fc4..afec8d909 100644
--- a/test/test_solver/test_sparse_matrix_product.cc
+++ b/test/test_solver/test_sparse_matrix_product.cc
@@ -1,121 +1,123 @@
/**
* @file test_sparse_matrix_product.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 17 2011
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Jan 01 2019
*
* @brief test the matrix vector product in parallel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 2;
const UInt nb_dof = 2;
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
mesh.read("bar.msh");
mesh.distribute();
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> test_synchronize(nb_nodes, nb_dof, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
if (prank == 0)
std::cout << "Creating a SparseMatrix" << std::endl;
auto & A = dynamic_cast<SparseMatrixAIJ &>(
dof_manager.getNewMatrix("A", _symmetric));
Array<Real> dof_vector(nb_nodes, nb_dof, "vector");
if (prank == 0)
std::cout << "Filling the matrix" << std::endl;
for (UInt i = 0; i < nb_nodes * nb_dof; ++i) {
if (dof_manager.isLocalOrMasterDOF(i))
A.add(i, i, 2.);
}
std::stringstream str;
str << "Matrix_" << prank << ".mtx";
A.saveMatrix(str.str());
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt d = 0; d < nb_dof; ++d) {
dof_vector(n, d) = 1.;
}
}
Array<Real> dof_vector_tmp(dof_vector);
if (prank == 0)
std::cout << "Computing x = A * x" << std::endl;
A.matVecMul(dof_vector, dof_vector_tmp);
dof_vector.copy(dof_vector_tmp);
auto & sync =
dynamic_cast<DOFManagerDefault &>(dof_manager).getSynchronizer();
if (prank == 0)
std::cout << "Gathering the results on proc 0" << std::endl;
if (psize > 1) {
if (prank == 0) {
Array<Real> gathered;
sync.gather(dof_vector, gathered);
debug::setDebugLevel(dblTest);
std::cout << gathered << std::endl;
debug::setDebugLevel(dblWarning);
} else {
sync.gather(dof_vector);
}
} else {
debug::setDebugLevel(dblTest);
std::cout << dof_vector << std::endl;
debug::setDebugLevel(dblWarning);
}
finalize();
return 0;
}
diff --git a/test/test_solver/test_sparse_matrix_profile.cc b/test/test_solver/test_sparse_matrix_profile.cc
index 7c31e21ad..9df8c129e 100644
--- a/test/test_solver/test_sparse_matrix_profile.cc
+++ b/test/test_solver/test_sparse_matrix_profile.cc
@@ -1,74 +1,76 @@
/**
* @file test_sparse_matrix_profile.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Dec 13 2010
- * @date last modification: Tue Aug 29 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Aug 29 2017
*
* @brief test the profile generation of the SparseMatrix class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
mesh.read("triangle.msh");
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> test_synchronize(nb_nodes, spatial_dimension, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
auto & A = dof_manager.getNewMatrix("A", _symmetric);
for (UInt i = 0; i < 10; ++i) {
A.add(i, i);
}
A.add(0, 9);
A.saveProfile("profile_hand.mtx");
for (UInt i = 0; i < 10; ++i) {
A.add(i, i, i * 10);
}
A.add(0, 9, 100);
A.saveMatrix("matrix_hand.mtx");
/* ------------------------------------------------------------------------ */
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_matrix_profile_parallel.cc b/test/test_solver/test_sparse_matrix_profile_parallel.cc
index 6fa06cbe7..77052e4b1 100644
--- a/test/test_solver/test_sparse_matrix_profile_parallel.cc
+++ b/test/test_solver/test_sparse_matrix_profile_parallel.cc
@@ -1,112 +1,114 @@
/**
* @file test_sparse_matrix_profile_parallel.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Sun Sep 12 2010
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Nov 08 2017
*
* @brief test the sparse matrix class in parallel
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communicator.hh"
#include "mesh.hh"
#include "mesh_io_msh.hh"
#include "mesh_partition_scotch.hh"
#include "solver_mumps.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
int dim = 2;
//#ifdef AKANTU_USE_IOHELPER
// akantu::ElementType type = akantu::_triangle_6;
//#endif //AKANTU_USE_IOHELPER
akantu::Mesh mesh(dim);
// akantu::debug::setDebugLevel(akantu::dblDump);
akantu::StaticCommunicator * comm =
akantu::Communicator::getStaticCommunicator();
akantu::Int psize = comm->getNbProc();
akantu::Int prank = comm->whoAmI();
akantu::UInt n = 0;
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
akantu::Communicator * communicator;
if (prank == 0) {
akantu::MeshIOMSH mesh_io;
mesh_io.read("triangle.msh", mesh);
akantu::MeshPartition * partition =
new akantu::MeshPartitionScotch(mesh, dim);
// partition->reorder();
mesh_io.write("triangle_reorder.msh", mesh);
n = mesh.getNbNodes();
partition->partitionate(psize);
communicator =
akantu::Communicator::createCommunicatorDistributeMesh(mesh, partition);
delete partition;
} else {
communicator =
akantu::Communicator::createCommunicatorDistributeMesh(mesh, NULL);
}
std::cout << "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA "
<< mesh.getNbGlobalNodes() << std::endl;
akantu::SparseMatrix sparse_matrix(mesh, akantu::_symmetric, 2, "mesh");
sparse_matrix.buildProfile();
akantu::Solver * solver = new akantu::SolverMumps(sparse_matrix);
if (prank == 0) {
for (akantu::UInt i = 0; i < n; ++i) {
solver->getRHS().storage()[i] = 1.;
}
}
akantu::debug::setDebugLevel(akantu::dblDump);
solver->initialize();
std::stringstream sstr;
sstr << "profile_" << prank << ".mtx";
sparse_matrix.saveProfile(sstr.str());
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_solver_mumps.cc b/test/test_solver/test_sparse_solver_mumps.cc
index 39ce688b8..3ab355a0d 100644
--- a/test/test_solver/test_sparse_solver_mumps.cc
+++ b/test/test_solver/test_sparse_solver_mumps.cc
@@ -1,167 +1,169 @@
/**
* @file test_sparse_solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 19 2017
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Sun Dec 30 2018
*
* @brief test the matrix vector product in parallel
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_partition_scotch.hh"
#include "sparse_matrix_aij.hh"
#include "sparse_solver_mumps.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 1;
const UInt nb_global_dof = 11;
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
if (prank == 0) {
genMesh(mesh, nb_global_dof);
RandomGenerator<UInt>::seed(1496137735);
} else {
RandomGenerator<UInt>::seed(2992275470);
}
mesh.distribute();
UInt node = 0;
for (auto pos : mesh.getNodes()) {
std::cout << prank << " " << node << " pos: " << pos << " ["
<< mesh.getNodeGlobalId(node) << "] " << mesh.getNodeFlag(node)
<< std::endl;
++node;
}
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> x(nb_nodes);
dof_manager.registerDOFs("x", x, _dst_nodal);
const auto & local_equation_number =
dof_manager.getLocalEquationsNumbers("x");
auto & A = dof_manager.getNewMatrix("A", _symmetric);
Array<Real> b(nb_nodes);
TermsToAssemble terms;
for (UInt i = 0; i < nb_nodes; ++i) {
if (dof_manager.isLocalOrMasterDOF(i)) {
auto li = local_equation_number(i);
auto gi = dof_manager.localToGlobalEquationNumber(li);
terms(i, i) = 1. / (1. + gi);
}
}
dof_manager.assemblePreassembledMatrix("x", "x", "A", terms);
std::stringstream str;
str << "Matrix_" << prank << ".mtx";
A.saveMatrix(str.str());
for (UInt n = 0; n < nb_nodes; ++n) {
b(n) = 1.;
}
SparseSolverMumps solver(dof_manager, "A");
solver.solve(x, b);
auto && check = [&](auto && xs) {
debug::setDebugLevel(dblTest);
std::cout << xs << std::endl;
debug::setDebugLevel(dblWarning);
UInt d = 1.;
for (auto x : xs) {
if (std::abs(x - d) / d > 1e-15)
AKANTU_EXCEPTION("Error in the solution: " << x << " != " << d << " ["
<< (std::abs(x - d) / d)
<< "].");
++d;
}
};
if (psize > 1) {
auto & sync =
dynamic_cast<DOFManagerDefault &>(dof_manager).getSynchronizer();
if (prank == 0) {
Array<Real> x_gathered(dof_manager.getSystemSize());
sync.gather(x, x_gathered);
check(x_gathered);
} else {
sync.gather(x);
}
} else {
check(x);
}
finalize();
return 0;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
}
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
mesh_accessor.makeReady();
}
diff --git a/test/test_synchronizer/CMakeLists.txt b/test/test_synchronizer/CMakeLists.txt
index e4ab7a943..ecb0c4a0a 100644
--- a/test/test_synchronizer/CMakeLists.txt
+++ b/test/test_synchronizer/CMakeLists.txt
@@ -1,83 +1,93 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
-# @date creation: Fri Sep 03 2010
-# @date last modification: Fri Jan 26 2018
+# @date creation: Sun Oct 19 2014
+# @date last modification: Wed Mar 18 2020
#
# @brief configuration for synchronizer tests
#
-# @section LICENSE
-#
-# Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne) Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# Akantu is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# @section LICENSE
#
-# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+# Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
-# You should have received a copy of the GNU Lesser General Public License along with Akantu. If not, see <http://www.gnu.org/licenses/>.
+# Akantu is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License along
+# with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
# @section DESCRIPTION
#
#===============================================================================
+
add_mesh(test_synchronizer_communication_mesh
cube.geo 3 2)
register_test(test_dof_synchronizer
SOURCES test_dof_synchronizer.cc test_data_accessor.hh
FILES_TO_COPY bar.msh
PACKAGE parallel
PARALLEL
)
# if(DEFINED AKANTU_DAMAGE_NON_LOCAL)
# add_executable(test_grid_synchronizer_check_neighbors test_grid_synchronizer_check_neighbors.cc test_grid_tools.hh)
# target_link_libraries(test_grid_synchronizer_check_neighbors akantu)
# if(AKANTU_EXTRA_CXX_FLAGS)
# set_target_properties(test_grid_synchronizer_check_neighbors PROPERTIES COMPILE_FLAGS ${AKANTU_EXTRA_CXX_FLAGS})
# endif()
# endif()
# register_test(test_grid_synchronizer
# SOURCES test_grid_synchronizer.cc test_data_accessor.hh
# DEPENDS test_synchronizer_communication_mesh test_grid_synchronizer_check_neighbors
# EXTRA_FILES test_grid_synchronizer_check_neighbors.cc test_grid_tools.hh
# PACKAGE damage_non_local
# )
register_gtest_sources(
SOURCES test_communicator.cc
PACKAGE parallel
)
register_gtest_sources(
SOURCES test_synchronizer_communication.cc test_data_accessor.hh test_synchronizers_fixture.hh
PACKAGE parallel
)
register_gtest_sources(
SOURCES test_node_synchronizer.cc test_synchronizers_fixture.hh
PACKAGE parallel
)
register_gtest_sources(
SOURCES test_data_distribution.cc test_synchronizers_fixture.hh
DEPENDS test_synchronizer_communication_mesh
PACKAGE parallel
)
add_mesh(test_facet_synchronizer_mesh
facet.geo 3 2)
register_gtest_sources(
SOURCES test_facet_synchronizer.cc test_data_accessor.hh test_synchronizers_fixture.hh
DEPENDS test_facet_synchronizer_mesh
PACKAGE parallel cohesive_element
)
register_gtest_test(test_synchronizers
DEPENDS test_synchronizer_communication_mesh
PARALLEL)
diff --git a/test/test_synchronizer/test_communicator.cc b/test/test_synchronizer/test_communicator.cc
index 744f41803..3ce704aa8 100644
--- a/test/test_synchronizer/test_communicator.cc
+++ b/test/test_synchronizer/test_communicator.cc
@@ -1,137 +1,141 @@
/**
* @file test_communicator.cc
*
- * @author Nicolas Richart
+ * @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation Thu Feb 21 2019
+ * @date creation: Tue Feb 26 2019
+ * @date last modification: Tue Nov 17 2020
*
- * @brief A Documented file.
+ * @brief Test the communicators
*
*
- * Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2018-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
+
/* -------------------------------------------------------------------------- */
#include <aka_iterators.hh>
#include <communication_tag.hh>
#include <communicator.hh>
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
#include <random>
/* -------------------------------------------------------------------------- */
using namespace akantu;
TEST(Communicator, Bcast) {
auto r = 0xdeadbeef;
auto & c = Communicator::getStaticCommunicator();
c.broadcast(r);
EXPECT_EQ(r, 0xdeadbeef);
}
TEST(Communicator, ReceiveAny) {
std::random_device rd;
std::mt19937 gen(rd());
std::uniform_int_distribution<> dis(1, 10);
std::vector<CommunicationRequest> reqs;
auto & c = Communicator::getStaticCommunicator();
auto && rank = c.whoAmI();
auto && size = c.getNbProc();
for (auto n [[gnu::unused]] : arange(100)) {
AKANTU_DEBUG_INFO("ROUND " << n);
auto tag = Tag::genTag(0, 1, 0);
if (rank == 0) {
std::vector<int> sends(size - 1);
for (auto & s : sends) {
s = dis(gen);
}
c.broadcast(sends);
AKANTU_DEBUG_INFO("Messages " << [&]() {
std::string msgs;
for (auto s : enumerate(sends)) {
if (std::get<0>(s) != 0)
msgs += ", ";
msgs += std::to_string(std::get<0>(s) + 1) + ": " +
std::to_string(std::get<1>(s));
}
return msgs;
}());
int nb_recvs = 0;
for (auto && data : enumerate(sends)) {
auto & send = std::get<1>(data);
int p = std::get<0>(data) + 1;
if (send > 5) {
reqs.push_back(
c.asyncSend(send, p, tag, CommunicationMode::_synchronous));
}
if (p <= send) {
++nb_recvs;
}
}
c.receiveAnyNumber<int>(reqs,
[&](auto && proc, auto && msg) {
EXPECT_EQ(msg[0], sends[proc - 1] + 100 * proc);
EXPECT_LE(proc, sends[proc - 1]);
--nb_recvs;
},
tag);
EXPECT_EQ(nb_recvs, 0);
} else {
std::vector<int> recv(size - 1);
c.broadcast(recv);
AKANTU_DEBUG_INFO("Messages " << [&]() {
std::string msgs;
for (auto s : enumerate(recv)) {
if (std::get<0>(s) != 0)
msgs += ", ";
msgs += std::to_string(std::get<0>(s) + 1) + ": " +
std::to_string(std::get<1>(s));
}
return msgs;
}());
auto send = recv[rank - 1] + 100 * rank;
if (rank <= recv[rank - 1]) {
reqs.push_back(
c.asyncSend(send, 0, tag, CommunicationMode::_synchronous));
}
bool has_recv = false;
c.receiveAnyNumber<int>(reqs,
[&](auto && proc, auto && msg) {
EXPECT_EQ(msg[0], recv[rank - 1]);
EXPECT_EQ(proc, 0);
has_recv = true;
},
tag);
bool should_recv = (recv[rank - 1] > 5);
EXPECT_EQ(has_recv, should_recv);
}
reqs.clear();
}
}
diff --git a/test/test_synchronizer/test_data_accessor.hh b/test/test_synchronizer/test_data_accessor.hh
index e26488b10..7a0b0fc00 100644
--- a/test/test_synchronizer/test_data_accessor.hh
+++ b/test/test_synchronizer/test_data_accessor.hh
@@ -1,123 +1,125 @@
/**
* @file test_data_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Thu Apr 11 2013
- * @date last modification: Fri Jan 26 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Jan 26 2018
*
* @brief Data Accessor class for testing
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
class TestAccessor : public DataAccessor<Element> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline TestAccessor(const Mesh & mesh,
const ElementTypeMapArray<Real> & barycenters);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Barycenter, barycenters, Real);
/* ------------------------------------------------------------------------ */
/* Ghost Synchronizer inherited members */
/* ------------------------------------------------------------------------ */
protected:
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const ElementTypeMapArray<Real> & barycenters;
const Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/* TestSynchronizer implementation */
/* -------------------------------------------------------------------------- */
inline TestAccessor::TestAccessor(const Mesh & mesh,
const ElementTypeMapArray<Real> & barycenters)
: barycenters(barycenters), mesh(mesh) {}
inline UInt TestAccessor::getNbData(const Array<Element> & elements,
const SynchronizationTag &) const {
if (elements.size())
// return Mesh::getSpatialDimension(elements(0).type) * sizeof(Real) *
// elements.size();
return mesh.getSpatialDimension() * sizeof(Real) * elements.size();
else
return 0;
}
inline void TestAccessor::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag &) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Array<Element>::const_iterator<Element> bit = elements.begin();
Array<Element>::const_iterator<Element> bend = elements.end();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> bary(
this->barycenters(element.type, element.ghost_type).storage() +
element.element * spatial_dimension,
spatial_dimension);
buffer << bary;
}
}
inline void TestAccessor::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag &) {
UInt spatial_dimension = mesh.getSpatialDimension();
for (const auto & element : elements) {
Vector<Real> barycenter_loc(
this->barycenters(element.type, element.ghost_type).storage() +
element.element * spatial_dimension,
spatial_dimension);
Vector<Real> bary(spatial_dimension);
buffer >> bary;
auto dist = (barycenter_loc - bary).template norm<L_inf>();
EXPECT_NEAR(0, dist, 1e-15);
}
}
diff --git a/test/test_synchronizer/test_data_distribution.cc b/test/test_synchronizer/test_data_distribution.cc
index e584f60e3..f1082a2ec 100644
--- a/test/test_synchronizer/test_data_distribution.cc
+++ b/test/test_synchronizer/test_data_distribution.cc
@@ -1,87 +1,89 @@
/**
* @file test_data_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Sep 05 2014
- * @date last modification: Fri Jan 26 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Dec 28 2018
*
* @brief Test the mesh distribution on creation of a distributed synchonizer
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_synchronizers_fixture.hh"
/* -------------------------------------------------------------------------- */
TEST_F(TestSynchronizerFixture, DataDistribution) {
auto & barycenters = this->mesh->getElementalData<Real>("barycenters");
auto spatial_dimension = this->mesh->getSpatialDimension();
barycenters.initialize(*this->mesh, _spatial_dimension = _all_dimensions,
_nb_component = spatial_dimension);
this->initBarycenters(barycenters, *this->mesh);
auto & gids = this->mesh->getNodalData<UInt>("gid");
gids.resize(this->mesh->getNbNodes());
for (auto && data : enumerate(gids)) {
std::get<1>(data) = std::get<0>(data);
}
this->distribute();
for (auto && ghost_type : ghost_types) {
for (const auto & type :
this->mesh->elementTypes(_all_dimensions, ghost_type)) {
auto & barycenters =
this->mesh->getData<Real>("barycenters", type, ghost_type);
for (auto && data :
enumerate(make_view(barycenters, spatial_dimension))) {
Element element{type, UInt(std::get<0>(data)), ghost_type};
Vector<Real> barycenter(spatial_dimension);
this->mesh->getBarycenter(element, barycenter);
auto dist = (std::get<1>(data) - barycenter).template norm<L_inf>();
EXPECT_NEAR(dist, 0, 1e-7);
}
}
}
if (psize > 1) {
for (auto && data : zip(gids, this->mesh->getGlobalNodesIds())) {
EXPECT_EQ(std::get<0>(data), std::get<1>(data));
}
}
}
TEST_F(TestSynchronizerFixture, DataDistributionTags) {
this->distribute();
for (const auto & type : this->mesh->elementTypes(_all_dimensions)) {
auto & tags = this->mesh->getData<UInt>("tag_0", type);
Array<UInt>::const_vector_iterator tags_it = tags.begin(1);
Array<UInt>::const_vector_iterator tags_end = tags.end(1);
// The number of tags should match the number of elements on rank"
EXPECT_EQ(this->mesh->getNbElement(type), tags.size());
}
}
diff --git a/test/test_synchronizer/test_dof_data_accessor.hh b/test/test_synchronizer/test_dof_data_accessor.hh
index 9ec1c1ecb..a8219d7fb 100644
--- a/test/test_synchronizer/test_dof_data_accessor.hh
+++ b/test/test_synchronizer/test_dof_data_accessor.hh
@@ -1,117 +1,119 @@
/**
* @file test_dof_data_accessor.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Dec 09 2014
- * @date last modification: Tue Feb 20 2018
+ * @date last modification: Tue Feb 20 2018
*
* @brief data accessor class for testing the
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class TestDOFAccessor : public DataAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline TestDOFAccessor(const Array<Int> & global_dof_equation_numbers);
/* ------------------------------------------------------------------------ */
/* Ghost Synchronizer inherited members */
/* ------------------------------------------------------------------------ */
protected:
inline UInt getNbDataForDOFs(const Array<UInt> & dofs,
SynchronizationTag tag) const;
inline void packDOFData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
SynchronizationTag tag) const;
inline void unpackDOFData(CommunicationBuffer & buffer,
const Array<UInt> & dofs, SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const Array<Int> & global_dof_equation_numbers;
};
/* -------------------------------------------------------------------------- */
/* TestDOFSynchronizer implementation */
/* -------------------------------------------------------------------------- */
inline TestDOFAccessor::TestDOFAccessor(
const Array<Int> & global_dof_equation_numbers)
: global_dof_equation_numbers(global_dof_equation_numbers) {}
inline UInt TestDOFAccessor::getNbDataForDOFs(const Array<UInt> & dofs,
__attribute__((unused))
SynchronizationTag tag) const {
if (dofs.size())
// return Mesh::getSpatialDimension(elements(0).type) * sizeof(Real) *
// elements.size();
return sizeof(Int) * dofs.size();
else
return 0;
}
inline void TestDOFAccessor::packDOFData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
__attribute__((unused))
SynchronizationTag tag) const {
Array<UInt>::const_scalar_iterator bit = dofs.begin();
Array<UInt>::const_scalar_iterator bend = dofs.end();
for (; bit != bend; ++bit) {
buffer << this->global_dof_equation_numbers[*bit];
}
}
inline void TestDOFAccessor::unpackDOFData(CommunicationBuffer & buffer,
const Array<UInt> & dofs,
__attribute__((unused))
SynchronizationTag tag) {
Array<UInt>::const_scalar_iterator bit = dofs.begin();
Array<UInt>::const_scalar_iterator bend = dofs.end();
for (; bit != bend; ++bit) {
Int global_dof_eq_nb_local = global_dof_equation_numbers[*bit];
Int global_dof_eq_nb = 0;
buffer >> global_dof_eq_nb;
std::cout << *bit << global_dof_eq_nb_local << std::endl;
Real tolerance = Math::getTolerance();
if (!(std::abs(global_dof_eq_nb - global_dof_eq_nb_local) <= tolerance))
AKANTU_ERROR(
"Unpacking an unknown value for the dof: "
<< *bit << "(global_dof_equation_number = " << global_dof_eq_nb_local
<< " and buffer = " << global_dof_eq_nb << ") - tag: " << tag);
}
}
} // namespace akantu
diff --git a/test/test_synchronizer/test_dof_synchronizer.cc b/test/test_synchronizer/test_dof_synchronizer.cc
index 6bf580666..bfd711c23 100644
--- a/test/test_synchronizer/test_dof_synchronizer.cc
+++ b/test/test_synchronizer/test_dof_synchronizer.cc
@@ -1,146 +1,148 @@
/**
* @file test_dof_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Fri Jun 17 2011
- * @date last modification: Wed Nov 08 2017
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Wed Jan 15 2020
*
* @brief Test the functionality of the DOFSynchronizer class
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "communicator.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh_io.hh"
#include "mesh_partition_scotch.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "io_helper.hh"
#endif // AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
const UInt spatial_dimension = 2;
initialize(argc, argv);
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
if (prank == 0)
mesh.read("bar.msh");
mesh.distribute();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
UInt nb_nodes = mesh.getNbNodes();
/* ------------------------------------------------------------------------ */
/* test the synchronization */
/* ------------------------------------------------------------------------ */
Array<Real> test_synchronize(nb_nodes, spatial_dimension, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
auto & equation_number =
dof_manager.getLocalEquationsNumbers("test_synchronize");
DOFSynchronizer & dof_synchronizer = dof_manager.getSynchronizer();
std::cout << "Synchronizing a dof vector" << std::endl;
Array<Int> local_data_array(dof_manager.getLocalSystemSize(), 2);
auto it_data = local_data_array.begin(2);
for (UInt local_dof = 0; local_dof < dof_manager.getLocalSystemSize();
++local_dof) {
UInt equ_number = equation_number(local_dof);
Vector<Int> val;
if (dof_manager.isLocalOrMasterDOF(equ_number)) {
UInt global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
val = {0, 1};
val += global_dof * 2;
} else {
val = {-1, -1};
}
Vector<Int> data = it_data[local_dof];
data = val;
}
dof_synchronizer.synchronizeArray(local_data_array);
auto test_data = [&]() -> void {
auto it_data = local_data_array.begin(2);
for (UInt local_dof = 0; local_dof < dof_manager.getLocalSystemSize();
++local_dof) {
UInt equ_number = equation_number(local_dof);
Vector<Int> exp_val;
UInt global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
if (dof_manager.isLocalOrMasterDOF(equ_number) ||
dof_manager.isSlaveDOF(equ_number)) {
exp_val = {0, 1};
exp_val += global_dof * 2;
} else {
exp_val = {-1, -1};
}
Vector<Int> val = it_data[local_dof];
if (exp_val != val) {
std::cerr << "Failed !" << prank << " DOF: " << global_dof << " - l"
<< local_dof << " value:" << val << " expected: " << exp_val
<< std::endl;
exit(1);
}
}
};
test_data();
if (prank == 0) {
Array<Int> test_gathered(dof_manager.getSystemSize(), 2);
dof_synchronizer.gather(local_data_array, test_gathered);
local_data_array.set(-1);
dof_synchronizer.scatter(local_data_array, test_gathered);
} else {
dof_synchronizer.gather(local_data_array);
local_data_array.set(-1);
dof_synchronizer.scatter(local_data_array);
}
test_data();
finalize();
return 0;
}
diff --git a/test/test_synchronizer/test_dof_synchronizer_communication.cc b/test/test_synchronizer/test_dof_synchronizer_communication.cc
index a57bfe0d8..5cfa8bb89 100644
--- a/test/test_synchronizer/test_dof_synchronizer_communication.cc
+++ b/test/test_synchronizer/test_dof_synchronizer_communication.cc
@@ -1,108 +1,110 @@
/**
* @file test_dof_synchronizer_communication.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Dec 09 2014
- * @date last modification: Wed Nov 08 2017
+ * @date last modification: Sun Dec 30 2018
*
* @brief test to synchronize global equation numbers
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_paraview.hh"
#endif // AKANTU_USE_IOHELPER
#include "test_dof_data_accessor.hh"
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
bool wait = true;
if (argc > 1) {
if (prank == 0)
while (wait)
;
}
ElementSynchronizer * communicator = NULL;
if (prank == 0) {
mesh.read("cube.msh");
MeshPartition * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
/* --------------------------------------------------------------------------
*/
/* test the communications of the dof synchronizer */
/* --------------------------------------------------------------------------
*/
std::cout << "Initializing the synchronizer" << std::endl;
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
dof_synchronizer.initGlobalDOFEquationNumbers();
AKANTU_DEBUG_INFO("Creating TestDOFAccessor");
TestDOFAccessor test_dof_accessor(
dof_synchronizer.getGlobalDOFEquationNumbers());
SynchronizerRegistry synch_registry(test_dof_accessor);
synch_registry.registerSynchronizer(dof_synchronizer,
SynchronizationTag::_test);
AKANTU_DEBUG_INFO("Synchronizing tag");
synch_registry.synchronize(SynchronizationTag::_test);
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_facet_synchronizer.cc b/test/test_synchronizer/test_facet_synchronizer.cc
index e6f716b3b..fffad2d1c 100644
--- a/test/test_synchronizer/test_facet_synchronizer.cc
+++ b/test/test_synchronizer/test_facet_synchronizer.cc
@@ -1,96 +1,98 @@
/**
* @file test_facet_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
- * @date creation: Wed Nov 05 2014
- * @date last modification: Fri Jan 26 2018
+ * @date creation: Fri Oct 13 2017
+ * @date last modification: Sun Dec 30 2018
*
* @brief Facet synchronizer test
*
*
- * Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2015-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_data_accessor.hh"
#include "test_synchronizers_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <chrono>
#include <random>
#include <thread>
/* -------------------------------------------------------------------------- */
class TestFacetSynchronizerFixture : public TestSynchronizerFixture {
public:
void SetUp() override {
TestSynchronizerFixture::SetUp();
this->distribute();
this->mesh->initMeshFacets();
/// compute barycenter for each element
barycenters =
std::make_unique<ElementTypeMapArray<Real>>("barycenters");
this->initBarycenters(*barycenters, this->mesh->getMeshFacets());
test_accessor =
std::make_unique<TestAccessor>(*this->mesh, *this->barycenters);
}
void TearDown() override {
barycenters.reset(nullptr);
test_accessor.reset(nullptr);
}
protected:
std::unique_ptr<ElementTypeMapArray<Real>> barycenters;
std::unique_ptr<TestAccessor> test_accessor;
};
/* -------------------------------------------------------------------------- */
TEST_F(TestFacetSynchronizerFixture, SynchroneOnce) {
auto & synchronizer = this->mesh->getMeshFacets().getElementSynchronizer();
synchronizer.synchronizeOnce(*this->test_accessor, SynchronizationTag::_test);
}
/* -------------------------------------------------------------------------- */
TEST_F(TestFacetSynchronizerFixture, Synchrone) {
auto & synchronizer = this->mesh->getMeshFacets().getElementSynchronizer();
synchronizer.synchronize(*this->test_accessor, SynchronizationTag::_test);
}
/* -------------------------------------------------------------------------- */
TEST_F(TestFacetSynchronizerFixture, Asynchrone) {
auto & synchronizer = this->mesh->getMeshFacets().getElementSynchronizer();
synchronizer.asynchronousSynchronize(*this->test_accessor,
SynchronizationTag::_test);
std::random_device r;
std::default_random_engine engine(r());
std::uniform_int_distribution<int> uniform_dist(10, 100);
std::chrono::microseconds delay(uniform_dist(engine));
std::this_thread::sleep_for(delay);
synchronizer.waitEndSynchronize(*this->test_accessor,
SynchronizationTag::_test);
}
diff --git a/test/test_synchronizer/test_grid_synchronizer.cc b/test/test_synchronizer/test_grid_synchronizer.cc
index 90406863b..4b0ae9789 100644
--- a/test/test_synchronizer/test_grid_synchronizer.cc
+++ b/test/test_synchronizer/test_grid_synchronizer.cc
@@ -1,309 +1,311 @@
/**
* @file test_grid_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Wed Sep 01 2010
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Sun Dec 30 2018
*
* @brief test the GridSynchronizer object
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_grid_dynamic.hh"
#include "grid_synchronizer.hh"
#include "mesh.hh"
#include "mesh_partition.hh"
#include "synchronizer_registry.hh"
#include "test_data_accessor.hh"
#ifdef AKANTU_USE_IOHELPER
#include "io_helper.hh"
#endif // AKANTU_USE_IOHELPER
using namespace akantu;
const UInt spatial_dimension = 2;
typedef std::map<std::pair<Element, Element>, Real> pair_list;
#include "test_grid_tools.hh"
static void
updatePairList(const ElementTypeMapArray<Real> & barycenter,
const SpatialGrid<Element> & grid, Real radius,
pair_list & neighbors,
neighbors_map_t<spatial_dimension>::type & neighbors_map) {
AKANTU_DEBUG_IN();
GhostType ghost_type = _not_ghost;
Element e;
e.ghost_type = ghost_type;
// generate the pair of neighbor depending of the cell_list
ElementTypeMapArray<Real>::type_iterator it =
barycenter.firstType(_all_dimensions, ghost_type);
ElementTypeMapArray<Real>::type_iterator last_type =
barycenter.lastType(0, ghost_type);
for (; it != last_type; ++it) {
// loop over quad points
e.type = *it;
e.element = 0;
const Array<Real> & barycenter_vect = barycenter(*it, ghost_type);
UInt sp = barycenter_vect.getNbComponent();
Array<Real>::const_iterator<Vector<Real>> bary = barycenter_vect.begin(sp);
Array<Real>::const_iterator<Vector<Real>> bary_end =
barycenter_vect.end(sp);
for (; bary != bary_end; ++bary, e.element++) {
#if !defined(AKANTU_NDEBUG)
Point<spatial_dimension> pt1(*bary);
#endif
SpatialGrid<Element>::CellID cell_id = grid.getCellID(*bary);
SpatialGrid<Element>::neighbor_cells_iterator first_neigh_cell =
grid.beginNeighborCells(cell_id);
SpatialGrid<Element>::neighbor_cells_iterator last_neigh_cell =
grid.endNeighborCells(cell_id);
// loop over neighbors cells of the one containing the current element
for (; first_neigh_cell != last_neigh_cell; ++first_neigh_cell) {
SpatialGrid<Element>::Cell::const_iterator first_neigh_el =
grid.beginCell(*first_neigh_cell);
SpatialGrid<Element>::Cell::const_iterator last_neigh_el =
grid.endCell(*first_neigh_cell);
// loop over the quadrature point in the current cell of the cell list
for (; first_neigh_el != last_neigh_el; ++first_neigh_el) {
const Element & elem = *first_neigh_el;
Array<Real>::const_iterator<Vector<Real>> neigh_it =
barycenter(elem.type, elem.ghost_type).begin(sp);
const Vector<Real> & neigh_bary = neigh_it[elem.element];
Real distance = bary->distance(neigh_bary);
if (distance <= radius) {
#if !defined(AKANTU_NDEBUG)
Point<spatial_dimension> pt2(neigh_bary);
neighbors_map[pt1].push_back(pt2);
#endif
std::pair<Element, Element> pair = std::make_pair(e, elem);
pair_list::iterator p = neighbors.find(pair);
if (p != neighbors.end()) {
AKANTU_ERROR("Pair already registered ["
<< e << " " << elem << "] -> " << p->second << " "
<< distance);
} else {
neighbors[pair] = distance;
}
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
Real radius = 0.001;
Mesh mesh(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
ElementSynchronizer * dist = NULL;
if (prank == 0) {
mesh.read("bar.msh");
MeshPartition * partition =
new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
dist =
ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
dist = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
spacing[i] = radius * 1.2;
}
SpatialGrid<Element> grid(spatial_dimension, spacing, center);
GhostType ghost_type = _not_ghost;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, ghost_type);
ElementTypeMapArray<Real> barycenters("", "");
mesh.initElementTypeMapArray(barycenters, spatial_dimension,
spatial_dimension);
Element e;
e.ghost_type = ghost_type;
for (; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
e.type = *it;
Array<Real> & barycenter = barycenters(*it, ghost_type);
barycenter.resize(nb_element);
Array<Real>::iterator<Vector<Real>> bary_it =
barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem) {
mesh.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
e.element = elem;
grid.insert(e, *bary_it);
++bary_it;
}
}
std::stringstream sstr;
sstr << "mesh_" << prank << ".msh";
mesh.write(sstr.str());
Mesh grid_mesh(spatial_dimension, "grid_mesh", 0);
std::stringstream sstr_grid;
sstr_grid << "grid_mesh_" << prank << ".msh";
grid.saveAsMesh(grid_mesh);
grid_mesh.write(sstr_grid.str());
std::cout << "Pouet 1" << std::endl;
AKANTU_DEBUG_INFO("Creating TestAccessor");
TestAccessor test_accessor(mesh, barycenters);
SynchronizerRegistry synch_registry(test_accessor);
GridSynchronizer * grid_communicator =
GridSynchronizer::createGridSynchronizer(mesh, grid);
std::cout << "Pouet 2" << std::endl;
ghost_type = _ghost;
it = mesh.firstType(spatial_dimension, ghost_type);
last_type = mesh.lastType(spatial_dimension, ghost_type);
e.ghost_type = ghost_type;
for (; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
e.type = *it;
Array<Real> & barycenter = barycenters(*it, ghost_type);
barycenter.resize(nb_element);
Array<Real>::iterator<Vector<Real>> bary_it =
barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem) {
mesh.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
e.element = elem;
grid.insert(e, *bary_it);
++bary_it;
}
}
Mesh grid_mesh_ghost(spatial_dimension, "grid_mesh_ghost", 0);
std::stringstream sstr_gridg;
sstr_gridg << "grid_mesh_ghost_" << prank << ".msh";
grid.saveAsMesh(grid_mesh_ghost);
grid_mesh_ghost.write(sstr_gridg.str());
std::cout << "Pouet 3" << std::endl;
neighbors_map_t<spatial_dimension>::type neighbors_map;
pair_list neighbors;
updatePairList(barycenters, grid, radius, neighbors, neighbors_map);
pair_list::iterator nit = neighbors.begin();
pair_list::iterator nend = neighbors.end();
std::stringstream sstrp;
sstrp << "pairs_" << prank;
std::ofstream fout(sstrp.str().c_str());
for (; nit != nend; ++nit) {
fout << "[" << nit->first.first << "," << nit->first.second << "] -> "
<< nit->second << std::endl;
}
std::string file = "neighbors_ref";
std::stringstream sstrf;
sstrf << file << "_" << psize << "_" << prank;
file = sstrf.str();
std::ofstream nout;
nout.open(file.c_str());
neighbors_map_t<spatial_dimension>::type::iterator it_n =
neighbors_map.begin();
neighbors_map_t<spatial_dimension>::type::iterator end_n =
neighbors_map.end();
for (; it_n != end_n; ++it_n) {
std::sort(it_n->second.begin(), it_n->second.end());
std::vector<Point<spatial_dimension>>::iterator it_v = it_n->second.begin();
std::vector<Point<spatial_dimension>>::iterator end_v = it_n->second.end();
nout << "####" << std::endl;
nout << it_n->second.size() << std::endl;
nout << it_n->first << std::endl;
nout << "#" << std::endl;
for (; it_v != end_v; ++it_v) {
nout << *it_v << std::endl;
}
}
fout.close();
synch_registry.registerSynchronizer(*dist, SynchronizationTag::_smm_mass);
synch_registry.registerSynchronizer(*grid_communicator,
SynchronizationTag::_test);
AKANTU_DEBUG_INFO("Synchronizing tag on Dist");
synch_registry.synchronize(SynchronizationTag::_smm_mass);
AKANTU_DEBUG_INFO("Synchronizing tag on Grid");
synch_registry.synchronize(SynchronizationTag::_test);
delete grid_communicator;
delete dist;
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc b/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
index f0835da02..5cdc14aa4 100644
--- a/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
+++ b/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
@@ -1,130 +1,132 @@
/**
* @file test_grid_synchronizer_check_neighbors.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Mar 11 2013
- * @date last modification: Tue Feb 20 2018
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Tue Feb 20 2018
*
* @brief Test the generation of neighbors list based on a akaentu::Grid
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <fstream>
#include <iostream>
#include <string>
#include "aka_common.hh"
#include "communicator.hh"
using namespace akantu;
const UInt spatial_dimension = 3;
#include "test_grid_tools.hh"
void readNeighbors(
std::ifstream & nin,
neighbors_map_t<spatial_dimension>::type & neighbors_map_read) {
std::string line;
while (std::getline(nin, line)) {
std::getline(nin, line);
std::istringstream iss(line);
UInt nb_neig;
iss >> nb_neig;
std::getline(nin, line);
Point<spatial_dimension> pt;
pt.read(line);
std::getline(nin, line);
for (UInt i = 0; i < nb_neig; ++i) {
std::getline(nin, line);
Point<spatial_dimension> ne;
ne.read(line);
neighbors_map_read[pt].push_back(ne);
}
}
}
int main(int argc, char * argv[]) {
initialize(argc, argv);
const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
std::string file_ref = "neighbors_ref_1_0";
std::string file = "neighbors_ref";
std::stringstream sstr;
sstr << file << "_" << psize << "_" << prank;
file = sstr.str();
std::ifstream nin;
neighbors_map_t<spatial_dimension>::type neighbors_map_read;
nin.open(file_ref.c_str());
readNeighbors(nin, neighbors_map_read);
nin.close();
neighbors_map_t<spatial_dimension>::type neighbors_map;
nin.open(file.c_str());
readNeighbors(nin, neighbors_map);
nin.close();
neighbors_map_t<spatial_dimension>::type::iterator it_n =
neighbors_map.begin();
neighbors_map_t<spatial_dimension>::type::iterator end_n =
neighbors_map.end();
for (; it_n != end_n; ++it_n) {
std::sort(it_n->second.begin(), it_n->second.end());
std::vector<Point<spatial_dimension>>::iterator it_v = it_n->second.begin();
std::vector<Point<spatial_dimension>>::iterator end_v = it_n->second.end();
neighbors_map_t<spatial_dimension>::type::iterator it_nr =
neighbors_map_read.find(it_n->first);
if (it_nr == neighbors_map_read.end())
AKANTU_ERROR(
"Argh what is this point that is not present in the ref file "
<< it_n->first);
std::vector<Point<spatial_dimension>>::iterator it_vr =
it_nr->second.begin();
std::vector<Point<spatial_dimension>>::iterator end_vr =
it_nr->second.end();
for (; it_v != end_v && it_vr != end_vr; ++it_v, ++it_vr) {
if (*it_vr != *it_v)
AKANTU_ERROR("Neighbors does not match " << *it_v << " != " << *it_vr
<< " neighbor of "
<< it_n->first);
}
if (it_v == end_v && it_vr != end_vr) {
AKANTU_ERROR("Some neighbors of " << it_n->first << " are missing!");
}
if (it_v != end_v && it_vr == end_vr)
AKANTU_ERROR("Some neighbors of " << it_n->first << " are in excess!");
}
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_grid_tools.hh b/test/test_synchronizer/test_grid_tools.hh
index b831ffe10..4b8ecacb7 100644
--- a/test/test_synchronizer/test_grid_tools.hh
+++ b/test/test_synchronizer/test_grid_tools.hh
@@ -1,114 +1,116 @@
/**
* @file test_grid_tools.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
- * @date creation: Mon Mar 11 2013
- * @date last modification: Wed Feb 03 2016
+ * @date creation: Sun Oct 19 2014
+ * @date last modification: Fri Jan 15 2016
*
* @brief Tools to help for the akantu::Grid class tests
*
*
- * Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2014-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include <map>
#include "aka_common.hh"
#include "aka_types.hh"
#define TOLERANCE 1e-7
template <UInt dim> class Point {
public:
Point() : id(0), tol(TOLERANCE) {
for (UInt i = 0; i < dim; ++i)
pos[i] = 0.;
}
Point(const Point & pt) : id(pt.id), tol(pt.tol) {
for (UInt i = 0; i < dim; ++i)
pos[i] = pt.pos[i];
}
Point(const Vector<Real> & pt, UInt id = 0) : id(id), tol(TOLERANCE) {
for (UInt i = 0; i < dim; ++i)
pos[i] = pt(i);
}
bool operator==(const Point & pt) const {
for (UInt i = 0; i < dim; ++i) {
// std::cout << i << " " << pos[i] << " " << pt.pos[i] << " " <<
// std::abs(pos[i] - pt.pos[i]);
if (std::abs(pos[i] - pt.pos[i]) > tol) {
// std::cout << " " << false << std::endl;
return false;
} // else
// std::cout << " " << true << std::endl;
}
return true;
}
bool operator<(const Point & pt) const {
UInt i = 0, j = 0;
for (; (i < dim) && (j < dim); i++, j++) {
if (pos[i] < pt.pos[j])
return true;
if (pt.pos[j] < pos[i])
return false;
}
return (i == dim) && (j != dim);
}
bool operator!=(const Point & pt) const { return !(operator==(pt)); }
Real & operator()(UInt d) { return pos[d]; }
const Real & operator()(UInt d) const { return pos[d]; }
void read(const std::string & str) {
std::stringstream sstr(str);
for (UInt i = 0; i < dim; ++i)
sstr >> pos[i];
}
void write(std::ostream & ostr) const {
for (UInt i = 0; i < dim; ++i) {
if (i != 0)
ostr << " ";
// ostr << std::setprecision(std::numeric_limits<Real>::digits) <<
// pos[i];
ostr << std::setprecision(9) << pos[i];
}
}
private:
UInt id;
Real pos[dim];
double tol;
};
template <UInt dim> struct neighbors_map_t {
typedef std::map<Point<dim>, std::vector<Point<dim>>> type;
};
template <UInt dim>
inline std::ostream & operator<<(std::ostream & stream,
const Point<dim> & _this) {
_this.write(stream);
return stream;
}
diff --git a/test/test_synchronizer/test_node_synchronizer.cc b/test/test_synchronizer/test_node_synchronizer.cc
index b6fdcd801..f4a2cca96 100644
--- a/test/test_synchronizer/test_node_synchronizer.cc
+++ b/test/test_synchronizer/test_node_synchronizer.cc
@@ -1,211 +1,213 @@
/**
* @file test_node_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu May 11 2017
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Wed Jan 15 2020
*
* @brief test the default node synchronizer present in the mesh
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_synchronizers_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
#include "data_accessor.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <chrono>
#include <limits>
#include <random>
#include <thread>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class DataAccessorTest : public DataAccessor<UInt> {
public:
explicit DataAccessorTest(Array<int> & data) : data(data) {}
UInt getNbData(const Array<UInt> & nodes, const SynchronizationTag &) const {
return nodes.size() * sizeof(int);
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag &) const {
for (auto node : nodes) {
buffer << data(node);
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag &) {
for (auto node : nodes) {
buffer >> data(node);
}
}
protected:
Array<int> & data;
};
class TestNodeSynchronizerFixture : public TestSynchronizerFixture {
public:
static constexpr int max_int = std::numeric_limits<int>::max();
void SetUp() override {
TestSynchronizerFixture::SetUp();
this->distribute();
UInt nb_nodes = this->mesh->getNbNodes();
node_data = std::make_unique<Array<int>>(nb_nodes);
for (auto && data : enumerate(*node_data)) {
auto n = std::get<0>(data);
auto & d = std::get<1>(data);
UInt gn = this->mesh->getNodeGlobalId(n);
if (this->mesh->isMasterNode(n))
d = gn;
else if (this->mesh->isLocalNode(n))
d = -gn;
else if (this->mesh->isSlaveNode(n))
d = max_int;
else
d = -max_int;
}
data_accessor = std::make_unique<DataAccessorTest>(*node_data);
}
void TearDown() override {
data_accessor.reset(nullptr);
node_data.reset(nullptr);
}
void checkData() {
for (auto && data : enumerate(*this->node_data)) {
auto n = std::get<0>(data);
auto & d = std::get<1>(data);
UInt gn = this->mesh->getNodeGlobalId(n);
if (this->mesh->isMasterNode(n))
EXPECT_EQ(d, gn);
else if (this->mesh->isLocalNode(n))
EXPECT_EQ(d, -gn);
else if (this->mesh->isSlaveNode(n))
EXPECT_EQ(d, gn);
else
EXPECT_EQ(d, -max_int);
}
}
protected:
std::unique_ptr<Array<int>> node_data;
std::unique_ptr<DataAccessorTest> data_accessor;
};
/* -------------------------------------------------------------------------- */
constexpr int TestNodeSynchronizerFixture::max_int;
/* -------------------------------------------------------------------------- */
TEST_F(TestNodeSynchronizerFixture, SynchroneOnce) {
auto & synchronizer = this->mesh->getNodeSynchronizer();
synchronizer.synchronizeOnce(*this->data_accessor, SynchronizationTag::_test);
this->checkData();
}
/* -------------------------------------------------------------------------- */
TEST_F(TestNodeSynchronizerFixture, Synchrone) {
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronize(*this->data_accessor,
SynchronizationTag::_test);
this->checkData();
}
/* -------------------------------------------------------------------------- */
TEST_F(TestNodeSynchronizerFixture, Asynchrone) {
auto & synchronizer = this->mesh->getNodeSynchronizer();
synchronizer.asynchronousSynchronize(*this->data_accessor,
SynchronizationTag::_test);
std::random_device r;
std::default_random_engine engine(r());
std::uniform_int_distribution<int> uniform_dist(10, 100);
std::chrono::microseconds delay(uniform_dist(engine));
std::this_thread::sleep_for(delay);
synchronizer.waitEndSynchronize(*this->data_accessor,
SynchronizationTag::_test);
this->checkData();
}
/* -------------------------------------------------------------------------- */
TEST_F(TestNodeSynchronizerFixture, Gather) {
auto & synchronizer = this->mesh->getNodeSynchronizer();
const auto & comm = akantu::Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
if (prank == 0) {
Array<int> all_data(this->mesh->getNbGlobalNodes());
synchronizer.gather(*(this->node_data), all_data);
for (auto && data : enumerate(all_data)) {
EXPECT_EQ(std::get<0>(data), std::abs(std::get<1>(data)));
}
} else {
synchronizer.gather(*(this->node_data));
}
}
/* -------------------------------------------------------------------------- */
TEST_F(TestNodeSynchronizerFixture, Scatter) {
Array<int> local_data(this->mesh->getNbNodes(), 1, this->max_int);
auto & synchronizer = this->mesh->getNodeSynchronizer();
if (prank == 0) {
Array<int> all_data(this->mesh->getNbGlobalNodes());
for (auto && data : enumerate(all_data)) {
std::get<1>(data) = std::get<0>(data);
}
synchronizer.scatter(local_data, all_data);
} else {
synchronizer.scatter(local_data);
}
for (auto && data : enumerate(local_data)) {
auto && n = std::get<0>(data);
auto && d = std::get<1>(data);
UInt gn = this->mesh->getNodeGlobalId(n);
if(this->mesh->isPureGhostNode(n)) {
EXPECT_EQ(d, this->max_int);
} else {
EXPECT_EQ(d, gn);
}
}
}
diff --git a/test/test_synchronizer/test_synchronizer_communication.cc b/test/test_synchronizer/test_synchronizer_communication.cc
index 8f84eff8a..2593c2d0d 100644
--- a/test/test_synchronizer/test_synchronizer_communication.cc
+++ b/test/test_synchronizer/test_synchronizer_communication.cc
@@ -1,94 +1,96 @@
/**
* @file test_synchronizer_communication.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
- * @date last modification: Fri Jan 26 2018
+ * @date last modification: Sun Dec 30 2018
*
* @brief test to synchronize barycenters
*
*
- * Copyright (©) 2010-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "test_data_accessor.hh"
#include "test_synchronizers_fixture.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <chrono>
#include <random>
#include <thread>
/* -------------------------------------------------------------------------- */
class TestElementSynchronizerFixture : public TestSynchronizerFixture {
public:
void SetUp() override {
TestSynchronizerFixture::SetUp();
this->distribute();
/// compute barycenter for each element
barycenters =
std::make_unique<ElementTypeMapArray<Real>>("barycenters");
this->initBarycenters(*barycenters, *mesh);
test_accessor =
std::make_unique<TestAccessor>(*this->mesh, *this->barycenters);
}
void TearDown() override {
barycenters.reset(nullptr);
test_accessor.reset(nullptr);
}
protected:
std::unique_ptr<ElementTypeMapArray<Real>> barycenters;
std::unique_ptr<TestAccessor> test_accessor;
};
/* -------------------------------------------------------------------------- */
TEST_F(TestElementSynchronizerFixture, SynchroneOnce) {
auto & synchronizer = this->mesh->getElementSynchronizer();
synchronizer.synchronizeOnce(*this->test_accessor, SynchronizationTag::_test);
}
/* -------------------------------------------------------------------------- */
TEST_F(TestElementSynchronizerFixture, Synchrone) {
auto & synchronizer = this->mesh->getElementSynchronizer();
synchronizer.synchronize(*this->test_accessor, SynchronizationTag::_test);
}
/* -------------------------------------------------------------------------- */
TEST_F(TestElementSynchronizerFixture, Asynchrone) {
auto & synchronizer = this->mesh->getElementSynchronizer();
synchronizer.asynchronousSynchronize(*this->test_accessor,
SynchronizationTag::_test);
std::random_device r;
std::default_random_engine engine(r());
std::uniform_int_distribution<int> uniform_dist(10, 100);
std::chrono::microseconds delay(uniform_dist(engine));
std::this_thread::sleep_for(delay);
synchronizer.waitEndSynchronize(*this->test_accessor,
SynchronizationTag::_test);
}
diff --git a/test/test_synchronizer/test_synchronizers_fixture.hh b/test/test_synchronizer/test_synchronizers_fixture.hh
index fba747cb8..b507d2e3b 100644
--- a/test/test_synchronizer/test_synchronizers_fixture.hh
+++ b/test/test_synchronizer/test_synchronizers_fixture.hh
@@ -1,80 +1,83 @@
/**
* @file test_synchronizers_fixture.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jan 26 2018
+ * @date last modification: Wed Feb 28 2018
*
* @brief Fixture for synchronizer tests
*
*
- * Copyright (©) 2016-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
+ * @section LICENSE
+ *
+ * Copyright (©) 2016-2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
- * Akantu is free software: you can redistribute it and/or modify it under the
- * terms of the GNU Lesser General Public License as published by the Free
+ * Akantu is free software: you can redistribute it and/or modify it under the
+ * terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
- *
- * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
+ *
+ * Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+ * A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
- *
- * You should have received a copy of the GNU Lesser General Public License
+ *
+ * You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_iterators.hh"
#include "communicator.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <gtest/gtest.h>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class TestSynchronizerFixture : public ::testing::Test {
public:
virtual void SetUp() {
const UInt spatial_dimension = 3;
mesh = std::make_unique<Mesh>(spatial_dimension);
const auto & comm = Communicator::getStaticCommunicator();
prank = comm.whoAmI();
psize = comm.getNbProc();
if (prank == 0) {
this->mesh->read("cube.msh");
}
}
virtual void TearDown() { this->mesh.reset(nullptr); }
void initBarycenters(ElementTypeMapArray<Real> & barycenters, Mesh & mesh) {
auto spatial_dimension = mesh.getSpatialDimension();
barycenters.initialize(mesh, _spatial_dimension = _all_dimensions,
_nb_component = spatial_dimension,
_with_nb_element = true);
for (auto && ghost_type : ghost_types) {
for (const auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
for (auto && data : enumerate(
make_view(barycenters(type, ghost_type), spatial_dimension))) {
Element element{type, UInt(std::get<0>(data)), ghost_type};
mesh.getBarycenter(element, std::get<1>(data));
}
}
}
}
void distribute() { this->mesh->distribute(); }
protected:
std::unique_ptr<Mesh> mesh;
Int prank;
Int psize;
};
diff --git a/third-party/akantu_iterators/include/aka_tuple_tools.hh b/third-party/akantu_iterators/include/aka_tuple_tools.hh
index b6773b150..38eac8e3c 100644
--- a/third-party/akantu_iterators/include/aka_tuple_tools.hh
+++ b/third-party/akantu_iterators/include/aka_tuple_tools.hh
@@ -1,409 +1,407 @@
/**
* @file aka_tuple_tools.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Aug 11 2017
* @date last modification: Mon Jan 29 2018
*
* @brief iterator interfaces
*
*
* Copyright 2019 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_compatibilty_with_cpp_standard.hh"
#include "aka_str_hash.hh"
/* -------------------------------------------------------------------------- */
#include <tuple>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_TUPLE_TOOLS_HH
#define AKANTU_AKA_TUPLE_TOOLS_HH
#ifndef AKANTU_ITERATORS_NAMESPACE
#define AKANTU_ITERATORS_NAMESPACE akantu
#endif
namespace AKANTU_ITERATORS_NAMESPACE {
namespace tuple {
/* ---------------------------------------------------------------------- */
template <typename tag, typename type> struct named_tag {
using _tag = tag; ///< key
using _type = type; ///< value type
template <
typename T,
std::enable_if_t<not std::is_same<named_tag, T>::value> * = nullptr>
explicit named_tag(T && value) // NOLINT
: _value(std::forward<T>(value)) {}
type _value;
};
namespace details {
/* ---------------------------------------------------------------------- */
#if (defined(__GNUC__) || defined(__GNUG__))
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Weffc++"
#endif
template <typename tag> struct named_tag_proxy {
using _tag = tag;
template <typename T> decltype(auto) operator=(T && value) {
return named_tag<_tag, T>{std::forward<T>(value)};
}
};
#if (defined(__GNUC__) || defined(__GNUG__))
#pragma GCC diagnostic pop
#endif
} // namespace details
/* ---------------------------------------------------------------------- */
template <typename T> struct is_named_tag : public std::false_type {};
template <typename tag>
struct is_named_tag<details::named_tag_proxy<tag>> : public std::true_type {};
template <typename tag, typename type>
struct is_named_tag<named_tag<tag, type>> : public std::true_type {};
/* ---------------------------------------------------------------------- */
template <class... Params>
struct named_tuple : public std::tuple<typename Params::_type...> {
using Names_t = std::tuple<typename Params::_tag...>;
using parent = std::tuple<typename Params::_type...>;
named_tuple(Params &&... params)
: parent(std::forward<typename Params::_type>(params._value)...) {}
named_tuple(typename Params::_type &&... args)
: parent(std::forward<typename Params::_type>(args)...) {}
private:
template <typename tag, std::size_t Idx,
std::enable_if_t<Idx == sizeof...(Params)> * = nullptr>
static constexpr std::size_t get_element_index() noexcept {
return -1;
}
template <typename tag, std::size_t Idx,
std::enable_if_t<(Idx < sizeof...(Params))> * = nullptr>
static constexpr std::size_t get_element_index() noexcept {
using _tag = std::tuple_element_t<Idx, Names_t>;
return (std::is_same<_tag, tag>::value)
? Idx
: get_element_index<tag, Idx + 1>();
}
public:
template <typename NT,
std::enable_if_t<is_named_tag<NT>::value> * = nullptr>
constexpr decltype(auto) get(NT && /*unused*/) noexcept {
const auto index = get_element_index<typename NT::_tag, 0>();
static_assert((index != -1), "wrong named_tag");
return (std::get<index>(*this));
}
template <typename NT,
std::enable_if_t<is_named_tag<NT>::value> * = nullptr>
constexpr decltype(auto) get(NT && /*unused*/) const noexcept {
const auto index = get_element_index<typename NT::_tag, 0>();
static_assert((index != -1), "wrong named_tag");
return std::get<index>(*this);
}
};
/* ---------------------------------------------------------------------- */
template <typename T> struct is_named_tuple : public std::false_type {};
template <typename... Params>
struct is_named_tuple<named_tuple<Params...>> : public std::true_type {};
/* ---------------------------------------------------------------------- */
template <typename... Params>
constexpr decltype(auto) make_named_tuple(Params &&... params) noexcept {
return named_tuple<Params...>(std::forward<Params>(params)...);
}
template <typename tag> constexpr decltype(auto) make_named_tag() noexcept {
return details::named_tag_proxy<tag>{};
}
template <size_t HashCode> constexpr decltype(auto) get() {
return make_named_tag<std::integral_constant<size_t, HashCode>>();
}
template <size_t HashCode, class Tuple>
constexpr decltype(auto) get(Tuple && tuple) {
return tuple.get(get<HashCode>());
}
template <typename Param, typename Tuple,
std::enable_if_t<is_named_tag<Param>::value> * = nullptr>
constexpr decltype(auto) get(Tuple && tuple) noexcept {
return tuple.template get<typename Param::hash>();
}
-#if defined(__INTEL_COMPILER)
-// intel warnings here
-#elif defined(__clang__)
+#if !defined(__INTEL_COMPILER)
+# if defined(__clang__)
// clang warnings here
-#pragma clang diagnostic push
-#pragma clang diagnostic ignored "-Wgnu-string-literal-operator-template"
-#elif (defined(__GNUC__) || defined(__GNUG__))
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wgnu-string-literal-operator-template"
+# elif (defined(__GNUC__) || defined(__GNUG__))
// gcc warnings here
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wpedantic"
-#endif
+# pragma GCC diagnostic push
+# pragma GCC diagnostic ignored "-Wpedantic"
+# endif
/// this is a GNU exstension
/// http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2013/n3599.html
template <class CharT, CharT... chars>
constexpr decltype(auto) operator"" _n() {
return make_named_tag<std::integral_constant<
std::size_t, string_literal<CharT, chars...>::hash>>();
}
-#if defined(__INTEL_COMPILER)
-#elif defined(__clang__)
-#pragma clang diagnostic pop
-#elif (defined(__GNUC__) || defined(__GNUG__))
-#pragma GCC diagnostic pop
+# if defined(__clang__)
+# pragma clang diagnostic pop
+# elif (defined(__GNUC__) || defined(__GNUG__))
+# pragma GCC diagnostic pop
+# endif
#endif
-
/* ------------------------------------------------------------------------ */
namespace details {
template <std::size_t N> struct Foreach {
template <class Tuple>
static constexpr inline auto not_equal(Tuple && a, Tuple && b) -> bool {
if (std::get<N - 1>(std::forward<Tuple>(a)) ==
std::get<N - 1>(std::forward<Tuple>(b))) {
return false;
}
return Foreach<N - 1>::not_equal(std::forward<Tuple>(a),
std::forward<Tuple>(b));
}
template <class Tuple, class V>
static constexpr inline auto find(Tuple && tuple, V && value)
-> std::size_t {
constexpr auto size = std::tuple_size<std::decay_t<Tuple>>::value;
if (std::get<size - N>(std::forward<Tuple>(tuple)) == value) {
return size - N;
}
return Foreach<N - 1>::find(std::forward<Tuple>(tuple),
std::forward<V>(value));
}
};
/* ---------------------------------------------------------------------- */
template <> struct Foreach<0> {
template <class Tuple>
static constexpr inline auto not_equal(Tuple && a, Tuple && b) -> bool {
return std::get<0>(std::forward<Tuple>(a)) !=
std::get<0>(std::forward<Tuple>(b));
}
template <class Tuple, class V>
static constexpr inline auto find(Tuple && tuple, V && value)
-> std::size_t {
constexpr auto size = std::tuple_size<std::decay_t<Tuple>>::value;
if (std::get<size - 1>(std::forward<Tuple>(tuple)) == value) {
return size - 1;
}
return size;
}
};
template <typename... Ts>
decltype(auto) make_tuple_no_decay(Ts &&... args) {
return std::tuple<Ts...>(std::forward<Ts>(args)...);
}
template <typename... Names, typename... Ts>
constexpr decltype(auto)
make_named_tuple_no_decay(std::tuple<Names...> /*unused*/, Ts &&... args) {
return named_tuple<named_tag<Names, Ts>...>(std::forward<Ts>(args)...);
}
template <class F, class Tuple, std::size_t... Is>
constexpr void foreach_impl(F && func, Tuple && tuple,
std::index_sequence<Is...> && /*unused*/) {
(void)std::initializer_list<int>{
(std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple))),
0)...};
}
template <class F, class Tuple, std::size_t... Is>
constexpr decltype(auto)
transform_impl(F && func, Tuple && tuple,
std::index_sequence<Is...> && /*unused*/) {
return make_tuple_no_decay(
std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple)))...);
}
template <class F, class Tuple, std::size_t... Is>
constexpr decltype(auto)
transform_impl(F && func, Tuple && tuple1, Tuple && tuple2,
std::index_sequence<Is...> && /*unused*/) {
return make_tuple_no_decay(
std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple1)),
std::get<Is>(std::forward<Tuple>(tuple2)))...);
}
template <class F, class Tuple, std::size_t... Is>
constexpr decltype(auto)
transform_named_impl(F && func, Tuple && tuple,
std::index_sequence<Is...> && /*unused*/) {
return make_named_tuple_no_decay(
typename std::decay_t<Tuple>::Names_t{},
std::forward<F>(func)(std::get<Is>(std::forward<Tuple>(tuple)))...);
}
} // namespace details
/* ------------------------------------------------------------------------
*/
template <class Tuple,
std::enable_if_t<not is_named_tuple<std::decay_t<Tuple>>::value> * =
nullptr>
constexpr auto are_not_equal(Tuple && a, Tuple && b) -> bool {
return details::Foreach<std::tuple_size<std::decay_t<Tuple>>::value>::
not_equal(std::forward<Tuple>(a), std::forward<Tuple>(b));
}
template <
class Tuple,
std::enable_if_t<is_named_tuple<std::decay_t<Tuple>>::value> * = nullptr>
constexpr auto are_not_equal(Tuple && a, Tuple && b) -> bool {
return details::Foreach<
std::tuple_size<typename std::decay_t<Tuple>::parent>::value>::
not_equal(std::forward<Tuple>(a), std::forward<Tuple>(b));
}
template <class Tuple, class V>
constexpr decltype(auto) find(Tuple && tuple, V && value) {
return details::Foreach<std::tuple_size<std::decay_t<Tuple>>::value>::find(
std::forward<Tuple>(tuple), std::forward<V>(value));
}
template <class F, class Tuple,
std::enable_if_t<not is_named_tuple<std::decay_t<Tuple>>::value> * =
nullptr>
constexpr void foreach (F && func, Tuple && tuple) {
return details::foreach_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>{});
}
template <
class F, class Tuple,
std::enable_if_t<is_named_tuple<std::decay_t<Tuple>>::value> * = nullptr>
constexpr void foreach (F && func, Tuple && tuple) {
return details::foreach_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<typename std::decay_t<Tuple>::parent>::value>{});
}
template <class F, class Tuple,
std::enable_if_t<not is_named_tuple<std::decay_t<Tuple>>::value> * =
nullptr>
constexpr decltype(auto) transform(F && func, Tuple && tuple) {
return details::transform_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>{});
}
template <class F, class Tuple,
std::enable_if_t<not is_named_tuple<std::decay_t<Tuple>>::value> * =
nullptr>
constexpr decltype(auto) transform(F && func, Tuple && tuple1,
Tuple && tuple2) {
return details::transform_impl(
std::forward<F>(func), std::forward<Tuple>(tuple1),
std::forward<Tuple>(tuple2),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>{});
}
template <
class F, class Tuple,
std::enable_if_t<is_named_tuple<std::decay_t<Tuple>>::value> * = nullptr>
constexpr decltype(auto) transform(F && func, Tuple && tuple) {
return details::transform_named_impl(
std::forward<F>(func), std::forward<Tuple>(tuple),
std::make_index_sequence<
std::tuple_size<typename std::decay_t<Tuple>::parent>::value>{});
}
namespace details {
template <class Tuple, std::size_t... Is>
constexpr decltype(auto) flatten(Tuple && tuples,
std::index_sequence<Is...> /*unused*/) {
return std::tuple_cat(std::get<Is>(tuples)...);
}
} // namespace details
template <class Tuple> constexpr decltype(auto) flatten(Tuple && tuples) {
return details::flatten(std::forward<Tuple>(tuples),
std::make_index_sequence<
std::tuple_size<std::decay_t<Tuple>>::value>());
}
namespace details {
template <size_t n, class Tuple>
decltype(auto) dynamic_get_impl(size_t i, Tuple && tuple) {
constexpr auto size = std::tuple_size<std::decay_t<Tuple>>::value;
if (i == n) {
return std::get<n>(tuple);
} else if (n == size - 1) {
throw std::out_of_range("Tuple element out of range.");
} else {
return dynamic_get_impl<(n < size - 1 ? n + 1 : 0)>(i, tuple);
}
}
} // namespace details
template <class Tuple>
constexpr decltype(auto) dynamic_get(std::size_t i, Tuple && tuple) {
return details::dynamic_get_impl<0>(i, std::forward<Tuple>(tuple));
}
} // namespace tuple
} // namespace AKANTU_ITERATORS_NAMESPACE
/* -------------------------------------------------------------------------- */
#include <iterator>
/* -------------------------------------------------------------------------- */
namespace std {
template <typename tag, typename type>
struct iterator_traits<
::AKANTU_ITERATORS_NAMESPACE::tuple::named_tag<tag, type>> {
using iterator_category = typename type::iterator_category;
using value_type = typename type::value_type;
using difference_type = typename type::difference_type;
using pointer = typename type::pointer;
using reference = typename type::reference;
};
} // namespace std
#endif /* AKANTU_AKA_TUPLE_TOOLS_HH */
diff --git a/third-party/iohelper/CMakeLists.txt b/third-party/iohelper/CMakeLists.txt
index da2daf7da..0cfe0d4ca 100644
--- a/third-party/iohelper/CMakeLists.txt
+++ b/third-party/iohelper/CMakeLists.txt
@@ -1,81 +1,81 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
# @date creation: Thu Oct 11 2012
# @date last modification: Fri Jun 13 2014
#
# @brief main configuration file
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# IOHelper is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# IOHelper is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with IOHelper. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
#===============================================================================
# CMake Project
#===============================================================================
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.0)
project(IOHelper)
enable_language(CXX)
#===============================================================================
# Misc.
#===============================================================================
set(BUILD_SHARED_LIBS ON CACHE BOOL "Build shared libraries.")
find_package (ZLIB)
if(ZLIB_FOUND)
set (IOHELPER_EXTERNAL_LIBS ${IOHELPER_EXTERNAL_LIBS} ${ZLIB_LIBRARIES})
include_directories(${ZLIB_INCLUDE_DIR})
endif()
#===============================================================================
# Version Number
#===============================================================================
# IOHelper version number. An even minor number corresponds to releases.
set(IOHELPER_MAJOR_VERSION 1)
set(IOHELPER_MINOR_VERSION 1)
include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/CMakeVersionGenerator.cmake)
-define_project_version()
+#define_project_version()
#==============================================================================
# Library
#===============================================================================
add_subdirectory(src)
#==============================================================================
# Packaging
#===============================================================================
include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/IOHelperCPack.cmake)
#===============================================================================
# Tests
#===============================================================================
option(IOHELPER_TESTS "Activate tests" OFF)
if(IOHELPER_TESTS)
enable_testing()
include(CTest)
add_subdirectory(test)
endif()

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