diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7de70155a..1f6989bd3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,186 +1,186 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jun 14 2010
# @date last modification: Mon Sep 15 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)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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
#-------------------------------------------------------------------------------
# _ _
# | | | |
# __ _| | ____ _ _ __ | |_ _ _
# / _` | |/ / _` | '_ \| __| | | |
# | (_| | < (_| | | | | |_| |_| |
# \__,_|_|\_\__,_|_| |_|\__|\__,_|
#
#===============================================================================
#===============================================================================
# CMake Project
#===============================================================================
cmake_minimum_required(VERSION 2.8)
# add this options before PROJECT keyword
set(CMAKE_DISABLE_SOURCE_CHANGES ON)
set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
project(Akantu)
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.")
mark_as_advanced(BUILD_SHARED_LIBS)
if(NOT AKANTU_TARGETS_EXPORT)
set(AKANTU_TARGETS_EXPORT AkantuLibraryDepends)
endif()
include(CMakeVersionGenerator)
include(CMakePackagesSystem)
include(CMakeFlagsHandling)
include(AkantuMacros)
#cmake_activate_debug_message()
#===============================================================================
# Version Number
#===============================================================================
# AKANTU version number. An even minor number corresponds to releases.
set(AKANTU_MAJOR_VERSION 2)
set(AKANTU_MINOR_VERSION 2)
set(AKANTU_PATCH_VERSION 0)
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")
#Profiling
set(CMAKE_CXX_FLAGS_PROFILING "-g -pg -DNDEBUG -DAKANTU_NDEBUG -O2"
CACHE STRING "Flags used by the compiler during profiling builds")
set(CMAKE_C_FLAGS_PROFILING "-g -pg -DNDEBUG -DAKANTU_NDEBUG -O2"
CACHE STRING "Flags used by the compiler during profiling builds")
set(CMAKE_Fortran_FLAGS_PROFILING "-g -pg -DNDEBUG -DAKANTU_NDEBUG -O2"
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
)
include(CMakeDetermineCCompiler)
cmake_deactivate_debug_message(PackagesSystem)
#===============================================================================
# Dependencies
#===============================================================================
option(AKANTU_PYTHON_INTERFACE "Generates the Akantu Python module" OFF)
if(AKANTU_PYTHON_INTERFACE)
list(APPEND AKANTU_BOOST_COMPONENTS python)
endif()
package_list_packages(${PROJECT_SOURCE_DIR}/packages
EXTRA_PACKAGES_FOLDER ${PROJECT_SOURCE_DIR}/extra_packages)
## meta option \todo better way to do it when multiple package give enable the
## same feature
if(AKANTU_SCOTCH)
set(AKANTU_PARTITIONER ON)
else()
set(AKANTU_PARTITIONER OFF)
endif()
if(AKANTU_MUMPS)
set(AKANTU_SOLVER ON)
else()
set(AKANTU_SOLVER OFF)
endif()
#===============================================================================
# Akantu library
#===============================================================================
add_subdirectory(src)
#===============================================================================
# Documentation
#===============================================================================
if(AKANTU_DOCUMENTATION_DOXYGEN OR AKANTU_DOCUMENTATION_MANUAL)
add_subdirectory(doc)
else()
set(AKANTU_DOC_EXCLUDE_FILES "${PROJECT_SOURCE_DIR}/doc/manual" CACHE INTERNAL "")
endif()
#===============================================================================
# Examples and tests
#===============================================================================
option(AKANTU_EXAMPLES "Activate examples" OFF)
option(AKANTU_TESTS "Activate tests" OFF)
include(AkantuTestAndExamples)
if(AKANTU_EXAMPLES OR AKANTU_TESTS)
find_package(GMSH REQUIRED)
endif()
if(AKANTU_EXAMPLES)
add_subdirectory(examples)
endif()
add_test_tree(test)
#===============================================================================
# Install and Packaging
#===============================================================================
include(AkantuInstall)
if(NOT AKANTU_DISABLE_CPACK)
include(AkantuCPack)
endif()
#===============================================================================
# Install and Packaging
#===============================================================================
mark_as_advanced(AKANTU_PYTHON_INTERFACE)
if(AKANTU_PYTHON_INTERFACE)
-# add_subdirectory(python)
- add_subdirectory(akantu4py)
+ add_subdirectory(python)
+# add_subdirectory(akantu4py)
endif()
diff --git a/cmake/AkantuTestAndExamples.cmake b/cmake/AkantuTestAndExamples.cmake
index 47430143a..8a6e50b0d 100644
--- a/cmake/AkantuTestAndExamples.cmake
+++ b/cmake/AkantuTestAndExamples.cmake
@@ -1,318 +1,321 @@
#===============================================================================
# @file AkantuTestAndExamples.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Oct 25 2010
# @date last modification: Tue Jun 24 2014
#
# @brief macros for tests and examples
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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(AKANTU_DIFF_SCRIPT ${AKANTU_CMAKE_DIR}/akantu_diff.sh)
#===============================================================================
function(manage_test_and_example et_name desc build_all label)
string(TOUPPER ${et_name} upper_name)
cmake_parse_arguments(manage_test_and_example
""
"PACKAGE"
""
${ARGN}
)
set(_activated ON)
if(manage_test_and_example_PACKAGE)
list(FIND ${_project}_PACKAGE_SYSTEM_PACKAGES_ON ${manage_test_and_example_PACKAGE} _ret)
if(_ret EQUAL -1)
set(_activated OFF)
file(RELATIVE_PATH _dir ${PROJECT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/${et_name})
list(APPEND AKANTU_TESTS_EXCLUDE_FILES /${_dir})
set(AKANTU_TESTS_EXCLUDE_FILES ${AKANTU_TESTS_EXCLUDE_FILES} CACHE INTERNAL "")
endif()
endif()
if(NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${et_name} AND _activated)
# message("Example or test ${et_name} not present")
return()
endif()
option(AKANTU_BUILD${label}${upper_name} "${desc}")
mark_as_advanced(AKANTU_BUILD_${upper_name})
if(${build_all} OR NOT _activated)
set(AKANTU_BUILD${label}${upper_name}_OLD
${AKANTU_BUILD${label}${upper_name}}
CACHE INTERNAL "${desc}" FORCE)
set(AKANTU_BUILD${label}${upper_name} ${_activated}
CACHE INTERNAL "${desc}" FORCE)
else()
if(DEFINED AKANTU_BUILD${label}${upper_name}_OLD)
set(AKANTU_BUILD${label}${upper_name}
${AKANTU_BUILD${label}${upper_name}_OLD}
CACHE BOOL "${desc}" FORCE)
unset(AKANTU_BUILD${label}${upper_name}_OLD
CACHE)
endif(DEFINED AKANTU_BUILD${label}${upper_name}_OLD)
endif()
if(AKANTU_BUILD${label}${upper_name})
add_subdirectory(${et_name})
endif(AKANTU_BUILD${label}${upper_name})
endfunction()
#===============================================================================
# Tests
#===============================================================================
if(AKANTU_TESTS)
option(AKANTU_BUILD_ALL_TESTS "Build all tests" ON)
mark_as_advanced(AKANTU_BUILD_ALL_TESTS)
endif(AKANTU_TESTS)
#===============================================================================
# Examples
#===============================================================================
if(AKANTU_EXAMPLES)
option(AKANTU_BUILD_ALL_EXAMPLES "Build all examples")
# mark_as_advanced(AKANTU_BUILD_ALL_EXAMPLES)
endif(AKANTU_EXAMPLES)
#===============================================================================
macro(register_example example_name)
add_executable(${example_name} ${ARGN})
target_link_libraries(${example_name} akantu ${AKANTU_EXTERNAL_LIBRARIES})
endmacro()
#===============================================================================
macro(add_example example_name desc)
manage_test_and_example(${example_name} ${desc} AKANTU_BUILD_ALL_EXAMPLES _EXAMPLE_ ${ARGN})
endmacro()
# ==============================================================================
# this should be a macro due to the enable_testing
macro(add_test_tree dir)
if(AKANTU_TESTS)
enable_testing()
include(CTest)
mark_as_advanced(BUILD_TESTING)
set(AKANTU_TESTS_EXCLUDE_FILES "" CACHE INTERNAL "")
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()
else()
set(AKANTU_TESTS_EXCLUDE_FILES "${CMAKE_CURRENT_BINARY_DIR}/${dir}" CACHE INTERNAL "")
endif()
endmacro()
# ==============================================================================
function(add_akantu_test dir desc)
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 ${_my_parent_dir} CACHE INTERNAL "Current test folder" FORCE)
endfunction()
# ==============================================================================
function(register_test test_name)
set(multi_variables
SOURCES FILES_TO_COPY DEPENDENCIES DIRECTORIES_TO_CREATE COMPILE_OPTIONS EXTRA_FILES
)
cmake_parse_arguments(_register_test
""
"PACKAGE"
"${multi_variables}"
${ARGN}
)
if(NOT _register_test_PACKAGE)
message(FATAL_ERROR "No reference package was defined for the test ${test_name} in folder ${CMAKE_CURRENT_SOURCE_DIR}")
endif()
package_is_activated(${_register_test_PACKAGE} _act)
if(_act)
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)
string(TOUPPER ${_akantu_current_parent_test} _u_parent)
if(AKANTU_BUILD_${_u_parent})
+ # 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(
AKANTU_EXTERNAL_INCLUDE_DIR
AKANTU_EXTERNAL_LIBRARIES
)
+
# set the proper includes to build most of the tests
include_directories(
${AKANTU_INCLUDE_DIRS}
${AKANTU_EXTERNAL_LIB_INCLUDE_DIR}
)
# Register the executable to compile
add_executable(${test_name} ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS})
set_property(TARGET ${test_name} APPEND
PROPERTY INCLUDE_DIRECTORIES ${AKANTU_LIBRARY_INCLUDE_DIRS} ${AKANTU_EXTERNAL_INCLUDE_DIR})
target_link_libraries(${test_name} akantu ${AKANTU_EXTERNAL_LIBRARIES})
# add the extra compilation options
if(_register_test_COMPILE_OPTIONS)
set_target_properties(${test_name}
PROPERTIES COMPILE_DEFINITIONS "${_register_test_COMPILE_OPTIONS}")
endif()
set(_test_all_files)
# add the different dependencies (meshes, local libraries, ...)
foreach(_dep ${_register_test_DEPENDENCIES})
add_dependencies(${test_name} ${_dep})
get_target_property(_dep_in_ressources ${_dep} RESSOURCES)
if(_dep_in_ressources)
list(APPEND _test_all_files ${_dep_in_ressources})
endif()
endforeach()
# copy the needed files to the build folder
if(_register_test_FILES_TO_COPY)
foreach(_file ${_register_test_FILES_TO_COPY})
file(COPY ${_file} DESTINATION .)
list(APPEND _test_all_files ${CMAKE_CURRENT_SOURCE_DIR}/${_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()
# add the source files in the list of all files
foreach(_file ${_register_test_SOURCES} ${_register_test_UNPARSED_ARGUMENTS} ${_register_test_EXTRA_FILES})
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
list(APPEND _test_all_files ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
else()
message("The file \"${_file}\" registred by the test \"${test_name}\" does not exists")
endif()
endforeach()
# register the test for ctest
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh)
file(COPY ${test_name}.sh DESTINATION .)
list(APPEND _test_all_files ${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.sh)
add_test(${test_name}_run
${CMAKE_CURRENT_BINARY_DIR}/${test_name}.sh)
elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified)
list(APPEND _test_all_files ${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified)
add_test(${test_name}_run
${AKANTU_DIFF_SCRIPT} ${test_name} ${CMAKE_CURRENT_SOURCE_DIR}/${test_name}.verified)
else()
add_test(${test_name}_run
${CMAKE_CURRENT_BINARY_DIR}/${test_name})
endif()
# add the executable as a dependency of the run
set_tests_properties(${test_name}_run PROPERTIES DEPENDS ${test_name})
# clean the list of all files for this test and add them in the total list
set(_tmp ${AKANTU_TESTS_FILES})
foreach(_file ${_source_file})
get_filename_component(_full ${_file} ABSOLUTE)
file(RELATIVE_PATH __file ${PROJECT_SOURCE_DIR} ${_full})
list(APPEND _tmp ${__file})
list(APPEND _pkg_tmp ${__file})
endforeach()
set(AKANTU_TESTS_FILES ${_tmp} CACHE INTERNAL "")
endif()
endif()
endfunction()
\ No newline at end of file
diff --git a/cmake/Modules/CMakePackagesSystem.cmake b/cmake/Modules/CMakePackagesSystem.cmake
index 2b92f3d0e..333cc7f1b 100644
--- a/cmake/Modules/CMakePackagesSystem.cmake
+++ b/cmake/Modules/CMakePackagesSystem.cmake
@@ -1,1635 +1,1637 @@
#===============================================================================
# @file CMakePackagesSystem.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
# @date creation: Thu Dec 20 2012
# @date last modification: Wed Sep 10 2014
#
# @brief Set of macros used by akantu to handle the package system
#
# @section DESCRIPTION
#
# 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:
# 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
#
# 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 <flags>]
# [SYSTEM <bool> [ <script_to_compile> ]])
#
# It can also declare multiple informations:
# source files:
# package_declare_sources(<package real name>
# <src1> <src2> ... <srcn>)
#
# a LaTeX documentation:
# package_declare_documentation(<package real name>
# <line1> <line2> ...<linen>)
#
# 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
# package_get_name(<pkg> <retval>)
# package_get_real_name(<pkg> <retval>)
#
# package_get_option_name(<pkg> <retval>)
#
# package_use_system(<pkg> <retval>)
#
# package_get_nature(<pkg> <retval>)
#
# package_get_description(<pkg> <retval>)
#
# package_get_filename(<pkg> <retval>)
#
# package_get_sources_folder(<pkg> <retval>)
# package_get_tests_folder(<pkg> <retval>)
# package_get_manual_folder(<pkg> <retval>)
#
# package_get_find_package_extra_options(<pkg> <retval>)
#
# package_get_compile_flags(<pkg> <retval>)
#
# package_get_include_dir(<pkg> <retval>)
# package_set_include_dir(<pkg> <inc1> <inc2> ... <incn>)
#
# package_get_libraries(<pkg> <retval>)
# package_set_libraries(<pkg> <lib1> <lib2> ... <libn>)
#
# package_add_extra_dependency(pkg <dep1> <dep2> ... <depn>)
# package_rm_extra_dependency(<pkg> <dep>)
# package_get_extra_dependencies(<pkg> <retval>)
#
# package_is_activated(<pkg> <retval>)
# package_is_deactivated(<pkg> <retval>)
#
# package_get_dependencies(<pkg> <retval>)
# package_add_dependencies(<pkg> <dep1> <dep2> ... <depn>)
#
# package_get_all_source_files(<srcs> <public_headers> <private_headers>)
# package_get_all_include_directories(<inc_dirs>)
# package_get_all_external_informations(<include_dir> <libraries>)
# package_get_all_definitions(<definitions>)
# package_get_all_extra_dependencies(<dependencies>)
# package_get_all_test_folders(<test_dirs>)
# package_get_all_documentation_files(<doc_files>)
# package_get_all_activated_packages(<activated_list>)
# package_get_all_packages(<packages_list>)
#
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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(CMakeParseArguments)
#===============================================================================
# Package Management
#===============================================================================
if(__CMAKE_PACKAGES_SYSTEM)
return()
endif()
set(__CMAKE_PACKAGES_SYSTEM TRUE)
include(CMakeDebugMessages)
cmake_register_debug_message_module(PackagesSystem)
#===============================================================================
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)
# ==============================================================================
# "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} ${ARGN} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Nature
# ------------------------------------------------------------------------------
function(package_get_nature pkg ret)
package_get_name(${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} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Source folder
# ------------------------------------------------------------------------------
function(package_get_sources_folder pkg ret)
package_get_name(${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} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Compilation flags
# ------------------------------------------------------------------------------
function(package_get_compile_flags pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_compile_flags(${_pkg_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Include dir
# ------------------------------------------------------------------------------
function(package_get_include_dir pkg ret)
package_get_name(${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} ${ARGN})
endfunction()
# ------------------------------------------------------------------------------
# Libraries
# ------------------------------------------------------------------------------
function(package_get_libraries pkg ret)
package_get_name(${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)
set(_tmp_dep ${${_pkg_name}_EXTRA_DEPENDS})
list(APPEND _tmp_dep ${ARGN})
list(REMOVE_DUPLICATES _tmp_dep)
set(${_pkg_name}_EXTRA_DEPENDENCY "${_tmp_dep}"
CACHE INTERNAL "External dependencies")
endfunction()
function(package_rm_extra_dependency pkg DEP)
package_get_name(${pkg} _pkg_name)
if(${_pkg_name}_EXTRA_DEPENDENCY)
set(_tmp_dep ${${_pkg_name}_EXTRA_DEPENDENCY})
list(REMOVE_ITEM _tmp_dep ${DEP})
set(${_pkg_name}_EXTRA_DEPENDENCY "${_tmp_dep}"
CACHE INTERNAL "External dependencies" FORCE)
endif()
endfunction()
function(package_get_extra_dependencies pkg ret)
package_get_name(${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} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Direct dependencies
# ------------------------------------------------------------------------------
function(package_get_dependencies pkg ret)
package_get_name(${pkg} _pkg_name)
_package_get_dependencies(${_pkg_name} _tmp_name)
_package_get_real_name(${_tmp_name} _tmp)
set(${ret} ${_tmp} PARENT_SCOPE)
endfunction()
function(package_add_dependencies pkg)
package_get_name(${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} ${_tmp_deps})
endfunction()
# ------------------------------------------------------------------------------
# Documentation related functions
# ------------------------------------------------------------------------------
function(package_declare_documentation pkg)
# \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_get_name(${pkg} _pkg_name)
set(${_pkg_name}_DOCUMENTATION "${_doc_escaped}"
CACHE INTERNAL "Latex doc of package ${pkg}" FORCE)
endfunction()
function(package_declare_documentation_files pkg)
package_get_name(${pkg} _pkg_name)
set(${_pkg_name}_DOCUMENTATION_FILES "${ARGN}"
CACHE INTERNAL "Latex doc files for package ${pkg}" FORCE)
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)
set(tmp_SRCS)
set(tmp_PUBLIC_HEADERS)
set(tmp_PRIVATE_HEADERS)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_source_files(${_pkg_name}
_tmp_SRCS
_tmp_PUBLIC_HEADERS
_tmp_PRIVATE_HEADERS
)
list(APPEND tmp_SRCS ${_tmp_SRCS})
list(APPEND tmp_PUBLIC_HEADERS ${tmp_PUBLIC_HEADERS})
list(APPEND tmp_PRIVATE_HEADERS ${tmp_PRIVATE_HEADERS})
endforeach()
set(${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)
string(TOUPPER ${PROJECT_NAME} _project)
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 "${_path}")
endforeach()
endforeach()
endforeach()
list(REMOVE_DUPLICATES _tmp)
set(${inc_dirs} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get external libraries informations
# ------------------------------------------------------------------------------
function(package_get_all_external_informations INCLUDE_DIR LIBRARIES)
string(TOUPPER ${PROJECT_NAME} _project)
set(tmp_INCLUDE_DIR)
set(tmp_LIBRARIES)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_nature(${_pkg_name} _nature)
if(${_nature} MATCHES "external")
_package_get_include_dir(${_pkg_name} _inc)
- _package_get_libraries (${_pkg_name} _lib)
+ _package_get_libraries (${_pkg_name} _libraries)
list(APPEND tmp_INCLUDE_DIR ${_inc})
- list(APPEND tmp_LIBRARIES ${_lib})
+ list(APPEND tmp_LIBRARIES ${_libraries})
endif()
endforeach()
set(${INCLUDE_DIR} ${tmp_INCLUDE_DIR} PARENT_SCOPE)
set(${LIBRARIES} ${tmp_LIBRARIES} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get definitions like external projects
# ------------------------------------------------------------------------------
function(package_get_all_definitions definitions)
set(_tmp)
string(TOUPPER ${PROJECT_NAME} _project)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_option_name(${_pkg_name} _option_name)
list(APPEND _tmp ${_option_name})
endforeach()
set(${definitions} ${_tmp} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get extra dependencies like external projects
# ------------------------------------------------------------------------------
function(package_get_all_extra_dependencies DEPS)
string(TOUPPER ${PROJECT_NAME} _project)
set(_tmp_DEPS)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_extra_dependencies(${_pkg_name} _dep)
list(APPEND _tmp_DEPS ${_dep})
endforeach()
if(_tmp_DEPS)
list(REMOVE_DUPLICATES _tmp_DEPS)
endif()
set(${DEPS} ${_tmp_DEPS} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Get extra infos
# ------------------------------------------------------------------------------
function(package_get_all_test_folders TEST_DIRS)
string(TOUPPER ${PROJECT_NAME} _project)
set(_tmp_TEST_DIRS)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
_package_get_tests_folder(${_pkg_name} _test_dir)
list(APPEND _tmp_TEST_DIRS ${_test_dir})
endforeach()
if(_tmp_TEST_DIRS)
list(REMOVE_DUPLICATES _tmp_TEST_DIRS)
endif()
set(${TEST_DIRS} ${_tmp_TEST_DIRS} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Documentation informations
# ------------------------------------------------------------------------------
function(package_get_all_documentation_files doc_files)
string(TOUPPER ${PROJECT_NAME} _project)
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()
# ------------------------------------------------------------------------------
# List packages
# ------------------------------------------------------------------------------
function(package_get_all_activated_packages activated_list)
string(TOUPPER ${PROJECT_NAME} _project)
set(${activated_list} ${${_project}_ACTIVATED_PACKAGE_LIST} PARENT_SCOPE)
endfunction()
function(package_get_all_packages packages_list)
string(TOUPPER ${PROJECT_NAME} _project)
set(${packages_list} ${${_project}_ALL_PACKAGES_LIST} PARENT_SCOPE)
endfunction()
# ==============================================================================
# User Functions
# ==============================================================================
# ------------------------------------------------------------------------------
# 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
""
"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(${_pkg_name})
_package_unset_activated(${_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()
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 ${_pkg_file_stripped})
package_get_name(${_pkg} _pkg_name)
_package_set_filename(${_pkg_name} "${PACKAGE_FOLDER}/${_pkg_file}")
_package_set_sources_folder(${_pkg_name} "${_abs_src_folder}")
_package_set_tests_folder(${_pkg_name} "${_abs_test_folder}")
_package_set_manual_folder(${_pkg_name} "${_abs_manual_folder}")
list(APPEND _packages_list_all ${_pkg_name})
include("${PACKAGE_FOLDER}/${_pkg_file}")
endforeach()
# check the extra_packages if they exists
if(_opt_pkg_EXTRA_PACKAGES_FOLDER)
file(GLOB _extra_package_list RELATIVE
"${_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}/${_pkg}/package.cmake")
_package_set_sources_folder(${_pkg_name}
"${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/src")
if(EXISTS "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/test")
_package_set_tests_folder(${_pkg_name}
"${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/test")
endif()
if(EXISTS "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/manual")
_package_set_manual_folder(${_pkg_name}
"${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/manual")
endif()
list(APPEND _extra_pkg_src_folders "${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/src")
list(APPEND _packages_list_all ${_pkg_name})
include("${_opt_pkg_EXTRA_PACKAGES_FOLDER}/${_pkg}/package.cmake")
endif()
endforeach()
endif()
# Store the list of packages
string(TOUPPER ${PROJECT_NAME} _project)
set(${_project}_ALL_PACKAGES_LIST ${_packages_list_all}
CACHE INTERNAL "List of available packages" FORCE)
_package_build_rdependencies()
_package_load_packages()
_package_check_files_exists()
_package_check_files_registered(${_abs_src_folder} ${_extra_pkg_src_folders})
# Load boost components if boost was loaded
package_is_activated(Boost _ret)
if(_ret)
_package_load_boost_components()
endif()
endfunction()
# ------------------------------------------------------------------------------
# macro to include internal/external packages packages
# package_declare(<package real name>
# [EXTERNAL] [META] [ADVANCED] [NOT_OPTIONAL]
# [DESCRIPTION <description>] [DEFAULT <default_value>]
# [DEPENDS <pkg> ...]
# [BOOST_COMPONENTS <pkg> ...]
# [EXTRA_PACKAGE_OPTIONS <opt> ...]
# [COMPILE_FLAGS <flags>]
# [SYSTEM <bool> [ <script_to_compile> ]])
# ------------------------------------------------------------------------------
function(package_declare pkg)
package_get_name(${pkg} _pkg_name)
_package_set_real_name(${_pkg_name} ${pkg})
cmake_parse_arguments(_opt_pkg
"EXTERNAL;NOT_OPTIONAL;META;ADVANCED"
"DEFAULT;DESCRIPTION"
"DEPENDS;EXTRA_PACKAGE_OPTIONS;COMPILE_FLAGS;BOOST_COMPONENTS;SYSTEM"
${ARGN})
if(_opt_pkg_UNPARSED_ARGUMENTS)
message("You gave to many arguments while registering the package ${pkg} \"${_opt_pkg_UNPARSED_ARGUMENTS}\"")
endif()
# set description
if(_opt_pkg_DESCRIPTION)
_package_set_description(${_pkg_name} ${_opt_pkg_DESCRIPTION})
else()
_package_set_description(${_pkg_name} "")
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(${_pkg_name} "internal")
endif()
_package_get_option_name(${_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)
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(_depends)
foreach(_dep ${_opt_pkg_DEPENDS})
package_get_name(${_dep} _dep_pkg_name)
list(APPEND _depends ${_dep_pkg_name})
endforeach()
_package_add_dependencies(${_pkg_name} ${_depends})
endif()
# keep the extra option for the future find package
if(_opt_pkg_EXTRA_PACKAGE_OPTIONS)
_package_set_find_package_extra_options(${_pkg_name} "${_opt_pkg_EXTRA_PACKAGE_OPTIONS}")
endif()
# register the compilation flags
if(_opt_pkg_COMPILE_FLAGS)
_package_set_compile_flags(${_pkg_name} "${_opt_pkg_COMPILE_FLAGS}")
endif()
# set the boost dependencies
if(_opt_pkg_BOOST_COMPONENTS)
_package_set_boost_component_needed(${_pkg_name} "${_opt_pkg_BOOST_COMPONENTS}")
endif()
endfunction()
# ------------------------------------------------------------------------------
# declare the source files of a given package
#
# package_declare_sources(<package> <list of sources>
# SOURCES <source file> ...
# PUBLIC_HEADER <header file> ...
# PRIVATE_HEADER <header file> ...)
# ------------------------------------------------------------------------------
function(package_declare_sources pkg)
package_get_name(${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
list(APPEND ${_type} "${_src_folder}/${_file}")
endforeach()
endforeach()
set(${_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 "${_pri_hdrs}"
CACHE INTERNAL "List of private header files" FORCE)
endfunction()
# ==============================================================================
# "Private" Accessors
# ==============================================================================
# ------------------------------------------------------------------------------
# Real name
# ------------------------------------------------------------------------------
function(_package_get_real_name pkg_name real_name)
set(${real_name} ${${pkg_name}} PARENT_SCOPE)
endfunction()
function(_package_set_real_name pkg_name real_name)
set(${pkg_name} ${real_name} CACHE INTERNAL "" FORCE)
endfunction()
# ------------------------------------------------------------------------------
# Option name
# ------------------------------------------------------------------------------
function(_package_get_option_name pkg_name opt_name)
string(TOUPPER "${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} PARENT_SCOPE)
elseif(${_nature} MATCHES "external")
set(${opt_name} ${_project}_USE_${_u_package} PARENT_SCOPE)
else()
set(${opt_name} UNKNOWN_NATURE_${_project}_${_u_package} PARENT_SCOPE)
endif()
endfunction()
# ------------------------------------------------------------------------------
# Set if system package or compile external lib
# ------------------------------------------------------------------------------
function(_package_set_system_option pkg_name default)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
option(${_project}_USE_SYSTEM_${_u_package}
"Should akantu compile the third-party: \"${_real_name}\"" ${default})
mark_as_advanced(${_project}_USE_SYSTEM_${_u_package})
endfunction()
function(_package_use_system pkg_name use)
string(TOUPPER "${PROJECT_NAME}" _project)
_package_get_real_name(${pkg_name} _real_name)
string(TOUPPER "${_real_name}" _u_package)
if(DEFINED ${_project}_USE_SYSTEM_${_u_package})
set(${use} ${${_project}_USE_SYSTEM_${_u_package}} PARENT_SCOPE)
else()
set(${use} TRUE PARENT_SCOPE)
endif()
endfunction()
function(_package_set_system_script pkg_name script)
set(${_pkg_name}_COMPILE_SCRIPT "${script}"
CACHE INTERNAL "Script associated to package ${pkg_name}" FORCE)
endfunction()
function(_package_add_third_party_script_variable pkg var)
set(${_pkg_name}_VARIABLE_${var} "${ARGN}"
CACHE INTERNAL "Script associated to package ${pkg_name}" FORCE)
set(${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 " (version ${${_opt_name}_VERSION})")
elseif(${_u_name}_VERSION)
set(_version " (version ${${_u_name}_VERSION})")
endif()
# load the script
message(STATUS "${_name}: building as third-party${_version}")
include(ExternalProject)
include(${${pkg_name}_COMPILE_SCRIPT})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Nature
# ------------------------------------------------------------------------------
function(_package_set_nature pkg_name NATURE)
set(${pkg_name}_NATURE ${NATURE} CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_nature pkg_name NATURE)
if(${pkg_name}_NATURE)
set(${NATURE} ${${pkg_name}_NATURE} PARENT_SCOPE)
else()
set(${NATURE} "unknown" PARENT_SCOPE)
endif()
endfunction()
# ------------------------------------------------------------------------------
# Description
# ------------------------------------------------------------------------------
function(_package_set_description pkg_name DESC)
set(${pkg_name}_DESC ${DESC} CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_description pkg_name DESC)
if(${pkg_name}_DESC)
set(${DESC} ${${pkg_name}_DESC} PARENT_SCOPE)
else()
message("No description set for the package ${${pkg_name}} (${pkg_name})")
endif()
endfunction()
# ------------------------------------------------------------------------------
# Package file name
# ------------------------------------------------------------------------------
function(_package_set_filename pkg_name FILE)
set(${pkg_name}_FILE ${FILE} CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_filename pkg_name FILE)
if(${pkg_name}_FILE)
set(${FILE} ${${pkg_name}_FILE} PARENT_SCOPE)
else()
message(ERROR "No filename set for the package ${${pkg_name}}")
endif()
endfunction()
# ------------------------------------------------------------------------------
# Source folder
# ------------------------------------------------------------------------------
function(_package_set_sources_folder pkg_name src_folder)
set(${pkg_name}_SRCS_FOLDER "${src_folder}" CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_sources_folder pkg_name src_folder)
set(${src_folder} ${${pkg_name}_SRCS_FOLDER} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Test folder
# ------------------------------------------------------------------------------
function(_package_set_tests_folder pkg_name test_folder)
set(${pkg_name}_TESTS_FOLDER "${test_folder}" CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_tests_folder pkg_name test_folder)
set(${test_folder} ${${pkg_name}_TESTS_FOLDER} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Manual folder
# ------------------------------------------------------------------------------
function(_package_set_manual_folder pkg_name manual_folder)
set(${pkg_name}_MANUAL_FOLDER "${manual_folder}" CACHE INTERNAL "" FORCE)
endfunction()
function(_package_get_manual_folder pkg_name manual_folder)
set(${manual_folder} ${${pkg_name}_MANUAL_FOLDER} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Extra option for the find_package
# ------------------------------------------------------------------------------
function(_package_set_find_package_extra_options pkg_name)
set(${pkg_name}_FIND_PKG_OPTIONS "${ARGN}"
CACHE INTERNAL "Extra option for the fin_package function" FORCE)
endfunction()
function(_package_get_find_package_extra_options pkg_name options)
set(${options} "${${pkg_name}_FIND_PKG_OPTIONS}" PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Compilation flags
# ------------------------------------------------------------------------------
function(_package_set_compile_flags pkg_name)
set(${pkg_name}_COMPILE_FLAGS ${ARGN}
CACHE INTERNAL "Additional compile flags" FORCE)
endfunction()
function(_package_get_compile_flags pkg_name flags)
set(${flags} "${${pkg_name}_COMPILE_FLAGS}" PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Include dir
# ------------------------------------------------------------------------------
function(_package_set_include_dir pkg_name)
_package_get_real_name(${pkg_name} _real_name)
set(${pkg_name}_INCLUDE_DIR "${ARGN}"
CACHE INTERNAL "Include folder for the package ${_real_name}" FORCE)
endfunction()
function(_package_get_include_dir pkg_name include_dir)
set(${include_dir} ${${pkg_name}_INCLUDE_DIR} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Libraries
# ------------------------------------------------------------------------------
function(_package_set_libraries pkg_name)
_package_get_real_name(${pkg_name} _real_name)
set(${pkg_name}_LIBRARIES "${ARGN}"
CACHE INTERNAL "Libraries for the package ${_real_name}" FORCE)
endfunction()
function(_package_get_libraries pkg_name libraries)
- set(${libraries} ${${pkg_name}_LIBRARIES} PARENT_SCOPE)
+ if(${pkg_name}_LIBRARIES)
+ set(${libraries} ${${pkg_name}_LIBRARIES} PARENT_SCOPE)
+ else()
+ set(${libraries} "" PARENT_SCOPE)
+ endif()
endfunction()
# ------------------------------------------------------------------------------
# Extra dependencies like custom commands of ExternalProject
# ------------------------------------------------------------------------------
function(_package_get_extra_dependencies pkg deps)
if(${_pkg_name}_EXTRA_DEPENDENCY)
set(${deps} ${${_pkg_name}_EXTRA_DEPENDENCY} PARENT_SCOPE)
else()
set(${deps} PARENT_SCOPE)
endif()
endfunction()
function(_package_unset_extra_dependencies pkg_name)
unset(${pkg_name}_EXTRA_DEPENDENCY CACHE)
endfunction()
# ------------------------------------------------------------------------------
# Activate/deactivate
# ------------------------------------------------------------------------------
function(_package_activate pkg_name)
set(${pkg_name}_STATE ON CACHE INTERNAL "" FORCE)
endfunction()
function(_package_deactivate pkg_name)
set(${pkg_name}_STATE OFF CACHE INTERNAL "" FORCE)
endfunction()
function(_package_is_activated pkg_name _act)
if(DEFINED ${pkg_name}_STATE AND ${pkg_name}_STATE)
set(${_act} TRUE PARENT_SCOPE)
else()
set(${_act} FALSE PARENT_SCOPE)
endif()
endfunction()
function(_package_is_deactivated pkg_name _act)
if(DEFINED ${pkg_name}_STATE AND NOT ${pkg_name}_STATE)
set(${_act} TRUE PARENT_SCOPE)
else()
set(${_act} FALSE PARENT_SCOPE)
endif()
endfunction()
function(_package_unset_activated pkg_name)
unset(${pkg_name}_STATE CACHE)
endfunction()
# ------------------------------------------------------------------------------
# Direct dependencies
# ------------------------------------------------------------------------------
function(_package_add_dependencies pkg_name)
set(_tmp_deps ${${pkg_name}_DEPENDENCIES})
list(APPEND _tmp_deps ${ARGN})
list(REMOVE_DUPLICATES _tmp_deps)
set(${pkg_name}_DEPENDENCIES "${_tmp_deps}"
CACHE INTERNAL "List of dependencies for package ${_opt_name}" FORCE)
endfunction()
function(_package_get_dependencies pkg_name dependencies)
set(${dependencies} "${${pkg_name}_DEPENDENCIES}" PARENT_SCOPE)
endfunction()
function(_package_unset_dependencies pkg_name)
unset(${pkg_name}_DEPENDENCIES CACHE)
endfunction()
# ------------------------------------------------------------------------------
# Functions to handle reverse dependencies
# ------------------------------------------------------------------------------
function(_package_set_rdependencies pkg_name)
set(${pkg_name}_RDEPENDENCIES "${ARGN}"
CACHE INTERNAL "Dependencies ON with package ${pkg_name}" FORCE)
endfunction()
function(_package_get_rdependencies pkg_name RDEPENDENCIES)
set(${RDEPENDENCIES} "${${pkg_name}_RDEPENDENCIES}" PARENT_SCOPE)
endfunction()
function(_package_add_rdependency pkg_name rdep)
# store the reverse dependency
set(_rdeps ${${pkg_name}_RDEPENDENCIES})
list(APPEND _rdeps ${rdep})
list(REMOVE_DUPLICATES _rdeps)
_package_set_rdependencies(${pkg_name} ${_rdeps})
endfunction()
function(_package_remove_rdependency pkg_name rdep)
set(_rdeps ${${pkg_name}_RDEPENDENCIES})
list(FIND _rdeps ${rdep} pos)
if(NOT pos EQUAL -1)
list(REMOVE_AT _rdeps ${pos})
_package_set_rdependencies(${pkg_name} ${_rdeps})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Function to handle forcing dependencies (Package turn ON that enforce their
# dependencies ON)
# ------------------------------------------------------------------------------
function(_package_set_fdependencies pkg_name)
set(${pkg_name}_FDEPENDENCIES "${ARGN}"
CACHE INTERNAL "Dependencies ON with package ${pkg_name}" FORCE)
endfunction()
function(_package_get_fdependencies pkg_name fdependencies)
set(${fdependencies} "${${pkg_name}_FDEPENDENCIES}" PARENT_SCOPE)
endfunction()
function(_package_add_fdependency pkg_name fdep)
# store the enforcing dependency
set(_fdeps ${${pkg_name}_FDEPENDENCIES})
list(APPEND _fdeps ${fdep})
list(REMOVE_DUPLICATES _fdeps)
_package_set_fdependencies(${pkg_name} ${_fdeps})
endfunction()
function(_package_remove_fdependency pkg_name fdep)
set(_fdeps ${${pkg_name}_FDEPENDENCIES})
list(FIND _fdeps ${fdep} pos)
if(NOT pos EQUAL -1)
list(REMOVE_AT _fdeps ${pos})
_package_set_fdependencies(${pkg_name} ${_fdeps})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Documentation related functions
# ------------------------------------------------------------------------------
function(_package_get_documentation_files pkg_name doc_files)
if(DEFINED ${pkg_name}_DOCUMENTATION_FILES)
set(${doc_files} ${${pkg_name}_DOCUMENTATION_FILES} PARENT_SCOPE)
else()
set(${doc_files} "" PARENT_SCOPE)
endif()
endfunction()
function(_package_get_documentation pkg_name _doc)
# \n replaced by && and \\ by ££ to avoid cache problems
if (DEFINED ${_pkg_name}_DOCUMENTATION)
set(_doc_tmp ${${_pkg_name}_DOCUMENTATION})
string(REPLACE "££" "\\" _doc_escaped "${_doc_tmp}")
string(REPLACE "&&" "\n" _doc_newlines "${_doc_escaped}")
set(${_doc} "${_doc_newlines}" PARENT_SCOPE)
else()
set(${_doc} "" PARENT_SCOPE)
endif()
endfunction()
# ------------------------------------------------------------------------------
# Special boost thingy
# ------------------------------------------------------------------------------
function(_package_set_boost_component_needed pkg_name)
set(_tmp ${${pkg_name}_BOOST_COMPONENTS_NEEDED})
list(APPEND _tmp ${ARGN})
list(REMOVE_DUPLICATES _tmp)
set(${pkg_name}_BOOST_NEEDED_COMPONENTS ${_tmp}
CACHE INTERNAL "List of Boost component needed by package ${${pkg_name}}" FORCE)
package_get_name(Boost _boost_pkg_name)
_package_add_dependencies(${pkg_name} ${_boost_pkg_name})
endfunction()
-function(_package_get_boost_component_needed pkg_name)
- set(_tmp ${${_project}_BOOST_COMPONENTS_NEEDED})
- list(APPEND _tmp ${ARGN})
- list(REMOVE_DUPLICATES _tmp)
- set(${pkg_name}_BOOST_NEEDED_COMPONENTS ${_tmp}
- CACHE INTERNAL "List of Boost component needed by package ${${pkg_name}}" FORCE)
+function(_package_get_boost_component_needed pkg_name needed)
+ if(${pkg_name}_BOOST_NEEDED_COMPONENTS)
+ set(${needed} ${${pkg_name}_BOOST_NEEDED_COMPONENTS} PARENT_SCOPE)
+ else()
+ set(${needed} PARENT_SCOPE)
+ endif()
endfunction()
function(_package_load_boost_components)
string(TOUPPER ${PROJECT_NAME} _project)
package_get_name(Boost _pkg_name)
set(_boost_needed_components)
package_get_all_activated_packages(_activated_list)
foreach(_pkg_name ${_activated_list})
- _package_get_documentation_files(${_pkg_name} _doc_files)
+ _package_get_boost_component_needed(${_pkg_name} _boost_comp)
- foreach(_doc_file ${_doc_files})
- list(APPEND _tmp_DOC_FILES ${_doc_dir}/${_doc_file})
- endforeach()
+ list(APPEND _boost_needed_components ${_boost_comp})
endforeach()
- if(_boost_components_needed)
- message(STATUS "Looking for Boost liraries")
- foreach(_comp ${_boost_components_needed})
+ 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 " ${_comp}: FOUND")
set(${_project}_BOOST_${_u_comp} TRUE CACHE INTERNAL "" FORCE)
# Generate the libraries for the package
_package_set_libraries(${_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)
string(TOUPPER ${PROJECT_NAME} _project)
# set empty lists
foreach(_pkg_name ${${_project}_ALL_PACKAGES_LIST})
set(${_pkg_name}_rdeps)
endforeach()
# fill the dependencies list
foreach(_pkg_name ${${_project}_ALL_PACKAGES_LIST})
_package_get_dependencies(${_pkg_name} _deps)
foreach(_dep_name ${_deps})
list(APPEND ${_dep_name}_rdeps ${_pkg_name})
endforeach()
endforeach()
# clean and set the reverse dependencies
foreach(_pkg_name ${${_project}_ALL_PACKAGES_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)
string(TOUPPER ${PROJECT_NAME} _project)
# Activate the dependencies of activated package and generate an ordered list
# of dependencies
set(ordered_loading_list)
foreach(_pkg_name ${${_project}_ALL_PACKAGES_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)
_package_is_deactivated(${_pkg_name} _deactivated)
if(NOT _deactivated AND ${_option_name})
_package_load_package(${_pkg_name})
endif()
endforeach()
# generates the activated and unactivated lists of packages
set(_packages_activated)
set(_packages_deactivated)
foreach(_pkg_name ${${_project}_ALL_PACKAGES_LIST})
_package_is_activated(${_pkg_name} _act)
if(_act)
list(APPEND _packages_activated ${_pkg_name})
else()
list(APPEND _packages_deactivated ${_pkg_name})
endif()
endforeach()
# generate the list usable by the calling code
set(${_project}_ACTIVATED_PACKAGE_LIST "${_packages_activated}"
CACHE INTERNAL "List of activated packages" FORCE)
set(${_project}_DEACTIVATED_PACKAGE_LIST "${_packages_deactivated}"
CACHE INTERNAL "List of deactivated packages" FORCE)
endfunction()
# ------------------------------------------------------------------------------
# This load an external package and recursively all its dependencies
# ------------------------------------------------------------------------------
function(_package_load_dependencies_package pkg_name loading_list)
# Get packages informations
_package_get_option_name(${pkg_name} _pkg_option_name)
_package_get_dependencies(${pkg_name} _dependencies)
# 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(${_dep_option_name} ON CACHE BOOL "${_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} _pkg_comile_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_comile_flags)
add_flags(cxx ${_pkg_comile_flags})
endif()
else()
# deactivate the packages than can already be deactivated
_package_deactivate(${pkg_name})
#remove the comilation flags if needed
if(_pkg_comile_flags)
remove_flags(cxx ${_pkg_comile_flags})
endif()
endif()
endfunction()
# ------------------------------------------------------------------------------
# Load the package if it is an external one
# ------------------------------------------------------------------------------
function(_package_load_package pkg_name)
# load the package if it is an external
_package_get_nature(${pkg_name} _nature)
if(${_nature} MATCHES "external")
_package_use_system(${pkg_name} _use_system)
set(_activated TRUE)
if(_use_system)
_package_load_external_package(${pkg_name} _activated)
else()
_package_load_third_party_script(${pkg_name})
endif()
if(_activated)
_package_activate(${pkg_name})
elseif()
_package_deactivate(${pkg_name})
endif()
else(${_nature})
_package_activate(${pkg_name})
endif()
endfunction()
# ------------------------------------------------------------------------------
# Load external packages
# ------------------------------------------------------------------------------
function(_package_load_external_package pkg_name activate)
string(TOUPPER ${PROJECT_NAME} _project)
_package_get_find_package_extra_options(${pkg_name} _options)
if(_options)
cmake_parse_arguments(_opt_pkg "" "LANGUAGE" "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()
_package_get_real_name(${pkg_name} _real_name)
# find the package
find_package(${_real_name} REQUIRED ${_opt_pkg_ARGS})
# check if the package is found
if(_opt_pkg_PREFIX)
set(_package_prefix ${_opt_pkg_PREFIX})
else()
string(TOUPPER ${${pkg_name}} _u_package)
set(_package_prefix ${_u_package})
endif()
set(_act FALSE)
set(_prefix_to_consider)
if(_opt_pkg_FOUND)
set(_act TRUE)
set(_prefix_to_consider ${_package_prefix})
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(DEFINED ${_prefix}_LIBRARIES)
_package_set_libraries(${_pkg_name} ${${_prefix}_LIBRARIES})
elseif(DEFINED ${_prefix}_LIBRARY)
_package_set_libraries(${_pkg_name} ${${_prefix}_LIBRARY})
endif()
endforeach()
endif()
set(${activate} ${_act} PARENT_SCOPE)
endfunction()
# ------------------------------------------------------------------------------
# Sanity check functions
# ------------------------------------------------------------------------------
function(_package_check_files_exists)
string(TOUPPER ${PROJECT_NAME} _project)
set(_message FALSE)
foreach(_pkg_name ${${_project}_ALL_PACKAGES_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)
# generates a file list of registered files
foreach(_pkg_name ${${_project}_ALL_PACKAGES_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 ine 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_SOURCE_DIR}/tmp/)
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} ${PROJECT_SOURCE_DIR}/tmp/${_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_SOURCE_DIR}/tmp/")
endif()
message(SEND_ERROR "Please register them in the good package or clean the sources")
endif()
endfunction()
diff --git a/cmake/Modules/FindPETSc.cmake b/cmake/Modules/FindPETSc.cmake
index 191a76fef..3c96349ab 100644
--- a/cmake/Modules/FindPETSc.cmake
+++ b/cmake/Modules/FindPETSc.cmake
@@ -1,345 +1,345 @@
# - Try to find PETSc
# Once done this will define
#
# PETSC_FOUND - system has PETSc
# PETSC_INCLUDES - the PETSc include directories
# PETSC_LIBRARIES - Link these to use PETSc
# PETSC_COMPILER - Compiler used by PETSc, helpful to find a compatible MPI
# PETSC_DEFINITIONS - Compiler switches for using PETSc
# PETSC_MPIEXEC - Executable for running MPI programs
# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
#
# Usage:
# find_package(PETSc COMPONENTS CXX) - required if build --with-clanguage=C++ --with-c-support=0
# find_package(PETSc COMPONENTS C) - standard behavior of checking build using a C compiler
# find_package(PETSc) - same as above
#
# Setting these changes the behavior of the search
# PETSC_DIR - directory in which PETSc resides
# PETSC_ARCH - build architecture
#
# Redistribution and use is allowed according to the terms of the BSD license.
# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
#
set(PETSC_VALID_COMPONENTS
C
CXX)
if(NOT PETSc_FIND_COMPONENTS)
set(PETSC_LANGUAGE_BINDINGS "C")
else()
# Right now, this is designed for compatability with the --with-clanguage option, so
# only allow one item in the components list.
list(LENGTH ${PETSc_FIND_COMPONENTS} components_length)
if(${components_length} GREATER 1)
message(FATAL_ERROR "Only one component for PETSc is allowed to be specified")
endif()
# This is a stub for allowing multiple components should that time ever come. Perhaps
# to also test Fortran bindings?
foreach(component ${PETSc_FIND_COMPONENTS})
list(FIND PETSC_VALID_COMPONENTS ${component} component_location)
if(${component_location} EQUAL -1)
message(FATAL_ERROR "\"${component}\" is not a valid PETSc component.")
else()
list(APPEND PETSC_LANGUAGE_BINDINGS ${component})
endif()
endforeach()
endif()
function (petsc_get_version)
if (EXISTS "${PETSC_DIR}/include/petscversion.h")
file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
foreach (line ${vstrings})
string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
list (GET fields 1 var)
list (GET fields 2 val)
set (${var} ${val} PARENT_SCOPE)
set (${var} ${val}) # Also in local scope so we have access below
endforeach ()
if (PETSC_VERSION_RELEASE)
set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" PARENT_SCOPE)
else ()
# make dev version compare higher than any patch level of a released version
set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" PARENT_SCOPE)
endif ()
else ()
message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
endif ()
endfunction ()
find_path (PETSC_DIR include/petsc.h
HINTS ENV PETSC_DIR
PATHS
# Debian paths
/usr/lib/petscdir/3.3 /usr/lib/petscdir/3.2 /usr/lib/petscdir/3.1
/usr/lib/petscdir/3.0.0 /usr/lib/petscdir/2.3.3 /usr/lib/petscdir/2.3.2
$ENV{HOME}/petsc
DOC "PETSc Directory")
find_program (MAKE_EXECUTABLE NAMES make gmake)
if (NOT PETSC_ARCH)
if (NOT ENV{PETSC_ARCH})
set(_petsc_arches
linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
else()
set(_petsc_arches $ENV{PETSC_ARCH}) # If set, use environment variable first)
endif()
else()
set (_petsc_arches
${PETSC_ARCH})
endif()
if (NOT PETSC_DIR)
if (NOT ENV{PETSC_DIR})
set(PETSC_DIR /usr/lib/petsc)
else()
set(PETSC_DIR $ENV{PETSC_DIR}) # If set, use environment variable first)
endif()
endif()
foreach (arch ${_petsc_arches})
set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
find_path (petscconf petscconf.h
HINTS ${PETSC_DIR}
PATH_SUFFIXES ${arch}/include bmake/${arch}
NO_DEFAULT_PATH)
if(petscconf)
set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
set(_petsc_dir ${PETSC_DIR})
set (PETSC_DIR "${_petsc_dir}" CACHE STRING "PETSc build directory")
break()
endif()
endforeach()
set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
INCLUDE_DIR INCLUDE_CONF)
include (FindPackageMultipass)
#find_package_multipass (PETSc petsc_config_current
# STATES DIR ARCH
# DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC EXECUTABLE_RUNS ${petsc_slaves})
#
# Determine whether the PETSc layout is old-style (through 2.3.3) or
# new-style (>= 3.0.0)
if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
elseif (PETSC_DIR)
message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
endif ()
message(petsc_conf_rules ${petsc_conf_rules})
message(petsc_conf_variables ${petsc_conf_variables})
message(petsc_config_current ${petsc_config_current})
if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
petsc_get_version()
# Put variables into environment since they are needed to get
# configuration (petscvariables) in the PETSc makefile
set (ENV{PETSC_DIR} "${PETSC_DIR}")
set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
# A temporary makefile to probe the PETSc configuration
set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
file (WRITE "${petsc_config_makefile}"
"## This file was autogenerated by FindPETSc.cmake
# PETSC_DIR = ${PETSC_DIR}
# PETSC_ARCH = ${PETSC_ARCH}
include ${petsc_conf_rules}
include ${petsc_conf_variables}
show :
-@echo -n \${\${VARIABLE}}
")
macro (PETSC_GET_VARIABLE name var)
set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
OUTPUT_VARIABLE ${var}
RESULT_VARIABLE petsc_return)
endmacro (PETSC_GET_VARIABLE)
petsc_get_variable (PETSC_LIB_DIR petsc_lib_dir)
petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
petsc_get_variable (PETSC_CCPPFLAGS petsc_cpp_line)
petsc_get_variable (PETSC_INCLUDE petsc_include)
petsc_get_variable (PCC petsc_cc)
petsc_get_variable (PCC_FLAGS petsc_cc_flags)
petsc_get_variable (MPIEXEC petsc_mpiexec)
# We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
file (REMOVE ${petsc_config_makefile})
include (ResolveCompilerPaths)
# Extract include paths and libraries from compile command line
resolve_includes (petsc_includes_all "${petsc_cpp_line}")
#on windows we need to make sure we're linking against the right
#runtime library
if (WIN32)
if (petsc_cc_flags MATCHES "-MT")
set(using_md False)
foreach(flag_var
CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO
CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO)
if(${flag_var} MATCHES "/MD")
set(using_md True)
endif(${flag_var} MATCHES "/MD")
endforeach(flag_var)
if(${using_md} MATCHES "True")
message(WARNING "PETSc was built with /MT, but /MD is currently set.
See http://www.cmake.org/Wiki/CMake_FAQ#How_can_I_build_my_MSVC_application_with_a_static_runtime.3F")
endif(${using_md} MATCHES "True")
endif (petsc_cc_flags MATCHES "-MT")
endif (WIN32)
include (CorrectWindowsPaths)
convert_cygwin_path(petsc_lib_dir)
message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
macro (PETSC_FIND_LIBRARY suffix name)
set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
if (WIN32)
set (libname lib${name}) #windows expects "libfoo", linux expects "foo"
else (WIN32)
set (libname ${name})
endif (WIN32)
find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
mark_as_advanced (PETSC_LIBRARY_${suffix})
endmacro (PETSC_FIND_LIBRARY suffix name)
# Look for petscvec first, if it doesn't exist, we must be using single-library
petsc_find_library (VEC petscvec)
if (PETSC_LIBRARY_VEC)
petsc_find_library (SYS "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
petsc_find_library (MAT petscmat)
petsc_find_library (DM petscdm)
petsc_find_library (KSP petscksp)
petsc_find_library (SNES petscsnes)
petsc_find_library (TS petscts)
macro (PETSC_JOIN libs deps)
list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
endmacro (PETSC_JOIN libs deps)
petsc_join (VEC SYS)
petsc_join (MAT VEC)
petsc_join (DM MAT)
petsc_join (KSP DM)
petsc_join (SNES KSP)
petsc_join (TS SNES)
petsc_join (ALL TS)
else ()
- set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
petsc_find_library (SINGLE petsc)
foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
endforeach ()
+ set (PETSC_LIBRARY_VEC "${PETSC_LIBRARY_SINGLE}" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
endif ()
if (PETSC_LIBRARY_TS)
message (STATUS "Recognized PETSc install with separate libraries for each package")
else ()
message (STATUS "Recognized PETSc install with single library for all packages")
endif ()
include(Check${PETSC_LANGUAGE_BINDINGS}SourceRuns)
macro (PETSC_TEST_RUNS includes libraries runs)
if(${PETSC_LANGUAGE_BINDINGS} STREQUAL "C")
set(_PETSC_ERR_FUNC "CHKERRQ(ierr)")
elseif(${PETSC_LANGUAGE_BINDINGS} STREQUAL "CXX")
set(_PETSC_ERR_FUNC "CHKERRXX(ierr)")
endif()
if (PETSC_VERSION VERSION_GREATER 3.1)
set (_PETSC_TSDestroy "TSDestroy(&ts)")
else ()
set (_PETSC_TSDestroy "TSDestroy(ts)")
endif ()
set(_PETSC_TEST_SOURCE "
static const char help[] = \"PETSc test program.\";
#include <petscts.h>
int main(int argc,char *argv[]) {
PetscErrorCode ierr;
TS ts;
ierr = PetscInitialize(&argc,&argv,0,help);${_PETSC_ERR_FUNC};
ierr = TSCreate(PETSC_COMM_WORLD,&ts);${_PETSC_ERR_FUNC};
ierr = TSSetFromOptions(ts);${_PETSC_ERR_FUNC};
ierr = ${_PETSC_TSDestroy};${_PETSC_ERR_FUNC};
ierr = PetscFinalize();${_PETSC_ERR_FUNC};
return 0;
}
")
multipass_source_runs ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
if (${${runs}})
set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
"Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
endif (${${runs}})
endmacro (PETSC_TEST_RUNS)
find_path (PETSC_INCLUDE_DIR petscts.h HINTS "${PETSC_DIR}" PATH_SUFFIXES include NO_DEFAULT_PATH)
find_path (PETSC_INCLUDE_CONF petscconf.h HINTS "${PETSC_DIR}" PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}" NO_DEFAULT_PATH)
mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_minimal)
if (petsc_works_minimal)
message (STATUS "Minimal PETSc includes and libraries work. This probably means we are building with shared libs.")
set (petsc_includes_needed "${petsc_includes_minimal}")
else (petsc_works_minimal) # Minimal includes fail, see if just adding full includes fixes it
petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_allincludes)
if (petsc_works_allincludes) # It does, we just need all the includes (
message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries. This is an unexpected configuration (but it seems to work fine).")
set (petsc_includes_needed ${petsc_includes_all})
else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
list (APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
endforeach (pkg)
petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_alllibraries)
if (petsc_works_alllibraries)
message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies. This is expected when PETSc is built with static libraries.")
set (petsc_includes_needed ${petsc_includes_minimal})
else (petsc_works_alllibraries)
# It looks like we really need everything, should have listened to Matt
set (petsc_includes_needed ${petsc_includes_all})
petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_all)
if (petsc_works_all) # We fail anyways
message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies. This probably means you have static libraries and something unexpected in PETSc headers.")
else (petsc_works_all) # We fail anyways
message (STATUS "PETSc could not be used, maybe the install is broken.")
endif (petsc_works_all)
endif (petsc_works_alllibraries)
endif (petsc_works_allincludes)
endif (petsc_works_minimal)
# We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
if (${PETSC_VERSION} VERSION_LESS 3.1)
set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
else ()
set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
endif ()
# Sometimes this can be used to assist FindMPI.cmake
set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
# Note that we have forced values for all these choices. If you
# change these, you are telling the system to trust you that they
# work. It is likely that you will end up with a broken build.
mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
endif ()
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (PETSc
"PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH."
PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS)
diff --git a/doc/manual/CMakeLists.txt b/doc/manual/CMakeLists.txt
index 83cda0284..5edf520f2 100644
--- a/doc/manual/CMakeLists.txt
+++ b/doc/manual/CMakeLists.txt
@@ -1,135 +1,152 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Jun 09 2014
# @date last modification: Thu Jul 03 2014
#
# @brief Build the documentation
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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/>.
#
#===============================================================================
#------------------------------------------------------------------------------#
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}}\\xspace")
math(EXPR _sub_level "${LEVEL}+1")
_package_get_dependencies(${pkg_name} _dependencies)
foreach(_dep_pkg_name ${_dependencies})
generate_package_dependency_tex_doc(${_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)
- file(APPEND ${FILENAME} "{\\color{red} TODO}: No Documentation in {\\color{blue} \\href{${_file_path}}{${_file}}}\\\\")
- file(APPEND ${FILENAME} "looking for the sequence: \\code{\\\\package\\_declare\\_documentation(${_pkg} \" documentation text \" )}" )
+ string(REPLACE "_" "\\_" _escaped_pkg "${_pkg}")
+
+ set(_missing_doc
+ "{\\color{red} TODO}: No Documentation in {\\color{blue} \\href{${_file_path}}{${_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} _dependencies)
if(_dependencies)
file(APPEND ${FILENAME} "\n\\begin{AkantuPackageDependencies}")
foreach(_dep_pkg_name ${_dependencies})
generate_package_dependency_tex_doc(${_dep_pkg_name} ${FILENAME} 1)
endforeach()
file(APPEND ${FILENAME} "\n\\end{AkantuPackageDependencies}")
endif()
file(APPEND ${FILENAME} "\n\\end{AkantuPackage}
")
endfunction()
#------------------------------------------------------------------------------#
#------------------------------------------------------------------------------#
set(DOC_DEPS_TEX_FILENAME "${CMAKE_CURRENT_BINARY_DIR}/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)
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}/manual.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 -Wall manual
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMENT "Compiling the user's manual"
)
add_custom_target(manual ALL DEPENDS ${MANUAL_OUTPUT})
install(FILES ${MANUAL_OUTPUT} DESTINATION share/akantu/doc)
package_get_all_activated_packages(_package_list)
foreach (_pkg_name ${_package_list})
generate_package_tex_doc(${_pkg_name} ${DOC_DEPS_TEX_FILENAME})
endforeach()
diff --git a/doc/manual/manual-heattransfermodel.tex b/doc/manual/manual-heattransfermodel.tex
index 473878c24..359d8dbcc 100644
--- a/doc/manual/manual-heattransfermodel.tex
+++ b/doc/manual/manual-heattransfermodel.tex
@@ -1,166 +1,166 @@
\chapter{Heat Transfer Model}
The heat transfer model is a specific implementation of the \code{Model} interface
dedicated to handle the dynamic heat equation.
\section{Theory}
The strong form of the dynamic heat equation
can be expressed as
\begin{equation}
\rho c_v \dot{T} + \nabla \cdot \vec{\kappa} \nabla T = b
\end{equation}
with $T$ the scalar temperature field,
$c_v$ the specific heat capacity,
$\rho$ the mass density,
$\mat{\kappa}$ the conductivity tensor, and $b$ the heat generation per unit of volume.
The discretized weak form with a finite number of elements is
\begin{equation}
\forall i \quad
\sum_j \left( \int_\Omega \rho c_v N_j N_i d\Omega \right) \dot{T}_j
- \sum_j \left( \int_\Omega \vec{\kappa} \nabla N_j \nabla N_i d\Omega \right) T_j =
- \int_{\Gamma} N_i \vec{q} \cdot \vec{n} d\Gamma + \int_\Omega b N_i d\Omega
\end{equation}
with $i$ and $j$ the node indices, $\vec{n}$ the normal field to the surface
$\Gamma = \partial \Omega$.
To simplify, we can define the capacity and the conductivity matrices as
\begin{equation}
C_{ij} = \int_\Omega \rho c_v N_j N_i d\Omega \qquad \textrm{and} \qquad
K_{ij} = - \int_\Omega \vec{\kappa} \nabla N_j \nabla N_i d\Omega
\end{equation}
and the system to solve can be written
\begin{equation}
\mat{C} \cdot \vec{\dot{T}} = \vec{Q}^{\text{ext}} -\mat{K} \cdot \vec{T}~,
\end{equation}
with $\vec{Q}^{\text{ext}}$ the consistent heat generated.
\section{Using the Heat Transfer Model}
Currently, the \code{HeatTransferModel} object uses dynamic analysis
with an explicit time integration scheme. It can simply be created
like this
\begin{cpp}
HeatTransferModel model(mesh, spatial_dimension);
\end{cpp}
while an existing mesh has been used (see \ref{sect:common:mesh}).
Then the model object can be initialized with:
\begin{cpp}
model.initFull()
\end{cpp}
where a material file name has to be provided. This function will load the material
properties, and allocate / initialize the nodes and element \code{Array}s
More precisely, the heat transfer model contains 4 \code{Arrays}:
\begin{description}
\item[temperature] contains the nodal temperature $T$ (zero by default after the
initialization).
\item[temperature\_rate] contains the variations of temperature $\dot{T}$
(zero by default after the
initialization).
\item[blocked\_dofs] contains a Boolean value for each degree of
freedom specifying whether the degree is blocked or not. A Dirichlet
boundary condition can be prescribed by setting the
\textbf{blocked\_dofs} value of a degree of freedom to \code{true}.
The \textbf{temperature} and the \textbf{temperature\_rate} are
computed for all degrees of freedom where the \textbf{blocked\_dofs}
value is set to \code{false}. For the remaining degrees of freedom,
the imposed values (zero by default after initialization) are kept.
\item[residual] contains the difference between external and internal heat generations.
The \textbf{residual} contains the supported heat reactions ($\vec{R} = \vec{Q^{ext}} -\mat{K} \cdot \vec{T}$) on
the nodes that the temperature imposed.
\end{description}
Only a single material can be specified on the domain.
A material text file (\eg material.dat) provides the material properties as follows:
\begin{cpp}
heat %\emph{name\_material}% [
capacity = %\emph{XXX}%
density = %\emph{XXX}%
conductivity = [%\emph{XXX}% ... %\emph{XXX}%]
]
\end{cpp}
where the \code{capacity} and \code{density} are scalars, and the \code{conductivity} is specified as a $3\times 3$ tensor.
\subsection{Explicit Dynamic}
The explicit time integration scheme in \akantu uses a lumped capacity
matrix $\mat{C}$ (reducing the computational cost, see Chapter \ref{sect:smm}).
This matrix is assembled by
distributing the capacity of each element onto its nodes. Therefore, the resulting $\mat{C}$ is a diagonal matrix stored in the \code{capacity} \code{Array} of the model.
\begin{cpp}
model.assembleCapacityLumped();
\end{cpp}
\index{HeatTransferModel!assembleCapacityLumped}
\note{Currently, only the explicit time integration with lumped capacity matrix
-is implemented within \akantu.} \\
+is implemented within \akantu.}
The explicit integration scheme is \index{Forward Euler} \emph{Forward Euler}
\cite{curnier92a}.
\begin{itemize}
\item Predictor: $\vec{T}_{n+1} = \vec{T}_{n} + \Delta t \dot{\vec{T}}_{n}$
\item Update residual: $\vec{R}_{n+1} = \left( \vec{Q^{ext}_{n+1}} - \vec{K}\vec{T}_{n+1} \right)$
\item Corrector : $\dot{\vec{T}}_{n+1} = \mat{C}^{-1} \vec{R}_{n+1}$
\end{itemize}
The explicit integration scheme is conditionally stable. The time step has to be smaller than the stable time step,
and it can be obtained in \akantu as follows:
\begin{cpp}
time_step = model.getStableTimeStep();
\end{cpp}
\index{HeatTransferModel!StableTimeStep}
The stable time step is defined as:
\begin{equation}\label{eqn:htm:explicit:stabletime}
\Delta t_{\st{crit}} = 2 \Delta x^2 \frac{\rho c_v}{\mid\mid \mat{\kappa} \mid\mid^\infty}
\end{equation}
where $\Delta x$ is the characteristic length (\eg the inradius in the
case of linear triangle element), $\rho$ is the density,
$\mat{\kappa}$ is the conductivity tensor, and $c_v$ is the specific
heat capacity. It is necessary to impose a time step which is smaller
than the stable time step, for instance, by multiplying the stable
time step by a safety factor smaller than one.
\begin{cpp}
const Real safety_time_factor = 0.1;
Real applied_time_step = time_step * safety_time_factor;
model.setTimeStep(applied_time_step);
\end{cpp}
The following loop allows, for each time step, to update the \code{temperature}, \code{residual} and
\code{temperature\_rate} fields following the previously described integration scheme.
\begin{cpp}
for (UInt s = 1; (s-1)*applied_time_step < total_time; ++s) {
model.explicitPred();
model.updateResidual();
model.explicitCorr();
}
\end{cpp}
\index{HeatTransferModel!explicitPred}
\index{HeatTransferModel!explicitCorr}
\index{HeatTransferModel!updateResidual}
\index{HeatTransferModel!solveExplicitLumped}
An example of explicit dynamic heat propagation is presented in \\
\shellcode{\examplesdir/heat\_transfer/explicit\_heat\_transfer.cc}. \\
This example consists of a square 2D plate of \SI{1}{\metre^2}
having an initial temperature of \SI{100}{\kelvin} everywhere but a
none centered hot point maintained at
\SI{300}{\kelvin}. Figure~\ref{fig:htm:explicit:dynamic} presents
the geometry of this case. The material used is a linear fictitious
elastic material with a density of
\SI{8940}{\kilo\gram\per\metre^3}, a conductivity of
\SI{401}{\watt\per\metre\per\kelvin} and a specific heat capacity of
\SI{385}{\joule\per\kelvin\per\kilogram}. The time step used is
\SI{0.12}{\second}.
\begin{figure}[!htb]
\centering
\includegraphics[width=.4\textwidth]{figures/hot-point-1}
\hfill
\includegraphics[width=.4\textwidth]{figures/hot-point-2}
\caption{Initial temperature field (left) and after 15000 time steps = 30 minutes (right). The lines represent iso-surfaces.}
\label{fig:htm:explicit:dynamic}
\end{figure}
diff --git a/doc/manual/manual-parallel.tex b/doc/manual/manual-parallel.tex
index 588a6aa49..bfd89a089 100644
--- a/doc/manual/manual-parallel.tex
+++ b/doc/manual/manual-parallel.tex
@@ -1,113 +1,113 @@
\chapter{Parallel Computation}
This section explains how to launch a parallel computation.
The strategy adopted by \akantu uses a mesh partitioning
where elements are mapped to processors. Mesh partitions are
then distributed to available processors by adequate routines
as will be described below.
The sequence of additional operations to be performed by the user are:
\begin{itemize}
\item Initializing the parallel context
\item Partitioning the mesh
\item Distributing mesh partitions
\end{itemize}
After these steps, the \code{Model}
object proceeds with the interprocess communication automatically
without the user having to explicitly take care of them.
In what follows we show how it works on a \code{SolidMechanics} model.
\section{Initializing the Parallel Context}
The user must initialize \akantu by forwarding the arguments passed to the
program by using the function \code{initialize}, and close \akantu instances
-at the end of the program by calling the \code{finalize} function.\\
+at the end of the program by calling the \code{finalize} function.
\note{This step does not change from the sequential case as it was stated in
-Section \ref{sect:common:main}. It only gives a additional motivation in the parallel/MPI context.}\\
+Section \ref{sect:common:main}. It only gives a additional motivation in the parallel/MPI context.}
The \code{initialize} function builds a \code{StaticCommunicator} object
responsible for handling the interprocess communications later on. The
\code{StaticCommunicator} can, for instance, be used to ask the total number of
declared processors available for computations as well as the process rank
through the functions \code{getNbProc} and \code{whoAmI} respectively.
An example of the initializing sequence and basic usage of the
\code{StaticCommunicator} is:
\begin{cpp}
int main(int argc, char *argv[])
{
initialize("material.dat", argc, argv);
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
...
finalize();
}
\end{cpp}
\section{Partitioning the Mesh}
The mesh is partitioned after the correct initialization of the
processes playing a role in the computation. We assume that a
\code{Mesh} object is constructed as presented in
Section~\ref{sect:common:mesh}. Then a partition must be computed by
using an appropriate mesh partitioner. At present time, the only
partitioner available is \code{MeshPartitionScotch} which implements
the function \code{partitionate} using the
\textbf{Scotch}\cite{scotch} program. This is achieved by the
following code
\begin{cpp}
Mesh mesh(spatial_dimension);
MeshPartition * partition = NULL;
if(prank == 0) {
mesh.read("my_mesh.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
\end{cpp}
\note{Only the processor of rank $0$ should load the mesh file to
partition it. Nevertheless, the \code{Mesh} object must by declared
for all processors since the mesh distribution will store mesh pieces to that object.}
\section{Distributing Mesh Partitions}
The distribution of the mesh is done automatically by the
\code{SolidMechanicsModel} through the \code{initParallel} method. Thus,
after creating a \code{SolidMechanicsModel} with our mesh as the initial
parameter, the \code{initParallel} method must be called receiving the partition
as a parameter.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initParallel(partition);
\end{cpp}
After that point, everything remains as in the sequential case from
the user point of view. This allows the user to care only
about his simulation without concern for the parallelism.
An example of an explicit dynamic 2D bar in compression in a parallel
context can be found in \shellcode{\examplesdir/parallel\_2d}.
\section{Launching a Parallel Program}
Using \textbf{MPI} a parallel run can be launched from a shell
using the command
\begin{cpp}
mpirun -np #procs program_name parameter1 parameter2 ...
\end{cpp}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "manual"
%%% End:
diff --git a/doc/manual/manual-solidmechanicsmodel.tex b/doc/manual/manual-solidmechanicsmodel.tex
index d265c744d..06ffe06b0 100644
--- a/doc/manual/manual-solidmechanicsmodel.tex
+++ b/doc/manual/manual-solidmechanicsmodel.tex
@@ -1,1040 +1,1040 @@
\chapter{Solid Mechanics Model\index{SolidMechanicsModel}\label{sect:smm}}
The solid mechanics model is a specific implementation of the
\code{Model} interface dedicated to handle the equations of motion or
equations of equilibrium. The model is created for a given mesh. It
will create its own \code{FEEngine} object to compute the interpolation,
gradient, integration and assembly operations. A
\code{SolidMechanicsModel} object can simply be created like this:
\begin{cpp}
SolidMechanicsModel model(mesh);
\end{cpp}
where \code{mesh} is the mesh for which the equations are to be
solved. A second parameter called \code{spatial\_dimension} can be
added after \code{mesh} if the spatial dimension of the problem is
different than that of the mesh.
This model contains at least the the following six \code{Arrays}:
\begin{description}
\item[blocked\_dofs] contains a Boolean value for each degree of
freedom specifying whether that degree is blocked or not. A
Dirichlet boundary condition can be prescribed by setting the
\textbf{blocked\_dofs} value of a degree of freedom to \code{true}.
A Neumann boundary condition can be applied by setting the
\textbf{blocked\_dofs} value of a degree of freedom to \code{false}.
The \textbf{displacement}, \textbf{velocity} and
\textbf{acceleration} are computed for all degrees of freedom for
which the \textbf{blocked\_dofs} value is set to \code{false}. For
the remaining degrees of freedom, the imposed values (zero by
default after initialization) are kept.
\item[displacement] contains the displacements of all degrees of
freedom. It can be either a computed displacement for free degrees
of freedom or an imposed displacement in case of blocked ones
($\vec{u}$ in the following).
\item[velocity] contains the velocities of all degrees of freedom. As
\textbf{displacement}, it contains computed or imposed velocities
depending on the nature of the degrees of freedom ($\dot{\vec{u}}$
in the following).
\item[acceleration] contains the accelerations of all degrees of
freedom. As \textbf{displacement}, it contains computed or imposed
accelerations depending on the nature of the degrees of freedom
($\ddot{\vec{u}}$ in the following).
\item[force] contains the external forces applied on the nodes
($\vec{f}_{\st{ext}}$ in the following).
\item[residual] contains the difference between external and internal
forces. On blocked degrees of freedom, \textbf{residual} contains
the support reactions. ($\vec{r}$ in the following). It should be
mentioned that at equilibrium \textbf{residual} should be zero on
free degrees of freedom.
\end{description}
Some examples to help to understand how to use this model will be
presented in the next sections.
\section{Model Setup}
\subsection{Setting Initial Conditions \label{sect:smm:initial_condition}}
For a unique solution of the equations of motion, initial
displacements and velocities for all degrees of freedom must be
specified:
\begin{eqnarray}
\vec{u}(t=0) = \vec{u}_0\\
\dot{\vec u}(t=0) =\vec{v}_0
\end{eqnarray} The solid mechanics model can be initialized as
follows:
\begin{cpp}
model.initFull()
\end{cpp}
This function initializes the internal arrays and sets them to
zero. Initial displacements and velocities that are not equal to zero
can be prescribed by running a loop over the total number of
nodes. Here, the initial displacement in $x$-direction and the
initial velocity in $y$-direction for all nodes is set to $0.1$ and $1$,
respectively.
\begin{cpp}
Array<Real> & disp = model.getDisplacement();
Array<Real> & velo = model.getVelocity();
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
disp(i, 0) = 0.1;
velo(i, 1) = 1.;
}
\end{cpp}
\subsection{Setting Boundary Conditions\label{sect:smm:boundary}}
This section explains how to impose Dirichlet or Neumann boundary
conditions. A Dirichlet boundary condition specifies the values that
the displacement needs to take for every point $x$ at the boundary
($\Gamma_u$) of the problem domain (Fig.~\ref{fig:smm:boundaries}):
\begin{equation}
\vec{u} = \bar{\vec u} \quad \forall \vec{x}\in
\Gamma_{u}
\end{equation}
A Neumann boundary condition imposes the value of the gradient of the
solution at the boundary $\Gamma_t$ of the problem domain
(Fig.~\ref{fig:smm:boundaries}):
\begin{equation}
\vec{t} = \mat{\sigma} \vec{n} = \bar{\vec t} \quad
\forall \vec{x}\in \Gamma_{t}
\end{equation}
\begin{figure} \centering
\def\svgwidth{0.5\columnwidth}
\input{figures/problemDomain.pdf_tex}
\caption{Problem domain $\Omega$ with boundary in three
dimensions. The Dirchelet and the Neumann regions of the boundary
are denoted with $\Gamma_u$ and $\Gamma_t$,
respecitvely.\label{fig:smm:boundaries}}
\label{fig:problemDomain}
\end{figure}
Different ways of imposing these boundary conditions exist. A basic
way is to loop over nodes or elements at the boundary and apply local
values. A more advanced method consists of using the notion of the
boundary of the mesh. In the following both ways are presented.
Starting with the basic approach, as mentioned, the Dirichlet boundary
conditions can be applied by looping over the nodes and assigning the
required values. Figure~\ref{fig:smm:dirichlet_bc} shows a beam with a
fixed support on the left side. On the right end of the beam, a load
is applied. At the fixed support, the displacement has a given
value. For this example, the displacements in both the $x$ and the
$y$-direction are set to zero. Implementing this displacement boundary
condition is similar to the implementation of initial displacement
conditions described above. However, in order to impose a displacement
boundary condition for all time steps, the corresponding nodes need to
be marked as boundary nodes as shown in the following code:
\begin{cpp}
Array<bool> & blocked = model.getBlockedDOFs();
const Array<Real> & pos = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt i = 0; i < nb_nodes; ++i) {
if(Math::are_float_equal(pos(i, 0), 0)) {
blocked(i, 0) = true; //block displacement in x-direction
blocked(i, 1) = true; //block displacement in y-direction
disp(i, 0) = 0.; //fixed displacement in x-direction
disp(i, 1)= 0.; //fixed displacement in y-direction
}
}
\end{cpp}
\begin{figure}[!htb]
\centering
\includegraphics[scale=0.4]{figures/dirichlet}
\caption{Beam with fixed support.\label{fig:smm:dirichlet_bc}}
\end{figure}
For the more advanced approach, one needs the notion of a boundary in
the mesh. Therefore, the boundary should be created before boundary
condition functors can be applied. Generally the boundary can be
specified from the mesh file or the geometry. For the first case, the
function \code{createGroupsFromMeshData} is called. This function
can read any types of mesh data which are provided in the mesh
file. If the mesh file is created with Gmsh, the function takes one
input strings which is either \code{tag\_0}, \code{tag\_1} or
\code{physical\_names}. The first two tags are assigned by Gmsh to
each element which shows the physical group that they belong to. In
Gmsh, it is also possible to consider strings for different groups of
elements. These elements can be separated by giving a string
\code{physical\_names} to the function
\code{createGroupsFromMeshData}. Boundary conditions can also be
created from the geometry by calling
\code{createBoundaryGroupFromGeometry}. This function gathers all the
elements on the boundary of the geometry.
To apply the required boundary conditions, the function \code{applyBC}
needs to be called on a \code{SolidMechanicsModel}. This function
gets a Dirichlet or Neumann functor and a string which specifies the
desired boundary on which the boundary conditions is to be
applied. The functors specify the type of conditions to apply. Three
built-in functors for Dirichlet exist: \code{FlagOnly, FixedValue,}
and \code{IncrementValue}. The functor \code{FlagOnly} is used if a
point is fixed in a given direction. Therefore, the input parameter to
this functor is only the fixed direction. The \code{FixedValue}
functor is used when a displacement value is applied in a fixed
direction. The \code{IncrementValue} applies an increment to the
displacement in a given direction. The following code shows the
utilization of three functors for the top, bottom and side surface of
the mesh which were already defined in the Gmsh file:
\begin{cpp}
mesh.createGroupsFromMeshData<std::string>("physical_names");
model.applyBC(BC::Dirichlet::FixedValue(13.0, BC::_y), "Top");
model.applyBC(BC::Dirichlet::FlagOnly(BC::_x), "Bottom");
model.applyBC(BC::Dirichlet::IncrementValue(13.0, BC::_x), "Side");
\end{cpp}
To apply a Neumann boundary condition, the applied traction or stress
should be specified before. In case of specifying the traction on the
surface, the functor \code{FromTraction} of Neumann boundary
conditions is called. Otherwise, the functor \code{FromStress} should
be called which gets the stress tensor as an input parameter.
\begin{cpp}
Array<Real> surface_traction(3);
surface_traction(0)=0.0;
surface_traction(1)=0.0;
surface_traction(2)=-1.0;
-Array<Real> surface_stress(3, 3, 0.0);
+Matrix<Real> surface_stress(3, 3, 0.0);
surface_stress(0,0)=0.0;
surface_stress(1,1)=0.0;
surface_stress(2,2)=-1.0;
model.applyBC(BC::Neumann::FromTraction(surface_traction), "Bottom");
model.applyBC(BC::Neumann::FromStress(surface_stress), "Top");
\end{cpp}
If the boundary conditions need to be removed during the simulation, a
functor is called from the Neumann boundary condition to free those
boundary conditions from the desired boundary.
\begin{cpp}
model.applyBC(BC::Neumann::FreeBoundary(), "Side");
\end{cpp}
User specified functors can also be implemented. A full example for
setting both initial and boundary conditions can be found in
\shellcode{\examplesdir/boundary\_conditions.cc}. The problem solved
in this example is shown in Fig.~\ref{fig:smm:bc_and_ic}. It consists
of a plate that is fixed with movable supports on the left and bottom
side. On the right side, a traction, which increases linearly with the
number of time steps, is applied. The initial displacement and
velocity in $x$-direction at all free nodes is zero and two
respectively.
\begin{figure}[!htb]
\centering
\includegraphics[scale=0.8]{figures/bc_and_ic_example}
\caption{Plate on movable supports.\label{fig:smm:bc_and_ic}}
\end{figure}
\subsection{Material Selector\label{sect:smm:materialselector}}
If the user wants to assign different materials to the different
finite elements of choice in \akantu, a material selector has to be
used. By default, \akantu assigns the first valid material in the
material file to all elements present in the model (regular continuum
materials are assigned to the regular elements and cohesive materials
are assigned to cohesive elements or element facets).
To assign different materials to specific elements, mesh data
information such as tag information or specified pyhsical names can be
used. \code{MeshDataMaterialSelector} class uses this information to
assign different materials. With the proper physical name or tag name
and index, different materials can be assigned as demonstrated in the
examples below.
\begin{cpp}
MeshDataMaterialSelector<std::string> * mat_selector;
mat_selector = new MeshDataMaterialSelector<std::string>("physical_names", model);
model.setMaterialSelector(*mat_selector);
\end{cpp}
In this example the physical names specified in a GMSH geometry file will by
used to match the material names in the input file.
Another example would be:
\begin{cpp}
MeshDataMaterialSelector<UInt> * mat_selector;
mat_selector = new MeshDataMaterialSelector<UInt>("tag_1", model);
model.setMaterialSelector(*mat_selector);
\end{cpp}
where \code{tag\_1} of the mesh file is used as the classifier index
and the elements that have index value equal to one will be assigned
to the second material in the material file.
There are four different material selectors pre-defined in
\akantu. \code{MaterialSelector} and \code{DefaultMaterialSelector} is
used to assign a material to regular elements by default. For the
regular elements, as in the example above,
\code{MeshDataMaterialSelector} can be used to assign different
materials to different elements. However, for cohesive elements, it is
not possible to assign multiple cohesive materials automatically and
user has to write a custom class. \akantu has a pre-defined material
selector to assign the first cohesive material by default to the
cohesive elements which is called
\code{DefaultMaterialCohesiveSelector} and it inherits its properties
from \code{DefaultMaterialSelector}. This material selector first
checks if an element is a cohesive element or a facet. If there is,
then the first cohesive material in the material file is assigned to
that element. Otherwise, this material is assigned to the element
facet, to which, a cohesive element might be inserted later. Hence,
this material selector works for the extrinsic cohesive elements which
are dynamically inserted throughout the analysis. If the element of
interest is not a cohesive element or an element facet, then
\code{DefaultMaterialSelector} is used by default.
Apart from the \akantu's default material selectors, users can always
develop their own classes in the main code to tackle various
multi-material assignment situations.
% An application of \code{DefaultMaterialCohesiveSelector} and usage in
% a customly generated material selector class can be seen in
% \shellcode{\examplesdir/cohesive\_element/cohesive\_extrinsic\_IG\_TG/cohesive\_extrinsic\_IG\_TG.cc}.
\IfFileExists{manual-cohesive_elements_insertion.tex}{\input{manual-cohesive_elements_insertion}}{}
\section{Static Analysis\label{sect:smm:static}}
The \code{SolidMechanicsModel} class can handle different analysis
methods, the first one being presented is the static case. In this
case, the equation to solve is
\begin{equation}
\label{eqn:smm:static} \mat{K} \vec{u} =
\vec{f}_{\st{ext}}
\end{equation}
where $\mat{K}$ is the global stiffness matrix, $\vec{u}$ the
displacement vector and $\vec{f}_{\st{ext}}$ the vector of external
forces applied to the system.
To solve such a problem, the static solver of the
\code{SolidMechanicsModel}\index{SolidMechanicsModel} object is used.
First, a model has to be created and initialized. To create the
model, a mesh (which can be read from a file) is needed, as explained
in Section~\ref{sect:common:mesh}. Once an instance of a
\code{SolidMechanicsModel} is obtained, the easiest way to initialize
it is to use the \code{initFull}\index{SolidMechanicsModel!initFull}
method by giving the \code{SolidMechanicsModelOptions}. These options
specify the type of analysis to be performed and whether the materials
should be initialized or not.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(SolidMechanicsModelOptions(_static));
\end{cpp}
Here, a static analysis is chosen by passing the argument
\code{\_static} to the method. By default, the Boolean for no
initialization of the materials is set to false, so that they are
initialized during the \code{initFull}. The method \code{initFull}
also initializes all appropriate vectors to zero. Once the model is
created and initialized, the boundary conditions can be set as
explained in Section~\ref{sect:smm:boundary}. Boundary conditions
will prescribe the external forces for some free degrees of freedom
$\vec{f}_{\st{ext}}$ and displacements for some others. At this point
of the analysis, the function
\code{solveStep}\index{SolidMechanicsModel!solveStep} can be called:
\begin{cpp}
model.solveStep<_scm_newton_raphson_tangent_modified, _scc_residual>(1e-4, 1);
\end{cpp}
This function is templated by the solving method and the convergence
criterion and takes two arguments: the tolerance and the maximum
number of iterations, which are $\num{1e-4}$ and $1$ for this example. The
modified Newton-Raphson method is chosen to solve the system. In this
method, the equilibrium equation (\ref{eqn:smm:static}) is modified in
order to apply a Newton-Raphson convergence algorithm:
\begin{align}\label{eqn:smm:static-newton-raphson}
\mat{K}^{i+1}\delta\vec{u}^{i+1} &= \vec{r} \\
&= \vec{f}_{\st{ext}} -\vec{f}_{\st{int}}\\
&= \vec{f}_{\st{ext}} - \mat{K}^{i} \vec{u}^{i}\\
\vec{u}^{i+1} &= \vec{u}^{i} + \delta\vec{u}^{i+1}~,\nonumber
\end{align}
where $\delta\vec{u}$ is the increment of displacement to be added
from one iteration to the other, and $i$ is the Newton-Raphson
iteration counter. By invoking the \code{solveStep} method in the
first step, the global stiffness matrix $\mat{K}$ from
Equation~(\ref{eqn:smm:static}) is automatically assembled. A
Newton-Raphson iteration is subsequently started, $\mat{K}$ is updated
according to the displacement computed at the previous iteration and
one loops until the forces are balanced (\code{\_scc\_residual}), \ie
$||\vec{r}|| < \mbox{\code{\_scc\_residual}}$. One can also iterate
until the increment of displacement is zero (\code{\_scc\_increment})
which also means that the equilibrium is found. For a linear elastic
problem, the solution is obtained in one iteration and therefore the
maximum number of iterations can be set to one. But for a non-linear
case, one needs to iterate as long as the norm of the residual exceeds
the tolerance threshold and therefore the maximum number of iterations
has to be higher, e.g. $100$:
\begin{cpp}
model.solveStep<_scm_newton_raphson_tangent_modified,_scc_residual>(1e-4, 100)
\end{cpp}
At the end of the analysis, the final solution is stored in the
\textbf{displacement} vector. A full example of how to solve a static
problem is presented in the code \code{\examplesdir/static/static.cc}.
This example is composed of a 2D plate of steel, blocked with rollers
on the left and bottom sides as shown in Figure \ref{fig:smm:static}.
The nodes from the right side of the sample are displaced by $0.01\%$
of the length of the plate.
\begin{figure}[!htb]
\centering
\includegraphics[scale=1.05]{figures/static}
\caption{Numerical setup\label{fig:smm:static}}
\end{figure}
The results of this analysis is depicted in
Figure~\ref{fig:smm:implicit:static_solution}.
\begin{figure}[!htb]
\centering
\includegraphics[width=.7\linewidth]{figures/static_analysis}
\caption{Solution of the static analysis. Left: the initial
condition, right: the solution (deformation magnified 50 times)}
\label{fig:smm:implicit:static_solution}
\end{figure}
\section{Dynamic Methods} \label{sect:smm:Dynamic_methods}
Different ways to solve the equations of motion are implemented in the
solid mechanics model. The complete equations that should be solved
are:
\begin{equation}
\label{eqn:equation-motion}
\mat{M}\ddot{\vec{u}} +
\mat{C}\dot{\vec{u}} + \mat{K}\vec{u} = \vec{f}_{\st{ext}}~,
\end{equation}
where $\mat{M}$, $\mat{C}$ and $\mat{K}$ are the mass,
damping and stiffness matrices, respectively.
In the previous section, it has already been discussed how to solve this
equation in the static case, where $\ddot{\vec{u}} = \dot{\vec{u}} = 0$. Here
the method to solve this equation in the general case will be presented. For
this purpose, a time discretization has to be specified. The most common
discretization method in solid mechanics is the Newmark-$\beta$ method, which is
also the default in \akantu.
For the Newmark-$\beta$ method, (\ref{eqn:equation-motion}) becomes a
system of three equations (see \cite{curnier92a} \cite{hughes-83a} for
more details):
\begin{align}
\mat{M} \ddot{\vec{u}}_{n+1} + \mat{C}\dot{\vec{u}}_{n+1} + \mat{K} \vec{u}_{n+1} &={\vec{f}_{\st{ext}}}_{\, n+1}
\label{eqn:equation-motion-discret} \\
\vec{u}_{n+1} &=\vec{u}_{n} + \left(1 - \alpha\right) \Delta t \dot{\vec{u}}_{n} +
\alpha \Delta t \dot{\vec{u}}_{n+1} + \left(\frac{1}{2} -
\alpha\right) \Delta t^2
\ddot{\vec{u}}_{n} \label{eqn:finite-difference-1}\\
\dot{\vec{u}}_{n+1} &= \dot{\vec{u}}_{n} + \left(1 - \beta\right)
\Delta t \ddot{\vec{u}}_{n} + \beta \Delta t
\ddot{\vec{u}}_{n+1} \label{eqn:finite-difference-2}
\end{align}
In these new equations, $\ddot{\vec{u}}_{n}$, $\dot{\vec{u}}_{n}$ and
$\vec{u}_{n}$ are the approximations of $\ddot{\vec{u}}(t_n)$,
$\dot{\vec{u}}(t_n)$ and $\vec{u}(t_n)$.
Equation~(\ref{eqn:equation-motion-discret}) is the equation of motion
discretized in space (finite-element discretization), and equations
(\ref{eqn:finite-difference-1}) and (\ref{eqn:finite-difference-2})
are discretized in both space and time (Newmark discretization). The
$\alpha$ and $\beta$ parameters determine the stability and the
accuracy of the algorithm. Classical values for $\alpha$ and $\beta$
are usually $\beta = 1/2$ for no numerical damping and $0 < \alpha <
1/2$.
\begin{center}
\begin{tabular}{cll}
\toprule
$\alpha$ & Method ($\beta = 1/2$) & Type\\
\midrule
$0$ & central difference & explicit\\
$1/6$ & Fox-Goodwin (royal road) &implicit\\
$1/3$ & Linear acceleration &implicit\\
$1/2$ & Average acceleration (trapezoidal rule)& implicit\\
\bottomrule
\end{tabular}
\end{center}
The solution of this system of equations,
(\ref{eqn:equation-motion-discret})-(\ref{eqn:finite-difference-2}) is
split into a predictor and a corrector system of equations. Moreover,
in the case of a non-linear equations, an iterative algorithm such as
the Newton-Raphson method is applied. The system of equations can be
written as:
\begin{enumerate}
\item \textit{Predictor:}
\begin{align}
\vec{u}_{n+1}^{0} &= \vec{u}_{n} + \Delta t
\dot{\vec{u}}_{n} + \frac{\Delta t^2}{2} \ddot{\vec{u}}_{n} \\
\dot{\vec{u}}_{n+1}^{0} &= \dot{\vec{u}}_{n} + \Delta t
\ddot{\vec{u}}_{n} \\
\ddot{\vec{u}}_{n+1}^{0} &= \ddot{\vec{u}}_{n}
\end{align}
\item \textit{Solve:}
\begin{align}
\left(c \mat{M} + d \mat{C} + e \mat{K}_{n+1}^i\right)
\vec{w} = {\vec{f}_{\st{ext}}}_{\,n+1} - {\vec{f}_{\st{int}}}_{\,n+1}^i -
\mat{C} \dot{\vec{u}}_{n+1}^i - \mat{M} \ddot{\vec{u}}_{n+1}^i = \vec{r}_{n+1}^i
\end{align}
\item \textit{Corrector:}
\begin{align}
\ddot{\vec{u}}_{n+1}^{i+1} &= \ddot{\vec{u}}_{n+1}^{i} +c \vec{w} \\
\dot{\vec{u}}_{n+1}^{i+1} &= \dot{\vec{u}}_{n+1}^{i} + d\vec{w} \\
\vec{u}_{n+1}^{i+1} &= \vec{u}_{n+1}^{i} + e \vec{w}
\end{align}
\end{enumerate}
where $i$ is the Newton-Raphson iteration counter and $c$, $d$ and $e$
are parameters depending on the method used to solve the equations
\begin{center}
\begin{tabular}{lcccc}
\toprule
& $\vec{w}$ & $e$ & $d$ & $c$\\
\midrule
in acceleration &$ \delta\ddot{\vec{u}}$ & $\alpha \beta\Delta t^2$ &$\beta \Delta t$ &$1$\\
in velocity & $ \delta\dot{\vec{u}}$& $\frac{1}{\beta} \Delta t$ & $1$ & $\alpha\Delta t$\\
in displacement &$\delta\vec{u}$ & $ 1$ & $\frac{1}{\alpha} \Delta t$ & $\frac{1}{\alpha \beta} \Delta t^2$\\
\bottomrule
\end{tabular}
\end{center}
%\note{If you want to use the implicit solver \akantu should be compiled at least with one sparse matrix solver such as Mumps\cite{mumps}.}
\subsection{Implicit Time Integration}
To solve a problem with an implicit time integration scheme, first a
\code{SolidMechanicsModel} object has to be created and initialized.
Then the initial and boundary conditions have to be set. Everything
is similar to the example in the static case
(Section~\ref{sect:smm:static}), however, in this case the implicit
dynamic scheme is selected at the initialization of the model.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(SolidMechanicsModelOptions(_implicit_dynamic));
/*Boundary conditions see Section~%\ref{sect:smm:boundary}% */
\end{cpp}
Because a dynamic simulation is conducted, an integration time step
$\Delta t$ has to be specified. In the case of implicit simulations,
\akantu implements a trapezoidal rule by default. That is to say
$\alpha = 1/2$ and $\beta = 1/2$ which is unconditionally
stable. Therefore the value of the time step can be chosen arbitrarily
within reason. \index{SolidMechanicsModel!setTimeStep}
\begin{cpp}
model.setTimeStep(time_step);
\end{cpp}
Since the system has to be solved for a given amount of time, the
method \code{solveStep()}, (which has already been used in the static
example in Section~\ref{sect:smm:static}), is called inside a time
loop:
\begin{cpp}
/// time loop
Real time = 0.;
for (UInt s = 1; time <max_time; ++s, time += time_step) {
model.solveStep<_scm_newton_raphson_tangent_modified,_scc_increment>(1e-12, 100);
}
\end{cpp}
An example of solid mechanics with an implicit time integration scheme
is presented in
\shellcode{\examplesdir/implicit/implicit\_dynamic.cc}. This example
consists of a 3D beam of
$\SI{10}{\metre}\,\times\,\SI{1}{\metre}\,\times\,\SI{1}{\metre}$
blocked on one side and is on a roller on the other side. A constant
force of \SI{5}{\kilo\newton} is applied in its middle.
Figure~\ref{fig:smm:implicit:dynamic} presents the geometry of this
case. The material used is a fictitious linear elastic material with a
density of \SI{1000}{\kilo\gram\per\cubic\metre}, a Young's Modulus of
\SI{120}{\mega\pascal} and Poisson's ratio of $0.3$. These values
were chosen to simplify the analytical solution.
An approximation of the dynamic response of the middle point of the
beam is given by:
\begin{equation}
\label{eqn:smm:implicit}
u\left(\frac{L}{2}, t\right)
= \frac{1}{\pi^4} \left(1 - cos\left(\pi^2 t\right) +
\frac{1}{81}\left(1 - cos\left(3^2 \pi^2 t\right)\right) +
\frac{1}{625}\left(1 - cos\left(5^2 \pi^2 t\right)\right)\right)
\end{equation}
\begin{figure}[!htb]
\centering
\includegraphics[scale=.6]{figures/implicit_dynamic}
\caption{Numerical setup}
\label{fig:smm:implicit:dynamic}
\end{figure}
Figure \ref{fig:smm:implicit:dynamic_solution} presents the deformed
beam at 3 different times during the simulation: time steps 0, 1000 and
2000.
\begin{figure}[!htb]
\centering
\setlength{\unitlength}{0.1\textwidth}
\begin{tikzpicture}
\node[above right] (img) at (0,0)
{\includegraphics[width=.6\linewidth]{figures/dynamic_analysis}};
\node[left] at (0pt,20pt) {$0$}; \node[left] at (0pt,60pt) {$1000$};
\node[left] at (0pt,100pt) {$2000$};
\end{tikzpicture}
\caption{Deformed beam at 3 different times (displacement are
magnified by a factor 10).}
\label{fig:smm:implicit:dynamic_solution}
\end{figure}
\subsection{Explicit Time Integration}
\label{ssect:smm:expl-time-integr}
The explicit dynamic time integration scheme is based on the
Newmark-$\beta$ scheme with $\alpha=0$ (see equations
\ref{eqn:equation-motion-discret}-\ref{eqn:finite-difference-2}). In
\akantu, $\beta$ is defaults to $\beta=1/2$, see section
\ref{sect:smm:Dynamic_methods}.
The initialization of the simulation is similar to the static and
implicit dynamic version. The model is created from the
\code{SolidMechanicsModel} class. In the initialization, the explicit
scheme is selected using the \code{\_explicit\_lumped\_mass} constant.
\begin{cpp}
SolidMechanicsModel model(mesh);
model.initFull(SolidMechanicsModelOptions(_explicit_lumped_mass));
\end{cpp}
\index{SolidMechanicsModel!initFull}
\note{Writing \code{model.initFull()} or \code{model.initFull(SolidMechanicsModelOptions());} is
equivalent to use the \code{\_explicit\_lumped\_mass} keyword, as this
is the default case.}
The explicit time integration scheme implemented in \akantu uses a
lumped mass matrix $\mat{M}$ (reducing the computational cost). This
matrix is assembled by distributing the mass of each element onto its
nodes. The resulting $\mat{M}$ is therefore a diagonal matrix stored
in the \textbf{mass} vector of the model.
The explicit integration scheme is conditionally stable. The time step
has to be smaller than the stable time step which is obtained in
\akantu as follows:
\begin{cpp}
time_step = model.getStableTimeStep();
\end{cpp} \index{SolidMechanicsModel!StableTimeStep}
The stable time step is defined as:
\begin{equation}
\label{eqn:smm:explicit:stabletime}
\Delta t_{\st{crit}} = \Delta x \sqrt{\frac{\rho}{2 \mu + \lambda}}
\end{equation}
where $\Delta x$ is a characteristic length (\eg the inradius in the
case of linear triangle element), $\mu$ and $\lambda$ are the first
and second Lame's coefficients and $\rho$ is the density. The stable
time step corresponds to the time the fastest wave (the compressive
wave) needs to travel the characteristic length of the mesh.
However, it is recommended to impose a time step that is smaller than the stable time step, for
instance, by multiplying the stable time step by a safety factor
smaller than one.
\begin{cpp}
const Real safety_time_factor = 0.8;
Real applied_time_step = time_step * safety_time_factor;
model.setTimeStep(applied_time_step);
\end{cpp}
\index{SolidMechanicsModel!setTimeStep} The initial displacement and
velocity fields are, by default, equal to zero if not given
specifically by the user (see \ref{sect:smm:initial_condition}).
Like in implicit dynamics, a time loop is used in which the
displacement, velocity and acceleration fields are updated at each
time step. The values of these fields are obtained from the
Newmark$-\beta$ equations with $\beta=1/2$ and $\alpha=0$. In \akantu
these computations at each time step are invoked by calling the
function \code{solveStep}:
\begin{cpp}
for (UInt s = 1; (s-1)*applied_time_step < total_time; ++s) {
model.solveStep();
}
\end{cpp} \index{SolidMechanicsModel!solveStep}
The method
\code{solveStep} wraps the four following functions:
\begin{itemize}
\item \code{model.explicitPred()} allows to compute the displacement
field at $t+1$ and a part of the velocity field at $t+1$, denoted by
$\vec{\dot{u}^{\st{p}}}_{n+1}$, which will be used later in the method
\code{model.explicitCorr()}. The equations are:
\begin{align}
\vec{u}_{n+1} &= \vec{u}_{n} + \Delta t
\vec{\dot{u}}_{n} + \frac{\Delta t^2}{2} \vec{\ddot{u}}_{n}\\
\vec{\dot{u}^{\st{p}}}_{n+1} &= \vec{\dot{u}}_{n} + \Delta t
\vec{\ddot{u}}_{n}
\label{eqn:smm:explicit:onehalfvelocity}
\end{align}
\item \code{model.updateResidual()} and
\code{model.updateAcceleration()} compute the acceleration increment
$\delta \vec{\ddot{u}}$:
\begin{equation}
\left(\mat{M} + \frac{1}{2} \Delta t \mat{C}\right)
\delta \vec{\ddot{u}} = \vec{f_{\st{ext}}} - \vec{f}_{\st{int}\, n+1}
- \mat{C} \vec{\dot{u}}_{n} - \mat{M} \vec{\ddot{u}}_{n}
\end{equation}
\note{The internal force $\vec{f}_{\st{int}\, n+1}$ is computed from
the displacement $\vec{u}_{n+1}$ based on the constitutive law.}
\item \code{model.explicitCorr()} computes the velocity and
acceleration fields at $t+1$:
\begin{align}
\vec{\dot{u}}_{n+1} &= \vec{\dot{u}^{\st{p}}}_{n+1} + \frac{\Delta t}{2}
\delta \vec{\ddot{u}} \\ \vec{\ddot{u}}_{n+1} &=
\vec{\ddot{u}}_{n} + \delta \vec{\ddot{u}}
\end{align}
\end{itemize}
The use of an explicit time integration scheme is illustrated by the
example:\par
\noindent \shellcode{\examplesdir/explicit/explicit\_dynamic.cc}\par
\noindent This example models the propagation of a wave in a steel beam. The
beam and the applied displacement in the $x$ direction are shown in
Figure~\ref{fig:smm:explicit}.
\begin{figure}[!htb] \centering
\begin{tikzpicture}
\coordinate (c) at (0,2);
\draw[shift={(c)},thick, color=blue] plot [id=x, domain=-5:5, samples=50] ({\x, {(40 * sin(0.1*pi*3*\x) * exp(- (0.1*pi*3*\x)*(0.1*pi*3*\x) / 4))}});
\draw[shift={(c)},-latex] (-6,0) -- (6,0) node[right, below] {$x$};
\draw[shift={(c)},-latex] (0,-0.7) -- (0,1) node[right] {$u$};
\draw[shift={(c)}] (-0.1,0.6) node[left] {$A$}-- (1.5,0.6);
\coordinate (l) at (0,0.6);
\draw[shift={(0,-0.7)}] (-5, 0) -- (5,0) -- (5, 1) -- (-5, 1) -- cycle;
\draw[shift={(l)}, latex-latex] (-5,0)-- (5,0) node [midway, above] {$L$};
\draw[shift={(l)}] (5,0.2)-- (5,-0.2);
\draw[shift={(l)}] (-5,0.2)-- (-5,-0.2);
\coordinate (h) at (5.3,-0.7);
\draw[shift={(h)}, latex-latex] (0,0)-- (0,1) node [midway, right] {$h$};
\draw[shift={(h)}] (-0.2,1)-- (0.2,1);
\draw[shift={(h)}] (-0.2,0)-- (0.2,0);
\end{tikzpicture}
\caption{Numerical setup \label{fig:smm:explicit}}
\end{figure}
The length and height of the beam are $L=\SI{10}{\metre}$ and
$h = \SI{1}{\metre}$, respectively. The material is linear elastic,
homogeneous and isotropic (density:
\SI{7800}{\kilo\gram\per\cubic\metre}, Young's modulus:
\SI{210}{\giga\pascal} and Poisson's ratio: $0.3$). The imposed
displacement follow a Gaussian function with a maximum amplitude of $A = \SI{0.01}{\meter}$. The
potential, kinetic and total energies are computed. The safety factor
is equal to $0.8$.
\input{manual-constitutive-laws}
\section{Adding a New Constitutive Law}\index{Material!create a new
material}
There are several constitutive laws in \akantu as described in the
previous Section~\ref{sect:smm:CL}. It is also possible to use a
user-defined material for the simulation. These materials are referred
to as local materials since they are local to the example of the user
and not part of the \akantu library. To define a new local material,
two files (\code {material\_XXX.hh} and \code{material\_XXX.cc}) have
to be provided where \code{XXX} is the name of the new material. The
header file \code {material\_XXX.hh} defines the interface of your
custom material. Its implementation is provided in the
\code{material\_XXX.cc}. The new law must inherit from the
\code{Material} class or any other existing material class. It is
therefore necessary to include the interface of the parent material
in the header file of your local material and indicate the inheritance
in the declaration of the class:
\begin{cpp}
/* ---------------------------------------------------------------------- */
#include "material.hh"
/* ---------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_XXX_HH__
#define __AKANTU_MATERIAL_XXX_HH__
__BEGIN_AKANTU__
class MaterialXXX : public Material {
/// declare here the interface of your material
};
\end{cpp}
In the header file the user also needs to declare all the members of the new
material. These include the parameters that a read from the
material input file, as well as any other material parameters that will be computed during the simulation and internal variables.\\
In the following the example of adding a new damage material will be presented. In this
case the parameters in the material will consist of the Young's modulus, the
Poisson coefficient, the resistance to damage and the damage threshold. The
material will then from these values compute its Lam\'{e} coefficients and its
bulk modulus. Furthermore, the user has to add a new internal variable
\code{damage} in order to store the amount of damage at each quadrature point in
each step of the simulation. For this specific material the member declaration
inside the class will look as follows:
\begin{cpp}
class LocalMaterialDamage : public Material {
/// declare constructors/destructors here
/// declare methods and accessors here
/* -------------------------------------------------------------------- */
/* Class Members */
/* -------------------------------------------------------------------- */
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
private:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lame coefficient
Real lambda;
/// Second Lame coefficient (shear modulus)
Real mu;
/// resistance to damage
Real Yd;
/// damage threshold
Real Sd;
/// Bulk modulus
Real kpa;
/// damage internal variable
InternalField<Real> damage;
};
\end{cpp}
In order to enable to print the material parameters at any point in
the user's example file using the standard output stream by typing:
\begin{cpp}
for (UInt m = 0; m < model.getNbMaterials(); ++m)
std::cout << model.getMaterial(m) << std::endl;
\end{cpp}
the standard output stream operator has to be redefined. This should be done at the end of the header file:
\begin{cpp}
class LocalMaterialDamage : public Material {
/// declare here the interace of your material
}:
/* ---------------------------------------------------------------------- */
/* inline functions */
/* ---------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const LocalMaterialDamage & _this)
{
_this.printself(stream);
return stream;
}
\end{cpp}
However, the user still needs to register the material parameters that
should be printed out. The registration is done during the call of the
constructor. Like all definitions the implementation of the
constructor has to be written in the \code{material\_XXX.cc}
file. However, the declaration has to be provided in the
\code{material\_XXX.hh} file:
\begin{cpp}
class LocalMaterialDamage : public Material {
/* -------------------------------------------------------------------- */
/* Constructors/Destructors */
/* -------------------------------------------------------------------- */
public:
LocalMaterialDamage(SolidMechanicsModel & model, const ID & id = "");
};
\end{cpp}
The user can now define the implementation of the constructor in the
\code{material\_XXX.cc} file:
\begin{cpp}
/* ---------------------------------------------------------------------- */
#include "local_material_damage.hh"
#include "solid_mechanics_model.hh"
__BEGIN_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 Lame coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lame 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();
}
\end{cpp}
During the intializer list the reference to the model and the material id are
assigned and the constructor of the internal field is called. Inside the scope
of the constructor the internal values have to be initialized and the
parameters, that should be printed out, are registered with the function:
\code{registerParam}\index{Material!registerParam}:
\begin{cpp}
void registerParam(name of the parameter (key in the material file),
member variable,
default value (optional parameter),
access permissions,
description);
\end{cpp}
The available access permissions are as follows:
\begin{itemize}
\item \code{\_pat\_internal}: Parameter can only be output when the material is printed.
\item \code{\_pat\_writable}: User can write into the parameter. The parameter is output when the material is printed.
\item \code{\_pat\_readable}: User can read the parameter. The parameter is output when the material is printed.
\item \code{\_pat\_modifiable}: Parameter is writable and readable.
\item \code{\_pat\_parsable}: Parameter can be parsed, \textit{i.e.} read from the input file.
\item \code{\_pat\_parsmod}: Parameter is modifiable and parsable.
\end{itemize}
In order to implement the new constitutive law the user needs to
specify how the additional material parameters, that are not
defined in the input material file, should be calculated. Furthermore,
it has to be defined how stresses and the stable time step should be
computed for the new local material. In the case of implicit
simulations, in addition, the computation of the tangent stiffness needs
to be defined. Therefore, the user needs to redefine the following
functions of the parent material:
\begin{cpp}
void initMaterial();
// for explicit and implicit simulations void
computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
// for implicit simulations
void computeTangentStiffness(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
// for explicit and implicit simulations
Real getStableTimeStep(Real h, const Element & element);
\end{cpp}
In the following a detailed description of these functions is provided:
\begin{itemize}
\item \code{initMaterial}:~ This method is called after the material
file is fully read and the elements corresponding to each material
are assigned. Some of the frequently used constant parameters are
calculated in this method. For example, the Lam\'{e} constants of
elastic materials can be considered as such parameters.
\item \code{computeStress}:~ In this method, the stresses are
computed based on the constitutive law as a function of the strains of the
quadrature points. For example, the stresses for the elastic
material are calculated based on the following formula:
\begin{equation}
\label{eqn:smm:constitutive_elastic}
\mat{\sigma } =\lambda\mathrm{tr}(\mat{\varepsilon})\mat{I}+2 \mu \mat{\varepsilon}
\end{equation}
Therefore, this method contains a loop on all quadrature points
assigned to the material using the two macros:\par
\code{MATERIAL\_STRESS\_QUADRATURE\_POINT\_LOOP\_BEGIN}\par
\code{MATERIAL\_STRESS\_QUADRATURE\_POINT\_LOOP\_END}
\begin{cpp}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(element_type);
// sigma <- f(grad_u)
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
\end{cpp}
\note{The strain vector in \akantu contains the values of $\nabla
\vec{u}$, i.e. it is really the \emph{displacement gradient},}
\item \code{computeTangentStiffness}:~ This method is called when
the tangent to the stress-strain curve is desired (see Fig \ref
{fig:smm:AL:K}). For example, it is called in the implicit solver
when the stiffness matrix for the regular elements is assembled
based on the following formula:
\begin{equation}
\label{eqn:smm:constitutive_elasc} \mat{K }
=\int{\mat{B^T}\mat{D(\varepsilon)}\mat{B}}
\end{equation}
Therefore, in this method, the \code{tangent} matrix (\mat{D}) is
computed for a given strain.
\note{ The \code{tangent} matrix is a $4^{th}$ order tensor which is
stored as a matrix in Voigt notation.}
\begin{figure}[!htb]
\begin{center}
\includegraphics[width=0.4\textwidth,keepaspectratio=true]{figures/tangent.pdf}
\caption{Tangent to the stress-strain curve.}
\label{fig:smm:AL:K}
\end{center}
\end{figure}
\item \code{getStableTimeStep}:~ The stable time step should be
calculated based on \eqref{eqn:smm:explicit:stabletime} for the
conditionally stable methods. This function depends on the longitudinal wave
speed which changes for different materials and strains. Therefore,
the value of this velocity should be defined in this method for
each new material.
\note {In case of need, the calculation of the longitudinal and
shear wave speeds can be done in separate functions
(\code{getPushWaveSpeed} and \code{getShearWaveSpeed}).
Therefore, the first function can be called for calculation of the
stable time step.}
\end{itemize}
Once the declaration and implementation of the new material has been
completed, this material can be used in the user's example by including the header file:
\begin{cpp}
#include "material_XXX.hh"
\end{cpp}
For existing materials, as mentioned in Section~\ref{sect:smm:CL}, by
default, the materials are initialized inside the method
\code{initFull}. If a local material should be used instead, the
initialization of the material has to be postponed until the local
material is registered in the model. Therefore, the model is
initialized with the boolean for skipping the material initialization
equal to true:
\begin{cpp}
/// model initialization
model.initFull(SolidMechanicsModelOptions(_explicit_lumped_mass,true));
\end{cpp}
Once the model has been initialized, the local material needs
to be registered in the model:
\begin{cpp}
model.registerNewCustomMaterials<XXX>("name_of_local_material");
\end{cpp}
Only at this point the material can be initialized:
\begin{cpp}
model.initMaterials();
\end{cpp}
A full example for adding a new damage law can be found in
\shellcode{\examplesdir/new\_material}.
%%% Local Variables: %%% mode: latex %%% TeX-master: "manual" %%% End:
diff --git a/doc/manual/manual-structuralmechanicsmodel.tex b/doc/manual/manual-structuralmechanicsmodel.tex
index 1c73c6712..145c28d1a 100644
--- a/doc/manual/manual-structuralmechanicsmodel.tex
+++ b/doc/manual/manual-structuralmechanicsmodel.tex
@@ -1,251 +1,249 @@
\chapter{Structural Mechanics Model}
Static structural mechanics problems can be handled using the
-\code{StructuralMechanicsModel}. So far, \akantu\ provides 2D and 3D
-Bernoulli beam elements \cite{frey2009}. Just as for the
-\code{SolidMechanicsModel}, this model is created for a given
-\code{Mesh}. The model will create its own \code{FEEngine} object to
+class \code{StructuralMechanicsModel}. So far, \akantu provides 2D and 3D
+Bernoulli beam elements \cite{frey2009}. This model is instantiated for a given
+\code{Mesh}, as for the \code{SolidMechanicsModel}. The model will create its own \code{FEEngine} object to
compute the interpolation, gradient, integration and assembly
operations. The \code{StructuralMechanicsModel} constructor is called
in the following way:
\begin{cpp}
StructuralMechanicsModel model(mesh, spatial_dimension);
\end{cpp}
where \code{mesh} is a \code{Mesh} object defining the structure for
which the equations of statics are to be solved, and
\code{spatial\_dimension} is the dimensionality of the problem. If
\code{spatial\_dimension} is omitted, the problem is assumed to have
the same dimensionality as the one specified by the mesh.
\note[\ 1]{Dynamic computations are not supported to date.}
\note[\ 2]{Structural meshes are created and loaded as described in
Section~\ref{sect:common:mesh} with \code{MeshIOMSHStruct} instead of \code{MeshIOMSH}.}
\vspace{1cm}
This model contains at least the following \code{Arrays}:
\begin{description}
\item[blocked\_dofs] contains a Boolean value for each degree of
freedom specifying whether that degree is blocked or not. A
Dirichlet boundary condition can be prescribed by setting the
\textbf{blocked\_dofs} value of a degree of freedom to
\code{true}. The \textbf{displacement} is computed for all degrees
of freedom for which the \textbf{blocked\_dofs} value is set to
\code{false}. For the remaining degrees of freedom, the imposed
values (zero by default after initialization) are kept.
\item[displacement\_rotation] contains the generalized displacements
(\textit{i.e.} displacements and rotations) of all degrees of freedom. It can be
either a computed displacement for free degrees of freedom or an
imposed displacement in case of blocked ones ($\vec{u}$ in the
following).
\item[force\_moment] contains the generalized external forces (forces
and moments) applied to the nodes ($\vec{f_{\st{ext}}}$ in the
following).
\item[residual] contains the difference between the generalized external and internal
forces and moments. On the blocked degrees of freedom,
\textbf{residual} contains the support reactions ($\vec{r}$ in the
following). It should be mentioned that, at equilibrium,
\textbf{residual} should be zero on the free degrees of freedom.
\end{description}
An example to help understand how to use this model will be presented in the
next section.
\section{Model Setup}
\label{sec:structMechMod:setup}
\subsection{Initialization}
The easiest way to initialize the structural mechanics model is:
\begin{cpp}
model.initFull();
\end{cpp}
The method \code{initFull} computes the shape functions, initializes
the internal vectors mentioned above and allocates the memory for the
stiffness matrix.
Material properties are defined using the \code{StructuralMaterial}
structure described in
Table~\ref{tab:structMechMod:strucMaterial}. Such a definition could,
for instance, look like
\begin{cpp}
StructuralMaterial mat1;
mat.E=3e10;
mat.I=0.0025;
mat.A=0.01;
\end{cpp}
\begin{table}[htb] \centering
\begin{tabular}{cl}
\toprule
Field & Description \\
\midrule
\code{E} & Young's modulus \\
\code{A} & Cross section area \\
\code{I} & Second cross sectional moment of inertia (for 2D elements)\\
\code{Iy} & \code{I} around beam $y$--axis (for 3D elements)\\
\code{Iz} & \code{I} around beam $z$--axis (for 3D elements)\\
\code{GJ} & Polar moment of inertia of beam cross section (for 3D elements)\\
\bottomrule
\end{tabular}
- \caption{Material properties for structural elements as defined by
-the structure \code{StructuralMaterial}.}
+ \caption{Material properties for structural elements defined in
+the class \code{StructuralMaterial}.}
\label{tab:structMechMod:strucMaterial}
\end{table}
Materials can be added to the model's \code{element\_material} vector using
\begin{cpp}
model.addMaterial(mat1);
\end{cpp}
They are successively numbered and then assigned to specific elements.
\begin{cpp}
for (UInt i = 0; i < nb_element_mat_1; ++i) {
model.getElementMaterial(_bernoulli_beam_2)(i,0) = 1;
}
\end{cpp}
\subsection{Setting Boundary Conditions}\label{sect:structMechMod:boundary}
-As explained before, the Dirichlet boundary conditions are applied
-through the array \textbf{blocked\_dofs}. Two options exist to define
-Neumann conditions. If a nodal force is applied, it has to be
-directly set in the array \textbf{force\_momentum}. For loads
-distributed along the beam length, the method
-\code{computeForcesFromFunction} integrates them into nodal forces.
-The method takes as input a function describing the distribution of
-loads along the beam and a \code{BoundaryFunctionType} specifing if
-the function is expressed in the local coordinates
-(\code{\_bft\_traction\_local}) or in the global system of coordinates
-(\code{\_bft\_traction}).
+
+As explained before, the Dirichlet boundary conditions are applied through the
+array \textbf{blocked\_dofs}. Two options exist to define Neumann conditions.
+If a nodal force is applied, it has to be directly set in the array
+\textbf{force\_momentum}. For loads distributed along the beam length, the
+method \code{computeForcesFromFunction} integrates them into nodal forces. The
+method takes as input a function describing the distribution of loads along the
+beam and a functor \code{BoundaryFunctionType} specifing if the function is
+expressed in the local coordinates (\code{\_bft\_traction\_local}) or in the
+global system of coordinates (\code{\_bft\_traction}).
\begin{cpp}
static void lin_load(double * position, double * load,
Real * normal, UInt surface_id){
memset(load,0,sizeof(Real)*3);
load[1] = position[0]*position[0]-250;
}
int main(int argc, char *argv[]){
...
model.computeForcesFromFunction<_bernoulli_beam_2>(lin_load,
_bft_traction_local);
...}
\end{cpp}
\section{Static Analysis\label{sect:structMechMod:static}}
The \code{StructuralMechanicsModel} class can perform static analyses
of structures. In this case, the equation to solve is the same as for
the \code{SolidMechanicsModel} used for static analyses
\begin{equation}\label{eqn:structMechMod:static}
\mat{K} \vec{u} = \vec{f_{\st{ext}}}~,
\end{equation}
where $\mat{K}$ is the global stiffness matrix, $\vec{u}$ the
generalized displacement vector and $\vec{f_{\st{ext}}}$ the vector of
generalized external forces applied to the system.
To solve such a problem, the static solver of the
\code{StructuralMechanicsModel}\index{StructuralMechanicsModel} object
is used. First a model has to be created and initialized.
\begin{cpp}
StructuralMechanicsModel model(mesh);
model.initFull();
\end{cpp}
\begin{itemize}
\item \code{model.initFull} initializes all internal vectors to zero.
\end{itemize}
Once the model is created and initialized, the boundary conditions can
be set as explained in Section~\ref{sect:structMechMod:boundary}.
Boundary conditions will prescribe the external forces or moments for
the free degrees of freedom $\vec{f_{\st{ext}}}$ and displacements or
rotations for the others. To completely define the system represented
by equation (\ref{eqn:structMechMod:static}), the global stiffness
matrix $\mat{K}$ must be assembled.
\index{StructuralMechanicsModel!assembleStiffnessMatrix}
\begin{cpp}
model.assembleStiffnessMatrix();
\end{cpp}
The computation of the static equilibrium is performed using the same
Newton-Raphson algorithm as described in
Section~\ref{sect:smm:static}.
\note{To date,
\code{StructuralMechanicsModel} handles only constitutively and
geometrically linear problems, the algorithm is therefore guaranteed
to converge in two iterations.}
\begin{cpp}
model.updateResidual();
model.solve();
\end{cpp}
\index{StructuralMechanicsModel!updateResidual}
\index{StructuralMechanicsModel!solve}
\begin{itemize}
\item \code{model.updateResidual} assembles the internal forces and
removes them from the external forces.
\item \code{model.solve} solves the Equation (\ref{eqn:structMechMod:static}).
The \textbf{increment} vector of the model will contain the new
increment of displacements, and the \textbf{displacement\_rotation}
vector is also updated to the new displacements.
\end{itemize}
%At the end of the analysis, the final solution is stored in the
%\textbf{displacement} vector. A full example of how to solve a
%structural mechanics problem is presented in the code
%\shellcode{\examplesdir/structural\_mechanics/test\_structural\_mechanics\_model\_bernoulli\_beam\_2\_exemple\_1\_1.cc}.
%This example is composed of a 2D beam, clamped at the left end and
%supported by two rollers as shown in Figure
%\ref{fig:structMechMod:exem1_1}. The problem is defined by the
%applied load $q=\SI{6}{\kilo\newton\per\metre}$, moment $\bar{M} =
%\SI{3.6}{\kilo\newton\metre}$, moments of inertia $I_1 =
%\SI{250\,000}{\power{\centi\metre}{4}}$ and $I_2 =
%\SI{128\,000}{\power{\centi\metre}{4}}$ and lengths $L_1 =
%\SI{10}{\metre}$ and $L_2 = \SI{8}{\metre}$. The resulting
%rotations at node two and three are $ \varphi_2 = 0.001\,167\
%\mbox{and}\ \varphi_3 = -0.000\,771.$
At the end of the analysis, the final solution is stored in the
\textbf{displacement\_rotation} vector. A full example of how to
solve a structural mechanics problem is presented in the code
\shellcode{\examplesdir/structural\_mechanics/bernoulli\_beam\_2\_example.cc}.
This example is composed of a 2D beam, clamped at the left end and
supported by two rollers as shown in Figure
\ref{fig:structMechMod:exem1_1}. The problem is defined by the
applied load $q=\SI{6}{\kilo\newton\per\metre}$, moment $\bar{M} =
\SI{3.6}{\kilo\newton\metre}$, moments of inertia $I_1 =
\SI{250\,000}{\centi\metre\tothe{4}}$ and $I_2 =
\SI{128\,000}{\centi\metre\tothe{4}}$ and lengths $L_1 =
\SI{10}{\metre}$ and $L_2 = \SI{8}{\metre}$. The resulting
rotations at node two and three are $ \varphi_2 = 0.001\,167\
\mbox{and}\ \varphi_3 = -0.000\,771.$
\begin{figure}[htb]
\centering
\includegraphics[scale=1.1]{figures/beam_example}
\caption{2D beam example}
\label{fig:structMechMod:exem1_1}
\end{figure}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "manual"
%%% End:
diff --git a/doc/manual/manual.sty b/doc/manual/manual.sty
index 6855a85ab..36dcb2425 100644
--- a/doc/manual/manual.sty
+++ b/doc/manual/manual.sty
@@ -1,312 +1,328 @@
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pdfauthor={Computational Solid Mechanics Laboratory - EPFL},
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diff --git a/doc/manual/manual.tex b/doc/manual/manual.tex
index f9cd426e9..d4e9562e6 100644
--- a/doc/manual/manual.tex
+++ b/doc/manual/manual.tex
@@ -1,47 +1,48 @@
\documentclass[openright,a4paper,11pt,fleqn]{manual}
\usepackage{manual}
\usepackage{manual-macros}
+
\newcommand{\version}{}
\graphicspath{ {./figures/} }
%%% For references \todo check the coherency
%% section 3.5 -> Section 3.5
%% figure 3.5 -> Figure 3.5
%% equation 3.5 -> Equation (3.5)
% Title pages and Table of Contents (includes \begin{document})
\input{manual-titlepages}
% Introduction chapter
\input{manual-introduction}
% The planning to write the documentation
%\input{manual-planning}
% The documentation chapter (split in parts)
\input{manual-gettingstarted}
\input{manual-elements}
%\IfFileExists{manual-lumping.tex}{}{\input{manual-lumping}}
\input{manual-solidmechanicsmodel}
\IfFileExists{manual-structuralmechanicsmodel.tex}{\input{manual-structuralmechanicsmodel}}{}
\IfFileExists{manual-heattransfermodel.tex}{\input{manual-heattransfermodel}}{}
\input{manual-io}
\IfFileExists{manual-parallel.tex}{\input{manual-parallel}}{}
\IfFileExists{manual-contact.tex}{\input{manual-contact}}{}
% The appendices
\appendix
\input{manual-appendix-elements}
\input{manual-appendix-materials}
\input{manual-appendix-packages}
% The backmatter material (index/bibliography, included \end{document})
\input{manual-backmatter}
diff --git a/extra_packages/extra-materials b/extra_packages/extra-materials
index 27835edcf..ce1204216 160000
--- a/extra_packages/extra-materials
+++ b/extra_packages/extra-materials
@@ -1 +1 @@
-Subproject commit 27835edcf205dedb552ddb9d82d3bc9e39b0156a
+Subproject commit ce1204216c5b64a145c011b619d9ceedc89eb2b4
diff --git a/extra_packages/traction-at-split-node-contact b/extra_packages/traction-at-split-node-contact
index ef51588f2..d72a71d49 160000
--- a/extra_packages/traction-at-split-node-contact
+++ b/extra_packages/traction-at-split-node-contact
@@ -1 +1 @@
-Subproject commit ef51588f2c24f3a1307085941eda060408d1d3d5
+Subproject commit d72a71d4913205050dee2a871e9a9a9fa452bccf
diff --git a/packages/cgal.cmake b/packages/cgal.cmake
index 68e7c13fd..bbc128aa9 100644
--- a/packages/cgal.cmake
+++ b/packages/cgal.cmake
@@ -1,62 +1,57 @@
#===============================================================================
# @file cgal.cmake
#
# @author Lucas Frérot <lucas.frerot@epfl.ch>
#
# @date creation: Thu Feb 19 2015
# @date last modification: Mon Mar 2 2015
#
# @brief package description for CGAL
#
# @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/>.
#
#===============================================================================
package_declare(CGAL EXTERNAL
DESCRIPTION "Add CGAL support in akantu"
COMPILE_FLAGS "-frounding-math"
BOOST_COMPONENTS system
)
package_declare_sources(CGAL
geometry/mesh_geom_abstract.hh
geometry/mesh_geom_abstract.cc
+
geometry/mesh_geom_factory.hh
geometry/mesh_geom_factory_tmpl.hh
- geometry/mesh_geom_container.hh
- geometry/mesh_geom_container.cc
+
+ geometry/mesh_geom_intersector.hh
+ geometry/mesh_geom_intersector_tmpl.hh
+
+ geometry/mesh_segment_intersector.hh
+ geometry/mesh_segment_intersector_tmpl.hh
geometry/tree_type_helper.hh
geometry/geom_helper_functions.hh
geometry/aabb_primitives/triangle.hh
- geometry/aabb_primitives/triangle_tmpl.hh
geometry/aabb_primitives/tetrahedron.hh
- geometry/aabb_primitives/tetrahedron_tmpl.hh
geometry/aabb_primitives/aabb_primitive.hh
)
-
-
-## Adding CGAL library
-#find_package(CGAL COMPONENTS Core)
-#if (NOT CGAL_FOUND)
-#message(STATUS "This project requires the CGAL library, and will not be compiled.")
-#return()
-#endif()
diff --git a/packages/cohesive_element.cmake b/packages/cohesive_element.cmake
index 2853335df..246c77c10 100644
--- a/packages/cohesive_element.cmake
+++ b/packages/cohesive_element.cmake
@@ -1,92 +1,93 @@
#===============================================================================
# @file 20_cohesive_element.cmake
#
# @author Marco Vocialta <marco.vocialta@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Tue Oct 16 2012
# @date last modification: Tue Sep 02 2014
#
# @brief package description for cohesive elements
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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(cohesive_element
DESCRIPTION "Use cohesive_element package of Akantu"
DEPENDS lapack)
package_declare_sources(cohesive_element
model/solid_mechanics/materials/material_cohesive_includes.hh
mesh_utils/cohesive_element_inserter.hh
mesh_utils/cohesive_element_inserter.cc
fe_engine/cohesive_element.cc
fe_engine/shape_cohesive.hh
fe_engine/cohesive_element.hh
fe_engine/fe_engine_template_cohesive.cc
fe_engine/shape_cohesive_inline_impl.cc
model/solid_mechanics/materials/material_cohesive/cohesive_internal_field_tmpl.hh
model/solid_mechanics/materials/material_cohesive/cohesive_internal_field.hh
model/solid_mechanics/materials/material_cohesive/material_cohesive_inline_impl.cc
model/solid_mechanics/solid_mechanics_model_cohesive.cc
model/solid_mechanics/solid_mechanics_model_cohesive_inline_impl.cc
model/solid_mechanics/fragment_manager.cc
model/solid_mechanics/materials/material_cohesive/material_cohesive.cc
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
+ model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.cc
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.cc
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.cc
model/solid_mechanics/solid_mechanics_model_cohesive.hh
model/solid_mechanics/fragment_manager.hh
model/solid_mechanics/materials/material_cohesive/material_cohesive.hh
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.hh
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.hh
model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.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/embedded.cmake b/packages/embedded.cmake
index aeb711a3c..aefb0fdfe 100644
--- a/packages/embedded.cmake
+++ b/packages/embedded.cmake
@@ -1,51 +1,51 @@
#===============================================================================
# @file embedded.cmake
#
# @author Lucas Frérot <lucas.frerot@epfl.ch>
#
# @date creation: Tue Oct 16 2012
# @date last modification: Thu Jun 12 2014
#
# @brief package descrition for embedded model use
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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(embedded
DESCRIPTION "Add support for the embedded solid mechanics model"
DEPENDS CGAL)
package_declare_sources(embedded
model/solid_mechanics/materials/material_embedded/material_embedded_includes.hh
- model/solid_mechanics/embedded_interface.hh
- model/solid_mechanics/embedded_interface.cc
+ model/solid_mechanics/embedded_interface_intersector.hh
+ model/solid_mechanics/embedded_interface_intersector.cc
model/solid_mechanics/embedded_interface_model.hh
model/solid_mechanics/embedded_interface_model.cc
model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
model/solid_mechanics/materials/material_embedded/material_reinforcement_inline_impl.cc
model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
model/solid_mechanics/materials/material_embedded/material_reinforcement_template_inline_impl.cc
)
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
index 215a96a2c..c723c34e4 100644
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -1,204 +1,205 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date Wed Jul 9 17:22:12 2014
#
# @brief CMake file for the python wrapping of akantu
#
# @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/>.
#
#===============================================================================
#===============================================================================
# Configuration
#===============================================================================
set(AKANTU_SWIG_FLAGS -w309,325,401)
set(AKANTU_SWIG_OUTDIR ${CMAKE_CURRENT_SOURCE_DIR})
set(AKANTU_SWIG_MODULES swig/akantu.i)
#===============================================================================
# Swig wrapper
#===============================================================================
find_package(SWIG REQUIRED)
find_package(PythonLibs)
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}/swig
${PYTHON_INCLUDE_PATH}
${AKANTU_INCLUDE_DIRS}
${Boost_INCLUDE_DIRS}
)
include(CMakeParseArguments)
function(swig_generate_dependencies _module _depedencies)
set(_dependencies_script "${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/_swig_generate_dependencies.cmake")
file(WRITE ${_dependencies_script} "
set(_include_directories ${_include_directories})
list(APPEND _include_directories \"./\")
set(_dep)
set(_files_to_process \${_module})
while(_files_to_process)
list(GET _files_to_process 0 _file)
list(REMOVE_AT _files_to_process 0)
file(STRINGS \${_file} _file_content REGEX \"^%include *\\\"(.*)\\\"\")
set(_includes)
foreach(_line \${_file_content})
string(REGEX REPLACE \"^%include *\\\"(.*)\\\"\" \"\\\\1\" _inc \${_line})
if(_inc)
list(APPEND _includes \${_inc})
endif()
endforeach()
foreach(_include \${_includes})
unset(_found)
foreach(_inc_dir \${_include_directories})
if(EXISTS \${_inc_dir}/\${_include})
set(_found \${_inc_dir}/\${_include})
break()
endif()
endforeach()
if(_found)
list(APPEND _files_to_process \${_found})
list(APPEND _dep \${_found})
endif()
endforeach()
endwhile()
get_filename_component(_module_we \"\${_module}\" NAME_WE)
set(_dependencies_file \${CMAKE_CURRENT_BINARY_DIR}\${CMAKE_FILES_DIRECTORY}/_swig_\${_module_we}_depends.cmake)
file(WRITE \"\${_dependencies_file}\"
\"set(_swig_\${_module_we}_depends\")
foreach(_d \${_dep})
file(APPEND \"\${_dependencies_file}\" \"
\${_d}\")
endforeach()
file(APPEND \"\${_dependencies_file}\" \"
)\")
")
get_directory_property(_include_directories INCLUDE_DIRECTORIES)
get_filename_component(_module_absolute "${_module}" ABSOLUTE)
get_filename_component(_module_we "${_module}" NAME_WE)
set(_dependencies_file ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/_swig_${_module_we}_depends.cmake)
if(EXISTS ${_dependencies_file})
include(${_dependencies_file})
else()
execute_process(COMMAND ${CMAKE_COMMAND}
-D_module=${_module_absolute}
-P ${_dependencies_script}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
include(${_dependencies_file})
endif()
add_custom_command(OUTPUT ${_dependencies_file}
COMMAND ${CMAKE_COMMAND}
-D_module=${_module_absolute}
-P ${_dependencies_script}
COMMENT "Scannong dependencies for swig module ${_module_we}"
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
MAIN_DEPENDENCY ${_module_absolute}
DEPENDS ${_swig_${_module_we}_depends}
)
set(${_depedencies} ${_dependencies_file} PARENT_SCOPE)
endfunction()
function(swig_generate_wrappers project _wrappers)
cmake_parse_arguments(_swig_opt "" "OUTPUT_DIR" "EXTRA_FLAGS" ${ARGN})
if(_swig_opt_OUTPUT_DIR)
set(_output_dir ${_swig_opt_OUTPUT_DIR})
else()
set(_output_dir ${CMAKE_CURRENT_BINARY_DIR})
endif()
set(_swig_wrappers)
get_directory_property(_include_directories INCLUDE_DIRECTORIES)
if(_include_directories)
string(REPLACE ";" ";-I" _swig_include_directories "${_include_directories}")
endif()
foreach(_module ${_swig_opt_UNPARSED_ARGUMENTS})
swig_generate_dependencies(${_module} _module_dependencies)
get_filename_component(_module_absolute "${_module}" ABSOLUTE)
get_filename_component(_module_path "${_module_absolute}" PATH)
get_filename_component(_module_name "${_module}" NAME)
get_filename_component(_module_we "${_module}" NAME_WE)
set(_wrapper "${_output_dir}/${_module_we}_wrapper.cc")
set(_extra_wrapper "${_output_dir}/${_module_we}.py")
set(_extra_wrapper_bin "${CMAKE_CURRENT_BINARY_DIR}/${_module_we}.py")
+
if(SWIG_FOUND)
set_source_files_properties("${_wrapper}" PROPERTIES GENERATED 1)
set_source_files_properties("${_extra_wrapper}" PROPERTIES GENERATED 1)
set(_dependencies_file ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/_swig_${_module_we}_depends.cmake)
+ set(_ouput "${_wrapper}" "${_extra_wrapper}" "${_extra_wrapper_bin}")
add_custom_command(
- OUTPUT "${_wrapper}" "${_extra_wrapper}" "${_extra_wrapper_bin}"
+ OUTPUT ${_ouput}
COMMAND "${SWIG_EXECUTABLE}"
ARGS -python -c++
${_swig_opt_EXTRA_FLAGS}
-outdir ${_output_dir}
-I${_swig_include_directories} -I${_module_path}
-o "${_wrapper}"
"${_module_absolute}"
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_extra_wrapper} ${_extra_wrapper_bin}
# MAIN_DEPENDENCY "${_module_absolute}"
DEPENDS ${_module_dependencies}
COMMENT "Generating swig wrapper ${_module} -> ${_wrapper}"
)
list(APPEND _swig_wrappers ${_wrapper})
else()
if(NOT EXISTS ${_wrapper} OR NOT EXISTS "${_extra_wrapper}")
message(FATAL_ERROR "The file ${_wrapper} and/or ${_extra_wrapper} does not exists and they cannot be generated. Install swig in order to generate them")
else()
list(APPEND _swig_wrappers ${_wrapper})
endif()
endif()
endforeach()
add_custom_target(${project}_generate_swig_wrappers DEPENDS ${_swig_wrappers})
set(${_wrappers} ${_swig_wrappers} PARENT_SCOPE)
endfunction()
swig_generate_wrappers(akantu AKANTU_SWIG_WRAPPERS
${AKANTU_SWIG_MODULES}
- OUTPUT_DIR ${AKANTU_SWIG_OUTDIR}
EXTRA_FLAGS ${AKANTU_SWIG_FLAGS})
if(AKANTU_SWIG_WRAPPERS)
add_library(_akantu MODULE ${AKANTU_SWIG_WRAPPERS})
target_link_libraries(_akantu akantu ${PYTHON_LIBRARIES})
set_target_properties(_akantu PROPERTIES PREFIX "")
endif()
diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh
index a77eaf50e..5d5fce77e 100644
--- a/src/common/aka_array.hh
+++ b/src/common/aka_array.hh
@@ -1,373 +1,375 @@
/**
* @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 Jun 24 2014
*
* @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
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_VECTOR_HH__
#define __AKANTU_VECTOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
//#include <cstring>
#include <vector>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/// class that afford to store vectors in static memory
class ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ArrayBase(const ID & id = "");
virtual ~ArrayBase();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the amount of space allocated in bytes
inline UInt getMemorySize() const;
/// set the size to zero without freeing the allocated space
inline void empty();
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the real size allocated in memory
AKANTU_GET_MACRO(AllocatedSize, allocated_size, UInt);
/// Get the Size of the Array
AKANTU_GET_MACRO(Size, size, UInt);
/// 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 &);
// AKANTU_GET_MACRO(Tag, tag, const std::string &);
// AKANTU_SET_MACRO(Tag, tag, const std::string &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the vector
ID id;
/// the size allocated
UInt allocated_size;
/// the size used
UInt size;
/// number of components
UInt nb_component;
/// size of the stored type
UInt size_of_type;
// /// User defined tag
// std::string tag;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template<typename T, bool is_scal>
class Array : public ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef T value_type;
typedef value_type & reference;
typedef value_type * pointer_type;
typedef const value_type & const_reference;
/// Allocation of a new vector
inline Array(UInt size = 0, UInt nb_component = 1,
const ID & id = "");
/// Allocation of a new vector with a default value
Array(UInt size, UInt nb_component,
const value_type def_values[], const ID & id = "");
/// Allocation of a new vector with a default value
Array(UInt size, UInt nb_component,
const_reference value, const ID & id = "");
/// Copy constructor (deep copy if deep=true)
Array(const Array<value_type, is_scal>& vect, bool deep = true, const ID & id = "");
#ifndef SWIG
/// Copy constructor (deep copy)
Array(const std::vector<value_type> & vect);
#endif
virtual inline ~Array();
Array & operator=(const Array & a) {
/// this is to let STL allocate and copy arrays in the case of std::vector::resize
AKANTU_DEBUG_ASSERT(this->size == 0,"Cannot copy akantu::Array");
return const_cast<Array&>(a);
}
/* ------------------------------------------------------------------------ */
/* Iterator */
/* ------------------------------------------------------------------------ */
/// \todo protected: does not compile with intel check why
public:
template <class R, class IR = R, bool issame = is_same<IR, T>::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
typedef iterator< T > scalar_iterator;
/// const_iterator for Array of nb_component = 1
typedef const_iterator< T > const_scalar_iterator;
/// iterator rerturning Vectors of size n on entries of Array with nb_component = n
typedef iterator< Vector<T> > vector_iterator;
/// const_iterator rerturning Vectors of n size on entries of Array with nb_component = n
typedef const_iterator< Vector<T> > const_vector_iterator;
/// iterator rerturning Matrices of size (m, n) on entries of Array with nb_component = m*n
typedef iterator< Matrix<T> > matrix_iterator;
/// const iterator rerturning Matrices of size (m, n) on entries of Array with nb_component = m*n
typedef const_iterator< Matrix<T> > const_matrix_iterator;
/* ------------------------------------------------------------------------ */
/// Get an iterator that behaves like a pointer T * to the first entry
inline iterator<T> begin();
/// Get an iterator that behaves like a pointer T * to the end of the Array
inline iterator<T> end();
/// Get a const_iterator to the beginging of an Array of scalar
inline const_iterator<T> begin() const;
/// Get a const_iterator to the end of an Array of scalar
inline const_iterator<T> end() const;
/* ------------------------------------------------------------------------ */
/// Get a vector_iterator on the begining of the Array
inline vector_iterator begin(UInt n);
/// Get a vector_iterator on the end of the Array
inline vector_iterator end(UInt n);
/// Get a vector_iterator on the begining of the Array
inline const_vector_iterator begin(UInt n) const;
/// Get a vector_iterator on the end of the Array
inline const_vector_iterator end(UInt n) const;
/// Get a vector_iterator on the begining of the Array considered of shape (new_size, n)
inline vector_iterator begin_reinterpret(UInt n, UInt new_size);
/// Get a vector_iterator on the end of the Array considered of shape (new_size, n)
inline vector_iterator end_reinterpret(UInt n, UInt new_size);
/// Get a const_vector_iterator on the begining of the Array considered of shape (new_size, n)
inline const_vector_iterator begin_reinterpret(UInt n, UInt new_size) const;
/// Get a const_vector_iterator on the end of the Array considered of shape (new_size, n)
inline const_vector_iterator end_reinterpret(UInt n, UInt new_size) const;
/* ------------------------------------------------------------------------ */
/// Get a matrix_iterator on the begining of the Array (Matrices of size (m, n))
inline matrix_iterator begin(UInt m, UInt n);
/// Get a matrix_iterator on the end of the Array (Matrices of size (m, n))
inline matrix_iterator end(UInt m, UInt n);
/// Get a const_matrix_iterator on the begining of the Array (Matrices of size (m, n))
inline const_matrix_iterator begin(UInt m, UInt n) const;
/// Get a const_matrix_iterator on the end of the Array (Matrices of size (m, n))
inline const_matrix_iterator end(UInt m, UInt n) const;
/// Get a matrix_iterator on the begining of the Array considered of shape (new_size, m*n)
inline matrix_iterator begin_reinterpret(UInt m, UInt n, UInt size);
/// Get a matrix_iterator on the end of the Array considered of shape (new_size, m*n)
inline matrix_iterator end_reinterpret(UInt m, UInt n, UInt size);
/// Get a const_matrix_iterator on the begining of the Array considered of shape (new_size, m*n)
inline const_matrix_iterator begin_reinterpret(UInt m, UInt n, UInt size) const;
/// Get a const_matrix_iterator on the end of the Array considered of shape (new_size, m*n)
inline const_matrix_iterator end_reinterpret(UInt m, UInt n, UInt size) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
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>
inline void push_back(const C<T> & new_elem);
/// append the value of the iterator
template<typename Ret>
inline void push_back(const iterator<Ret> & 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);
/// change the size of the Array
void resize(UInt size);
/// change the number of components by interlacing data
void extendComponentsInterlaced(UInt multiplicator, UInt stride);
/// search elem in the vector, return the position of the first occurrence or -1 if not found
Int find(const_reference elem) const;\
/// @see Array::find(const_reference elem) const
Int find(T elem[]) const;
/// set all entries of the array to 0
inline void clear() { std::fill_n(values, size*nb_component, T()); }
/// 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(values, size*nb_component, t); }
/// 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>
inline void set(const C<T> & vm);
/// 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);
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// perform the allocation for the constructors
void allocate(UInt size, UInt nb_component = 1);
/// resize without initializing the memory
void resizeUnitialized(UInt new_size);
/* ------------------------------------------------------------------------ */
/* 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;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the number of tuples contained in the array
UInt getSize() const{ return this->size; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// array of values
T * values; // /!\ very dangerous
};
__END_AKANTU__
#include "aka_types.hh"
__BEGIN_AKANTU__
#include "aka_array_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* 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;
}
__END_AKANTU__
#endif /* __AKANTU_VECTOR_HH__ */
diff --git a/src/common/aka_common_inline_impl.cc b/src/common/aka_common_inline_impl.cc
index 6eb33206b..dedf81ea0 100644
--- a/src/common/aka_common_inline_impl.cc
+++ b/src/common/aka_common_inline_impl.cc
@@ -1,238 +1,238 @@
/**
* @file aka_common_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Dec 01 2011
* @date last modification: Wed Jul 23 2014
*
* @brief inline implementations of common akantu type descriptions
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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
*
* All common things to be included in the projects files
*
*/
#include <algorithm>
#include <iomanip>
#include <cctype>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementType type)
{
#define STRINGIFY(type) \
stream << BOOST_PP_STRINGIZE(type)
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, \
STRINGIFY, \
AKANTU_ALL_ELEMENT_TYPE)
case _not_defined: stream << "_not_defined"; break;
case _max_element_type: stream << "_max_element_type"; break;
}
#undef STRINGIFY
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementKind kind )
{
#define STRINGIFY(kind) \
stream << BOOST_PP_STRINGIZE(kind)
AKANTU_BOOST_ALL_KIND_SWITCH(STRINGIFY);
#undef STRINGIFY
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for InterpolationType
inline std::ostream & operator <<(std::ostream & stream, InterpolationType type)
{
switch(type)
{
case _itp_lagrange_point_1 : stream << "_itp_lagrange_point_1" ; break;
case _itp_lagrange_segment_2 : stream << "_itp_lagrange_segment_2" ; break;
case _itp_lagrange_segment_3 : stream << "_itp_lagrange_segment_3" ; break;
case _itp_lagrange_triangle_3 : stream << "_itp_lagrange_triangle_3" ; break;
case _itp_lagrange_triangle_6 : stream << "_itp_lagrange_triangle_6" ; break;
case _itp_lagrange_quadrangle_4 : stream << "_itp_lagrange_quadrangle_4" ; break;
case _itp_serendip_quadrangle_8 : stream << "_itp_serendip_quadrangle_8" ; break;
case _itp_lagrange_tetrahedron_4 : stream << "_itp_lagrange_tetrahedron_4" ; break;
case _itp_lagrange_tetrahedron_10 : stream << "_itp_lagrange_tetrahedron_10"; break;
case _itp_lagrange_hexahedron_8 : stream << "_itp_lagrange_hexahedron_8" ; break;
case _itp_lagrange_pentahedron_6 : stream << "_itp_lagrange_pentahedron_6" ; break;
case _itp_serendip_hexahedron_20 : stream << "_itp_serendip_hexahedron_20" ; break;
case _itp_lagrange_pentahedron_15 : stream << "_itp_lagrange_pentahedron_15"; break;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _itp_bernoulli_beam : stream << "_itp_bernoulli_beam" ; break;
case _itp_kirchhoff_shell : stream << "_itp_kirchhoff_shell" ; break;
#endif
case _itp_not_defined : stream << "_itp_not_defined" ; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// 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;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator <<(std::ostream & stream, SynchronizationTag type)
{
switch(type)
{
case _gst_smm_mass : stream << "_gst_smm_mass" ; break;
case _gst_smm_for_gradu : stream << "_gst_smm_for_gradu" ; break;
case _gst_smm_boundary : stream << "_gst_smm_boundary" ; break;
case _gst_smm_uv : stream << "_gst_smm_uv" ; break;
case _gst_smm_res : stream << "_gst_smm_res" ; break;
case _gst_smm_init_mat : stream << "_gst_smm_init_mat" ; break;
case _gst_smm_stress : stream << "_gst_smm_stress" ; break;
case _gst_smmc_facets : stream << "_gst_smmc_facets" ; break;
case _gst_smmc_facets_conn : stream << "_gst_smmc_facets_conn" ; break;
case _gst_smmc_facets_stress : stream << "_gst_smmc_facets_stress" ; break;
case _gst_smmc_damage : stream << "_gst_smmc_damage" ; break;
case _gst_ce_inserter : stream << "_gst_ce_inserter" ; break;
case _gst_gm_clusters : stream << "_gst_gm_clusters" ; break;
case _gst_htm_capacity : stream << "_gst_htm_capacity" ; break;
case _gst_htm_temperature : stream << "_gst_htm_temperature" ; break;
case _gst_htm_gradient_temperature : stream << "_gst_htm_gradient_temperature"; break;
case _gst_htm_phi : stream << "_gst_htm_phi" ; break;
case _gst_htm_gradient_phi : stream << "_gst_htm_gradient_phi" ; break;
case _gst_mnl_for_average : stream << "_gst_mnl_for_average" ; break;
case _gst_mnl_weight : stream << "_gst_mnl_weight" ; break;
case _gst_test : stream << "_gst_test" ; break;
- case _gst_user_1 : stream << "_gst_user_1" ; break;
- case _gst_user_2 : stream << "_gst_user_2" ; break;
+ case _gst_user_1 : stream << "_gst_user_1" ; break;
+ case _gst_user_2 : stream << "_gst_user_2" ; break;
case _gst_material_id : stream << "_gst_material_id" ; break;
case _gst_for_dump : stream << "_gst_for_dump" ; break;
case _gst_cf_nodal : stream << "_gst_cf_nodal" ; break;
case _gst_cf_incr : stream << "_gst_cf_incr" ; break;
case _gst_solver_solution : stream << "_gst_solver_solution" ; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SolveConvergenceCriteria
inline std::ostream & operator <<(std::ostream & stream, SolveConvergenceCriteria criteria)
{
switch(criteria) {
case _scc_residual : stream << "_scc_residual" ; break;
case _scc_increment: stream << "_scc_increment"; break;
case _scc_residual_mass_wgh: stream << "_scc_residual_mass_wgh"; 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;
}
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim) {
std::string trimed = to_trim;
//left trim
trimed.erase(trimed.begin(),
std::find_if(trimed.begin(),
trimed.end(),
std::not1(std::ptr_fun<int, int>(isspace))));
// right trim
trimed.erase(std::find_if(trimed.rbegin(),
trimed.rend(),
std::not1(std::ptr_fun<int, int>(isspace))).base(),
trimed.end());
return trimed;
}
__END_AKANTU__
#include <cmath>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template<typename T>
std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt 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;
switch(mult) {
case 0: sstr << ""; break;
case 1: sstr << "Ki"; break;
case 2: sstr << "Mi"; break;
case 3: sstr << "Gi"; break; // I started on this type of machines
// (32bit computers) (Nicolas)
case 4: sstr << "Ti"; break;
case 5: sstr << "Pi"; break;
case 6: sstr << "Ei"; break; // theoritical limit of RAM of the current
// computers in 2014 (64bit computers) (Nicolas)
case 7: sstr << "Zi"; break;
case 8: sstr << "Yi"; break;
default:
AKANTU_DEBUG_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 this switch case.");
}
sstr << "Byte";
return sstr.str();
}
__END_AKANTU__
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index 4ccfd7517..d92deb104 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,991 +1,1012 @@
/**
* @file aka_types.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 17 2011
* @date last modification: Tue Aug 19 2014
*
* @brief description of the "simple" types
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_error.hh"
#include "aka_fwd.hh"
#include "aka_math.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <iomanip>
#ifndef __INTEL_COMPILER
#include <tr1/unordered_map>
#else
#include <map>
#endif
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_TYPES_HH__
#define __AKANTU_AKA_TYPES_HH__
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
/* maps */
/* -------------------------------------------------------------------------- */
#ifndef __INTEL_COMPILER
template<class Key, class Ty>
struct unordered_map { typedef typename std::tr1::unordered_map<Key, Ty> type; };
#else
template<class Key, class Ty>
struct unordered_map { typedef typename std::map<Key, Ty> type; };
#endif
enum NormType {
L_1 = 1,
L_2 = 2,
L_inf = UInt(-1)
};
template<UInt dim>
struct DimHelper {
static inline void setDims(UInt m, UInt n, UInt p, UInt dims[dim]);
};
template<>
struct DimHelper<1> {
static inline void setDims(UInt m,
__attribute__((unused)) UInt n,
__attribute__((unused)) UInt p,
UInt dims[1]) {
dims[0] = m;
}
};
template<>
struct DimHelper<2> {
static inline void setDims(UInt m,
UInt n,
__attribute__((unused)) UInt p,
UInt dims[2]) {
dims[0] = m;
dims[1] = n;
}
};
template<>
struct DimHelper<3> {
static inline void setDims(UInt m,
UInt n,
UInt p,
UInt dims[3]) {
dims[0] = m;
dims[1] = n;
dims[2] = p;
}
};
/* -------------------------------------------------------------------------- */
template<typename T, UInt ndim, class RetType>
class TensorStorage;
/* -------------------------------------------------------------------------- */
template<typename T, UInt ndim, class RetType>
class TensorProxy {
protected:
TensorProxy(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->values = data;
}
TensorProxy(const TensorProxy & other) {
this->values = other.storage();
for (UInt i = 0; i < ndim; ++i)
this->n[i] = other.n[i];
}
inline TensorProxy(const TensorStorage<T, ndim, RetType> & other);
public:
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; }
+ void copyExternalMemory(T * data, UInt nb_values) {
+ AKANTU_DEBUG_ASSERT(nb_values == this->size(),
+ "You are trying to copy two tensors with differents sizes");
+ memcpy(this->values, data, nb_values * sizeof(T));
+ }
+
protected:
T * values;
UInt n[ndim];
};
/* -------------------------------------------------------------------------- */
template<typename T>
class VectorProxy : public TensorProxy<T, 1, Vector<T> > {
typedef TensorProxy<T, 1, Vector<T> > parent;
public:
VectorProxy(T * data = NULL, UInt n = 0) : parent(data, n, 0, 0) { }
VectorProxy(const VectorProxy & src) : parent(src) { }
VectorProxy(const Vector<T> & src) : parent(src) { }
+
+ VectorProxy & operator=(const Vector<T> & src) {
+ this->copyExternalMemory(src.storage(), src.size());
+ return *this;
+ }
};
template<typename T>
class MatrixProxy : public TensorProxy<T, 2, Matrix<T> > {
typedef TensorProxy<T, 2, Matrix<T> > parent;
public:
MatrixProxy(T * data = NULL, UInt m = 0, UInt n = 0) : parent(data, m, n, 0) { }
MatrixProxy(const MatrixProxy & src) : parent(src) { }
MatrixProxy(const Matrix<T> & src) : parent(src) { }
+
+ MatrixProxy & operator=(const Matrix<T> & src) {
+ this->copyExternalMemory(src.storage(), src.size());
+ return *this;
+ }
};
template<typename T>
class Tensor3Proxy : public TensorProxy<T, 3, Tensor3<T> > {
typedef TensorProxy<T, 3, Tensor3<T> > parent;
public:
Tensor3Proxy(T * data = NULL, UInt m = 0, UInt n = 0, UInt k = 0) :
parent(data, m, n, k) { }
Tensor3Proxy(const Tensor3Proxy & src) : parent(src) { }
Tensor3Proxy(const Tensor3<T> & src) : parent(src) { }
+
+ Tensor3Proxy & operator=(const Tensor3<T> & src) {
+ this->copyExternalMemory(src.storage(), src.size());
+ return *this;
+ }
};
/* -------------------------------------------------------------------------- */
/* Tensor base class */
/* -------------------------------------------------------------------------- */
template<typename T, UInt ndim, class RetType>
class TensorStorage {
public:
typedef T value_type;
protected:
template<class TensorType>
void copySize(const TensorType & src) {
for (UInt d = 0; d < ndim; ++d) this->n[d] = src.size(d);
this->_size = src.size();
}
TensorStorage() :
values(NULL), wrapped(false) {
for (UInt d = 0; d < ndim; ++d) this->n[d] = 0;
_size = 0;
}
TensorStorage(const TensorProxy<T, ndim, RetType> & proxy) {
this->copySize(proxy);
this->values = proxy.storage();
this->wrapped = true;
}
protected:
TensorStorage(const TensorStorage & src) { }
public:
TensorStorage(const TensorStorage & src, bool deep_copy) :
values(NULL), wrapped(false) {
if(deep_copy) this->deepCopy(src);
else this->shallowCopy(src);
}
protected:
TensorStorage(UInt m, UInt n, UInt p, const T & def) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = new T[this->_size];
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;
this->values = new T[this->_size];
memcpy(this->values, src.storage(), this->_size * sizeof(T));
this->wrapped = false;
}
virtual ~TensorStorage() {
if(!this->wrapped)
delete [] this->values;
}
inline TensorStorage & operator=(const RetType & src) {
if(this != &src) {
if (this->wrapped) {
AKANTU_DEBUG_ASSERT(this->_size == src.size(), "vectors of different size");
memcpy(this->values, src.storage(), this->_size * sizeof(T));
} 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));
}
/* ------------------------------------------------------------------------ */
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 clear() { memset(values, 0, _size * sizeof(T)); };
inline void set(const T & t) { std::fill_n(values, _size, t); };
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");
memcpy(values, other.storage(), _size * sizeof(T));
}
protected:
friend class Array<T>;
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);
}
};
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:
UInt n[ndim];
UInt _size;
T * values;
bool wrapped;
};
template<typename T, UInt ndim, class RetType>
inline TensorProxy<T, ndim, RetType>::TensorProxy(const TensorStorage<T, ndim, RetType> & other) {
this->values = other.storage();
for (UInt i = 0; i < ndim; ++i)
this->n[i] = other.size(i);
}
/* -------------------------------------------------------------------------- */
/* Vector */
/* -------------------------------------------------------------------------- */
template<typename T>
class Vector : public TensorStorage< T, 1, Vector<T> > {
typedef TensorStorage< T, 1, Vector<T> > parent;
public:
typedef typename parent::value_type value_type;
typedef VectorProxy<T> proxy;
public:
Vector() : parent() {}
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 VectorProxy<T> & src) : parent(src) { }
public:
virtual ~Vector() { };
/* ------------------------------------------------------------------------ */
inline Vector & operator=(const Vector & src) {
parent::operator=(src);
return *this;
}
/* ------------------------------------------------------------------------ */
inline T& operator()(UInt i) { return *(this->values + i); };
inline const T& operator()(UInt i) const { return *(this->values + i); };
inline T& operator[](UInt i) { return *(this->values + i); };
inline const T& operator[](UInt i) const { return *(this->values + 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) {
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 void solve(Matrix<T> & A, const Vector<T> & b) {
AKANTU_DEBUG_ASSERT(this->size() == A.rows() && this->_size = A.cols(),
"The solution vector as a mismatch in size with the matrix");
AKANTU_DEBUG_ASSERT(this->_size == b._size, "The rhs vector as 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,
Real alpha = 1.0);
/* ------------------------------------------------------------------------ */
inline Real norm() const {
return parent::template norm<L_2>();
}
template<NormType nt>
inline Real norm() const {
return parent::template norm<nt>();
}
/* ------------------------------------------------------------------------ */
inline void normalize() {
Real n = norm();
operator/=(n);
}
/* ------------------------------------------------------------------------ */
/// 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) 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 compare(v) == -1; }
inline bool operator>(const Vector<T> & v) const { return compare(v) == 1; }
/* ------------------------------------------------------------------------ */
/// 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 << "Vector<" << debug::demangle(typeid(T).name()) << ">(" << this->_size <<") : [";
for (UInt i = 0; i < this->_size; ++i) {
if(i != 0) stream << ", ";
stream << this->values[i];
}
stream << "]";
}
friend class ::akantu::Array<T>;
};
typedef Vector<Real> RVector;
/* -------------------------------------------------------------------------- */
// support operations for the creation of other vectors
template <typename T> Vector<T> operator*(T scalar, const Vector<T> & a);
template <typename T> Vector<T> operator+(const Vector<T> & a, const Vector<T> & b);
template <typename T> Vector<T> operator-(const Vector<T> & a, const Vector<T> & b);
/* -------------------------------------------------------------------------- */
template <typename T>
Vector<T> operator*(T scalar, const Vector<T> & a) {
Vector<T> r(a.size());
r = a;
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator+(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a.size());
r = a;
r += b;
return r;
}
template <typename T>
Vector<T> operator-(const Vector<T>& a, const Vector<T>& b) {
Vector<T> r(a.size());
r = a;
r -= b;
return r;
}
template <typename T>
Matrix<T> operator*(T scalar, const Matrix<T>& a) {
Matrix<T> r(a.rows(), a.cols());
r = a;
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator+(const Matrix<T>& a, const Matrix<T>& b) {
Matrix<T> r(a.rows(), a.cols());
r = a;
r += b;
return r;
}
template <typename T>
Matrix<T> operator-(const Matrix<T>& a, const Matrix<T>& b) {
Matrix<T> r(a.rows(), a.cols());
r = a;
r -= b;
return r;
}
/* ------------------------------------------------------------------------ */
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;
}
/* ------------------------------------------------------------------------ */
/* Matrix */
/* ------------------------------------------------------------------------ */
template<typename T>
class Matrix : public TensorStorage< T, 2, Matrix<T> > {
typedef TensorStorage< T, 2, Matrix<T> > parent;
public:
typedef typename parent::value_type value_type;
typedef MatrixProxy<T> proxy;
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) { }
virtual ~Matrix() { }
/* ------------------------------------------------------------------------ */
inline Matrix & operator=(const Matrix & src) {
parent::operator=(src);
return *this;
}
public:
/* ---------------------------------------------------------------------- */
UInt rows() const { return this->n[0]; }
UInt cols() const { return this->n[1]; }
/* ---------------------------------------------------------------------- */
inline T& operator()(UInt i, UInt j) {
return this->at(i,j);
}
inline T& at(UInt i, UInt j) {
return *(this->values + i + j*this->n[0]);
}
inline const T& operator()(UInt i, UInt j) const {
return this->at(i,j);
}
inline T& at(UInt i, UInt j) const {
return *(this->values + i + j*this->n[0]);
}
/// give a line vector wrapped on the column i
inline VectorProxy<T> operator()(UInt j) {
return VectorProxy<T>(this->values + j*this->n[0], this->n[0]);
}
inline const VectorProxy<T> operator()(UInt j) const {
return VectorProxy<T>(this->values + j*this->n[0], this->n[0]);
}
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) {
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) 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() != NULL)
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());
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->clear();
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 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);
else if(this->cols() == 2) return Math::det2(this->values);
else if(this->cols() == 3) return Math::det3(this->values);
else 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());
else if(this->cols() == 2) return Math::matrixDoubleDot22(this->values, other.storage());
else if(this->cols() == 3) return Math::matrixDoubleDot33(this->values, other.storage());
else AKANTU_DEBUG_ERROR("doubleDot is not defined for other spatial dimensions"
<< " than 1, 2 or 3.");
return T();
}
/* ---------------------------------------------------------------------- */
/// 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 << "Matrix<" << debug::demangle(typeid(T).name())
<< ">(" << this->n[0] << "," << this->n[1] <<") :" << "[";
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,
Real 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> > {
typedef TensorStorage< T, 3, Tensor3<T> > parent;
public:
typedef typename parent::value_type value_type;
typedef Tensor3Proxy<T> proxy;
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) { }
public:
/* ------------------------------------------------------------------------ */
inline Tensor3 & operator=(const Tensor3 & src) {
parent::operator=(src);
return *this;
}
/* ---------------------------------------------------------------------- */
inline T& operator()(UInt i, UInt j, UInt k)
{ return *(this->values + (k*this->n[0] + i)*this->n[1] + j); };
inline const T& operator()(UInt i, UInt j, UInt k) const
{ return *(this->values + (k*this->n[0] + i)*this->n[1] + j); };
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 const MatrixProxy<T> operator()(UInt k) const
{ 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 Matrix<T>(this->values + k*this->n[0]*this->n[1], this->n[0], this->n[1]); }
inline const MatrixProxy<T> operator[](UInt k) const
{ return MatrixProxy<T>(this->values + k*this->n[0]*this->n[1], this->n[0], this->n[1]); }
};
__END_AKANTU__
#endif /* __AKANTU_AKA_TYPES_HH__ */
diff --git a/src/fe_engine/fe_engine.cc b/src/fe_engine/fe_engine.cc
index 753c477cf..66b8dd754 100644
--- a/src/fe_engine/fe_engine.cc
+++ b/src/fe_engine/fe_engine.cc
@@ -1,241 +1,275 @@
/**
* @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: Fri Jun 13 2014
*
* @brief Implementation of the FEEngine class
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "fe_engine.hh"
#include "mesh.hh"
#include "element_class.hh"
#include "static_communicator.hh"
#include "aka_math.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
FEEngine::FEEngine(Mesh & mesh, UInt element_dimension, ID id, MemoryID memory_id) :
Memory(id, memory_id), mesh(mesh), normals_on_quad_points("normals_on_quad_points", id) {
AKANTU_DEBUG_IN();
this->element_dimension = (element_dimension != _all_dimensions) ?
element_dimension : mesh.getSpatialDimension();
init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::init() {
}
/* -------------------------------------------------------------------------- */
FEEngine::~FEEngine() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::assembleArray(const Array<Real> & elementary_vect,
- Array<Real> & nodal_values,
- const Array<Int> & equation_number,
- UInt nb_degree_of_freedom,
- const ElementType & type,
- const GhostType & ghost_type,
- const Array<UInt> & filter_elements,
- Real scale_factor) const {
+ Array<Real> & nodal_values,
+ const Array<Int> & equation_number,
+ UInt nb_degree_of_freedom,
+ const ElementType & type,
+ const GhostType & ghost_type,
+ const Array<UInt> & filter_elements,
+ Real scale_factor) const {
AKANTU_DEBUG_IN();
UInt nb_element;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
Array<UInt>::const_iterator< Vector<UInt> > conn_it;
Array<UInt> * filtered_connectivity = NULL;
if(filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filtered_connectivity = new Array<UInt>(0, nb_nodes_per_element);
FEEngine::filterElementalData(mesh,
- mesh.getConnectivity(type, ghost_type),
- *filtered_connectivity,
- type, ghost_type,
- filter_elements);
+ mesh.getConnectivity(type, ghost_type),
+ *filtered_connectivity,
+ type, ghost_type,
+ filter_elements);
const Array<UInt> & cfiltered = *filtered_connectivity; // \todo temporary patch
conn_it = cfiltered.begin(nb_nodes_per_element);
} else {
nb_element = mesh.getNbElement(type, ghost_type);
conn_it = mesh.getConnectivity(type, ghost_type).begin(nb_nodes_per_element);
}
AKANTU_DEBUG_ASSERT(elementary_vect.getSize() == nb_element,
- "The vector elementary_vect(" << elementary_vect.getID()
- << ") has not the good size.");
+ "The vector elementary_vect(" << elementary_vect.getID()
+ << ") has not the good size.");
AKANTU_DEBUG_ASSERT(elementary_vect.getNbComponent()
- == nb_degree_of_freedom*nb_nodes_per_element,
- "The vector elementary_vect(" << elementary_vect.getID()
- << ") has not the good number of component."
- << "(" << elementary_vect.getNbComponent()
- << " != " << nb_degree_of_freedom*nb_nodes_per_element << ")");
+ == nb_degree_of_freedom*nb_nodes_per_element,
+ "The vector elementary_vect(" << elementary_vect.getID()
+ << ") has not the good number of component."
+ << "(" << elementary_vect.getNbComponent()
+ << " != " << nb_degree_of_freedom*nb_nodes_per_element << ")");
AKANTU_DEBUG_ASSERT(nodal_values.getNbComponent() == nb_degree_of_freedom,
- "The vector nodal_values(" << nodal_values.getID()
- << ") has not the good number of component."
- << "(" << nodal_values.getNbComponent()
- << " != " << nb_degree_of_freedom << ")");
+ "The vector nodal_values(" << nodal_values.getID()
+ << ") has not the good number of component."
+ << "(" << nodal_values.getNbComponent()
+ << " != " << nb_degree_of_freedom << ")");
nodal_values.resize(mesh.getNbNodes());
Real * nodal_it = nodal_values.storage();
Array<Real>::const_matrix_iterator elem_it = elementary_vect.begin(nb_degree_of_freedom,
- nb_nodes_per_element);
+ nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++elem_it, ++conn_it) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = (*conn_it)(n);
UInt offset_node = node * nb_degree_of_freedom;
const Vector<Real> & elem_data = (*elem_it)(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
nodal_it[equation_number(offset_node + d)]
+= scale_factor * elem_data(d);
}
}
}
delete filtered_connectivity;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::assembleMatrix(const Array<Real> & elementary_mat,
- SparseMatrix & matrix,
- UInt nb_degree_of_freedom,
- const ElementType & type,
- const GhostType & ghost_type,
- const Array<UInt> & filter_elements) const {
+ SparseMatrix & matrix,
+ UInt nb_degree_of_freedom,
+ const ElementType & type,
+ const GhostType & ghost_type,
+ const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element;
if(ghost_type == _not_ghost) {
nb_element = mesh.getNbElement(type);
} else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
if(filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
}
AKANTU_DEBUG_ASSERT(elementary_mat.getSize() == nb_element,
- "The vector elementary_mat(" << elementary_mat.getID()
- << ") has not the good size.");
+ "The vector elementary_mat(" << elementary_mat.getID()
+ << ") has not the good size.");
AKANTU_DEBUG_ASSERT(elementary_mat.getNbComponent()
- == nb_degree_of_freedom * nb_nodes_per_element * nb_degree_of_freedom * nb_nodes_per_element,
- "The vector elementary_mat(" << elementary_mat.getID()
- << ") has not the good number of component.");
+ == nb_degree_of_freedom * nb_nodes_per_element * nb_degree_of_freedom * nb_nodes_per_element,
+ "The vector elementary_mat(" << elementary_mat.getID()
+ << ") has not the good number of component.");
Real * elementary_mat_val = elementary_mat.storage();
UInt offset_elementary_mat = elementary_mat.getNbComponent();
UInt * connectivity_val = mesh.getConnectivity(type, ghost_type).storage();
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
UInt size = mesh.getNbGlobalNodes() * nb_degree_of_freedom;
Int * eq_nb_val = matrix.getDOFSynchronizer().getGlobalDOFEquationNumbers().storage();
Int * local_eq_nb_val = new Int[size_mat];
for (UInt e = 0; e < nb_element; ++e) {
UInt el = e;
if(filter_elements != empty_filter) el = filter_elements(e);
Int * tmp_local_eq_nb_val = local_eq_nb_val;
UInt * conn_val = connectivity_val + el * nb_nodes_per_element;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
UInt n = conn_val[i];
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
*tmp_local_eq_nb_val++ = eq_nb_val[n * nb_degree_of_freedom + d];
}
// memcpy(tmp_local_eq_nb_val, eq_nb_val + n * nb_degree_of_freedom, nb_degree_of_freedom * sizeof(Int));
// tmp_local_eq_nb_val += nb_degree_of_freedom;
}
- for (UInt i = 0; i < size_mat; ++i) {
- UInt c_irn = local_eq_nb_val[i];
- if(c_irn < size) {
- UInt j_start = (matrix.getSparseMatrixType() == _symmetric) ? i : 0;
- for (UInt j = j_start; j < size_mat; ++j) {
- UInt c_jcn = local_eq_nb_val[j];
- if(c_jcn < size) {
- matrix(c_irn, c_jcn) += elementary_mat_val[j * size_mat + i];
+ /// The matrix assembling for cohesive elements with degenerated nodes
+ /// (i.e. elements in correspondence of the crack tips) has to be done
+ /// without considering symmetry
+
+
+#if defined(AKANTU_COHESIVE_ELEMENT)
+ if (mesh.getKind(type) == _ek_cohesive){
+
+ /// matrix assembling procedure for cohesive elements
+ for (UInt i = 0; i < size_mat; ++i) {
+ UInt c_irn = local_eq_nb_val[i];
+ if(c_irn < size) {
+ for (UInt j = 0; j < size_mat; ++j) {
+ UInt c_jcn = local_eq_nb_val[j];
+ if(c_jcn < size) {
+ if (matrix.getSparseMatrixType() == _symmetric){
+ if (c_jcn >= c_irn){
+ matrix(c_irn, c_jcn) += elementary_mat_val[j * size_mat + i];
+ }
+ }else{
+ matrix(c_irn, c_jcn) += elementary_mat_val[j * size_mat + i];
+ }
+ }
}
}
}
+ elementary_mat_val += offset_elementary_mat;
+
+ }else{
+#endif
+ /// matrix assembling procedure for all the elements except cohesive ones
+ for (UInt i = 0; i < size_mat; ++i) {
+ UInt c_irn = local_eq_nb_val[i];
+ if(c_irn < size) {
+ UInt j_start = (matrix.getSparseMatrixType() == _symmetric) ? i : 0;
+ for (UInt j = j_start; j < size_mat; ++j) {
+ UInt c_jcn = local_eq_nb_val[j];
+ if(c_jcn < size) {
+ matrix(c_irn, c_jcn) += elementary_mat_val[j * size_mat + i];
+ }
+ }
+ }
+ }
+ elementary_mat_val += offset_elementary_mat;
}
- elementary_mat_val += offset_elementary_mat;
+#if defined(AKANTU_COHESIVE_ELEMENT)
}
+#endif
delete [] local_eq_nb_val;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += 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;
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/geometry/aabb_primitives/aabb_primitive.hh b/src/geometry/aabb_primitives/aabb_primitive.hh
index 98f6d85fc..e603bf47e 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.hh
+++ b/src/geometry/aabb_primitives/aabb_primitive.hh
@@ -1,77 +1,85 @@
/**
* @file aabb_primitive.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Fri Mar 13 2015
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AABB_PRIMITIVE_HH__
#define __AKANTU_AABB_PRIMITIVE_HH__
#include "aka_common.hh"
#include "triangle.hh"
#include "tetrahedron.hh"
__BEGIN_AKANTU__
-typedef CGAL::Cartesian<Real> Kernel;
-
-#define AKANTU_AABB_CLASS(name) \
+/**
+ * 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 { \
- typedef std::list< name<Kernel> >::iterator Iterator; \
+ typedef std::list< name<kernel> >::iterator Iterator; \
\
public: \
typedef UInt Id; \
- typedef Kernel::Point_3 Point; \
- typedef Kernel::name##_3 Datum; \
+ typedef kernel::Point_3 Point; \
+ typedef kernel::name##_3 Datum; \
\
public: \
name##_primitive() : meshId(0), primitive() {} \
name##_primitive(Iterator it) : meshId(it->id()), primitive(*it) {} \
\
public: \
const Datum & datum() const { return primitive; } \
const Point & reference_point() const { return primitive.vertex(0); } \
const Id & id() const { return meshId; } \
\
protected: \
Id meshId; \
- name<Kernel> primitive; \
+ name<kernel> primitive; \
\
}
// If the primitive is supported by CGAL::intersection() then the
// implementation process is really easy with this macro
-AKANTU_AABB_CLASS(Triangle);
-AKANTU_AABB_CLASS(Tetrahedron);
+AKANTU_AABB_CLASS(Triangle, CGAL::Cartesian<Real>);
#undef AKANTU_AABB_CLASS
__END_AKANTU__
#endif // __AKANTU_AABB_PRIMITIVE_HH__
diff --git a/src/geometry/aabb_primitives/tetrahedron.hh b/src/geometry/aabb_primitives/tetrahedron.hh
index e7006ad78..6609fd40b 100644
--- a/src/geometry/aabb_primitives/tetrahedron.hh
+++ b/src/geometry/aabb_primitives/tetrahedron.hh
@@ -1,71 +1,74 @@
/**
* @file tetrahedron.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Mar 10 2015
* @date last modification: Tue Mar 10 2015
*
* @brief Tetrahedron classe (geometry) for AABB CGAL algos
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TETRAHEDRON_HH__
#define __AKANTU_TETRAHEDRON_HH__
#include "aka_common.hh"
#include <CGAL/Cartesian.h>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
+/// Class used for substitution of CGAL::Tetrahedron_3 primitive
template<typename K>
class Tetrahedron : public CGAL::Tetrahedron_3<K> {
public:
/// Default constructor
- Tetrahedron();
+ Tetrahedron() :
+ CGAL::Tetrahedron_3<K>(), meshId(0) {}
/// Copy constructor
- Tetrahedron(const Tetrahedron & other);
+ 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);
+ const CGAL::Point_3<K> & d) :
+ CGAL::Tetrahedron_3<K>(a, b, c, d), meshId(0) {}
public:
- UInt id() const;
- void setId(UInt newId);
+ UInt id() const { return meshId; }
+ void setId(UInt newId) { meshId = newId; }
protected:
+ /// Id of the element represented by the primitive
UInt meshId;
};
__END_AKANTU__
-#include "tetrahedron_tmpl.hh"
-
#endif
diff --git a/src/geometry/aabb_primitives/tetrahedron_tmpl.hh b/src/geometry/aabb_primitives/tetrahedron_tmpl.hh
deleted file mode 100644
index d686cda02..000000000
--- a/src/geometry/aabb_primitives/tetrahedron_tmpl.hh
+++ /dev/null
@@ -1,74 +0,0 @@
-/**
- * @file tetrahedron_tmpl.hh
- *
- * @author Lucas Frérot <lucas.frerot@epfl.ch>
- *
- * @date creation: Tue Mar 10 2015
- * @date last modification: Tue Mar 10 2015
- *
- * @brief Tetrahedron class (geometry) for AABB CGAL algos, template impl
- *
- * @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/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_TETRAHEDRON_TMPL_HH__
-#define __AKANTU_TETRAHEDRON_TMPL_HH__
-
-#include "tetrahedron.hh"
-#include <CGAL/Cartesian.h>
-
-__BEGIN_AKANTU__
-
-template<typename K>
-Tetrahedron<K>::Tetrahedron() :
- CGAL::Tetrahedron_3<K>(),
- meshId(0)
-{}
-
-template<typename K>
-Tetrahedron<K>::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),
- meshId(0)
-{}
-
-template<typename K>
-Tetrahedron<K>::Tetrahedron(const Tetrahedron & other) :
- CGAL::Tetrahedron_3<K>(other),
- meshId(other.meshId)
-{}
-
-template<typename K>
-UInt Tetrahedron<K>::id() const {
- return meshId;
-}
-
-template<typename K>
-void Tetrahedron<K>::setId(UInt newId) {
- meshId = newId;
-}
-
-__END_AKANTU__
-
-#endif
diff --git a/src/geometry/aabb_primitives/triangle.hh b/src/geometry/aabb_primitives/triangle.hh
index 4b4112a65..30c6104d1 100644
--- a/src/geometry/aabb_primitives/triangle.hh
+++ b/src/geometry/aabb_primitives/triangle.hh
@@ -1,68 +1,71 @@
/**
* @file triangle.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Tue Mar 3 2015
* @date last modification: Tue Mar 3 2015
*
* @brief Triangle classe (geometry) for AABB CGAL algos
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TRIANGLE_HH__
#define __AKANTU_TRIANGLE_HH__
#include "aka_common.hh"
#include <CGAL/Cartesian.h>
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
+/// Class used for substitution of CGAL::Triangle_3 primitive
template<typename K>
class Triangle : public CGAL::Triangle_3<K> {
public:
/// Default constructor
- Triangle();
+ Triangle() :
+ CGAL::Triangle_3<K>(), meshId(0) {}
/// Copy constructor
- Triangle(const Triangle & other);
+ Triangle(const Triangle & other) :
+ CGAL::Triangle_3<K>(other), meshId(other.meshId) {}
/// Construct from 3 points
- Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b, const CGAL::Point_3<K> & c);
+ Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b, const CGAL::Point_3<K> & c):
+ CGAL::Triangle_3<K>(a, b, c), meshId(0) {}
public:
- UInt id() const;
- void setId(UInt newId);
+ UInt id() const { return meshId; }
+ void setId(UInt newId) { meshId = newId; }
protected:
+ /// Id of the element represented by the primitive
UInt meshId;
};
__END_AKANTU__
-#include "triangle_tmpl.hh"
-
#endif // __AKANTU_TRIANGLE_HH__
diff --git a/src/geometry/aabb_primitives/triangle_tmpl.hh b/src/geometry/aabb_primitives/triangle_tmpl.hh
deleted file mode 100644
index acd15ed8f..000000000
--- a/src/geometry/aabb_primitives/triangle_tmpl.hh
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * @file triangle_tmpl.hh
- *
- * @author Lucas Frérot <lucas.frerot@epfl.ch>
- *
- * @date creation: Tue Mar 3 2015
- * @date last modification: Tue Mar 3 2015
- *
- * @brief Triangle classe (geometry) for AABB CGAL algos, template impl
- *
- * @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/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_TRIANGLE_TMPL_HH__
-#define __AKANTU_TRIANGLE_TMPL_HH__
-
-#include "triangle.hh"
-#include <CGAL/Cartesian.h>
-
-__BEGIN_AKANTU__
-
-template<typename K>
-Triangle<K>::Triangle() :
- CGAL::Triangle_3<K>(),
- meshId(0)
-{}
-
-template<typename K>
-Triangle<K>::Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b, const CGAL::Point_3<K> & c) :
- CGAL::Triangle_3<K>(a, b, c),
- meshId(0)
-{}
-
-template<typename K>
-Triangle<K>::Triangle(const Triangle & other) :
- CGAL::Triangle_3<K>(other),
- meshId(other.meshId)
-{}
-
-template<typename K>
-UInt Triangle<K>::id() const {
- return meshId;
-}
-
-template<typename K>
-void Triangle<K>::setId(UInt newId) {
- meshId = newId;
-}
-
-__END_AKANTU__
-
-#endif // __AKANTU_TRIANGLE_TMPL_HH__
diff --git a/src/geometry/geom_helper_functions.hh b/src/geometry/geom_helper_functions.hh
index 8ab38bf3f..63337084c 100644
--- a/src/geometry/geom_helper_functions.hh
+++ b/src/geometry/geom_helper_functions.hh
@@ -1,125 +1,114 @@
/**
* @file geom_helper_functions.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 4 2015
* @date last modification: Thu Mar 5 2015
*
* @brief Helper functions for the computational geometry algorithms
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#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 <CGAL/Cartesian.h>
__BEGIN_AKANTU__
typedef CGAL::Cartesian<Real> K;
#define EPS 1e-10
+/// Fuzzy compare of two points
inline bool comparePoints(const K::Point_3 & a, const K::Point_3 & b) {
Math::setTolerance(EPS);
return Math::are_float_equal(a.x(), b.x()) && Math::are_float_equal(a.y(), b.y());
}
+/// Fuzzy compare of two segments
inline bool compareSegments(const K::Segment_3 & a, const K::Segment_3 & 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<K::Segment_3, UInt> & a, const std::pair<K::Segment_3, UInt> & b) {
return compareSegments(a.first, b.first);
}
+/// Pair ordering operator based on second member
inline bool comparePairElement(const std::pair<K::Segment_3, UInt> & a, const std::pair<K::Segment_3, UInt> & b) {
return a.second < b.second;
}
+/// Pair ordering operator based on first member
inline bool lessSegmentPair(const std::pair<K::Segment_3, UInt> & a, const std::pair<K::Segment_3, UInt> & b) {
return CGAL::compare_lexicographically(a.first.min(), b.first.min()) || CGAL::compare_lexicographically(a.first.max(), b.first.max());
}
/* -------------------------------------------------------------------------- */
/* Predicates */
/* -------------------------------------------------------------------------- */
-// Predicate used to eliminate faces of mesh not belonging to a specific element
-template <UInt dim, ElementType el_type>
+/// Predicate used to eliminate faces of mesh not belonging to a specific element
+template <class Primitive, class Kernel>
class BelongsNotToElement {
public:
BelongsNotToElement(UInt el):
el(el)
{}
- bool operator()(const typename TreeTypeHelper<dim, el_type>::primitive_type & primitive) {
+ bool operator()(const typename TreeTypeHelper<Primitive, Kernel>::primitive_type & primitive) {
return primitive.id() != el;
}
protected:
const UInt el;
};
-// Predicate used to determine if point is on edge of faces of mesh
-template <UInt dim, ElementType el_type>
-class HasOnEdge {
-
-public:
- HasOnEdge(const K::Point_3 & point):
- point(point)
- {}
-
- bool operator()(const typename TreeTypeHelper<dim, el_type>::primitive_type & primitive) {
- return primitive.has_on(point);
- }
-
-protected:
- const K::Point_3 & point;
-};
-
+/// Predicate used to determine if two segments are equal
class IsSameSegment {
public:
IsSameSegment(const K::Segment_3 & segment):
segment(segment)
{}
bool operator()(const std::pair<K::Segment_3, UInt> & test_pair) {
return compareSegments(segment, test_pair.first);
}
protected:
const K::Segment_3 segment;
};
__END_AKANTU__
#endif // _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
diff --git a/src/geometry/mesh_geom_abstract.hh b/src/geometry/mesh_geom_abstract.hh
index 0b89f05a4..b116ab725 100644
--- a/src/geometry/mesh_geom_abstract.hh
+++ b/src/geometry/mesh_geom_abstract.hh
@@ -1,76 +1,64 @@
/**
* @file mesh_geom_abstract.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Feb 26 2015
* @date last modification: Fri Mar 6 2015
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_GEOM_ABSTRACT_HH__
#define __AKANTU_MESH_GEOM_ABSTRACT_HH__
#include "aka_common.hh"
#include "mesh.hh"
-#include <CGAL/Cartesian.h>
-
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
-typedef CGAL::Cartesian<Real> K;
-
+/// Abstract class for mesh geometry operations
class MeshGeomAbstract {
-protected:
- typedef std::pair<K::Segment_3, std::string> Interface;
-
public:
/// Construct from mesh
explicit MeshGeomAbstract(const Mesh & mesh);
/// Destructor
virtual ~MeshGeomAbstract();
public:
/// Construct geometric data for computational geometry algorithms
virtual void constructData() = 0;
- /// Compute number of intersections with geometric interface
- virtual UInt numberOfIntersectionsWithInterface(const K::Segment_3 & interface) const = 0;
-
- /// Compute the mesh created by a linear interface
- virtual void meshOfLinearInterface(const Interface & interface, Mesh & interface_mesh) = 0;
-
protected:
/// Mesh used to construct the primitives
const Mesh & mesh;
};
__END_AKANTU__
#endif // __AKANTU_MESH_GEOM_ABSTRACT_HH__
diff --git a/src/geometry/mesh_geom_container.cc b/src/geometry/mesh_geom_container.cc
deleted file mode 100644
index 84925c1b5..000000000
--- a/src/geometry/mesh_geom_container.cc
+++ /dev/null
@@ -1,153 +0,0 @@
-/**
- * @file mesh_geom_container.cc
- *
- * @author Lucas Frérot <lucas.frerot@epfl.ch>
- *
- * @date creation: Fri Feb 27 2015
- * @date last modification: Fri Mar 6 2015
- *
- * @brief Contains the CGAL representation of a mesh
- *
- * @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/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#include "aka_common.hh"
-
-#include "mesh_geom_container.hh"
-#include "mesh_geom_factory.hh"
-#include "mesh.hh"
-
-#include <CGAL/Cartesian.h>
-
-/* -------------------------------------------------------------------------- */
-
-#define MESH_GEOM_CASE(d, type) \
- MeshGeomFactory<d, type> * factory = new MeshGeomFactory<d, type>(mesh); \
- factory_map(factory, type); \
- factory->constructData();
-
-#define MESH_GEOM_CASE_2D(type) MESH_GEOM_CASE(2, type)
-#define MESH_GEOM_CASE_3D(type) MESH_GEOM_CASE(3, type)
-
-/* -------------------------------------------------------------------------- */
-
-__BEGIN_AKANTU__
-
-typedef CGAL::Cartesian<Real> K;
-
-
-MeshGeomContainer::MeshGeomContainer(const Mesh & mesh):
- MeshGeomAbstract(mesh),
- factory_map(),
- interface_mesh(mesh.getSpatialDimension(), "mesh_geom")
-{
- interface_mesh.addConnectivityType(_segment_2, _not_ghost);
- interface_mesh.addConnectivityType(_segment_2, _ghost);
- interface_mesh.registerData<Element>("associated_element").alloc(0, 1, _segment_2);
- interface_mesh.registerData<std::string>("material").alloc(0, 1, _segment_2);
-}
-
-MeshGeomContainer::~MeshGeomContainer()
-{}
-
-void MeshGeomContainer::constructData() {
- AKANTU_DEBUG_IN();
-
- const UInt spatial_dim = mesh.getSpatialDimension();
-
- Mesh::type_iterator it = mesh.firstType(spatial_dim, _not_ghost);
- Mesh::type_iterator end = mesh.lastType(spatial_dim, _not_ghost);
-
- /// Loop over the element types of the mesh and construct the primitive trees
- for (; it != end ; ++it) {
- ElementType type = *it; // for AKANTU_BOOST_ELEMENT_SWITCH macro
- switch(spatial_dim) {
- case 1:
- AKANTU_DEBUG_WARNING("Geometry in 1D is undefined");
- break;
-
- case 2:
- // Expand the list of elements when they are implemented
- AKANTU_BOOST_ELEMENT_SWITCH(MESH_GEOM_CASE_2D, (_triangle_3));
- break;
-
- case 3:
- AKANTU_BOOST_ELEMENT_SWITCH(MESH_GEOM_CASE_3D, (_tetrahedron_4));
- break;
- }
- }
-
- AKANTU_DEBUG_OUT();
-}
-
-UInt MeshGeomContainer::numberOfIntersectionsWithInterface(const K::Segment_3 & interface) const {
- AKANTU_DEBUG_IN();
-
- UInt total = 0;
-
- GeomMap::type_iterator it = factory_map.firstType();
- GeomMap::type_iterator end = factory_map.lastType();
-
- for (; it != end ; ++it) {
- total += factory_map(*it)->numberOfIntersectionsWithInterface(interface);
- }
-
- AKANTU_DEBUG_OUT();
-
- return total;
-}
-
-void MeshGeomContainer::meshOfLinearInterface(const Interface & interface, Mesh & interface_mesh) {
- AKANTU_DEBUG_IN();
-
- GeomMap::type_iterator it = factory_map.firstType();
- GeomMap::type_iterator end = factory_map.lastType();
-
- for (; it != end ; ++it) {
- factory_map(*it)->meshOfLinearInterface(interface, interface_mesh);
- }
-
- AKANTU_DEBUG_OUT();
-}
-
-Mesh & MeshGeomContainer::meshOfLinearInterfaces(const std::list<Interface> & interfaces) {
- std::list<Interface>::const_iterator interfaces_it = interfaces.begin();
- std::list<Interface>::const_iterator interfaces_end = interfaces.end();
-
- for (; interfaces_it != interfaces_end ; ++interfaces_it) {
- meshOfLinearInterface(*interfaces_it, interface_mesh);
- }
-
- return interface_mesh;
-}
-
-const MeshGeomAbstract * MeshGeomContainer::getFactoryForElementType(ElementType el_type) const {
- return factory_map(el_type);
-}
-
-/* -------------------------------------------------------------------------- */
-
-#undef MESH_GEOM_CASE_2D
-#undef MESH_GEOM_CASE_3D
-#undef MESH_GEOM_CASE
-
-__END_AKANTU__
diff --git a/src/geometry/mesh_geom_container.hh b/src/geometry/mesh_geom_container.hh
deleted file mode 100644
index bb8fb2fd2..000000000
--- a/src/geometry/mesh_geom_container.hh
+++ /dev/null
@@ -1,82 +0,0 @@
-/**
- * @file mesh_geom_container.hh
- *
- * @author Lucas Frérot <lucas.frerot@epfl.ch>
- *
- * @date creation: Fri Feb 27 2015
- * @date last modification: Fri Mar 6 2015
- *
- * @brief Contains the CGAL representation of a mesh
- *
- * @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/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_MESH_GEOM_CONTAINER__
-#define __AKANTU_MESH_GEOM_CONTAINER__
-
-#include "aka_common.hh"
-#include "mesh.hh"
-#include "mesh_geom_abstract.hh"
-
-#include <CGAL/Cartesian.h>
-
-/* -------------------------------------------------------------------------- */
-
-__BEGIN_AKANTU__
-
-typedef CGAL::Cartesian<Real> K;
-
-class MeshGeomContainer : MeshGeomAbstract {
- typedef ElementTypeMap<MeshGeomAbstract *> GeomMap;
-
-public:
- /// Construct from mesh
- explicit MeshGeomContainer(const Mesh & mesh);
-
- /// Destructor
- virtual ~MeshGeomContainer();
-
-public:
- /// Constructs the geometric data from the mesh
- virtual void constructData();
-
- /// Compute the number of intersections with geometric interface
- virtual UInt numberOfIntersectionsWithInterface(const K::Segment_3 & interface) const;
-
- /// Compute the intersection mesh with linear interface
- virtual void meshOfLinearInterface(const Interface & interface, Mesh & interface_mesh);
-
- /// Construct the interface mesh from several segments
- Mesh & meshOfLinearInterfaces(const std::list<Interface> & interfaces);
-
- /// Get the factory object for an element type
- const MeshGeomAbstract * getFactoryForElementType(ElementType el_type) const;
-
-protected:
- GeomMap factory_map;
-
- Mesh interface_mesh;
-};
-
-__END_AKANTU__
-
-#endif // __AKANTU_MESH_GEOM_CONTAINER__
diff --git a/src/geometry/mesh_geom_factory.hh b/src/geometry/mesh_geom_factory.hh
index 143a49b2b..43387d45b 100644
--- a/src/geometry/mesh_geom_factory.hh
+++ b/src/geometry/mesh_geom_factory.hh
@@ -1,90 +1,109 @@
/**
* @file mesh_geom_factory.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Feb 26 2015
* @date last modification: Fri Mar 6 2015
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_GEOM_FACTORY_HH__
#define __AKANTU_MESH_GEOM_FACTORY_HH__
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_geom_abstract.hh"
#include "tree_type_helper.hh"
+#include "geom_helper_functions.hh"
+
+#include <algorithm>
#include <CGAL/Cartesian.h>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
-typedef CGAL::Cartesian<Real> K;
-
-template<UInt dim, ElementType el_type>
+/**
+ * @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(const Mesh & mesh);
/// Desctructor
virtual ~MeshGeomFactory();
public:
/// Construct AABB tree for fast intersection computing
virtual void constructData();
- /// Compute the number of intersections with primitive
- virtual UInt numberOfIntersectionsWithInterface(const K::Segment_3 & interface) const;
-
- /// Create a mesh of the intersection with a linear interface
- virtual void meshOfLinearInterface(const Interface & interface, Mesh & interface_mesh);
-
- /// Construct a primitive and add it to the list
- void addPrimitive(const Matrix<Real> & node_coordinates, UInt id);
-
- /// Construct segment list from intersections and remove duplicates
- void constructSegments(
- const std::list<typename TreeTypeHelper<dim, el_type>::linear_intersection> & intersections,
- std::list<std::pair<K::Segment_3, UInt> > & segments,
- const K::Segment_3 & interface);
-
- const typename TreeTypeHelper<dim, el_type>::tree & getTree() const { return *data_tree; }
+ /**
+ * @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,
+ typename TreeTypeHelper<Primitive, Kernel>::container_type & list
+ );
+
+ inline void addPrimitive(
+ const Matrix<Real> & node_coordinates,
+ UInt id
+ );
+
+ /// Getter for the AABB tree
+ const typename TreeTypeHelper<Primitive, Kernel>::tree & getTree() const { return *data_tree; }
+
+ /// Getter for primitive list
+ const typename TreeTypeHelper<Primitive, Kernel>::container_type & getPrimitiveList() const
+ { return primitive_list; }
protected:
- typename TreeTypeHelper<dim, el_type>::tree * data_tree;
- typename TreeTypeHelper<dim, el_type>::container_type primitive_list;
-};
+ /// AABB data tree
+ typename TreeTypeHelper<Primitive, Kernel>::tree * data_tree;
+ /// Primitive list
+ typename TreeTypeHelper<Primitive, Kernel>::container_type primitive_list;
+};
__END_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 545884d0e..889e379f5 100644
--- a/src/geometry/mesh_geom_factory_tmpl.hh
+++ b/src/geometry/mesh_geom_factory_tmpl.hh
@@ -1,271 +1,153 @@
/**
* @file mesh_geom_factory_tmpl.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Feb 26 2015
* @date last modification: Fri Mar 6 2015
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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/>.
*
*/
-/* -------------------------------------------------------------------------- */
-
-#ifndef _AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
-#define _AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
+#ifndef __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
+#define __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
-#include "mesh_geom_factory.hh"
+/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
-#include "tree_type_helper.hh"
-#include "triangle.hh"
-#include "geom_helper_functions.hh"
-
-#include <algorithm>
+#include "mesh_geom_factory.hh"
#include <CGAL/Cartesian.h>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
-typedef CGAL::Cartesian<Real> K;
+typedef CGAL::Cartesian<Real> Cartesian;
-template<UInt dim, ElementType type>
-MeshGeomFactory<dim, type>::MeshGeomFactory(const Mesh & mesh) :
+template<UInt dim, ElementType type, class Primitive, class Kernel>
+MeshGeomFactory<dim, type, Primitive, Kernel>::MeshGeomFactory(const Mesh & mesh) :
MeshGeomAbstract(mesh),
data_tree(NULL),
primitive_list()
{}
-template<UInt dim, ElementType type>
-MeshGeomFactory<dim, type>::~MeshGeomFactory() {
+template<UInt dim, ElementType type, class Primitive, class Kernel>
+MeshGeomFactory<dim, type, Primitive, Kernel>::~MeshGeomFactory() {
delete data_tree;
}
-template<UInt dim, ElementType type>
-void MeshGeomFactory<dim, type>::constructData() {
+/**
+ * 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() {
AKANTU_DEBUG_IN();
const GhostType ghost_type = _not_ghost;
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();
Array<UInt>::const_vector_iterator begin = connectivity.begin(nb_nodes_per_element);
Array<UInt>::const_vector_iterator it = connectivity.begin(nb_nodes_per_element);
Array<UInt>::const_vector_iterator end = connectivity.end(nb_nodes_per_element);
- /// This loop builds the list of primitives
+ // This loop builds the list of primitives
for (; it != end ; ++it) {
const Vector<UInt> & el_connectivity = *it;
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);
addPrimitive(node_coordinates, it - begin);
}
delete data_tree;
- data_tree = new typename TreeTypeHelper<dim, type>::tree(primitive_list.begin(), primitive_list.end());
+ data_tree = new typename TreeTypeHelper<Primitive, Kernel>::tree(primitive_list.begin(), primitive_list.end());
AKANTU_DEBUG_OUT();
}
+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);
+}
+
// 2D and _triangle_3 implementation
template<>
-void MeshGeomFactory<2, _triangle_3>::addPrimitive(const Matrix<Real> & node_coordinates, UInt id) {
- TreeTypeHelper<2, _triangle_3>::point_type a(node_coordinates(0, 0), node_coordinates(1, 0), 0.);
- TreeTypeHelper<2, _triangle_3>::point_type b(node_coordinates(0, 1), node_coordinates(1, 1), 0.);
- TreeTypeHelper<2, _triangle_3>::point_type c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
+inline void MeshGeomFactory<2, _triangle_3, Triangle<Cartesian>, Cartesian>::addPrimitive(
+ const Matrix<Real> & node_coordinates,
+ UInt id,
+ TreeTypeHelper<Triangle<Cartesian>, Cartesian>::container_type & list) {
+
+ TreeTypeHelper<Triangle<Cartesian>, Cartesian>::point_type
+ a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
+ b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
+ c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
- Triangle<K> t(a, b, c);
+ Triangle<Cartesian> t(a, b, c);
t.setId(id);
- primitive_list.push_back(t);
+ list.push_back(t);
}
-// 3D and _tetrahedron_4 implementation
+// 3D and _tetrahedron_4 with triangles implementation
template<>
-void MeshGeomFactory<3, _tetrahedron_4>::addPrimitive(const Matrix<Real> & node_coordinates, UInt id) {
- TreeTypeHelper<3, _tetrahedron_4>::point_type
+inline void MeshGeomFactory<3, _tetrahedron_4, Triangle<Cartesian>, Cartesian>::addPrimitive(
+ const Matrix<Real> & node_coordinates,
+ UInt id,
+ TreeTypeHelper<Triangle<Cartesian>, Cartesian>::container_type & list) {
+
+ TreeTypeHelper<Triangle<Cartesian>, Cartesian>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), node_coordinates(2, 0)),
b(node_coordinates(0, 1), node_coordinates(1, 1), node_coordinates(2, 1)),
c(node_coordinates(0, 2), node_coordinates(1, 2), node_coordinates(2, 2)),
d(node_coordinates(0, 3), node_coordinates(1, 3), node_coordinates(2, 3));
- Triangle<K>
+ Triangle<Cartesian>
t1(a, b, c),
t2(b, c, d),
t3(c, d, a),
t4(d, a, b);
t1.setId(id);
t2.setId(id);
t3.setId(id);
t4.setId(id);
- primitive_list.push_back(t1);
- primitive_list.push_back(t2);
- primitive_list.push_back(t3);
- primitive_list.push_back(t4);
-}
-
-template<UInt dim, ElementType el_type>
-UInt MeshGeomFactory<dim, el_type>::numberOfIntersectionsWithInterface(const K::Segment_3 & interface) const {
- return data_tree->number_of_intersected_primitives(interface);
+ list.push_back(t1);
+ list.push_back(t2);
+ list.push_back(t3);
+ list.push_back(t4);
}
-template<UInt dim, ElementType el_type>
-void MeshGeomFactory<dim, el_type>::meshOfLinearInterface(const Interface & interface_pair, Mesh & interface_mesh) {
- AKANTU_DEBUG_IN();
-
- const K::Segment_3 & interface = interface_pair.first;
-
- UInt number_of_intersections = this->numberOfIntersectionsWithInterface(interface);
-
- if (!number_of_intersections) {
- AKANTU_DEBUG_WARNING("No intersection with interface");
- return;
- }
-
- std::list<typename TreeTypeHelper<dim, el_type>::linear_intersection> list_of_intersections;
- /// TODO change this list to a set using lessSegmentPair for optimization
- std::list< std::pair<K::Segment_3, UInt> > list_of_segments; // Contains no duplicate elements
-
- /// Compute all the intersection pairs (segment + element id) and remove duplicates
- data_tree->all_intersections(interface, std::back_inserter(list_of_intersections));
- this->constructSegments(list_of_intersections, list_of_segments, interface);
-
- /// Arrays for storing nodes and connectivity
- Array<Real> & nodes = interface_mesh.getNodes();
- Array<UInt> & connectivity = interface_mesh.getConnectivity(_segment_2);
-
- /// Arrays for storing associated element id and type
- Array<Element> & associated_element = interface_mesh.getData<Element>("associated_element", _segment_2);
- Array<std::string> & associated_material = interface_mesh.getData<std::string>("material", _segment_2);
-
- std::list<std::pair<K::Segment_3, UInt> >::iterator it = list_of_segments.begin();
- std::list<std::pair<K::Segment_3, UInt> >::iterator end = list_of_segments.end();
-
- /// Loop over the intersections pairs (segment, id)
- for (; it != end ; ++it) {
- Vector<UInt> segment_connectivity(2);
- segment_connectivity(0) = interface_mesh.getNbNodes();
- segment_connectivity(1) = interface_mesh.getNbNodes() + 1;
- connectivity.push_back(segment_connectivity);
-
- /// Copy nodes
- Vector<Real> source(dim), 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
- associated_element.push_back(Element(el_type, it->second));
- associated_material.push_back(interface_pair.second);
- }
-
- AKANTU_DEBUG_OUT();
-}
-
-template<UInt dim, ElementType el_type>
-void MeshGeomFactory<dim, el_type>::constructSegments(
- const std::list< typename TreeTypeHelper<dim, el_type>::linear_intersection > & intersections,
- std::list<std::pair<K::Segment_3, UInt> > & segments,
- const K::Segment_3 & interface)
-{
- AKANTU_DEBUG_IN();
-
- typename std::list<typename TreeTypeHelper<dim, el_type>::linear_intersection>::const_iterator
- int_it = intersections.begin(),
- int_end = intersections.end();
-
- for (; int_it != int_end ; ++int_it) {
- UInt el = (*int_it)->second;
-
- if (const K::Segment_3 * segment = boost::get<K::Segment_3>(&((*int_it)->first))) {
- if (std::find_if(segments.begin(), segments.end(), IsSameSegment(*segment)) == segments.end()) {
- // Use min() and max() for ordering
- K::Segment_3 seg_ord(segment->min(), segment->max());
- segments.push_back(std::make_pair(seg_ord, (*int_it)->second));
- }
- }
-
- else if (const K::Point_3 * point = boost::get<K::Point_3>(&((*int_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 && el_type == _tetrahedron_4) {
- UInt nb_facets = Mesh::getNbFacetsPerElement(el_type);
- typename TreeTypeHelper<dim, el_type>::container_type facets(nb_facets);
-
- // TODO Use mesh facets instead of this (should make O(n²) go to O(n))
- std::remove_copy_if(primitive_list.begin(),
- primitive_list.end(),
- facets.begin(),
- BelongsNotToElement<dim, el_type>(el));
-
- typename TreeTypeHelper<dim, el_type>::tree * local_tree =
- new typename TreeTypeHelper<dim, el_type>::tree(facets.begin(), facets.end());
-
- std::list< typename TreeTypeHelper<dim, el_type>::linear_intersection>
- local_intersections;
-
- local_tree->all_intersections(interface, std::back_inserter(local_intersections));
-
- typename std::list<typename TreeTypeHelper<dim, el_type>::linear_intersection>::const_iterator
- local_it = local_intersections.begin(),
- local_end = local_intersections.end();
-
- for (; local_it != local_end ; ++local_it) {
- if (const K::Point_3 * local_point = boost::get<K::Point_3>(&((*local_it)->first))) {
- if (!comparePoints(*point, *local_point)) {
- K::Segment_3 seg(*point, *local_point);
- K::Segment_3 seg_ord(seg.min(), seg.max());
- if (std::find_if(segments.begin(), segments.end(), IsSameSegment(seg_ord)) == segments.end())
- segments.push_back(std::make_pair(seg_ord, el));
- }
- }
- }
-
- delete local_tree;
- }
- }
- }
-
- AKANTU_DEBUG_OUT();
-}
-
-
-
__END_AKANTU__
-#endif // _AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
+#endif // __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
diff --git a/src/geometry/mesh_geom_intersector.hh b/src/geometry/mesh_geom_intersector.hh
new file mode 100644
index 000000000..5475e6869
--- /dev/null
+++ b/src/geometry/mesh_geom_intersector.hh
@@ -0,0 +1,87 @@
+/**
+ * @file mesh_geom_intersector.hh
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief General class for intersection computations
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_HH__
+#define __AKANTU_MESH_GEOM_INTERSECTOR_HH__
+
+#include "aka_common.hh"
+#include "mesh_geom_abstract.hh"
+#include "mesh_geom_factory.hh"
+
+/* -------------------------------------------------------------------------- */
+
+__BEGIN_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 MeshGeomAbstract {
+
+protected:
+ /// Result of intersection function type
+ typedef typename IntersectionTypeHelper<TreeTypeHelper<Primitive, Kernel>, Query>::intersection_type result_type;
+
+public:
+ /// Construct from mesh
+ explicit MeshGeomIntersector(const Mesh & mesh);
+
+ /// Destructor
+ virtual ~MeshGeomIntersector();
+
+public:
+ /// Construct the primitive tree object
+ virtual void constructData();
+
+ /**
+ * @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 list of queries
+ virtual void computeIntersectionQueryList(const std::list<Query> & query_list);
+
+protected:
+ /// Factory object containing the primitive tree
+ MeshGeomFactory<dim, type, Primitive, Kernel> factory;
+};
+
+__END_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
new file mode 100644
index 000000000..63f36933b
--- /dev/null
+++ b/src/geometry/mesh_geom_intersector_tmpl.hh
@@ -0,0 +1,76 @@
+/**
+ * @file mesh_geom_intersector_tmpl.hh
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief General class for intersection computations
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
+#define __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
+
+#include "aka_common.hh"
+#include "mesh_geom_intersector.hh"
+
+__BEGIN_AKANTU__
+
+template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
+MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::MeshGeomIntersector(const Mesh & mesh) :
+ MeshGeomAbstract(mesh),
+ factory(mesh)
+{}
+
+template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
+MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::~MeshGeomIntersector()
+{}
+
+template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
+void MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::constructData() {
+ factory.constructData();
+}
+
+template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
+void MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::computeIntersectionQueryList(
+ const std::list<Query> & query_list) {
+ AKANTU_DEBUG_IN();
+
+ typename std::list<Query>::const_iterator
+ query_it = query_list.begin(),
+ query_end = query_list.end();
+
+ for (; query_it != query_end ; ++query_it) {
+ computeIntersectionQuery(*query_it);
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
+
+__END_AKANTU__
+
+#endif // __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
+
diff --git a/src/geometry/mesh_segment_intersector.hh b/src/geometry/mesh_segment_intersector.hh
new file mode 100644
index 000000000..88ce3fadb
--- /dev/null
+++ b/src/geometry/mesh_segment_intersector.hh
@@ -0,0 +1,99 @@
+/**
+ * @file mesh_segment_intersector.hh
+ *
+ * @author Lucas Frerot
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief Computation of mesh intersection with segments
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
+#define __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
+
+#include "aka_common.hh"
+#include "mesh_geom_intersector.hh"
+
+#include <CGAL/Cartesian.h>
+
+/* -------------------------------------------------------------------------- */
+
+__BEGIN_AKANTU__
+
+/// Here, we know what kernel we have to use
+typedef CGAL::Cartesian<Real> K;
+
+template<UInt dim, ElementType type>
+class MeshSegmentIntersector : public MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K> {
+ /// Parent class type
+ typedef MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K> parent_type;
+
+ /// Result of intersection type
+ typedef typename parent_type::result_type result_type;
+
+ /// Pair of segments and element id
+ typedef std::pair<K::Segment_3, UInt> pair_type;
+
+public:
+ /// Construct from mesh
+ explicit MeshSegmentIntersector(const Mesh & mesh, Mesh & result_mesh);
+
+ /// Destructor
+ virtual ~MeshSegmentIntersector();
+
+public:
+ /**
+ * @brief Computes the intersection of the mesh with a segment
+ *
+ * @param query the segment to compute the intersections with the mesh
+ */
+ virtual void computeIntersectionQuery(const K::Segment_3 & query);
+
+ /// Compute the list of queries
+ virtual void computeIntersectionQueryList(const std::list<K::Segment_3> & query_list);
+
+ /// Compute the list of queries and adds sets the physical name of the elements created
+ virtual void computeIntersectionQueryList(const std::list<K::Segment_3> & query_list,
+ const std::string & physical_name);
+
+protected:
+ /// Compute segments from intersection list
+ void computeSegments(const std::list<result_type> & intersections,
+ std::list<pair_type> & 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;
+};
+
+__END_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
new file mode 100644
index 000000000..15469b7a5
--- /dev/null
+++ b/src/geometry/mesh_segment_intersector_tmpl.hh
@@ -0,0 +1,276 @@
+/**
+ * @file mesh_segment_intersector_tmpl.hh
+ *
+ * @author Lucas Frerot
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief Computation of mesh intersection with segments
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
+#define __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
+
+#include "aka_common.hh"
+#include "tree_type_helper.hh"
+
+#include <CGAL/Cartesian.h>
+
+__BEGIN_AKANTU__
+
+typedef CGAL::Cartesian<Real> K;
+
+template<UInt dim, ElementType type>
+MeshSegmentIntersector<dim, type>::MeshSegmentIntersector(const Mesh & mesh, Mesh & result_mesh):
+ parent_type(mesh),
+ result_mesh(result_mesh),
+ current_physical_name()
+{
+ this->constructData();
+}
+
+template<UInt dim, ElementType type>
+MeshSegmentIntersector<dim, type>::~MeshSegmentIntersector()
+{}
+
+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::list<std::pair<K::Segment_3, UInt> > segment_list;
+
+ this->factory.getTree().all_intersections(query, std::back_inserter(result_list));
+ this->computeSegments(result_list, segment_list, 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 = NULL;
+ Array<std::string> * associated_physical_name = NULL;
+
+ 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;
+ }
+
+ std::list<pair_type>::iterator
+ it = segment_list.begin(),
+ end = segment_list.end();
+
+ // Loop over the segment pairs
+ for (; it != end ; ++it) {
+ 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), 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));
+ associated_physical_name->push_back(current_physical_name);
+ }
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
+template<UInt dim, ElementType type>
+void MeshSegmentIntersector<dim, type>::computeIntersectionQueryList(const std::list<K::Segment_3> & query_list,
+ const std::string & physical_name) {
+ AKANTU_DEBUG_IN();
+
+ current_physical_name = physical_name;
+ parent_type::computeIntersectionQueryList(query_list);
+
+ AKANTU_DEBUG_OUT();
+}
+
+template<UInt dim, ElementType type>
+void MeshSegmentIntersector<dim, type>::computeIntersectionQueryList(const std::list<K::Segment_3> & query_list) {
+ AKANTU_DEBUG_IN();
+
+ parent_type::computeIntersectionQueryList(query_list);
+
+ AKANTU_DEBUG_OUT();
+}
+
+template<UInt dim, ElementType type>
+void MeshSegmentIntersector<dim, type>::computeSegments(const std::list<result_type> & intersections,
+ std::list<pair_type> & 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.size() == 0) {
+ // 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::list<UInt> ray1_results, ray2_results;
+
+ this->factory.getTree().all_intersected_primitives(ray1, std::back_inserter(ray1_results));
+ this->factory.getTree().all_intersected_primitives(ray2, std::back_inserter(ray2_results));
+
+ std::set<UInt> id_set;
+ bool inside_primitive = false;
+ UInt primitive_id = 0;
+
+ std::list<UInt>::iterator
+ ray1_it = ray1_results.begin(),
+ ray2_it = ray2_results.begin(),
+ ray1_end = ray1_results.end(),
+ ray2_end = ray2_results.end();
+
+ // Populate the set with elements of first list
+ for (; ray1_it != ray1_end ; ++ray1_it)
+ id_set.insert(id_set.begin(), *ray1_it);
+
+ // Test if first list contains an element of second list
+ for (; ray2_it != ray2_end && !inside_primitive ; ++ray2_it) {
+ if (id_set.find(*ray2_it) != id_set.end()) {
+ inside_primitive = true;
+ primitive_id = *ray2_it;
+ }
+ }
+
+ if (inside_primitive) {
+ segments.push_back(std::make_pair(query, primitive_id));
+ }
+ }
+
+ else {
+ typename std::list<result_type>::const_iterator
+ it = intersections.begin(),
+ 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
+ if (std::find_if(segments.begin(), segments.end(), IsSameSegment(*segment)) == segments.end()) {
+ segments.push_back(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
+ TreeTypeHelper<Triangle<K>, K>::tree * 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));
+
+ if (local_intersections.size() == 1) {
+ TreeTypeHelper<Triangle<K>, K>::point_type
+ a(node_coordinates(0, 0), node_coordinates(1, 0), node_coordinates(2, 0)),
+ b(node_coordinates(0, 1), node_coordinates(1, 1), node_coordinates(2, 1)),
+ c(node_coordinates(0, 2), node_coordinates(1, 2), node_coordinates(2, 2)),
+ d(node_coordinates(0, 3), node_coordinates(1, 3), node_coordinates(2, 3));
+ K::Tetrahedron_3 tetra(a, b, c, d);
+ K::Point_3 inside_point =
+ (tetra.has_on_bounded_side(query.source())) ? query.source() : query.target();
+ K::Segment_3 seg(inside_point, *point);
+ segments.push_back(std::make_pair(seg, el));
+ }
+
+ else {
+ typename std::list<result_type>::const_iterator
+ local_it = local_intersections.begin(),
+ local_end = local_intersections.end();
+
+ for (; local_it != local_end ; ++local_it) {
+ if (const K::Point_3 * local_point = boost::get<K::Point_3>(&((*local_it)->first))) {
+ if (!comparePoints(*point, *local_point)) {
+ K::Segment_3 seg(*point, *local_point);
+ if(std::find_if(segments.begin(), segments.end(), IsSameSegment(seg)) == segments.end())
+ segments.push_back(std::make_pair(seg, el));
+ }
+ }
+ }
+ }
+
+ delete local_tree;
+ }
+ }
+ }
+ }
+ AKANTU_DEBUG_OUT();
+}
+
+__END_AKANTU__
+
+#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
+
diff --git a/src/geometry/tree_type_helper.hh b/src/geometry/tree_type_helper.hh
index e79f6f28f..d372306df 100644
--- a/src/geometry/tree_type_helper.hh
+++ b/src/geometry/tree_type_helper.hh
@@ -1,81 +1,95 @@
/**
* @file tree_type_helper.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Thu Mar 5 2015
*
* @brief Converts element types of a mesh to CGAL primitive types
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TREE_TYPE_HELPER_HH__
#define __AKANTU_TREE_TYPE_HELPER_HH__
#include "aka_common.hh"
#include "triangle.hh"
#include "tetrahedron.hh"
#include "aabb_primitive.hh"
#include <CGAL/Cartesian.h>
#include <CGAL/AABB_traits.h>
#include <CGAL/AABB_tree.h>
__BEGIN_AKANTU__
-typedef CGAL::Cartesian<Real> Kernel;
-
/* -------------------------------------------------------------------------- */
-template<UInt dim, ElementType el_type>
+typedef CGAL::Cartesian<Real> CartKern;
+
+/// Helper class used to ease the use of CGAL AABB tree algorithm
+template<class Primitive, class Kernel>
struct TreeTypeHelper;
-#define TREE_TYPE_HELPER_MACRO(dim, el_type, my_primitive) \
- template<> \
- struct TreeTypeHelper<dim, el_type> { \
- typedef my_primitive<Kernel> primitive_type; \
- typedef my_primitive##_primitive aabb_primitive_type; \
- typedef Kernel::Point_3 point_type; \
- \
- typedef std::list<primitive_type> container_type; \
- typedef container_type::iterator iterator; \
- typedef CGAL::AABB_traits<Kernel, aabb_primitive_type> aabb_traits_type; \
- typedef CGAL::AABB_tree<aabb_traits_type> tree; \
+/// 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>, my_kernel> { \
+ typedef my_primitive<my_kernel> primitive_type; \
+ typedef my_primitive##_primitive aabb_primitive_type; \
+ typedef CGAL::Point_3<my_kernel> point_type; \
\
- typedef boost::optional< \
- tree::Intersection_and_primitive_id< \
- CGAL::Segment_3<Kernel> \
- >::Type > linear_intersection; \
+ typedef std::list<primitive_type> container_type; \
+ typedef container_type::iterator iterator; \
+ typedef CGAL::AABB_traits<my_kernel, aabb_primitive_type> aabb_traits_type; \
+ typedef CGAL::AABB_tree<aabb_traits_type> tree; \
+ typedef tree::Primitive_id id_type; \
+ }; \
+ \
+ template<> \
+ struct IntersectionTypeHelper<TreeTypeHelper<my_primitive<my_kernel>, my_kernel>, my_query> { \
+ typedef boost::optional< \
+ TreeTypeHelper<my_primitive<my_kernel>, my_kernel>::tree::Intersection_and_primitive_id<my_query>::Type \
+ > intersection_type; \
}
-TREE_TYPE_HELPER_MACRO(2, _triangle_3, Triangle);
-TREE_TYPE_HELPER_MACRO(3, _tetrahedron_4, Triangle);
+TREE_TYPE_HELPER_MACRO(Triangle, CartKern::Segment_3, CartKern);
#undef TREE_TYPE_HELPER_MACRO
__END_AKANTU__
#endif // __AKANTU_TREE_TYPE_HELPER_HH__
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 032b42b07..20246f4d4 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,350 +1,348 @@
/**
* @file cohesive_element_inserter.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Tue Jul 29 2014
*
* @brief Cohesive element inserter functions
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 <algorithm>
#include <limits>
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh,
bool is_extrinsic,
DistributedSynchronizer * synchronizer,
const ID & id) :
id(id),
mesh(mesh),
mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
MeshUtils::buildAllFacets(mesh, mesh_facets, 0, synchronizer);
init(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() {
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
delete distributed_synchronizer;
#endif
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::init(bool is_extrinsic) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
MeshUtils::resetFacetToDouble(mesh_facets);
/// initialize facet insertion array
mesh_facets.initElementTypeMapArray(insertion_facets, 1,
spatial_dimension - 1,
false,
_ek_regular,
true);
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * (-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
if (is_extrinsic) {
mesh_facets.initElementTypeMapArray(check_facets, 1, spatial_dimension - 1);
initFacetsCheck();
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
facet_synchronizer = NULL;
distributed_synchronizer = NULL;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::initFacetsCheck() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & f_check = check_facets(facet_type, facet_gt);
const Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(facet_type, facet_gt);
UInt nb_facet = element_to_facet.getSize();
f_check.resize(nb_facet);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull ||
(element_to_facet(f)[0].ghost_type == _ghost &&
element_to_facet(f)[1].ghost_type == _ghost)) {
f_check(f) = false;
}
else f_check(f) = true;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
AKANTU_DEBUG_IN();
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 = check_facets(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);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) > insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) < insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit != spatial_dimension)
f_check(f) = false;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(SpacialDirection 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);
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
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) {
const ElementType type_facet = *it;
Array<bool> & f_insertion = insertion_facets(type_facet, ghost_type);
Array<std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type_facet, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull) continue;
mesh_facets.getBarycenter(f, type_facet, bary_facet.storage(), ghost_type);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) > insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) < insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit == spatial_dimension)
f_insertion(f) = true;
}
}
}
insertElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-void CohesiveElementInserter::insertElements() {
- AKANTU_DEBUG_IN();
-
+UInt CohesiveElementInserter::insertElements() {
NewNodesEvent node_event;
node_event.getList().extendComponentsInterlaced(2, 1);
NewElementsEvent element_event;
MeshUtils::insertCohesiveElements(mesh,
mesh_facets,
insertion_facets,
node_event.getList(),
element_event.getList());
UInt nb_new_nodes = node_event.getList().getSize();
UInt nb_new_elements = element_event.getList().getSize();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.getNodesType().getSize()) {
/// update nodes type
updateNodesType(mesh, node_event);
updateNodesType(mesh_facets, node_event);
/// update global ids
nb_new_nodes = updateGlobalIDs(node_event);
/// compute total number of new elements
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(&nb_new_elements, 1, _so_sum);
}
#endif
if (nb_new_nodes > 0) {
mesh.nb_global_nodes += nb_new_nodes;
mesh_facets.nb_global_nodes += nb_new_nodes;
mesh.sendEvent(node_event);
}
if (nb_new_elements > 0) {
updateInsertionFacets();
mesh.updateTypesOffsets(_not_ghost);
mesh.sendEvent(element_event);
MeshUtils::resetFacetToDouble(mesh_facets);
}
- AKANTU_DEBUG_OUT();
+ return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the extrinsic case
if (check_facets.exists(facet_type, facet_gt)) {
Array<bool> & f_check = check_facets(facet_type, facet_gt);
UInt nb_facets = f_check.getSize();
for (UInt f = 0; f < ins_facets.getSize(); ++f) {
if (ins_facets(f)) {
++nb_facets;
ins_facets(f) = false;
f_check(f) = false;
}
}
f_check.resize(nb_facets);
}
// and this the intrinsic one
else {
ins_facets.resize(mesh_facets.getNbElement(facet_type, facet_gt));
ins_facets.set(false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "CohesiveElementInserter [" << std::endl;
stream << space << " + mesh [" << std::endl;
mesh.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + mesh_facets [" << std::endl;
mesh_facets.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
__END_AKANTU__
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index b5b5fe5d1..03232e486 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,192 +1,193 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Tue Jul 29 2014
*
* @brief Cohesive element inserter
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_COHESIVE_ELEMENT_INSERTER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
/* -------------------------------------------------------------------------- */
#include <numeric>
#include "data_accessor.hh"
#include "mesh_utils.hh"
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "facet_synchronizer.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class CohesiveElementInserter : public DataAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh,
bool is_extrinsic = false,
DistributedSynchronizer * synchronizer = NULL,
const ID & id = "cohesive_element_inserter");
virtual ~CohesiveElementInserter();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// init function
void init(bool is_extrinsic);
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpacialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
void insertIntrinsicElements();
- /// insert extrinsic cohesive elements
- void insertElements();
+ /// insert extrinsic cohesive elements (returns the number of new
+ /// cohesive elements)
+ UInt insertElements();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// limit check facets to match given insertion limits
void limitCheckFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// init parallel variables
void initParallel(FacetSynchronizer * facet_synchronizer);
#endif
protected:
/// init facets check
void initFacetsCheck();
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// update nodes type and global ids for parallel simulations
UInt updateGlobalIDs(NewNodesEvent & node_event);
/// update nodes type
void updateNodesType(Mesh & mesh, NewNodesEvent & node_event);
/// functions for parallel communications
inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
template<bool pack_mode>
inline void packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
#endif
/* ------------------------------------------------------------------------ */
/* 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_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 &);
/* ------------------------------------------------------------------------ */
/* 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
Array<Real> insertion_limits;
/// vector containing facets in which extrinsic cohesive elements can be inserted
ElementTypeMapArray<bool> check_facets;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// facet synchronizer
FacetSynchronizer * facet_synchronizer;
/// distributed synchronizer
DistributedSynchronizer * distributed_synchronizer;
#endif
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "cohesive_element_inserter_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const CohesiveElementInserter & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index ddbf2615f..1464591d5 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,2051 +1,2048 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@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 Aug 20 2010
* @date last modification: Mon Jun 09 2014
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "mesh_utils.hh"
#include "aka_safe_enum.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
#include <queue>
/* -------------------------------------------------------------------------- */
__BEGIN_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();
AKANTU_DEBUG_ASSERT(mesh.firstType(spatial_dimension) !=
mesh.lastType(spatial_dimension),
"Some elements must be found in right dimension to compute facets!");
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
for (; first != last; ++first) {
ElementType type = *first;
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator< Vector<UInt> > conn_it =
mesh.getConnectivity(type, *gt).begin(Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it)
for (UInt n = 0; n < conn_it->size(); ++n)
++node_to_elem.rowOffset((*conn_it)(n));
}
}
node_to_elem.countToCSR();
node_to_elem.resizeCols();
/// rearrange element to get the node-element list
Element e;
node_to_elem.beginInsertions();
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
e.ghost_type = *gt;
for (; first != last; ++first) {
ElementType type = *first;
e.type = type;
e.kind = Mesh::getKind(type);
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator< Vector<UInt> > conn_it =
mesh.getConnectivity(type, *gt).begin(Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
for (UInt n = 0; n < conn_it->size(); ++n)
node_to_elem.insertInRow((*conn_it)(n), e);
}
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* This function should disappear in the future (used in mesh partitioning)
*/
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<UInt> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
if (spatial_dimension == _all_dimensions) spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes = mesh.getNbNodes();
const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
Mesh::ConnectivityTypeList::const_iterator it;
UInt nb_types = type_list.size();
UInt nb_good_types = 0;
UInt nb_nodes_per_element[nb_types];
UInt * conn_val[nb_types];
UInt nb_element[nb_types];
for(it = type_list.begin(); it != type_list.end(); ++it) {
ElementType type = *it;
if(Mesh::getSpatialDimension(type) != spatial_dimension) continue;
nb_nodes_per_element[nb_good_types] = Mesh::getNbNodesPerElement(type);
conn_val[nb_good_types] = mesh.getConnectivity(type, _not_ghost).storage();
nb_element[nb_good_types] = mesh.getConnectivity(type, _not_ghost).getSize();
nb_good_types++;
}
AKANTU_DEBUG_ASSERT(nb_good_types != 0,
"Some elements must be found in right dimension to compute facets!");
/// 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 t = 0; t < nb_good_types; ++t) {
for (UInt el = 0; el < nb_element[t]; ++el) {
UInt el_offset = el*nb_nodes_per_element[t];
for (UInt n = 0; n < nb_nodes_per_element[t]; ++n) {
++node_to_elem.rowOffset(conn_val[t][el_offset + n]);
}
}
}
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// rearrange element to get the node-element list
for (UInt t = 0, linearized_el = 0; t < nb_good_types; ++t)
for (UInt el = 0; el < nb_element[t]; ++el, ++linearized_el) {
UInt el_offset = el*nb_nodes_per_element[t];
for (UInt n = 0; n < nb_nodes_per_element[t]; ++n)
node_to_elem.insertInRow(conn_val[t][el_offset + n], linearized_el);
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
CSR<UInt> & node_to_elem,
const ElementType & type,
const 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).getSize();
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 (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh.lastType(spatial_dimension - 1, gt_facet);
for(; it != end; ++it) {
mesh.getConnectivity(*it, *gt).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,
DistributedSynchronizer * synchronizer) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension, synchronizer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh,
Mesh & mesh_facets,
UInt from_dimension,
UInt to_dimension,
DistributedSynchronizer * synchronizer) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
const ElementTypeMapArray<UInt> * prank_to_element = NULL;
if (synchronizer) {
synchronizer->buildPrankToElement();
prank_to_element = &synchronizer->getPrankToElement();
}
/// generate facets
buildFacetsDimension(mesh,
mesh_facets,
false,
from_dimension,
prank_to_element);
/// copy nodes type
mesh_facets.nodes_type.resize(mesh.nodes_type.getSize());
mesh_facets.nodes_type.copy(mesh.nodes_type);
/// sort facets and generate subfacets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets,
mesh_facets,
false,
i,
prank_to_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(const Mesh & mesh,
Mesh & mesh_facets,
bool boundary_only,
UInt dimension,
const ElementTypeMapArray<UInt> * prank_to_element){
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 subelements
// example: if the function is called with mesh = mesh_facets
const Mesh & mesh_facets_parent = mesh_facets.getMeshParent();
mesh_facets.defineMeshParent(mesh);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const Array<Real>::const_vector_iterator 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;
// init the SubelementToElement data to improve performance
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for(; first != last; ++first) {
ElementType type = *first;
ElementType facet_type = mesh.getFacetType(type);
mesh_facets.getSubelementToElementPointer(type, ghost_type);
mesh_facets.getElementToSubelementPointer(facet_type, ghost_type);
mesh_facets.getConnectivityPointer(facet_type, ghost_type);
}
}
Element current_element;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for(; first != last; ++first) {
ElementType type = *first;
ElementType facet_type = mesh.getFacetType(type);
current_element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array< std::vector<Element> > * element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
Array<UInt> * connectivity_facets = &mesh_facets.getConnectivity(facet_type, ghost_type);
UInt nb_facet_per_element = mesh.getNbFacetsPerElement(type);
const Array<UInt> & element_connectivity = mesh.getConnectivity(type, ghost_type);
const Matrix<UInt> facet_local_connectivity = mesh.getFacetLocalConnectivity(type);
UInt 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;
for (UInt f = 0; f < nb_facet_per_element; ++f) {
for (UInt n = 0; n < nb_nodes_per_facet; ++n)
facet(n) = element_connectivity(el, facet_local_connectivity(f, n));
UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
counter.resize(first_node_nb_elements);
counter.clear();
//loop over the other nodes to search intersecting elements,
//which are the elements that share another node with the
//starting element after first_node
CSR<Element>::iterator first_node_elements = node_to_elem.begin(facet(0));
CSR<Element>::iterator first_node_elements_end = node_to_elem.end(facet(0));
UInt local_el = 0;
for (; first_node_elements != first_node_elements_end;
++first_node_elements, ++local_el) {
for (UInt n = 1; n < nb_nodes_per_facet; ++n) {
CSR<Element>::iterator node_elements_begin = node_to_elem.begin(facet(n));
CSR<Element>::iterator node_elements_end = node_to_elem.end (facet(n));
counter(local_el) += std::count(node_elements_begin,
node_elements_end,
*first_node_elements);
}
}
// 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 (UInt el_f = 0; el_f < first_node_nb_elements; el_f++) {
Element real_el = node_to_elem(facet(0), el_f);
if (counter(el_f) == nb_nodes_per_facet - 1) {
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
}
if (minimum_el == current_element) {
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet && mesh.isPureGhostNode(facet(n))) ++n;
if (n == nb_nodes_per_facet) full_ghost_facet = true;
if (!full_ghost_facet) {
if (!boundary_only || (boundary_only && nb_element_connected_to_facet == 1)) {
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.push_back(current_element);
/// boundary facet
if (nb_element_connected_to_facet == 1)
elements.push_back(ElementNull);
/// internal facet
else if (nb_element_connected_to_facet == 2) {
elements.push_back(connected_elements[1]);
/// 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] + gt[1] == 1) {
if (prank_to_element) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
UInt current_el = connected_elements[el].element;
ElementType current_type = connected_elements[el].type;
GhostType current_gt = connected_elements[el].ghost_type;
const Array<UInt> & prank_to_el
= (*prank_to_element)(current_type, current_gt);
prank[el] = prank_to_el(current_el);
}
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_facets.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_facets.getElementToSubelement(facet_type, facet_ghost_type);
}
}
}
/// facet of facet
else {
for (UInt i = 1; i < nb_element_connected_to_facet; ++i) {
elements.push_back(connected_elements[i]);
}
}
element_to_subelement->push_back(elements);
connectivity_facets->push_back(facet);
/// current facet index
UInt current_facet = connectivity_facets->getSize() - 1;
/// loop on every element connected to current facet and
/// insert current facet in the first free spot of the
/// subelement_to_element vector
for (UInt elem = 0; elem < elements.size(); ++elem) {
Element loc_el = elements[elem];
if (loc_el.type != _not_defined) {
Array<Element> & subelement_to_element =
mesh_facets.getSubelementToElement(type, loc_el.ghost_type);
for (UInt f_in = 0; f_in < nb_facet_per_element; ++f_in) {
if (subelement_to_element(loc_el.element, f_in).type == _not_defined) {
subelement_to_element(loc_el.element, f_in).type = facet_type;
subelement_to_element(loc_el.element, f_in).element = current_facet;
subelement_to_element(loc_el.element, f_in).ghost_type = facet_ghost_type;
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_facets.getConnectivityPointer(facet_type, facet_ghost_type);
element_to_subelement = mesh_facets.getElementToSubelementPointer(facet_type, facet_ghost_type);
}
}
}
}
}
}
}
}
// restore the parent of mesh_facet
mesh_facets.defineMeshParent(mesh_facets_parent);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
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.getSize(); ++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);
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
old_nodes_numbers.resize(renumbering_map.size());
for (;it != end; ++it) {
old_nodes_numbers(it->second) = it->first;
}
renumbering_map.clear();
/// copy the renumbered connectivity to the right place
Array<UInt> * local_conn = mesh.getConnectivityPointer(type);
local_conn->resize(nb_local_element);
memcpy(local_conn->storage(),
local_connectivities,
nb_local_element * nb_nodes_per_element * sizeof(UInt));
Array<UInt> * ghost_conn = mesh.getConnectivityPointer(type, _ghost);
ghost_conn->resize(nb_ghost_element);
memcpy(ghost_conn->storage(),
local_connectivities + nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(UInt * list_nodes,
UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes;
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
std::map<UInt, UInt>::iterator 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);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
Mesh::type_iterator it = mesh.firstType(_all_dimensions, ghost_type, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for(; it != end; ++it) {
ElementType type(*it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity_vect = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity_vect.getSize());
UInt * connectivity = connectivity_vect.storage();
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));
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
for (; it != end; ++it) {
new_numbering(it->first) = it->second;
}
for (UInt i = 0; i < new_numbering.getSize(); ++i) {
if(new_numbering(i) == UInt(-1))
nodes_removed.push_back(i);
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
void MeshUtils::insertCohesiveElements(Mesh & mesh,
Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements) {
- AKANTU_DEBUG_IN();
-
UInt spatial_dimension = mesh.getSpatialDimension();
+ UInt elements_to_insert = updateFacetToDouble(mesh_facets, facet_insertion);
- if (updateFacetToDouble(mesh_facets, facet_insertion)) {
+ if (elements_to_insert > 0) {
if (spatial_dimension == 1) {
doublePointFacet(mesh, mesh_facets, doubled_nodes);
}
else {
doubleFacet(mesh, mesh_facets, spatial_dimension - 1,
doubled_nodes, true);
findSubfacetToDouble<false>(mesh, mesh_facets);
if (spatial_dimension == 2) {
doubleSubfacet<2>(mesh, mesh_facets, doubled_nodes);
}
else if (spatial_dimension == 3) {
doubleFacet(mesh, mesh_facets, 1, doubled_nodes, false);
findSubfacetToDouble<true>(mesh, mesh_facets);
doubleSubfacet<3>(mesh, mesh_facets, doubled_nodes);
}
}
updateCohesiveData(mesh, mesh_facets, new_elements);
}
-
- AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleNodes(Mesh & mesh,
const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
Array<Real> & position = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt old_nb_nodes = position.getSize();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
UInt new_nb_doubled_nodes = old_nb_doubled_nodes + old_nodes.size();
position.resize(new_nb_nodes);
doubled_nodes.resize(new_nb_doubled_nodes);
Array<Real>::iterator<Vector<Real> > position_begin
= position.begin(spatial_dimension);
for (UInt n = 0; n < old_nodes.size(); ++n) {
UInt new_node = old_nb_nodes + n;
/// store doubled nodes
doubled_nodes(old_nb_doubled_nodes + n, 0) = old_nodes[n];
doubled_nodes(old_nb_doubled_nodes + n, 1) = new_node;
/// update position
std::copy(position_begin + old_nodes[n],
position_begin + old_nodes[n] + 1,
position_begin + new_node);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleFacet(Mesh & mesh,
Mesh & mesh_facets,
UInt facet_dimension,
Array<UInt> & doubled_nodes,
bool facet_mode) {
AKANTU_DEBUG_IN();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(facet_dimension, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(facet_dimension, gt_facet);
for(; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0) continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
const UInt nb_subfacet_per_facet = Mesh::getNbFacetsPerElement(type_facet);
GhostType gt_subfacet = _casper;
Array<std::vector<Element> > * f_to_subfacet = NULL;
Array<Element> & subfacet_to_facet
= mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
UInt nb_nodes_per_facet = conn_facet.getNbComponent();
UInt old_nb_facet = conn_facet.getSize();
UInt new_nb_facet = old_nb_facet + nb_facet_to_double;
conn_facet.resize(new_nb_facet);
subfacet_to_facet.resize(new_nb_facet);
UInt new_facet = old_nb_facet - 1;
Element new_facet_el(type_facet, 0, gt_facet);
Array<Element>::iterator<Vector<Element> > subfacet_to_facet_begin
= subfacet_to_facet.begin(nb_subfacet_per_facet);
Array<UInt>::iterator<Vector<UInt> > conn_facet_begin
= conn_facet.begin(nb_nodes_per_facet);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
++new_facet;
/// adding a new facet by copying original one
/// copy connectivity in new facet
std::copy(conn_facet_begin + old_facet,
conn_facet_begin + old_facet + 1,
conn_facet_begin + new_facet);
/// update subfacet_to_facet
std::copy(subfacet_to_facet_begin + old_facet,
subfacet_to_facet_begin + old_facet + 1,
subfacet_to_facet_begin + new_facet);
new_facet_el.element = new_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet_per_facet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull) continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
f_to_subfacet = & mesh_facets.getElementToSubelement(type_subfacet,
subfacet.ghost_type);
}
/// update facet_to_subfacet array
(*f_to_subfacet)(subfacet.element).push_back(new_facet_el);
}
}
/// update facet_to_subfacet and _segment_3 facets if any
if (!facet_mode) {
updateSubfacetToFacet(mesh_facets, type_facet, gt_facet, true);
updateFacetToSubfacet(mesh_facets, type_facet, gt_facet, true);
updateQuadraticSegments<true>(mesh, mesh_facets, type_facet,
gt_facet, doubled_nodes);
}
else
updateQuadraticSegments<false>(mesh, mesh_facets, type_facet,
gt_facet, doubled_nodes);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-bool MeshUtils::updateFacetToDouble(Mesh & mesh_facets,
+UInt MeshUtils::updateFacetToDouble(Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
- bool facets_to_double = false;
+ UInt nb_facets_to_double = 0.;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for(; it != end; ++it) {
ElementType type_facet = *it;
const Array<bool> & f_insertion = facet_insertion(type_facet, gt_facet);
Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, gt_facet);
ElementType el_type = _not_defined;
GhostType el_gt = _casper;
UInt nb_facet_per_element = 0;
Element old_facet_el(type_facet, 0, gt_facet);
Array<Element> * facet_to_element = NULL;
for (UInt f = 0; f < f_insertion.getSize(); ++f) {
if (f_insertion(f) == false) continue;
- facets_to_double = true;
+ ++nb_facets_to_double;
if (element_to_facet(f)[1].type == _not_defined
#if defined(AKANTU_COHESIVE_ELEMENT)
|| element_to_facet(f)[1].kind == _ek_cohesive
#endif
) {
AKANTU_DEBUG_WARNING("attempt to double a facet on the boundary");
continue;
}
f_to_double.push_back(f);
UInt new_facet =
mesh_facets.getNbElement(type_facet, gt_facet) + f_to_double.getSize() - 1;
old_facet_el.element = f;
/// update facet_to_element vector
Element & elem_to_update = element_to_facet(f)[1];
UInt el = elem_to_update.element;
if (elem_to_update.ghost_type != el_gt || elem_to_update.type != el_type) {
el_type = elem_to_update.type;
el_gt = elem_to_update.ghost_type;
facet_to_element = & mesh_facets.getSubelementToElement(el_type, el_gt);
nb_facet_per_element = facet_to_element->getNbComponent();
}
Element * f_update
= std::find(facet_to_element->storage() + el * nb_facet_per_element,
facet_to_element->storage() + el * nb_facet_per_element
+ nb_facet_per_element,
old_facet_el);
AKANTU_DEBUG_ASSERT(facet_to_element->storage() + el * nb_facet_per_element !=
facet_to_element->storage() + el * nb_facet_per_element
+ nb_facet_per_element,
"Facet not found");
f_update->element = new_facet;
/// update elements connected to facet
std::vector<Element> first_facet_list = element_to_facet(f);
element_to_facet.push_back(first_facet_list);
/// set new and original facets as boundary facets
element_to_facet(new_facet)[0] = element_to_facet(new_facet)[1];
element_to_facet(f)[1] = ElementNull;
element_to_facet(new_facet)[1] = ElementNull;
}
}
}
AKANTU_DEBUG_OUT();
- return facets_to_double;
+ return nb_facets_to_double;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::resetFacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
Mesh::type_iterator it = mesh_facets.firstType(_all_dimensions, gt);
Mesh::type_iterator end = mesh_facets.lastType(_all_dimensions, gt);
for(; it != end; ++it) {
ElementType type = *it;
mesh_facets.getDataPointer<UInt>("facet_to_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element> >
("facets_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element> >
("elements_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element> >
("subfacets_to_subsubfacet_double", type, gt, 1, false);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool subsubfacet_mode>
void MeshUtils::findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
if (spatial_dimension == 1) return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for(; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0) continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
GhostType gt_subfacet = _casper;
ElementType type_subsubfacet = Mesh::getFacetType(type_subfacet);
GhostType gt_subsubfacet = _casper;
Array<UInt> * conn_subfacet = NULL;
Array<UInt> * sf_to_double = NULL;
Array<std::vector<Element> > * sf_to_subfacet_double = NULL;
Array<std::vector<Element> > * f_to_subfacet_double = NULL;
Array<std::vector<Element> > * el_to_subfacet_double = NULL;
UInt nb_subfacet = Mesh::getNbFacetsPerElement(type_facet);
UInt nb_subsubfacet;
UInt nb_nodes_per_sf_el;
if (subsubfacet_mode) {
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subsubfacet);
nb_subsubfacet = Mesh::getNbFacetsPerElement(type_subfacet);
}
else
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subfacet);
Array<Element> & subfacet_to_facet
= mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, gt_facet);
Array<Element> * subsubfacet_to_subfacet = NULL;
UInt old_nb_facet = subfacet_to_facet.getSize() - nb_facet_to_double;
Element current_facet(type_facet, 0, gt_facet);
std::vector<Element> element_list;
std::vector<Element> facet_list;
std::vector<Element> * subfacet_list;
if (subsubfacet_mode)
subfacet_list = new std::vector<Element>;
/// map to filter subfacets
Array< std::vector<Element> > * facet_to_subfacet = NULL;
/// this is used to make sure that both new and old facets are
/// checked
UInt facets[2];
/// loop on every facet
for (UInt f_index = 0; f_index < 2; ++f_index) {
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
facets[bool(f_index)] = f_to_double(facet);
facets[!bool(f_index)] = old_nb_facet + facet;
UInt old_facet = facets[0];
UInt new_facet = facets[1];
Element & starting_element = element_to_facet(new_facet)[0];
current_facet.element = old_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull) continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
if (subsubfacet_mode) {
subsubfacet_to_subfacet
= & mesh_facets.getSubelementToElement(type_subfacet,
gt_subfacet);
}
else {
conn_subfacet = & mesh_facets.getConnectivity(type_subfacet,
gt_subfacet);
sf_to_double = & mesh_facets.getData<UInt>("facet_to_double",
type_subfacet,
gt_subfacet);
f_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_subfacet,
gt_subfacet);
el_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("elements_to_subfacet_double",
type_subfacet,
gt_subfacet);
facet_to_subfacet
= & mesh_facets.getElementToSubelement(type_subfacet,
gt_subfacet);
}
}
if (subsubfacet_mode) {
/// loop on every subsubfacet
for (UInt ssf = 0; ssf < nb_subsubfacet; ++ssf) {
Element & subsubfacet
= (*subsubfacet_to_subfacet)(subfacet.element, ssf);
if (subsubfacet == ElementNull) continue;
if (gt_subsubfacet != subsubfacet.ghost_type) {
gt_subsubfacet = subsubfacet.ghost_type;
conn_subfacet = & mesh_facets.getConnectivity(type_subsubfacet,
gt_subsubfacet);
sf_to_double = & mesh_facets.getData<UInt>("facet_to_double",
type_subsubfacet,
gt_subsubfacet);
sf_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("subfacets_to_subsubfacet_double",
type_subsubfacet,
gt_subsubfacet);
f_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_subsubfacet,
gt_subsubfacet);
el_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("elements_to_subfacet_double",
type_subsubfacet,
gt_subsubfacet);
facet_to_subfacet
= & mesh_facets.getElementToSubelement(type_subsubfacet,
gt_subsubfacet);
}
UInt global_ssf = subsubfacet.element;
Vector<UInt> subsubfacet_connectivity(conn_subfacet->storage()
+ global_ssf
* nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subsubfacet is to be doubled
if (findElementsAroundSubfacet<true>(mesh, mesh_facets,
starting_element, current_facet,
subsubfacet_connectivity,
element_list,
facet_list,
subfacet_list) == false &&
removeElementsInVector(*subfacet_list,
(*facet_to_subfacet)(global_ssf)) == false) {
sf_to_double->push_back(global_ssf);
sf_to_subfacet_double->push_back(*subfacet_list);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
}
else {
const UInt global_sf = subfacet.element;
Vector<UInt> subfacet_connectivity(conn_subfacet->storage()
+ global_sf
* nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subfacet is to be doubled
if (findElementsAroundSubfacet<false>(mesh, mesh_facets,
starting_element, current_facet,
subfacet_connectivity,
element_list,
facet_list) == false &&
removeElementsInVector(facet_list,
(*facet_to_subfacet)(global_sf)) == false) {
sf_to_double->push_back(global_sf);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
}
}
}
if (subsubfacet_mode)
delete subfacet_list;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
void MeshUtils::updateCohesiveData(Mesh & mesh,
Mesh & mesh_facets,
Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
bool third_dimension = spatial_dimension == 3;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for(; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
if (nb_facet_to_double == 0) continue;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Array<Element> * facet_to_coh_element
= mesh_facets.getSubelementToElementPointer(type_cohesive, gt_facet);
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
Array<UInt> * conn_cohesive = mesh.getConnectivityPointer(type_cohesive,
gt_facet);
UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(type_facet);
Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, gt_facet);
UInt old_nb_cohesive_elements = conn_cohesive->getSize();
UInt new_nb_cohesive_elements = conn_cohesive->getSize() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.getSize() - nb_facet_to_double;
facet_to_coh_element->resize(new_nb_cohesive_elements);
conn_cohesive->resize(new_nb_cohesive_elements);
UInt new_elements_old_size = new_elements.getSize();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element(type_cohesive, 0, gt_facet, _ek_cohesive);
Element f_element(type_facet, 0, gt_facet);
UInt facets[2];
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
/// (in 3D cohesive elements connectivity is inverted)
facets[third_dimension] = f_to_double(facet);
facets[!third_dimension] = old_nb_facet + facet;
UInt cohesive_element = old_nb_cohesive_elements + facet;
/// store doubled facets
f_element.element = facets[0];
(*facet_to_coh_element)(cohesive_element, 0) = f_element;
f_element.element = facets[1];
(*facet_to_coh_element)(cohesive_element, 1) = f_element;
/// modify cohesive elements' connectivity
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
(*conn_cohesive)(cohesive_element, n) = conn_facet(facets[0], n);
(*conn_cohesive)(cohesive_element, n + nb_nodes_per_facet)
= conn_facet(facets[1], n);
}
/// update element_to_facet vectors
c_element.element = cohesive_element;
element_to_facet(facets[0])[1] = c_element;
element_to_facet(facets[1])[1] = c_element;
/// add cohesive element to the element event list
new_elements(new_elements_old_size + facet) = c_element;
}
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doublePointFacet(Mesh & mesh,
Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
if (spatial_dimension != 1) return;
Array<Real> & position = mesh.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for(; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, gt_facet);
const Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
UInt old_nb_facet = element_to_facet.getSize() - nb_facet_to_double;
UInt new_nb_facet = element_to_facet.getSize();
UInt old_nb_nodes = position.getSize();
UInt new_nb_nodes = old_nb_nodes + nb_facet_to_double;
position.resize(new_nb_nodes);
conn_facet.resize(new_nb_facet);
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
doubled_nodes.resize(old_nb_doubled_nodes + nb_facet_to_double);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt new_facet = old_nb_facet + facet;
ElementType type = element_to_facet(new_facet)[0].type;
UInt el = element_to_facet(new_facet)[0].element;
GhostType gt = element_to_facet(new_facet)[0].ghost_type;
UInt old_node = conn_facet(old_facet);
UInt new_node = old_nb_nodes + facet;
/// update position
position(new_node) = position(old_node);
conn_facet(new_facet) = new_node;
Array<UInt> & conn_segment = mesh.getConnectivity(type, gt);
UInt nb_nodes_per_segment = conn_segment.getNbComponent();
/// update facet connectivity
UInt i;
for (i = 0; conn_segment(el, i) != old_node
&& i <= nb_nodes_per_segment; ++i);
conn_segment(el, i) = new_node;
doubled_nodes(old_nb_doubled_nodes + facet, 0) = old_node;
doubled_nodes(old_nb_doubled_nodes + facet, 1) = new_node;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_segments>
void MeshUtils::updateQuadraticSegments(Mesh & mesh,
Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (type_facet != _segment_3) return;
Array<UInt> & f_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_facet,
gt_facet);
UInt nb_facet_to_double = f_to_double.getSize();
UInt old_nb_facet
= mesh_facets.getNbElement(type_facet, gt_facet) - nb_facet_to_double;
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet,
gt_facet);
Array< std::vector<Element> > & element_to_facet
= mesh_facets.getElementToSubelement(type_facet, gt_facet);
/// this ones matter only for segments in 3D
Array< std::vector<Element> > * el_to_subfacet_double = NULL;
Array< std::vector<Element> > * f_to_subfacet_double = NULL;
if (third_dim_segments) {
el_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("elements_to_subfacet_double",
type_facet,
gt_facet);
f_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_facet,
gt_facet);
}
std::vector<UInt> middle_nodes;
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt node = conn_facet(old_facet, 2);
if (!mesh.isPureGhostNode(node)) middle_nodes.push_back(node);
}
UInt n = doubled_nodes.getSize();
doubleNodes(mesh, middle_nodes, doubled_nodes);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt old_node = conn_facet(old_facet, 2);
if (mesh.isPureGhostNode(old_node)) continue;
UInt new_node = doubled_nodes(n, 1);
UInt new_facet = old_nb_facet + facet;
conn_facet(new_facet, 2) = new_node;
if (third_dim_segments) {
updateElementalConnectivity(mesh_facets,
old_node, new_node,
element_to_facet(new_facet));
updateElementalConnectivity(mesh,
old_node, new_node,
(*el_to_subfacet_double)(facet),
&(*f_to_subfacet_double)(facet));
}
else {
updateElementalConnectivity(mesh,
old_node, new_node,
element_to_facet(new_facet));
}
++n;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet,
bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_subfacet,
gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
Array<Element> * subfacet_to_facet = NULL;
UInt nb_subfacet_per_facet = 0;
UInt old_nb_subfacet
= mesh_facets.getNbElement(type_subfacet, gt_subfacet) - nb_subfacet_to_double;
Array<std::vector<Element> > * facet_list = NULL;
if (facet_mode)
facet_list = & mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_subfacet,
gt_subfacet);
else
facet_list = & mesh_facets.getData<std::vector<Element> >("subfacets_to_subsubfacet_double",
type_subfacet,
gt_subfacet);
Element old_subfacet_el(type_subfacet, 0, gt_subfacet);
Element new_subfacet_el(type_subfacet, 0, gt_subfacet);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
old_subfacet_el.element = sf_to_double(sf);
new_subfacet_el.element = old_nb_subfacet + sf;
for (UInt f = 0; f < (*facet_list)(sf).size(); ++f) {
Element & facet = (*facet_list)(sf)[f];
if (facet.type != type_facet || facet.ghost_type != gt_facet) {
type_facet = facet.type;
gt_facet = facet.ghost_type;
subfacet_to_facet = & mesh_facets.getSubelementToElement(type_facet,
gt_facet);
nb_subfacet_per_facet = subfacet_to_facet->getNbComponent();
}
Element * sf_update
= std::find(subfacet_to_facet->storage()
+ facet.element * nb_subfacet_per_facet,
subfacet_to_facet->storage()
+ facet.element * nb_subfacet_per_facet + nb_subfacet_per_facet,
old_subfacet_el);
AKANTU_DEBUG_ASSERT(subfacet_to_facet->storage()
+ facet.element * nb_subfacet_per_facet !=
subfacet_to_facet->storage()
+ facet.element * nb_subfacet_per_facet + nb_subfacet_per_facet,
"Subfacet not found");
*sf_update = new_subfacet_el;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet,
bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_subfacet,
gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
Array< std::vector<Element> > & facet_to_subfacet
= mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
Array< std::vector<Element> > * facet_to_subfacet_double = NULL;
if (facet_mode) {
facet_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_subfacet,
gt_subfacet);
}
else {
facet_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("subfacets_to_subsubfacet_double",
type_subfacet,
gt_subfacet);
}
UInt old_nb_subfacet = facet_to_subfacet.getSize();
facet_to_subfacet.resize(old_nb_subfacet + nb_subfacet_to_double);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf)
facet_to_subfacet(old_nb_subfacet + sf) = (*facet_to_subfacet_double)(sf);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MeshUtils::doubleSubfacet(Mesh & mesh,
Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (spatial_dimension == 1) return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_subfacet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(0, gt_subfacet);
Mesh::type_iterator end = mesh_facets.lastType(0, gt_subfacet);
for(; it != end; ++it) {
ElementType type_subfacet = *it;
Array<UInt> & sf_to_double = mesh_facets.getData<UInt>("facet_to_double",
type_subfacet,
gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.getSize();
if (nb_subfacet_to_double == 0) continue;
AKANTU_DEBUG_ASSERT(type_subfacet == _point_1,
"Only _point_1 subfacet doubling is supported at the moment");
Array<UInt> & conn_subfacet = mesh_facets.getConnectivity(type_subfacet,
gt_subfacet);
UInt old_nb_subfacet = conn_subfacet.getSize();
UInt new_nb_subfacet = old_nb_subfacet + nb_subfacet_to_double;
conn_subfacet.resize(new_nb_subfacet);
std::vector<UInt> nodes_to_double;
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
/// double nodes
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_subfacet = sf_to_double(sf);
nodes_to_double.push_back(conn_subfacet(old_subfacet));
}
doubleNodes(mesh, nodes_to_double, doubled_nodes);
/// add new nodes in connectivity
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt new_subfacet = old_nb_subfacet + sf;
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
conn_subfacet(new_subfacet) = new_node;
}
/// update facet and element connectivity
Array<std::vector<Element> > & f_to_subfacet_double =
mesh_facets.getData<std::vector<Element> >("facets_to_subfacet_double",
type_subfacet,
gt_subfacet);
Array<std::vector<Element> > & el_to_subfacet_double =
mesh_facets.getData<std::vector<Element> >("elements_to_subfacet_double",
type_subfacet,
gt_subfacet);
Array<std::vector<Element> > * sf_to_subfacet_double = NULL;
if (spatial_dimension == 3)
sf_to_subfacet_double
= & mesh_facets.getData<std::vector<Element> >("subfacets_to_subsubfacet_double",
type_subfacet,
gt_subfacet);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_node = doubled_nodes(old_nb_doubled_nodes + sf, 0);
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
updateElementalConnectivity(mesh,
old_node, new_node,
el_to_subfacet_double(sf),
&f_to_subfacet_double(sf));
updateElementalConnectivity(mesh_facets,
old_node, new_node,
f_to_subfacet_double(sf));
if (spatial_dimension == 3)
updateElementalConnectivity(mesh_facets,
old_node, new_node,
(*sf_to_subfacet_double)(sf));
}
if (spatial_dimension == 2) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, true);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, true);
}
else if (spatial_dimension == 3) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, false);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::flipFacets(Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & global_connectivity,
GhostType gt_facet) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
/// get global connectivity for local mesh
ElementTypeMapArray<UInt> global_connectivity_tmp;
mesh_facets.initElementTypeMapArray(global_connectivity_tmp, 1,
spatial_dimension - 1, gt_facet,
true, _ek_regular, true);
mesh_facets.getGlobalConnectivity(global_connectivity_tmp,
spatial_dimension - 1, gt_facet);
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, gt_facet);
/// loop on every facet
for(; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & connectivity = mesh_facets.getConnectivity(type_facet, gt_facet);
const Array<UInt> & g_connectivity = global_connectivity(type_facet, gt_facet);
Array<std::vector<Element> > & el_to_f =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
UInt nb_subfacet_per_facet = subfacet_to_facet.getNbComponent();
UInt nb_nodes_per_facet = connectivity.getNbComponent();
UInt nb_facet = connectivity.getSize();
UInt nb_nodes_per_P1_facet
= Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
Array<UInt> & global_conn_tmp = global_connectivity_tmp(type_facet, gt_facet);
Array<UInt>::iterator<Vector<UInt> > conn_it =
connectivity.begin(nb_nodes_per_facet);
Array<UInt>::iterator<Vector<UInt> > gconn_tmp_it =
global_conn_tmp.begin(nb_nodes_per_facet);
Array<UInt>::const_iterator<Vector<UInt> > conn_glob_it =
g_connectivity.begin(nb_nodes_per_facet);
Array<Element>::iterator<Vector<Element> > subf_to_f =
subfacet_to_facet.begin(nb_subfacet_per_facet);
UInt * conn_tmp_pointer = new UInt[nb_nodes_per_facet];
Vector<UInt> conn_tmp(conn_tmp_pointer, nb_nodes_per_facet);
Element el_tmp;
Element * subf_tmp_pointer = new Element[nb_subfacet_per_facet];
Vector<Element> subf_tmp(subf_tmp_pointer, nb_subfacet_per_facet);
for (UInt f = 0; f < nb_facet; ++f, ++conn_it, ++gconn_tmp_it,
++subf_to_f, ++conn_glob_it) {
Vector<UInt> & gconn_tmp = *gconn_tmp_it;
const Vector<UInt> & conn_glob = *conn_glob_it;
Vector<UInt> & conn_local = *conn_it;
/// skip facet if connectivities are the same
if (gconn_tmp == conn_glob) continue;
/// re-arrange connectivity
conn_tmp = conn_local;
UInt * begin = conn_glob.storage();
UInt * end = conn_glob.storage() + nb_nodes_per_facet;
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
UInt * new_node = std::find(begin, end, gconn_tmp(n));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
conn_local(new_position) = conn_tmp(n);
}
/// if 3D, check if facets are just rotated
if (spatial_dimension == 3) {
/// find first node
UInt * new_node = std::find(begin, end, gconn_tmp(0));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
UInt n = 1;
/// count how many nodes in the received connectivity follow
/// the same order of those in the local connectivity
for (; n < nb_nodes_per_P1_facet &&
gconn_tmp(n) == conn_glob((new_position + 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
el_tmp = el_to_f(f)[0];
el_to_f(f)[0] = el_to_f(f)[1];
el_to_f(f)[1] = el_tmp;
subf_tmp = (*subf_to_f);
(*subf_to_f)(0) = subf_tmp(1);
(*subf_to_f)(1) = subf_tmp(0);
}
delete [] subf_tmp_pointer;
delete [] conn_tmp_pointer;
}
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());
mesh.initElementTypeMapArray(barycenters,
spatial_dimension,
_all_dimensions);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
Mesh::type_iterator it = mesh.firstType(_all_dimensions, *gt);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, *gt);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, *gt);
Array<Real> & barycenters_arr = barycenters(*it, *gt);
barycenters_arr.resize(nb_element);
Array<Real>::vector_iterator bary = barycenters_arr.begin(spatial_dimension);
Array<Real>::vector_iterator bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
mesh.getBarycenter(el, *it, bary->storage(), *gt);
}
}
}
for(Int sp(spatial_dimension); sp >= 1; --sp) {
if(mesh.getNbElement(sp) == 0) continue;
for (ghost_type_t::iterator git = ghost_type_t::begin(); git != ghost_type_t::end(); ++git) {
Mesh::type_iterator tit = mesh.firstType(sp, *git);
Mesh::type_iterator tend = mesh.lastType(sp, *git);
for (;tit != tend; ++tit) {
mesh.getSubelementToElementPointer(*tit, *git)->resize(mesh.getNbElement(*tit, *git));
mesh.getSubelementToElement(*tit, *git).clear();
}
tit = mesh.firstType(sp - 1, *git);
tend = mesh.lastType(sp - 1, *git);
for (;tit != tend; ++tit) {
mesh.getElementToSubelementPointer(*tit, *git)->resize(mesh.getNbElement(*tit, *git));
mesh.getElementToSubelement(*tit, *git).clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (ghost_type_t::iterator git = ghost_type_t::begin(); git != ghost_type_t::end(); ++git) {
Mesh::type_iterator tit = mesh.firstType(sp - 1, *git);
Mesh::type_iterator tend = mesh.lastType(sp - 1, *git);
facet_element.ghost_type = *git;
for (;tit != tend; ++tit) {
facet_element.type = *tit;
Array< std::vector<Element> > & element_to_subelement = mesh.getElementToSubelement(*tit, *git);
const Array<UInt> & connectivity = mesh.getConnectivity(*tit, *git);
Array<UInt>::const_iterator< Vector<UInt> > fit = connectivity.begin(mesh.getNbNodesPerElement(*tit));
Array<UInt>::const_iterator< Vector<UInt> > fend = connectivity.end(mesh.getNbNodesPerElement(*tit));
UInt fid = 0;
for (;fit != fend; ++fit, ++fid) {
const Vector<UInt> & facet = *fit;
facet_element.element = fid;
std::map<Element, UInt> element_seen_counter;
UInt nb_nodes_per_facet = mesh.getNbNodesPerElement(Mesh::getP1ElementType(*tit));
for (UInt n(0); n < nb_nodes_per_facet; ++n) {
CSR<Element>::iterator eit = nodes_to_elements.begin(facet(n));
CSR<Element>::iterator eend = nodes_to_elements.end(facet(n));
for(;eit != eend; ++eit) {
Element & elem = *eit;
std::map<Element, UInt>::iterator cit = element_seen_counter.find(elem);
if(cit != element_seen_counter.end()) {
cit->second++;
} else {
element_seen_counter[elem] = 1;
}
}
}
std::vector<Element> connected_elements;
std::map<Element, UInt>::iterator cit = element_seen_counter.begin();
std::map<Element, UInt>::iterator cend = element_seen_counter.end();
for(;cit != cend; ++cit) {
if(cit->second == nb_nodes_per_facet) connected_elements.push_back(cit->first);
}
std::vector<Element>::iterator ceit = connected_elements.begin();
std::vector<Element>::iterator ceend = connected_elements.end();
for(;ceit != ceend; ++ceit)
element_to_subelement(fid).push_back(*ceit);
for (UInt ce = 0; ce < connected_elements.size(); ++ce) {
Element & elem = connected_elements[ce];
Array<Element> & subelement_to_element =
*(mesh.getSubelementToElementPointer(elem.type,
elem.ghost_type));
UInt f(0);
for(; f < mesh.getNbFacetsPerElement(elem.type) && subelement_to_element(elem.element, f) != ElementNull; ++f);
AKANTU_DEBUG_ASSERT(f < mesh.getNbFacetsPerElement(elem.type), "The element " << elem << " seems to have too many facets!! (" << f << " < " << mesh.getNbFacetsPerElement(elem.type) << ")");
subelement_to_element(elem.element, f) = facet_element;
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_points>
bool MeshUtils::findElementsAroundSubfacet(const Mesh & mesh,
const Mesh & mesh_facets,
const Element & starting_element,
const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list,
std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list) {
AKANTU_DEBUG_IN();
/// preallocated stuff before starting
bool facet_matched = false;
elem_list.clear();
facet_list.clear();
if (third_dim_points)
subfacet_list->clear();
elem_list.push_back(starting_element);
const Array<UInt> * facet_connectivity = NULL;
const Array<UInt> * sf_connectivity = NULL;
const Array<Element> * facet_to_element = NULL;
const Array<Element> * subfacet_to_facet = NULL;
ElementType current_type = _not_defined;
GhostType current_ghost_type = _casper;
ElementType current_facet_type = _not_defined;
GhostType current_facet_ghost_type = _casper;
ElementType current_subfacet_type = _not_defined;
GhostType current_subfacet_ghost_type = _casper;
const Array< std::vector<Element> > * element_to_facet = NULL;
const Element * opposing_el = NULL;
std::queue<Element> elements_to_check;
elements_to_check.push(starting_element);
/// keep going until there are elements to check
while (!elements_to_check.empty()) {
/// check current element
Element & current_el = elements_to_check.front();
if (current_el.type != current_type ||
current_el.ghost_type != current_ghost_type) {
current_type = current_el.type;
current_ghost_type = current_el.ghost_type;
facet_to_element = & mesh_facets.getSubelementToElement(current_type,
current_ghost_type);
}
/// loop over each facet of the element
for (UInt f = 0; f < facet_to_element->getNbComponent(); ++f) {
const Element & current_facet = (*facet_to_element)(current_el.element, f);
if (current_facet == ElementNull) continue;
if (current_facet_type != current_facet.type ||
current_facet_ghost_type != current_facet.ghost_type) {
current_facet_type = current_facet.type;
current_facet_ghost_type = current_facet.ghost_type;
element_to_facet =
& mesh_facets.getElementToSubelement(current_facet_type,
current_facet_ghost_type);
facet_connectivity = & mesh_facets.getConnectivity(current_facet_type,
current_facet_ghost_type);
if (third_dim_points)
subfacet_to_facet =
& mesh_facets.getSubelementToElement(current_facet_type,
current_facet_ghost_type);
}
/// check if end facet is reached
if (current_facet == end_facet)
facet_matched = true;
/// add this facet if not already passed
if (std::find(facet_list.begin(),
facet_list.end(),
current_facet) == facet_list.end() &&
hasElement(*facet_connectivity, current_facet, subfacet_connectivity)) {
facet_list.push_back(current_facet);
if (third_dim_points) {
/// check subfacets
for (UInt sf = 0; sf < subfacet_to_facet->getNbComponent(); ++sf) {
const Element & current_subfacet
= (*subfacet_to_facet)(current_facet.element, sf);
if (current_subfacet == ElementNull) continue;
if (current_subfacet_type != current_subfacet.type ||
current_subfacet_ghost_type != current_subfacet.ghost_type) {
current_subfacet_type = current_subfacet.type;
current_subfacet_ghost_type = current_subfacet.ghost_type;
sf_connectivity
= & mesh_facets.getConnectivity(current_subfacet_type,
current_subfacet_ghost_type);
}
if (std::find(subfacet_list->begin(),
subfacet_list->end(),
current_subfacet) == subfacet_list->end() &&
hasElement(*sf_connectivity, current_subfacet, subfacet_connectivity))
subfacet_list->push_back(current_subfacet);
}
}
}
else
continue;
/// consider opposing element
if ( (*element_to_facet)(current_facet.element)[0] == current_el)
opposing_el = & (*element_to_facet)(current_facet.element)[1];
else
opposing_el = & (*element_to_facet)(current_facet.element)[0];
/// skip null elements since they are on a boundary
if (*opposing_el == ElementNull) continue;
/// skip this element if already added
if ( std::find(elem_list.begin(),
elem_list.end(),
*opposing_el) != elem_list.end() ) continue;
/// only regular elements have to be checked
if (opposing_el->kind == _ek_regular)
elements_to_check.push(*opposing_el);
elem_list.push_back(*opposing_el);
#ifndef AKANTU_NDEBUG
const Array<UInt> & conn_elem = mesh.getConnectivity(opposing_el->type,
opposing_el->ghost_type);
AKANTU_DEBUG_ASSERT(hasElement(conn_elem, *opposing_el, subfacet_connectivity),
"Subfacet doesn't belong to this element");
#endif
}
/// erased checked element from the list
elements_to_check.pop();
}
AKANTU_DEBUG_OUT();
return facet_matched;
}
__END_AKANTU__
// LocalWords: ElementType
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index 48a1a1100..7848bd139 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,277 +1,278 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@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 Aug 20 2010
* @date last modification: Mon Jun 23 2014
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "mesh.hh"
#include "aka_csr.hh"
#include "distributed_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_UTILS_HH__
#define __AKANTU_MESH_UTILS_HH__
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshUtils();
virtual ~MeshUtils();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<UInt> that contains for each node the linearized number of
/// the connected elements of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh,
CSR<UInt> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<Element> that contains for each node the list of connected
/// elements ofr 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,
const ElementType & type,
const 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,
DistributedSynchronizer * synchronizer = NULL);
/// 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,
DistributedSynchronizer * synchronizer = NULL);
/// build facets for a given spatial dimension
static void buildFacetsDimension(const Mesh & mesh,
Mesh & mesh_facets,
bool boundary_only,
UInt dimension,
const ElementTypeMapArray<UInt> * prank_to_element = NULL);
/// 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,
UInt * local_connectivities,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes);
/// compute pbc pair for on given a direction
static void computePBCMap(const Mesh & mymesh, const UInt dir,
std::map<UInt,UInt> & pbc_pair);
/// compute pbc pair for a surface pair
static void computePBCMap(const Mesh & mymesh,
const std::pair<Surface, Surface> & surface_pair,
std::map<UInt,UInt> & pbc_pair);
/// create a multimap of nodes per surfaces
static void buildNodesPerSurface(const Mesh & mesh, CSR<UInt> & nodes_per_surface);
/// remove not connected nodes /!\ this functions renumbers the nodes.
static void purifyMesh(Mesh & mesh);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// function to insert cohesive elements on the selected facets
static void insertCohesiveElements(Mesh & mesh,
Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements);
#endif
/// 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> & global_connectivity,
GhostType gt_facet);
/// provide list of elements around a node and check if a given
/// facet is reached
template <bool third_dim_points>
static bool findElementsAroundSubfacet(const Mesh & mesh,
const Mesh & mesh_facets,
const Element & starting_element,
const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list,
std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list = NULL);
/// function to check if a node belongs to a given element
static inline bool hasElement(const Array<UInt> & connectivity,
const Element & el,
const Vector<UInt> & nodes);
/// reset facet_to_double arrays in the Mesh
static void resetFacetToDouble(Mesh & mesh_facets);
private:
/// match pairs that are on the associated pbc's
static void matchPBCPairs(const Mesh & mymesh,
const 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(UInt * list_nodes,
UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map);
/// update facet_to_subfacet
static void updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet,
bool facet_mode);
/// update subfacet_to_facet
static void updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet,
bool facet_mode);
/// function to double a given facet and update the list of doubled
/// nodes
static void doubleFacet(Mesh & mesh,
Mesh & mesh_facets,
UInt facet_dimension,
Array<UInt> & doubled_nodes,
bool facet_mode);
/// function to double a subfacet given start and end index for
/// local facet_to_subfacet vector, and update the list of doubled
/// nodes
template <UInt spatial_dimension>
static void doubleSubfacet(Mesh & mesh,
Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
/// double a node
static void doubleNodes(Mesh & mesh,
const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes);
/// fill facet_to_double array in the mesh
- static bool updateFacetToDouble(Mesh & mesh_facets,
+ /// returns the number of facets to be doubled
+ static UInt updateFacetToDouble(Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion);
/// find subfacets to be doubled
template <bool subsubfacet_mode>
static void findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets);
/// double facets (points) in 1D
static void doublePointFacet(Mesh & mesh,
Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// update cohesive element data
static void updateCohesiveData(Mesh & mesh,
Mesh & mesh_facets,
Array<Element> & new_elements);
#endif
/// update elemental connectivity after doubling a node
inline static void updateElementalConnectivity(Mesh & mesh,
UInt old_node,
UInt new_node,
const std::vector<Element> & element_list,
const std::vector<Element> * facet_list = NULL);
/// double middle nodes if facets are _segment_3
template <bool third_dim_segments>
static void updateQuadraticSegments(Mesh & mesh,
Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes);
/// remove elements on a vector
inline static bool removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "mesh_utils_inline_impl.cc"
__END_AKANTU__
#endif /* __AKANTU_MESH_UTILS_HH__ */
diff --git a/src/model/boundary_condition_functor.hh b/src/model/boundary_condition_functor.hh
index e1e300106..279dc72a2 100644
--- a/src/model/boundary_condition_functor.hh
+++ b/src/model/boundary_condition_functor.hh
@@ -1,205 +1,202 @@
/**
* @file boundary_condition_functor.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Fri Sep 19 2014
*
* @brief XXX
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_BOUNDARY_CONDITION_FUNCTOR_HH__
#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
#include "aka_common.hh"
#include "fe_engine.hh"
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
namespace BC {
typedef ::akantu::SpacialDirection Axis;
struct Functor {
enum Type {
_dirichlet,
_neumann
};
};
/* ------------------------------------------------------------------------ */
/* Dirichlet */
/* ------------------------------------------------------------------------ */
namespace Dirichlet {
/* ---------------------------------------------------------------------- */
class DirichletFunctor : public Functor {
protected:
DirichletFunctor() : axis(_x) {}
DirichletFunctor(Axis ax) : axis(ax) {}
public:
void operator()(UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
public:
static const Type type = _dirichlet;
protected:
Axis axis;
};
/* ---------------------------------------------------------------------- */
class FlagOnly : public DirichletFunctor {
public:
FlagOnly(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public DirichletFunctor {
public:
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;
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;
inline void setIncrement(Real val) { this->value = val; }
protected:
Real value;
};
} //end namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
/* ---------------------------------------------------------------------- */
class NeumannFunctor : public Functor {
protected:
NeumannFunctor() {}
public:
- void operator()(UInt node,
- Vector<bool> & flags,
- Vector<Real> & primal,
- const Vector<Real> & coord) const {
- AKANTU_DEBUG_TO_IMPLEMENT();
- }
-
+ virtual void operator()(const QuadraturePoint & quad_point,
+ Vector<Real> & dual,
+ const Vector<Real> & coord,
+ const Vector<Real> & normals) const = 0;
public:
static const Type type = _neumann;
};
/* ---------------------------------------------------------------------- */
class FromHigherDim : public NeumannFunctor {
public:
FromHigherDim(const Matrix<Real> & mat) : bc_data(mat) {}
public:
inline void operator()(const QuadraturePoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
public:
inline void operator()(const QuadraturePoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const;
protected:
Vector<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public NeumannFunctor {
public:
inline void operator()(const QuadraturePoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const;
};
} //end namespace Neumann
} //end namespace BC
__END_AKANTU__
#include "boundary_condition_functor_inline_impl.cc"
#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__ */
diff --git a/src/model/model.cc b/src/model/model.cc
index 3c0388268..2d7a9c7d8 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,373 +1,373 @@
/**
* @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: Fri Sep 05 2014
*
* @brief implementation of model common parts
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "model.hh"
#include "element_group.hh"
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
Model::Model(Mesh& m, UInt dim, const ID & id,
const MemoryID & memory_id) :
Memory(id, memory_id), mesh(m),
spatial_dimension(dim == _all_dimensions ? m.getSpatialDimension() : dim),
synch_registry(NULL),is_pbc_slave_node(0,1,"is_pbc_slave_node") ,
parser(&getStaticParser()) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Model::~Model() {
AKANTU_DEBUG_IN();
FEEngineMap::iterator it;
for (it = fems.begin(); it != fems.end(); ++it) {
if(it->second) delete it->second;
}
for (it = fems_boundary.begin(); it != fems_boundary.end(); ++it) {
if(it->second) delete it->second;
}
delete synch_registry;
delete dof_synchronizer;
dof_synchronizer = NULL;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::setParser(Parser & parser){
this->parser = &parser;
}
/* -------------------------------------------------------------------------- */
void Model::initFull(const ModelOptions & options) {
AKANTU_DEBUG_IN();
initModel();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::createSynchronizerRegistry(DataAccessor * data_accessor){
synch_registry = new SynchronizerRegistry(*data_accessor);
}
/* -------------------------------------------------------------------------- */
void Model::setPBC(UInt x, UInt y, UInt z){
mesh.computeBoundingBox();
if (x) MeshUtils::computePBCMap(this->mesh, 0, this->pbc_pair);
if (y) MeshUtils::computePBCMap(this->mesh, 1, this->pbc_pair);
if (z) MeshUtils::computePBCMap(this->mesh, 2, this->pbc_pair);
}
/* -------------------------------------------------------------------------- */
void Model::setPBC(SurfacePairList & surface_pairs){
SurfacePairList::iterator s_it;
for(s_it = surface_pairs.begin(); s_it != surface_pairs.end(); ++s_it) {
MeshUtils::computePBCMap(this->mesh, *s_it, this->pbc_pair);
}
}
/* -------------------------------------------------------------------------- */
void Model::initPBC() {
std::map<UInt,UInt>::iterator it = pbc_pair.begin();
std::map<UInt,UInt>::iterator end = pbc_pair.end();
is_pbc_slave_node.resize(mesh.getNbNodes());
#ifndef AKANTU_NDEBUG
Real * coords = mesh.getNodes().storage();
UInt dim = mesh.getSpatialDimension();
#endif
while(it != end){
UInt i1 = (*it).first;
is_pbc_slave_node(i1) = true;
#ifndef AKANTU_NDEBUG
UInt i2 = (*it).second;
AKANTU_DEBUG_INFO("pairing " << i1 << " ("
<< coords[dim*i1] << "," << coords[dim*i1+1] << ","
<< coords[dim*i1+2]
<< ") with "
<< i2 << " ("
<< coords[dim*i2] << "," << coords[dim*i2+1] << ","
<< coords[dim*i2+2]
<< ")");
#endif
++it;
}
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer & Model::createParallelSynch(MeshPartition * partition,
__attribute__((unused)) DataAccessor * data_accessor){
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
StaticCommunicator & comm =
StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
DistributedSynchronizer * synch = NULL;
if(prank == 0)
synch =
DistributedSynchronizer::createDistributedSynchronizerMesh(getFEEngine().getMesh(),
partition);
else
synch =
DistributedSynchronizer::createDistributedSynchronizerMesh(getFEEngine().getMesh(),
NULL);
AKANTU_DEBUG_OUT();
return *synch;
}
/* -------------------------------------------------------------------------- */
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() {
GroupManager::element_group_iterator bit = mesh.element_group_begin();
GroupManager::element_group_iterator bend = mesh.element_group_end();
for(; bit != bend; ++bit) {
bit->second->dump();
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory) {
GroupManager::element_group_iterator bit = mesh.element_group_begin();
GroupManager::element_group_iterator bend = mesh.element_group_end();
for (; bit != bend; ++bit) {
bit->second->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,
dumper::Field * field,
DumperIOHelper & dumper) {
#ifdef AKANTU_USE_IOHELPER
dumper.registerField(field_id,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",_ek_regular,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,_ek_regular,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",_ek_regular,3);
}
/* -------------------------------------------------------------------------- */
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,_ek_regular,true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name,field_id,"all",_ek_regular,true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
- const std::string & field_id,
- const std::string & group_name,
- const ElementKind & element_kind,
- bool padding_flag) {
+ const std::string & field_id,
+ const std::string & group_name,
+ const ElementKind & element_kind,
+ bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
dumper::Field * field = NULL;
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,element_kind);
+ if (!field) field = this->createElementalField(field_id,group_name,padding_flag,this->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);
if (!field) AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name,group_name);
this->addDumpGroupFieldToDumper(field_id,field,dumper);
}
#endif
}
/* -------------------------------------------------------------------------- */
void Model::dump() {
mesh.dump();
}
/* -------------------------------------------------------------------------- */
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);
}
__END_AKANTU__
diff --git a/src/model/model.hh b/src/model/model.hh
index ee38ae66e..86d658102 100644
--- a/src/model/model.hh
+++ b/src/model/model.hh
@@ -1,316 +1,317 @@
/**
* @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: Tue Jul 27 2010
* @date last modification: Fri Sep 05 2014
*
* @brief Interface of a model
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_MODEL_HH__
#define __AKANTU_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "mesh.hh"
#include "fe_engine.hh"
#include "mesh_utils.hh"
#include "synchronizer_registry.hh"
#include "distributed_synchronizer.hh"
#include "static_communicator.hh"
#include "mesh_partition.hh"
#include "dof_synchronizer.hh"
#include "pbc_synchronizer.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
struct ModelOptions {
virtual ~ModelOptions() {}
};
class DumperIOHelper;
class Model : public Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef Mesh mesh_type;
Model(Mesh& mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "model",
const MemoryID & memory_id = 0);
virtual ~Model();
typedef std::map<std::string, FEEngine *> FEEngineMap;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initFull(const ModelOptions & options);
virtual void initModel() = 0;
/// create the synchronizer registry object
void createSynchronizerRegistry(DataAccessor * data_accessor);
/// create a parallel synchronizer and distribute the mesh
DistributedSynchronizer & createParallelSynch(MeshPartition * partition,
DataAccessor * data_accessor);
/// change local equation number so that PBC is assembled properly
void changeLocalEquationNumberForPBC(std::map<UInt,UInt> & pbc_pair,UInt dimension);
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
/// initialize the model for PBC
void setPBC(UInt x, UInt y, UInt z);
void setPBC(SurfacePairList & surface_pairs);
virtual void initPBC();
/// set the parser to use
void setParser(Parser & parser);
/* ------------------------------------------------------------------------ */
/* 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);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get id of model
AKANTU_GET_MACRO(ID, id, const ID)
/// get the number of surfaces
AKANTU_GET_MACRO(Mesh, mesh, Mesh&);
/// return the object handling equation numbers
AKANTU_GET_MACRO(DOFSynchronizer, *dof_synchronizer, const DOFSynchronizer &)
/// return the object handling synchronizers
AKANTU_GET_MACRO(SynchronizerRegistry, *synch_registry, SynchronizerRegistry &)
/// 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 = "");
/// 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 pbc pairs
std::map<UInt,UInt> & getPBCPairs(){return pbc_pair;};
/// returns if node is slave in pbc
inline bool isPBCSlaveNode(const UInt node) const;
/// returns the array of pbc slave nodes (boolean information)
AKANTU_GET_MACRO(IsPBCSlaveNode, is_pbc_slave_node, const Array<bool> &)
/* ------------------------------------------------------------------------ */
/* Pack and unpack helper functions */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbQuadraturePoints(const Array<Element> & elements,
const ID & fem_id = ID()) const;
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
virtual void addDumpGroupFieldToDumper(const std::string & field_id,
dumper::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 & basename);
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,
const 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 dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag){return NULL;}
virtual dumper::Field * createNodalFieldUInt(const std::string & field_name,
const std::string & group_name,
bool padding_flag){return NULL;}
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag){return NULL;}
virtual dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
+ const UInt & spatial_dimension,
const ElementKind & kind){return NULL;}
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
virtual void dump();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// 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;
/// synchronizer registry
SynchronizerRegistry * synch_registry;
/// handle the equation number things
DOFSynchronizer * dof_synchronizer;
/// pbc pairs
std::map<UInt,UInt> pbc_pair;
/// flag per node to know is pbc slave
Array<bool> is_pbc_slave_node;
/// parser to the pointer to use
Parser * parser;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "model_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const Model & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#endif /* __AKANTU_MODEL_HH__ */
diff --git a/src/model/solid_mechanics/embedded_interface.cc b/src/model/solid_mechanics/embedded_interface.cc
deleted file mode 100644
index 812bfff4a..000000000
--- a/src/model/solid_mechanics/embedded_interface.cc
+++ /dev/null
@@ -1,71 +0,0 @@
-/**
- * @file embedded_interface.cc
- *
- * @author Lucas Frerot <lucas.frerot@epfl.ch>
- *
- * @date creation: Mon Mar 23 2015
- * @date last modification: Mon Mar 23 2015
- *
- * @brief Class used to represent embedded interfaces
- *
- * @section LICENSE
- *
- * Copyright (©) 2010-2015 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 "aka_common.hh"
-#include "embedded_interface.hh"
-
-#include <CGAL/Cartesian.h>
-
-__BEGIN_AKANTU__
-
-typedef CGAL::Cartesian<Real> K;
-
-EmbeddedInterface::EmbeddedInterface(UInt dim, const ID & id) :
- Parsable(_st_embedded_interface, id),
- points(2, dim)
-{
- registerParam<std::string>("name", name, _pat_parsable | _pat_readable, "ID");
- registerParam<std::string>("material", mat_name, _pat_parsable | _pat_readable, "Material Name");
- registerParam< Matrix<Real> >("points", points, _pat_parsable | _pat_readable, "Interface Points");
-}
-
-EmbeddedInterface::~EmbeddedInterface()
-{}
-
-K::Segment_3 EmbeddedInterface::getPrimitive() const {
- AKANTU_DEBUG_INFO("Creating interface " << points);
-
- if (points.cols() == 2) {
- K::Point_3 a(points(0, 0), points(0, 1), 0.);
- K::Point_3 b(points(1, 0), points(1, 1), 0.);
- return K::Segment_3(a, b);
- } else if (points.cols() == 3) {
- K::Point_3 a(points(0, 0), points(0, 1), points(0, 2));
- K::Point_3 b(points(1, 0), points(1, 1), points(1, 2));
- return K::Segment_3(a, b);
- } else {
- AKANTU_DEBUG_ERROR("Error in reading embedded interface : wrong number of components");
- return K::Segment_3(CGAL::ORIGIN, CGAL::ORIGIN);
- }
-}
-
-__END_AKANTU__
diff --git a/src/model/solid_mechanics/embedded_interface.hh b/src/model/solid_mechanics/embedded_interface.hh
deleted file mode 100644
index b9edbeb5e..000000000
--- a/src/model/solid_mechanics/embedded_interface.hh
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * @file embedded_interface.hh
- *
- * @author Lucas Frerot <lucas.frerot@epfl.ch>
- *
- * @date creation: Mon Mar 23 2015
- * @date last modification: Mon Mar 23 2015
- *
- * @brief Class used to represent embedded interfaces
- *
- * @section LICENSE
- *
- * Copyright (©) 2010-2015 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/>.
- *
- */
-
-/* -------------------------------------------------------------------------- */
-
-#ifndef __AKANTU_EMBEDDED_INTERFACE_HH__
-#define __AKANTU_EMBEDDED_INTERFACE_HH__
-
-#include "aka_common.hh"
-#include "parsable.hh"
-
-#include <CGAL/Cartesian.h>
-
-/* -------------------------------------------------------------------------- */
-
-__BEGIN_AKANTU__
-
-class EmbeddedInterface : public Parsable {
-
- typedef CGAL::Cartesian<Real> K;
-
- /* ------------------------------------------------------------------------ */
- /* Constructors/Destructors */
- /* ------------------------------------------------------------------------ */
-public:
- EmbeddedInterface(UInt dim, const ID & id = "");
-
- virtual ~EmbeddedInterface();
-
- /* ------------------------------------------------------------------------ */
- /* Methods */
- /* ------------------------------------------------------------------------ */
-public:
- K::Segment_3 getPrimitive() const;
-
- /* ------------------------------------------------------------------------ */
- /* Accessors */
- /* ------------------------------------------------------------------------ */
-public:
- AKANTU_GET_MACRO(Name, name, const std::string &);
- AKANTU_GET_MACRO(MaterialName, mat_name, const std::string &);
-
- /* ------------------------------------------------------------------------ */
- /* Class Members */
- /* ------------------------------------------------------------------------ */
-protected:
- std::string name;
- std::string mat_name;
- Matrix<Real> points;
-
-
-};
-
-__END_AKANTU__
-
-#endif // __AKANTU_EMBEDDED_INTERFACE_HH__
diff --git a/src/model/solid_mechanics/embedded_interface_intersector.cc b/src/model/solid_mechanics/embedded_interface_intersector.cc
new file mode 100644
index 000000000..38b7e7eef
--- /dev/null
+++ b/src/model/solid_mechanics/embedded_interface_intersector.cc
@@ -0,0 +1,151 @@
+/**
+ * @file embedded_interface_intersector.cc
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief Class that loads the interface from mesh and computes intersections
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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 "embedded_interface_intersector.hh"
+#include "mesh_segment_intersector.hh"
+
+#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.computeIntersectionQueryList( \
+ name_to_primitives_it->second, \
+ name_to_primitives_it->first); \
+ } } while(0)
+
+#define INTERFACE_INTERSECTOR_CASE_2D(type) INTERFACE_INTERSECTOR_CASE(2, type)
+#define INTERFACE_INTERSECTOR_CASE_3D(type) INTERFACE_INTERSECTOR_CASE(3, type)
+
+__BEGIN_AKANTU__
+
+EmbeddedInterfaceIntersector::EmbeddedInterfaceIntersector(const Mesh & mesh, const Mesh & primitive_mesh) :
+ MeshGeomAbstract(mesh),
+ interface_mesh(mesh.getSpatialDimension(), "interface_mesh"),
+ primitive_mesh(primitive_mesh)
+{
+ interface_mesh.addConnectivityType(_segment_2, _not_ghost);
+ interface_mesh.addConnectivityType(_segment_2, _ghost);
+ interface_mesh.registerData<Element>("associated_element").alloc(0, 1, _segment_2);
+ interface_mesh.registerData<std::string>("physical_names").alloc(0, 1, _segment_2);
+}
+
+EmbeddedInterfaceIntersector::~EmbeddedInterfaceIntersector()
+{}
+
+void EmbeddedInterfaceIntersector::constructData() {
+ AKANTU_DEBUG_IN();
+
+ const UInt dim = this->mesh.getSpatialDimension();
+
+ Array<std::string> * physical_names = NULL;
+
+ try {
+ physical_names = &const_cast<Array<std::string> &>(this->primitive_mesh.getData<std::string>("physical_names", _segment_2));
+ } catch (debug::Exception & e) {
+ AKANTU_DEBUG_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);
+ Array<UInt>::const_vector_iterator connectivity = primitive_mesh.getConnectivity(_segment_2).begin(nb_nodes_per_element);
+
+ Array<std::string>::scalar_iterator
+ names_it = physical_names->begin(),
+ names_end = physical_names->end();
+
+ std::map<std::string, std::list<K::Segment_3> > 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
+ Mesh::type_iterator
+ type_it = this->mesh.firstType(dim, _not_ghost),
+ type_end = this->mesh.lastType(dim, _not_ghost);
+
+ std::map<std::string, std::list<K::Segment_3> >::iterator
+ name_to_primitives_it,
+ name_to_primitives_end = name_to_primitives_map.end();
+
+ for (; type_it != type_end ; ++type_it) {
+ ElementType type = *type_it;
+
+ switch(dim) {
+ case 1:
+ AKANTU_DEBUG_ERROR("No embedded model in 1D");
+ break;
+
+ case 2:
+ AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_2D, (_triangle_3));
+ break;
+
+ case 3:
+ 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();
+
+ K::Point_3 * source = NULL, * target = NULL;
+ const Array<Real> & nodes = this->primitive_mesh.getNodes();
+
+ if (this->mesh.getSpatialDimension() == 2) {
+ source = new K::Point_3(nodes(connectivity(0), 0), nodes(connectivity(0), 1), 0.);
+ target = new K::Point_3(nodes(connectivity(1), 0), nodes(connectivity(1), 1), 0.);
+ } else if (this->mesh.getSpatialDimension() == 3) {
+ source = new K::Point_3(nodes(connectivity(0), 0), nodes(connectivity(0), 1), nodes(connectivity(0), 2));
+ target = new K::Point_3(nodes(connectivity(1), 0), nodes(connectivity(1), 1), nodes(connectivity(1), 2));
+ }
+
+ K::Segment_3 segment(*source, *target);
+ delete source;
+ delete target;
+
+ AKANTU_DEBUG_OUT();
+ return segment;
+}
+
+__END_AKANTU__
+
+#undef INTERFACE_INTERSECTOR_CASE
+#undef INTERFACE_INTERSECTOR_CASE_2D
+#undef INTERFACE_INTERSECTOR_CASE_3D
diff --git a/src/model/solid_mechanics/embedded_interface_intersector.hh b/src/model/solid_mechanics/embedded_interface_intersector.hh
new file mode 100644
index 000000000..b12e2443b
--- /dev/null
+++ b/src/model/solid_mechanics/embedded_interface_intersector.hh
@@ -0,0 +1,92 @@
+/**
+ * @file embedded_interface_intersector.hh
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: Wed Apr 29 2015
+ * @date last modification: Wed Apr 29 2015
+ *
+ * @brief Class that loads the interface from mesh and computes intersections
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
+#define __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
+
+#include "aka_common.hh"
+#include "mesh_geom_abstract.hh"
+#include "mesh_segment_intersector.hh"
+
+#include <CGAL/Cartesian.h>
+
+/* -------------------------------------------------------------------------- */
+
+__BEGIN_AKANTU__
+
+typedef CGAL::Cartesian<Real> K;
+
+/**
+ * @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(const Mesh & mesh, const Mesh & primitive_mesh);
+
+ /// Destructor
+ virtual ~EmbeddedInterfaceIntersector();
+
+public:
+ /// Generate the interface mesh
+ virtual void constructData();
+
+ /// 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;
+
+};
+
+__END_AKANTU__
+
+#endif // __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
diff --git a/src/model/solid_mechanics/embedded_interface_model.cc b/src/model/solid_mechanics/embedded_interface_model.cc
index 945b80f1d..ad82a8875 100644
--- a/src/model/solid_mechanics/embedded_interface_model.cc
+++ b/src/model/solid_mechanics/embedded_interface_model.cc
@@ -1,171 +1,186 @@
/**
* @file embedded_interface_model.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Mon Mar 9 2015
* @date last modification: Mon Mar 9 2015
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "embedded_interface_model.hh"
#include "material_reinforcement.hh"
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
# include "dumpable_inline_impl.hh"
#endif
#include <CGAL/Cartesian.h>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
typedef CGAL::Cartesian<Real> K;
EmbeddedInterfaceModel::EmbeddedInterfaceModel(Mesh & mesh,
+ Mesh & primitive_mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id) :
SolidMechanicsModel(mesh, spatial_dimension, id, memory_id),
interface_mesh(NULL),
+ primitive_mesh(primitive_mesh),
interface_material_selector(NULL),
- interface_container(mesh)
-{}
+ intersector(mesh, primitive_mesh)
+{
+ // This pointer should be deleted by ~SolidMechanicsModel()
+ MaterialSelector * mat_sel_pointer = new MeshDataMaterialSelector<std::string>("physical_names", *this);
+ this->setMaterialSelector(*mat_sel_pointer);
+}
EmbeddedInterfaceModel::~EmbeddedInterfaceModel() {
delete interface_material_selector;
}
-void EmbeddedInterfaceModel::initModel() {
- interface_container.constructData();
- instanciateInterfaces();
+void EmbeddedInterfaceModel::initFull(const ModelOptions & options) {
+ const SolidMechanicsModelOptions & smm_options =
+ dynamic_cast<const SolidMechanicsModelOptions &>(options);
+
+ // We don't want to initiate materials before shape functions are initialized
+ SolidMechanicsModelOptions dummy_options(smm_options.analysis_method, true);
+
+ interface_mesh = &(intersector.getInterfaceMesh());
+ registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine", *interface_mesh, 1);
+
+ SolidMechanicsModel::initFull(dummy_options);
+
+ intersector.constructData();
+
+ FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
+ engine.initShapeFunctions(_not_ghost);
+ engine.initShapeFunctions(_ghost);
+
+ this->initMaterials();
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("reinforcement", id);
this->mesh.addDumpMeshToDumper("reinforcement", *interface_mesh,
- spatial_dimension, _not_ghost, _ek_regular);
+ 1, _not_ghost, _ek_regular);
#endif
-
- SolidMechanicsModel::initModel();
}
void EmbeddedInterfaceModel::initMaterials() {
- delete interface_material_selector;
- interface_material_selector = new EmbeddedInterfaceMaterialSelector<std::string>("material", *this);
- this->setMaterialSelector(*interface_material_selector);
-
Element element;
- //Material ** mat_val = &(materials.at(0));
+
+ delete interface_material_selector;
+ interface_material_selector = new InterfaceMeshDataMaterialSelector<std::string>("physical_names", *this);
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
element.ghost_type = *gt;
Mesh::type_iterator it = interface_mesh->firstType(1, *gt);
Mesh::type_iterator end = interface_mesh->lastType(1, *gt);
for (; it != end ; ++it) {
UInt nb_element = interface_mesh->getNbElement(*it, *gt);
element.type = *it;
Array<UInt> & mat_indexes = material_index.alloc(nb_element, 1, *it, *gt);
for (UInt el = 0 ; el < nb_element ; el++) {
element.element = el;
UInt mat_index = (*interface_material_selector)(element);
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The material selector returned an index that does not exist");
mat_indexes(element.element) = mat_index;
materials.at(mat_index)->addElement(*it, el, *gt);
}
}
}
SolidMechanicsModel::initMaterials();
}
-void EmbeddedInterfaceModel::instanciateInterfaces() {
- const std::pair<Parser::const_section_iterator, Parser::const_section_iterator> &
- sub_sect = this->parser->getSubSections(_st_embedded_interface);
+ElementTypeMap<UInt> EmbeddedInterfaceModel::getInternalDataPerElem(const std::string & field_name,
+ const ElementKind & kind) {
+ if (!(this->isInternal(field_name,kind))) AKANTU_EXCEPTION("unknown internal " << field_name);
- Parser::const_section_iterator section_it = sub_sect.first;
+ for (UInt m = 0; m < materials.size() ; ++m) {
+ if (materials[m]->isInternal(field_name, kind)) {
+ Material * mat = NULL;
- std::list<std::pair<K::Segment_3, std::string> > interface_list;
+ switch(this->spatial_dimension) {
+ case 1:
+ mat = dynamic_cast<MaterialReinforcement<1> *>(materials[m]);
+ break;
- for (; section_it != sub_sect.second ; ++section_it) {
- EmbeddedInterface interface(this->spatial_dimension);
- interface.parseSection(*section_it);
+ case 2:
+ mat = dynamic_cast<MaterialReinforcement<2> *>(materials[m]);
+ break;
- interface_list.push_back(std::make_pair(interface.getPrimitive(), interface.getMaterialName()));
+ case 3:
+ mat = dynamic_cast<MaterialReinforcement<3> *>(materials[m]);
+ break;
+ }
+
+ if (mat == NULL && field_name != "stress_embedded")
+ return materials[m]->getInternalDataPerElem(field_name,kind);
+ else if (mat != NULL && field_name == "stress_embedded")
+ return mat->getInternalDataPerElem(field_name, kind, "EmbeddedInterfaceFEEngine");
+ }
}
- initInterface(interface_list);
+ return ElementTypeMap<UInt>();
}
-void EmbeddedInterfaceModel::initInterface(const std::list<std::pair<K::Segment_3, std::string> > & interface_list) {
- AKANTU_DEBUG_IN();
-
- interface_mesh = &(interface_container.meshOfLinearInterfaces(interface_list));
-
- registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine", *interface_mesh, 1);
- FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
- engine.initShapeFunctions(_not_ghost);
- engine.initShapeFunctions(_ghost);
+void EmbeddedInterfaceModel::addDumpGroupFieldToDumper(const std::string & dumper_name,
+ const std::string & field_id,
+ const std::string & group_name,
+ const ElementKind & element_kind,
+ bool padding_flag) {
+#ifdef AKANTU_USE_IOHELPER
+ dumper::Field * field = NULL;
- AKANTU_DEBUG_OUT();
-}
+ if (field_id == "stress_embedded")
+ field = this->createElementalField(field_id, group_name, padding_flag, 1, element_kind);
+ else
+ SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id, group_name, element_kind, padding_flag);
-void EmbeddedInterfaceModel::assembleStiffnessMatrix() {
- SolidMechanicsModel::assembleStiffnessMatrix();
-}
-
-dumper::Field * EmbeddedInterfaceModel::createElementalField(const std::string & field_name,
- const std::string & group_name,
- bool padding_flag,
- const ElementKind & kind,
- const std::string & fe_engine_id) {
-
- if (field_name == "stress_embedded") {
- return SolidMechanicsModel::createElementalField(field_name,
- group_name,
- padding_flag,
- kind,
- "EmbeddedInterfaceFEEngine");
- } else {
- return SolidMechanicsModel::createElementalField(field_name,
- group_name,
- padding_flag,
- kind,
- fe_engine_id);
+ if (field) {
+ DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name,group_name);
+ Model::addDumpGroupFieldToDumper(field_id,field,dumper);
}
+
+#endif
}
__END_AKANTU__
diff --git a/src/model/solid_mechanics/embedded_interface_model.hh b/src/model/solid_mechanics/embedded_interface_model.hh
index d1e233c5c..11eab4f80 100644
--- a/src/model/solid_mechanics/embedded_interface_model.hh
+++ b/src/model/solid_mechanics/embedded_interface_model.hh
@@ -1,162 +1,150 @@
/**
* @file embedded_interface_model.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Mon Mar 9 2015
* @date last modification: Mon Mar 9 2015
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_EMBEDDED_INTERFACE_MODEL_HH__
#define __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
#include "aka_common.hh"
#include "solid_mechanics_model.hh"
#include "mesh.hh"
-#include "parsable.hh"
-#include "embedded_interface.hh"
-#include "mesh_geom_container.hh"
+#include "embedded_interface_intersector.hh"
#include <CGAL/Cartesian.h>
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
typedef CGAL::Cartesian<Real> K;
+/**
+ * @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 {
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular> MyFEEngineType;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
- /// Constructor
+ /**
+ * @brief Constructor
+ *
+ * @param mesh main mesh (concrete)
+ * @param primitive_mesh mesh of the embedded reinforcement
+ */
EmbeddedInterfaceModel(Mesh & mesh,
+ Mesh & primitive_mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "embedded_interface_model",
const MemoryID & memory_id = 0);
/// Destructor
virtual ~EmbeddedInterfaceModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialise the model
- virtual void initModel();
+ virtual void initFull(const ModelOptions & options = default_solid_mechanics_model_options);
/// Initialise the materials
virtual void initMaterials();
- /// Instanciate the interfaces
- virtual void instanciateInterfaces();
-
- /// Initialise the interface mesh
- void initInterface(const std::list<std::pair<K::Segment_3, std::string> > & interface_list);
-
- /// Assemble the stiffness matrix of the model
- virtual void assembleStiffnessMatrix();
-
- /// Dump
- virtual dumper::Field * createElementalField(const std::string & field_name,
- const std::string & group_name,
- bool padding_flag,
- const ElementKind & kind,
- const std::string & fe_engine_id = "");
-
-
+#ifndef SWIG
+ /// give the amount of data per element
+ ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
+ const ElementKind & kind);
+#endif
+
+ virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
+ const std::string & field_id,
+ const std::string & group_name,
+ const ElementKind & element_kind,
+ bool padding_flag);
/* ------------------------------------------------------------------------ */
/* 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:
/// 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;
- /// Geom object to build the interface mesh
- MeshGeomContainer interface_container;
+ /// Intersector object to build the interface mesh
+ EmbeddedInterfaceIntersector intersector;
};
-/// Material selector for EmbeddedInterfaceModel
-template <typename T> class EmbeddedInterfaceMaterialSelector : public DefaultMaterialSelector {};
-
-/// Material selector based on associated material name
-template<>
-class EmbeddedInterfaceMaterialSelector<std::string> : public DefaultMaterialSelector {
-
+template<typename T>
+class InterfaceMeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
- EmbeddedInterfaceMaterialSelector(const std::string & name, const EmbeddedInterfaceModel & model):
- DefaultMaterialSelector(model.getMaterialByElement()),
- names(model.getInterfaceMesh().getData<std::string>(name)),
- model(model)
+ InterfaceMeshDataMaterialSelector(const std::string & name, const EmbeddedInterfaceModel & model, UInt first_index = 1) :
+ ElementDataMaterialSelector<T>(model.getInterfaceMesh().getData<T>(name), model, first_index)
{}
-
- UInt operator() (const Element & element) {
- try {
- DebugLevel dbl = debug::getDebugLevel();
- debug::setDebugLevel(dblError);
-
- std::string material_name = names(element.type, element.ghost_type)(element.element);
-
- debug::setDebugLevel(dbl);
-
- return model.getMaterialIndex(material_name);
- } catch (debug::Exception& e) {
- /// TODO this returns the last material, which should be a bulk material. Try to find cleaner way
- return model.getNbMaterials() - 1;
- }
- }
-
-protected:
- const ElementTypeMapArray<std::string> & names;
- const EmbeddedInterfaceModel & model;
};
__END_AKANTU__
#endif // __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
diff --git a/src/model/solid_mechanics/material.cc b/src/model/solid_mechanics/material.cc
index 3b8ae9092..2a3041210 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1663 +1,1667 @@
/**
* @file material.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Sep 16 2014
*
* @brief Implementation of the common part of the material class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, const ID & id) :
Memory(id, model.getMemoryID()),
Parsable(_st_material, id),
is_init(false),
finite_deformation(false),
name(""),
model(&model),
spatial_dimension(this->model->getSpatialDimension()),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this),
eigenstrain("eigenstrain", *this),
gradu("grad_u", *this),
green_strain("green_strain",*this),
piola_kirchhoff_2("piola_kirchhoff_2", *this),
// potential_energy_vector(false),
potential_energy("potential_energy", *this),
is_non_local(false),
use_previous_stress(false),
use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse coordinates", *this),
interpolation_points_matrices("interpolation points matrices", *this) {
AKANTU_DEBUG_IN();
/// for each connectivity types allocate the element filer array of the material
model.getMesh().initElementTypeMapArray(element_filter,
1,
spatial_dimension,
false,
_ek_regular);
registerParam("rho" , rho , 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
eigenstrain.initialize(spatial_dimension * spatial_dimension);
gradu.initialize(spatial_dimension * spatial_dimension);
stress.initialize(spatial_dimension * spatial_dimension);
model.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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();
for (std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.begin();
it != internal_vectors_real.end();
++it) it->second->resize();
for (std::map<ID, InternalField<UInt> *>::iterator it = internal_vectors_uint.begin();
it != internal_vectors_uint.end();
++it) it->second->resize();
is_init = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::savePreviousState() {
AKANTU_DEBUG_IN();
for (std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.begin();
it != internal_vectors_real.end();
++it) {
if(it->second->hasHistory()) it->second->saveCurrentValues();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the residual by assembling @f$\int_{e} \sigma_e \frac{\partial
* \varphi}{\partial X} dX @f$
*
* @param[in] displacements nodes displacements
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::updateResidual(GhostType ghost_type) {
AKANTU_DEBUG_IN();
computeAllStresses(ghost_type);
assembleResidual(ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::assembleResidual(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model->getSpatialDimension();
if(!finite_deformation){
Array<Real> & residual = const_cast<Array<Real> &>(model->getResidual());
Mesh & mesh = model->getFEEngine().getMesh();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
const Array<Real> & shapes_derivatives = model->getFEEngine().getShapesDerivatives(*it, ghost_type);
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
Array<Real> * sigma_dphi_dx =
new Array<Real>(nb_element*nb_quadrature_points,
size_of_shapes_derivatives, "sigma_x_dphi_/_dX");
Array<Real> * shapesd_filtered =
new Array<Real>(0, size_of_shapes_derivatives, "filtered shapesd");
FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
*it, ghost_type, elem_filter);
Array<Real> & stress_vect = stress(*it, ghost_type);
Array<Real>::matrix_iterator sigma =
stress_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator B =
shapesd_filtered->begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_sigma_it =
sigma_dphi_dx->begin(spatial_dimension, nb_nodes_per_element);
for (UInt q = 0; q < nb_element*nb_quadrature_points; ++q, ++sigma, ++B, ++Bt_sigma_it)
Bt_sigma_it->mul<false,false>(*sigma, *B);
delete shapesd_filtered;
/**
* 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$
*/
Array<Real> * int_sigma_dphi_dx = new Array<Real>(nb_element,
nb_nodes_per_element * spatial_dimension,
"int_sigma_x_dphi_/_dX");
model->getFEEngine().integrate(*sigma_dphi_dx, *int_sigma_dphi_dx,
size_of_shapes_derivatives,
*it, ghost_type,
elem_filter);
delete sigma_dphi_dx;
/// assemble
model->getFEEngine().assembleArray(*int_sigma_dphi_dx, residual,
model->getDOFSynchronizer().getLocalDOFEquationNumbers(),
residual.getNbComponent(),
*it, ghost_type, elem_filter, -1);
delete int_sigma_dphi_dx;
}
}
else{
switch (spatial_dimension){
case 1:
this->assembleResidual<1>(ghost_type);
break;
case 2:
this->assembleResidual<2>(ghost_type);
break;
case 3:
this->assembleResidual<3>(ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] current_position nodes postition + displacements
* @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();
Mesh::type_iterator it = model->getFEEngine().getMesh().firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = model->getFEEngine().getMesh().lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
Array<Real> & gradu_vect = gradu(*it, ghost_type);
/// compute @f$\nabla u@f$
model->getFEEngine().gradientOnQuadraturePoints(model->getDisplacement(), gradu_vect,
spatial_dimension,
*it, ghost_type, elem_filter);
gradu_vect -= eigenstrain(*it, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(*it, 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.");
//resizeInternalArray(stress);
Mesh::type_iterator it = model->getFEEngine().getMesh().firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = model->getFEEngine().getMesh().lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it)
switch (spatial_dimension){
case 1:
this->computeCauchyStress<1>(*it, ghost_type);
break;
case 2:
this->computeCauchyStress<2>(*it, ghost_type);
break;
case 3:
this->computeCauchyStress<3>(*it, ghost_type);
break;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::computeCauchyStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::matrix_iterator gradu_it =
this->gradu(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator gradu_end =
this->gradu(el_type, ghost_type).end(dim, dim);
Array<Real>::matrix_iterator piola_it =
this->piola_kirchhoff_2(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator stress_it =
this->stress(el_type, ghost_type).begin(dim, dim);
Matrix<Real> F_tensor(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;
gradUToF<dim > (grad_u, F_tensor);
this->computeCauchyStressOnQuad<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();
Mesh::type_iterator it = model->getFEEngine().getMesh().firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = model->getFEEngine().getMesh().lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
Array<Real> & gradu_vect = gradu(*it, ghost_type);
/// compute @f$\nabla u@f$
model->getFEEngine().gradientOnQuadraturePoints(displacement, gradu_vect,
spatial_dimension,
*it, ghost_type, elem_filter);
setToSteadyState(*it, 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] current_position nodes postition + displacements
* @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();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
if(finite_deformation){
switch (spatial_dimension) {
case 1:
{
assembleStiffnessMatrixNL < 1 > (*it, ghost_type);
assembleStiffnessMatrixL2 < 1 > (*it, ghost_type);
break;
}
case 2:
{
assembleStiffnessMatrixNL < 2 > (*it, ghost_type);
assembleStiffnessMatrixL2 < 2 > (*it, ghost_type);
break;
}
case 3:
{
assembleStiffnessMatrixNL < 3 > (*it, ghost_type);
assembleStiffnessMatrixL2 < 3 > (*it, ghost_type);
break;
}
}
} else {
switch(spatial_dimension) {
case 1: { assembleStiffnessMatrix<1>(*it, ghost_type); break; }
case 2: { assembleStiffnessMatrix<2>(*it, ghost_type); break; }
case 3: { assembleStiffnessMatrix<3>(*it, ghost_type); break; }
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::assembleStiffnessMatrix(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
SparseMatrix & K = const_cast<SparseMatrix &>(model->getStiffnessMatrix());
const Array<Real> & shapes_derivatives = model->getFEEngine().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.getSize();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(type,
ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
model->getFEEngine().gradientOnQuadraturePoints(model->getDisplacement(),
gradu_vect, dim, type, ghost_type,
elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_stiffness_matrix =
new Array<Real>(nb_element*nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
tangent_stiffness_matrix->clear();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
Array<Real> * shapesd_filtered =
new Array<Real>(0, dim * nb_nodes_per_element, "filtered shapesd");
FEEngine::filterElementalData(model->getFEEngine().getMesh(), shapes_derivatives,
*shapesd_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;
Array<Real> * 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> Bt_D(dim * nb_nodes_per_element, tangent_size);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_D_B_it
= bt_d_b->begin(dim*nb_nodes_per_element, dim*nb_nodes_per_element);
Array<Real>::matrix_iterator D_it
= tangent_stiffness_matrix->begin(tangent_size, tangent_size);
Array<Real>::matrix_iterator 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) {
Matrix<Real> & D = *D_it;
Matrix<Real> & Bt_D_B = *Bt_D_B_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
Bt_D.mul<true, false>(B, D);
Bt_D_B.mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e = new Array<Real>(nb_element,
bt_d_b_size * bt_d_b_size,
"K_e");
model->getFEEngine().integrate(*bt_d_b, *K_e,
bt_d_b_size * bt_d_b_size,
type, ghost_type,
elem_filter);
delete bt_d_b;
model->getFEEngine().assembleMatrix(*K_e, K, spatial_dimension, type, ghost_type,
elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::assembleStiffnessMatrixNL(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
SparseMatrix & K = const_cast<SparseMatrix &> (model->getStiffnessMatrix());
const Array<Real> & shapes_derivatives = model->getFEEngine().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.getSize();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
//gradu_vect.resize(nb_quadrature_points * nb_element);
// model->getFEEngine().gradientOnQuadraturePoints(model->getIncrement(), gradu_vect,
// dim, type, ghost_type, &elem_filter);
Array<Real> * shapes_derivatives_filtered = new Array<Real > (nb_element * nb_quadrature_points,
dim * nb_nodes_per_element,
"shapes derivatives filtered");
Array<Real>::const_matrix_iterator shapes_derivatives_it = shapes_derivatives.begin(spatial_dimension,
nb_nodes_per_element);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(spatial_dimension,
nb_nodes_per_element);
UInt * elem_filter_val = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
for (UInt q = 0; q < nb_quadrature_points; ++q, ++shapes_derivatives_filtered_it)
*shapes_derivatives_filtered_it = shapes_derivatives_it[*elem_filter_val * nb_quadrature_points + q];
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_s_b_size = dim * nb_nodes_per_element;
Array<Real> * 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);
shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_S_B_it = bt_s_b->begin(bt_s_b_size,
bt_s_b_size);
Array<Real>::matrix_iterator Bt_S_B_end = bt_s_b->end(bt_s_b_size,
bt_s_b_size);
Array<Real>::matrix_iterator 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) {
Matrix<Real> & Bt_S_B = *Bt_S_B_it;
Matrix<Real> & 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.mul < true, false > (B, S);
Bt_S_B.mul < false, false > (Bt_S, B);
}
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e = new Array<Real > (nb_element,
bt_s_b_size * bt_s_b_size,
"K_e");
model->getFEEngine().integrate(*bt_s_b, *K_e,
bt_s_b_size * bt_s_b_size,
type, ghost_type,
elem_filter);
delete bt_s_b;
model->getFEEngine().assembleMatrix(*K_e, K, spatial_dimension, type, ghost_type, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::assembleStiffnessMatrixL2(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
SparseMatrix & K = const_cast<SparseMatrix &> (model->getStiffnessMatrix());
const Array<Real> & shapes_derivatives = model->getFEEngine().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.getSize();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
model->getFEEngine().gradientOnQuadraturePoints(model->getDisplacement(), gradu_vect,
dim, type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_stiffness_matrix =
new Array<Real > (nb_element*nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
tangent_stiffness_matrix->clear();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
Array<Real> * shapes_derivatives_filtered = new Array<Real > (nb_element * nb_quadrature_points,
dim * nb_nodes_per_element,
"shapes derivatives filtered");
Array<Real>::const_matrix_iterator shapes_derivatives_it = shapes_derivatives.begin(spatial_dimension,
nb_nodes_per_element);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(spatial_dimension,
nb_nodes_per_element);
UInt * elem_filter_val = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
for (UInt q = 0; q < nb_quadrature_points; ++q, ++shapes_derivatives_filtered_it)
*shapes_derivatives_filtered_it = shapes_derivatives_it[*elem_filter_val * nb_quadrature_points + q];
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
Array<Real> * 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);
shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_D_B_it = bt_d_b->begin(dim*nb_nodes_per_element,
dim * nb_nodes_per_element);
Array<Real>::matrix_iterator grad_u_it = gradu_vect.begin(dim, dim);
Array<Real>::matrix_iterator D_it = tangent_stiffness_matrix->begin(tangent_size,
tangent_size);
Array<Real>::matrix_iterator 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) {
Matrix<Real> & grad_u = *grad_u_it;
Matrix<Real> & D = *D_it;
Matrix<Real> & 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.mul < true, false > (B, D);
Bt_D_B.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$
Array<Real> * K_e = new Array<Real > (nb_element,
bt_d_b_size * bt_d_b_size,
"K_e");
model->getFEEngine().integrate(*bt_d_b, *K_e,
bt_d_b_size * bt_d_b_size,
type, ghost_type,
elem_filter);
delete bt_d_b;
model->getFEEngine().assembleMatrix(*K_e, K, spatial_dimension, type, ghost_type, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::assembleResidual(GhostType ghost_type){
AKANTU_DEBUG_IN();
Array<Real> & residual = const_cast<Array<Real> &> (model->getResidual());
Mesh & mesh = model->getFEEngine().getMesh();
Mesh::type_iterator it = element_filter.firstType(dim, ghost_type);
Mesh::type_iterator last_type = element_filter.lastType(dim, ghost_type);
for (; it != last_type; ++it) {
const Array<Real> & shapes_derivatives = model->getFEEngine().getShapesDerivatives(*it, ghost_type);
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.getSize();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(*it, ghost_type);
Array<Real> * shapesd_filtered =
new Array<Real>(0, size_of_shapes_derivatives, "filtered shapesd");
FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
*it, 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;
Array<Real> * bt_s = new Array<Real > (nb_element * nb_quadrature_points,
bt_s_size,
"B^t*S");
Array<Real>::matrix_iterator grad_u_it = this->gradu(*it, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator grad_u_end = this->gradu(*it, ghost_type).end(dim, dim);
Array<Real>::matrix_iterator stress_it = this->piola_kirchhoff_2(*it, 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> S_vect(stress_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) {
Matrix<Real> & grad_u = *grad_u_it;
Matrix<Real> & r_it = *bt_s_it;
Matrix<Real> & S_it = *stress_it;
SetCauchyStressArray <dim> (S_it, S_vect);
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;
r_it.mul < true, false > (B_tensor, S_vect);
}
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * r_e = new Array<Real > (nb_element,
bt_s_size, "r_e");
model->getFEEngine().integrate(*bt_s, *r_e,
bt_s_size,
*it, ghost_type,
elem_filter);
delete bt_s;
model->getFEEngine().assembleArray(*r_e, residual,
model->getDOFSynchronizer().getLocalDOFEquationNumbers(),
residual.getNbComponent(),
*it, ghost_type, elem_filter, -1);
delete r_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllStressesFromTangentModuli(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model->getSpatialDimension();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
switch(spatial_dimension) {
case 1: { computeAllStressesFromTangentModuli<1>(*it, ghost_type); break; }
case 2: { computeAllStressesFromTangentModuli<2>(*it, ghost_type); break; }
case 3: { computeAllStressesFromTangentModuli<3>(*it, ghost_type); break; }
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void Material::computeAllStressesFromTangentModuli(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives = model->getFEEngine().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.getSize();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
Array<Real> & disp = model->getDisplacement();
model->getFEEngine().gradientOnQuadraturePoints(disp, gradu_vect,
dim, type, ghost_type, elem_filter);
UInt tangent_moduli_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_moduli_tensors =
new Array<Real>(nb_element*nb_quadrature_points, tangent_moduli_size * tangent_moduli_size,
"tangent_moduli_tensors");
tangent_moduli_tensors->clear();
computeTangentModuli(type, *tangent_moduli_tensors, ghost_type);
Array<Real> * shapesd_filtered =
new Array<Real>(0, dim* nb_nodes_per_element, "filtered shapesd");
FEEngine::filterElementalData(model->getFEEngine().getMesh(), shapes_derivatives, *shapesd_filtered,
type, ghost_type, elem_filter);
Array<Real> filtered_u(nb_element, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(model->getFEEngine().getMesh(), disp, filtered_u,
type, ghost_type, elem_filter);
/// compute @f$\mathbf{D} \mathbf{B} \mathbf{u}@f$
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator D_it = tangent_moduli_tensors->begin(tangent_moduli_size,
tangent_moduli_size);
Array<Real>::matrix_iterator sigma_it = stress(type, ghost_type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::vector_iterator u_it = filtered_u.begin(spatial_dimension * nb_nodes_per_element);
Matrix<Real> B(tangent_moduli_size, spatial_dimension * nb_nodes_per_element);
Vector<Real> Bu(tangent_moduli_size);
Vector<Real> DBu(tangent_moduli_size);
for (UInt e = 0; e < nb_element; ++e, ++u_it) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it, ++shapes_derivatives_filtered_it, ++sigma_it) {
Vector<Real> & u = *u_it;
Matrix<Real> & sigma = *sigma_it;
Matrix<Real> & D = *D_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
Bu.mul<false>(B, u);
DBu.mul<false>(D, Bu);
// Voigt notation to full symmetric tensor
for (UInt i = 0; i < dim; ++i) sigma(i, i) = DBu(i);
if(dim == 2) {
sigma(0,1) = sigma(1,0) = DBu(2);
} else if(dim == 3) {
sigma(1,2) = sigma(2,1) = DBu(3);
sigma(0,2) = sigma(2,0) = DBu(4);
sigma(0,1) = sigma(1,0) = DBu(5);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergyByElements() {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension);
Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension);
for(; it != last_type; ++it) {
computePotentialEnergy(*it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergy(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
if(!potential_energy.exists(el_type, ghost_type)) {
UInt nb_element = element_filter(el_type, ghost_type).getSize();
UInt nb_quadrature_points = model->getFEEngine().getNbQuadraturePoints(el_type, _not_ghost);
potential_energy.alloc(nb_element * nb_quadrature_points, 1,
el_type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real epot = 0.;
computePotentialEnergyByElements();
/// integrate the potential energy for each type of elements
Mesh::type_iterator it = element_filter.firstType(spatial_dimension);
Mesh::type_iterator last_type = element_filter.lastType(spatial_dimension);
for(; it != last_type; ++it) {
epot += model->getFEEngine().integrate(potential_energy(*it, _not_ghost), *it,
_not_ghost, element_filter(*it, _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(model->getFEEngine().getNbQuadraturePoints(type));
computePotentialEnergyByElement(type, index, epot_on_quad_points);
epot = model->getFEEngine().integrate(epot_on_quad_points, type, element_filter(type)(index));
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(std::string type) {
AKANTU_DEBUG_IN();
if(type == "potential") return getPotentialEnergy();
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(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::computeQuadraturePointsCoordinates(ElementTypeMapArray<Real> & quadrature_points_coordinates,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
const Mesh & mesh = this->model->getMesh();
Array<Real> nodes_coordinates(mesh.getNodes(), true);
nodes_coordinates += this->model->getDisplacement();
Mesh::type_iterator it = this->element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = this->element_filter.lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
const Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nb_tot_quad = this->model->getFEEngine().getNbQuadraturePoints(*it, ghost_type) * nb_element;
Array<Real> & quads = quadrature_points_coordinates(*it, ghost_type);
quads.resize(nb_tot_quad);
this->model->getFEEngine().interpolateOnQuadraturePoints(nodes_coordinates,
quads, spatial_dimension,
*it, ghost_type, elem_filter);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::initElementalFieldInterpolation(const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
AKANTU_DEBUG_IN();
const Mesh & mesh = model->getFEEngine().getMesh();
ElementTypeMapArray<Real> quadrature_points_coordinates("quadrature_points_coordinates_for_interpolation", getID());
mesh.initElementTypeMapArray(quadrature_points_coordinates, spatial_dimension, spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
computeQuadraturePointsCoordinates(quadrature_points_coordinates, ghost_type);
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = element_filter.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) continue;
const Array<Real> & interp_points_coord = interpolation_points_coordinates(type, ghost_type);
UInt nb_interpolation_points_per_elem = interp_points_coord.getSize() / nb_element;
AKANTU_DEBUG_ASSERT(interp_points_coord.getSize() % nb_element == 0,
"Number of interpolation points is wrong");
#define AKANTU_INIT_INTERPOLATE_ELEMENTAL_FIELD(type) \
initElementalFieldInterpolation<type>(quadrature_points_coordinates(type, ghost_type), \
interp_points_coord, \
nb_interpolation_points_per_elem, \
ghost_type) \
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(AKANTU_INIT_INTERPOLATE_ELEMENTAL_FIELD);
#undef AKANTU_INIT_INTERPOLATE_ELEMENTAL_FIELD
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void Material::initElementalFieldInterpolation(const Array<Real> & quad_coordinates,
const Array<Real> & interpolation_points_coordinates,
const UInt nb_interpolation_points_per_elem,
const GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_fil = element_filter(type, ghost_type);
UInt nb_element = elem_fil.getSize();
UInt nb_quad_per_element = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
if(!interpolation_inverse_coordinates.exists(type, ghost_type))
interpolation_inverse_coordinates.alloc(nb_element,
nb_quad_per_element*nb_quad_per_element,
type, ghost_type);
+ else
+ interpolation_inverse_coordinates(type, ghost_type).resize(nb_element);
if(!interpolation_points_matrices.exists(type, ghost_type))
interpolation_points_matrices.alloc(nb_element,
nb_interpolation_points_per_elem * nb_quad_per_element,
type, ghost_type);
+ else
+ interpolation_points_matrices(type, ghost_type).resize(nb_element);
Array<Real> & interp_inv_coord = interpolation_inverse_coordinates(type, ghost_type);
Array<Real> & interp_points_mat = interpolation_points_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 =
quad_coordinates.begin_reinterpret(spatial_dimension,
nb_quad_per_element,
nb_element);
Array<Real>::const_matrix_iterator points_coords_begin =
interpolation_points_coordinates.begin_reinterpret(spatial_dimension,
nb_interpolation_points_per_elem,
interpolation_points_coordinates.getSize() / nb_interpolation_points_per_elem);
Array<Real>::matrix_iterator inv_quad_coord_it =
interp_inv_coord.begin(nb_quad_per_element, nb_quad_per_element);
Array<Real>::matrix_iterator inv_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; ++el, ++inv_quad_coord_it,
++inv_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
buildElementalFieldInterpolationCoodinates<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[elem_fil(el)];
/// matrix to store the interpolation points coordinates
/// compatible with these functions
Matrix<Real> & inv_points_coord_matrix = *inv_points_mat_it;
/// insert the quad coordinates in a matrix compatible with the interpolation
buildElementalFieldInterpolationCoodinates<type>(points_coords,
inv_points_coord_matrix);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
interpolateElementalField(stress, result, ghost_type);
}
/* -------------------------------------------------------------------------- */
void Material::interpolateElementalField(const ElementTypeMapArray<Real> & field,
ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = element_filter.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
Array<UInt> & elem_fil = element_filter(type, ghost_type);
UInt nb_element = elem_fil.getSize();
UInt nb_quad_per_element = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
const Array<Real> & field_vec = field(type, ghost_type);
Array<Real> & result_vec = result(type, ghost_type);
Matrix<Real> coefficients(nb_quad_per_element, field_vec.getNbComponent());
const Array<Real> & interp_inv_coord = interpolation_inverse_coordinates(type, ghost_type);
const Array<Real> & interp_points_coord = interpolation_points_matrices(type, ghost_type);
UInt nb_interpolation_points_per_elem
= interp_points_coord.getNbComponent() / nb_quad_per_element;
Array<Real>::const_matrix_iterator field_it
= field_vec.begin_reinterpret(field_vec.getNbComponent(),
nb_quad_per_element,
nb_element);
Array<Real>::const_matrix_iterator interpolation_points_coordinates_it =
interp_points_coord.begin(nb_interpolation_points_per_elem, nb_quad_per_element);
Array<Real>::matrix_iterator result_begin
= result_vec.begin_reinterpret(field_vec.getNbComponent(),
nb_interpolation_points_per_elem,
result_vec.getSize() / nb_interpolation_points_per_elem);
Array<Real>::const_matrix_iterator inv_quad_coord_it =
interp_inv_coord.begin(nb_quad_per_element, nb_quad_per_element);
/// loop over the elements of the current material 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 Matrix<Real> & 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 Matrix<Real> & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the result
Matrix<Real> res(result_begin[elem_fil(el)]);
res.mul<true, true>(coefficients, coord);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStressOnFacets(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
interpolateElementalFieldOnFacets(stress, result, ghost_type);
}
/* -------------------------------------------------------------------------- */
void Material::interpolateElementalFieldOnFacets(const ElementTypeMapArray<Real> & field,
ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt sp2 = spatial_dimension * spatial_dimension;
const Mesh & mesh = this->model->getMesh();
const Mesh & mesh_facets = mesh.getMeshFacets();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = element_filter.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
Array<UInt> & elem_fil = element_filter(type, ghost_type);
UInt nb_element = elem_fil.getSize();
UInt nb_quad_per_element = model->getFEEngine().getNbQuadraturePoints(type, ghost_type);
const Array<Real> & field_vec = field(type, ghost_type);
Matrix<Real> coefficients(nb_quad_per_element, field_vec.getNbComponent());
const Array<Real> & interp_inv_coord = interpolation_inverse_coordinates(type, ghost_type);
const Array<Real> & interp_points_coord = interpolation_points_matrices(type, ghost_type);
UInt nb_interpolation_points_per_elem
= interp_points_coord.getNbComponent() / nb_quad_per_element;
Array<Real>::const_matrix_iterator field_it
= field_vec.begin_reinterpret(field_vec.getNbComponent(),
nb_quad_per_element,
nb_element);
Array<Real>::const_matrix_iterator interpolation_points_coordinates_it =
interp_points_coord.begin(nb_interpolation_points_per_elem, nb_quad_per_element);
Array<Real>::const_matrix_iterator inv_quad_coord_it =
interp_inv_coord.begin(nb_quad_per_element, nb_quad_per_element);
Matrix<Real> result_tmp(sp2, nb_interpolation_points_per_elem);
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 = NULL;
GhostType current_ghost_type = _casper;
Array<Real> * result_vec = NULL;
/// loop over the elements of the current material 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 Matrix<Real> & 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 Matrix<Real> & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the result
result_tmp.mul<true, true>(coefficients, coord);
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()
+ is_second_element * sp2,
sp2);
result_local = result_tmp(f * nb_quad_per_facet + q);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & Material::getArray(const ID & vect_id, const ElementType & type, const GhostType & ghost_type) const {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost) ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch(debug::Exception & e) {
AKANTU_EXCEPTION("The material " << name << "(" <<getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
Array<Real> & Material::getArray(const ID & vect_id, const ElementType & type, const GhostType & ghost_type) {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost) ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch(debug::Exception & e) {
AKANTU_EXCEPTION("The material " << name << "(" << getID() << ") does not contain a vector " << vect_id << "(" << fvect_id << ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
const InternalField<Real> & Material::getInternal(const ID & int_id) const {
std::map<ID, InternalField<Real> *>::const_iterator it = internal_vectors_real.find(getID() + ":" + int_id);
if(it == internal_vectors_real.end()) {
AKANTU_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " (" << (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
InternalField<Real> & Material::getInternal(const ID & int_id) {
std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.find(getID() + ":" + int_id);
if(it == internal_vectors_real.end()) {
AKANTU_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " (" << (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
void Material::addElements(const Array<Element> & elements_to_add) {
AKANTU_DEBUG_IN();
UInt mat_id = model->getInternalIndexFromID(getID());
Array<Element>::const_iterator<Element> el_begin = elements_to_add.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_add.end();
for(;el_begin != el_end; ++el_begin) {
const Element & element = *el_begin;
Array<UInt> & mat_indexes = model->getMaterialByElement (element.type, element.ghost_type);
Array<UInt> & mat_loc_num = model->getMaterialLocalNumbering(element.type, element.ghost_type);
UInt index = this->addElement(element.type, element.element, element.ghost_type);
mat_indexes(element.element) = mat_id;
mat_loc_num(element.element) = index;
}
this->resizeInternals();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::removeElements(const Array<Element> & elements_to_remove) {
AKANTU_DEBUG_IN();
Array<Element>::const_iterator<Element> el_begin = elements_to_remove.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_remove.end();
if(el_begin==el_end)
return;
ElementTypeMapArray<UInt> material_local_new_numbering("remove mat filter elem", getID());
Element element;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
element.ghost_type = ghost_type;
ElementTypeMapArray<UInt>::type_iterator it = element_filter.firstType(_all_dimensions, ghost_type, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end = element_filter.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for(; it != end; ++it) {
ElementType type = *it;
element.type = type;
Array<UInt> & elem_filter = this->element_filter(type, ghost_type);
Array<UInt> & mat_loc_num = this->model->getMaterialLocalNumbering(type, ghost_type);
if(!material_local_new_numbering.exists(type, ghost_type))
material_local_new_numbering.alloc(elem_filter.getSize(), 1, type, ghost_type);
Array<UInt> & mat_renumbering = material_local_new_numbering(type, ghost_type);
UInt nb_element = elem_filter.getSize();
element.kind=(*el_begin).kind;
Array<UInt> elem_filter_tmp;
UInt new_id = 0;
for (UInt el = 0; el < nb_element; ++el) {
element.element = elem_filter(el);
if(std::find(el_begin, el_end, element) == el_end) {
elem_filter_tmp.push_back(element.element);
mat_renumbering(el) = new_id;
mat_loc_num(element.element) = new_id;
++new_id;
} else {
mat_renumbering(el) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.getSize());
elem_filter.copy(elem_filter_tmp);
}
}
for (std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.begin();
it != internal_vectors_real.end();
++it) it->second->removeQuadraturePoints(material_local_new_numbering);
for (std::map<ID, InternalField<UInt> *>::iterator it = internal_vectors_uint.begin();
it != internal_vectors_uint.end();
++it) it->second->removeQuadraturePoints(material_local_new_numbering);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::resizeInternals() {
AKANTU_DEBUG_IN();
for (std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.begin();
it != internal_vectors_real.end();
++it) it->second->resize();
for (std::map<ID, InternalField<UInt> *>::iterator it = internal_vectors_uint.begin();
it != internal_vectors_uint.end();
++it) it->second->resize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsAdded(__attribute__((unused)) const Array<Element> & element_list,
__attribute__((unused)) const NewElementsEvent & event) {
this->resizeInternals();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
UInt my_num = model->getInternalIndexFromID(getID());
ElementTypeMapArray<UInt> material_local_new_numbering("remove mat filter elem", getID());
Array<Element>::const_iterator<Element> el_begin = element_list.begin();
Array<Element>::const_iterator<Element> el_end = element_list.end();
for (ghost_type_t::iterator g = ghost_type_t::begin(); g != ghost_type_t::end(); ++g) {
GhostType gt = *g;
ElementTypeMapArray<UInt>::type_iterator it = new_numbering.firstType(_all_dimensions, gt, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end = new_numbering.lastType (_all_dimensions, gt, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
if(element_filter.exists(type, gt)){
Array<UInt> & elem_filter = element_filter(type, gt);
Array<UInt> & mat_indexes = this->model->getMaterialByElement (*it, gt);
Array<UInt> & mat_loc_num = this->model->getMaterialLocalNumbering(*it, gt);
UInt 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.getSize(), 1, type, gt);
Array<UInt> & mat_renumbering = material_local_new_numbering(type, gt);
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<UInt> elem_filter_tmp;
UInt ni = 0;
Element el;
el.type = type;
el.ghost_type = gt;
for (UInt i = 0; i < elem_filter.getSize(); ++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.getSize());
elem_filter.copy(elem_filter);
}
}
}
for (std::map<ID, InternalField<Real> *>::iterator it = internal_vectors_real.begin();
it != internal_vectors_real.end();
++it) it->second->removeQuadraturePoints(material_local_new_numbering);
for (std::map<ID, InternalField<UInt> *>::iterator it = internal_vectors_uint.begin();
it != internal_vectors_uint.end();
++it) it->second->removeQuadraturePoints(material_local_new_numbering);
}
/* -------------------------------------------------------------------------- */
void Material::onBeginningSolveStep(const AnalysisMethod & method) {
this->savePreviousState();
}
/* -------------------------------------------------------------------------- */
void Material::onEndSolveStep(const AnalysisMethod & method) {
ElementTypeMapArray<UInt>::type_iterator it
= this->element_filter.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end
= element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);
for(; it != end; ++it) {
this->updateEnergies(*it, _not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDamageIteration() {
this->savePreviousState();
}
/* -------------------------------------------------------------------------- */
void Material::onDamageUpdate() {
ElementTypeMapArray<UInt>::type_iterator it
= this->element_filter.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end
= element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);
for(; it != end; ++it) {
if(!this->potential_energy.exists(*it, _not_ghost)) {
UInt nb_element = this->element_filter(*it, _not_ghost).getSize();
UInt nb_quadrature_points = this->model->getFEEngine().getNbQuadraturePoints(*it, _not_ghost);
this->potential_energy.alloc(nb_element * nb_quadrature_points, 1,
*it, _not_ghost);
}
this->updateEnergiesAfterDamage(*it, _not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDump(){
if(this->isFiniteDeformation())
this->computeAllCauchyStresses(_not_ghost);
}
/* -------------------------------------------------------------------------- */
void Material::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += 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;
}
/* -------------------------------------------------------------------------- */
void Material::flattenInternal(const std::string & field_id,
ElementTypeMapArray<Real> & internal_flat,
const GhostType ghost_type,
ElementKind element_kind){
typedef ElementTypeMapArray<UInt>::type_iterator iterator;
iterator tit = this->element_filter.firstType(this->spatial_dimension,
ghost_type, element_kind);
iterator end = this->element_filter.lastType(this->spatial_dimension,
ghost_type, element_kind);
for (; tit != end; ++tit) {
ElementType type = *tit;
try {
__attribute__((unused)) const Array<Real> & src_vect
= this->getArray(field_id,type,ghost_type);
} catch(debug::Exception & e) {
continue;
}
const Array<Real> & src_vect = this->getArray(field_id,type,ghost_type);
const Array<UInt> & filter = this->element_filter(type,ghost_type);
// total number of elements for a given type
UInt nb_element = this->model->mesh.getNbElement(type,ghost_type);
// number of filtered elements
UInt nb_element_src = filter.getSize();
// number of quadrature points per elem
UInt nb_quad_per_elem = 0;
// number of data per quadrature point
UInt nb_data_per_quad = src_vect.getNbComponent();
if (!internal_flat.exists(type,ghost_type)) {
internal_flat.alloc(nb_element*nb_quad_per_elem,nb_data_per_quad,type,ghost_type);
}
if (nb_element_src == 0) continue;
nb_quad_per_elem = (src_vect.getSize()/nb_element_src);
// number of data per element
UInt nb_data = nb_quad_per_elem * src_vect.getNbComponent();
Array<Real> & dst_vect = internal_flat(type,ghost_type);
dst_vect.resize(nb_element*nb_quad_per_elem);
Array<UInt>::const_scalar_iterator it = filter.begin();
Array<UInt>::const_scalar_iterator end = filter.end();
Array<Real>::const_vector_iterator it_src =
src_vect.begin_reinterpret(nb_data,nb_element_src);
Array<Real>::vector_iterator it_dst =
dst_vect.begin_reinterpret(nb_data,nb_element);
for (; it != end ; ++it,++it_src) {
it_dst[*it] = *it_src;
}
}
};
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index 10d0d12a8..ef9f67ef4 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,600 +1,600 @@
/**
* @file material.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Sep 16 2014
*
* @brief Mother class for all materials
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_memory.hh"
#include "aka_voigthelper.hh"
#include "parser.hh"
#include "parsable.hh"
#include "data_accessor.hh"
#include "internal_field.hh"
#include "random_internal_field.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_HH__
#define __AKANTU_MATERIAL_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class SolidMechanicsModel;
}
__BEGIN_AKANTU__
/**
* 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(const ElementType & el_type,
* Array<Real> & tangent_matrix,
* GhostType ghost_type = _not_ghost);
* \endcode
*
*/
class Material : public Memory, public DataAccessor, public Parsable,
public MeshEventHandler,
protected SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Material(SolidMechanicsModel & model, const ID & id = "");
virtual ~Material();
/* ------------------------------------------------------------------------ */
/* Function that materials can/should reimplement */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law
virtual void computeStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the tangent stiffness matrix
virtual void computeTangentModuli(__attribute__((unused)) const ElementType & el_type,
__attribute__((unused)) Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the potential energy
virtual void computePotentialEnergy(ElementType el_type, GhostType ghost_type = _not_ghost);
/// compute the potential energy for an element
virtual void computePotentialEnergyByElement(__attribute__((unused)) ElementType type,
__attribute__((unused)) UInt index,
__attribute__((unused)) Vector<Real> & epot_on_quad_points) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
virtual void updateEnergies(__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type = _not_ghost) { }
virtual void updateEnergiesAfterDamage(__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type = _not_ghost) {}
/// set the material to steady state (to be implemented for materials that need it)
virtual void setToSteadyState(__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type = _not_ghost) { }
/// function called to update the internal parameters when the modifiable
/// parameters are modified
virtual void updateInternalParameters() {}
public:
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(const Element & element) const { AKANTU_DEBUG_TO_IMPLEMENT(); }
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(const Element & element) const { AKANTU_DEBUG_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(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
template<typename T>
void unregisterInternal(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_DEBUG_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 assembleResidual(GhostType ghost_type);
/// Operations before and after solveStep in implicit
virtual void beforeSolveStep() {}
virtual void afterSolveStep() {}
/// save the stress in the previous_stress if needed
virtual void savePreviousState();
/// compute the stresses for this material
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
virtual void computeAllNonLocalStresses(__attribute__((unused)) 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(const ElementType & type,
UInt element,
const GhostType & ghost_type);
/// 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
virtual void printself(std::ostream & stream, int indent = 0) const;
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points
*/
void interpolateStress(ElementTypeMapArray<Real> & result,
const 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,
const 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:
/// assemble the residual
template<UInt dim>
void assembleResidual(GhostType ghost_type);
/// Computation of Cauchy stress tensor in the case of finite deformation
template<UInt dim>
void computeCauchyStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type = _not_ghost);
template<UInt dim >
inline void computeCauchyStressOnQuad(const Matrix<Real> & F, const Matrix<Real> & S,
Matrix<Real> & cauchy,
const Real & C33 = 1.0 ) const;
template<UInt dim>
void computeAllStressesFromTangentModuli(const ElementType & type,
GhostType ghost_type);
template<UInt dim>
void assembleStiffnessMatrix(const ElementType & type,
GhostType ghost_type);
/// assembling in finite deformation
template<UInt dim>
void assembleStiffnessMatrixNL(const ElementType & type,
GhostType ghost_type);
template<UInt dim>
void assembleStiffnessMatrixL2(const ElementType & type,
GhostType ghost_type);
/// write the stress tensor in the Voigt notation.
template<UInt dim>
inline void SetCauchyStressArray(const Matrix<Real> & S_t, Matrix<Real> & Stress_vect);
inline UInt getTangentStiffnessVoigtSize(UInt spatial_dimension) const;
/// Size of the Stress matrix for the case of finite deformation see: Bathe et al, IJNME, Vol 9, 353-386, 1975
inline UInt getCauchyStressMatrixSize(UInt spatial_dimension) const;
/// Sets the stress matrix according to Bathe et al, IJNME, Vol 9, 353-386, 1975
template<UInt dim>
inline void setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & Stress_matrix);
/// compute the potential energy by element
void computePotentialEnergyByElements();
/// resize the intenals arrays
void resizeInternals();
public:
/// compute the coordinates of the quadrature points
void computeQuadraturePointsCoordinates(ElementTypeMapArray<Real> & quadrature_points_coordinates,
const GhostType & ghost_type) const;
protected:
/// interpolate an elemental field on given points for each element
void interpolateElementalField(const ElementTypeMapArray<Real> & field,
ElementTypeMapArray<Real> & result,
const GhostType ghost_type);
/// interpolate an elemental field and store the results per facet
void interpolateElementalFieldOnFacets(const ElementTypeMapArray<Real> & field,
ElementTypeMapArray<Real> & result,
const GhostType ghost_type);
/// template function to initialize the elemental field interpolation
template <ElementType type>
void initElementalFieldInterpolation(const Array<Real> & quad_coordinates,
const Array<Real> & interpolation_points_coordinates,
const UInt nb_interpolation_points_per_elem,
const GhostType ghost_type);
/// build the coordinate matrix for the interpolation on elemental field
template <ElementType type>
inline void buildElementalFieldInterpolationCoodinates(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix);
/// build interpolation coordinates for basic linear elements
inline void buildElementalFieldInterpolationCoodinatesLinear(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix);
/// build interpolation coordinates for basic quadratic elements
inline void buildElementalFieldInterpolationCoodinatesQuadratic(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix);
public:
/* ------------------------------------------------------------------------ */
/* Conversion functions */
/* ------------------------------------------------------------------------ */
template<UInt dim>
static inline void gradUToF (const Matrix<Real> & grad_u, Matrix<Real> & F);
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 void gradUToGreenStrain(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
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 QuadraturePoint convertToLocalPoint(const QuadraturePoint & global_point) const;
/// converts local quadrature point to global quadrature point
inline QuadraturePoint convertToGlobalPoint(const QuadraturePoint & local_point) const;
/* ------------------------------------------------------------------------ */
/* 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);
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:
/* ------------------------------------------------------------------------ */
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
virtual void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void onBeginningSolveStep(const AnalysisMethod & method);
virtual void onEndSolveStep(const AnalysisMethod & method);
virtual void onDamageIteration();
virtual void onDamageUpdate();
virtual void onDump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Model, *model, const SolidMechanicsModel &)
AKANTU_GET_MACRO(ID, Memory::getID(), const ID &);
AKANTU_GET_MACRO(Rho, rho, Real);
AKANTU_SET_MACRO(Rho, rho, Real);
/// 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(std::string energy_id);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(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> &);
bool isNonLocal() const { return is_non_local; }
const Array<Real> & getArray(const ID & id, const ElementType & type, const GhostType & ghost_type = _not_ghost) const;
Array<Real> & getArray(const ID & id, const ElementType & type, const GhostType & ghost_type = _not_ghost);
const InternalField<Real> & getInternal(const ID & id) const;
InternalField<Real> & getInternal(const ID & id);
inline bool isInternal(const ID & id, const ElementKind & element_kind) const;
inline ElementTypeMap<UInt> getInternalDataPerElem(const ID & id, const ElementKind & element_kind, const ID & fe_engine_id = "") const;
bool isFiniteDeformation() const { return finite_deformation; }
bool isInelasticDeformation() const { return inelastic_deformation; }
template <typename T>
inline void setParam(const ID & param, T value);
template <typename T>
inline const T & getParam(const ID & param) const;
- void flattenInternal(const std::string & field_id,
- ElementTypeMapArray<Real> & internal_flat,
- const GhostType ghost_type = _not_ghost,
- ElementKind element_kind = _ek_not_defined);
+ virtual void flattenInternal(const std::string & field_id,
+ ElementTypeMapArray<Real> & internal_flat,
+ const GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
protected:
bool isInit() const { return is_init; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// boolean to know if the material has been initialized
bool is_init;
std::map<ID, InternalField<Real> *> internal_vectors_real;
std::map<ID, InternalField<UInt> *> internal_vectors_uint;
protected:
/// Finite deformation
bool finite_deformation;
/// Finite deformation
bool inelastic_deformation;
/// material name
std::string name;
/// The model to witch the material belong
SolidMechanicsModel * model;
/// density : rho
Real rho;
/// 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;
/// eigenstrain arrays ordered by element types
InternalField<Real> eigenstrain;
/// 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;
/// tell if the material need the previous stress state
bool use_previous_stress;
/// tell if the material need the previous strain state
bool use_previous_gradu;
/// elemental field interpolation coordinates
InternalField<Real> interpolation_inverse_coordinates;
/// elemental field interpolation points
InternalField<Real> interpolation_points_matrices;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const Material & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* Auto loop */
/* -------------------------------------------------------------------------- */
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
Array<Real>::matrix_iterator gradu_it = \
this->gradu(el_type, ghost_type).begin(this->spatial_dimension, \
this->spatial_dimension); \
Array<Real>::matrix_iterator gradu_end = \
this->gradu(el_type, ghost_type).end(this->spatial_dimension, \
this->spatial_dimension); \
\
this->stress(el_type, \
ghost_type).resize(this->gradu(el_type, \
ghost_type).getSize()); \
\
Array<Real>::iterator< Matrix<Real> > stress_it = \
this->stress(el_type, ghost_type).begin(this->spatial_dimension, \
this->spatial_dimension); \
\
if(this->isFiniteDeformation()){ \
this->piola_kirchhoff_2(el_type, \
ghost_type).resize(this->gradu(el_type, \
ghost_type).getSize()); \
stress_it = \
this->piola_kirchhoff_2(el_type, \
ghost_type).begin(this->spatial_dimension, \
this->spatial_dimension); \
} \
\
for(;gradu_it != gradu_end; ++gradu_it, ++stress_it) { \
Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
Matrix<Real> & __attribute__((unused)) sigma = *stress_it
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END \
} \
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
Array<Real>::matrix_iterator gradu_it = \
this->gradu(el_type, ghost_type).begin(this->spatial_dimension, \
this->spatial_dimension); \
Array<Real>::matrix_iterator gradu_end = \
this->gradu(el_type, ghost_type).end(this->spatial_dimension, \
this->spatial_dimension); \
Array<Real>::matrix_iterator sigma_it = \
this->stress(el_type, ghost_type).begin(this->spatial_dimension, \
this->spatial_dimension); \
\
tangent_mat.resize(this->gradu(el_type, ghost_type).getSize()); \
\
UInt tangent_size = \
this->getTangentStiffnessVoigtSize(this->spatial_dimension); \
Array<Real>::matrix_iterator tangent_it = \
tangent_mat.begin(tangent_size, \
tangent_size); \
\
for(;gradu_it != gradu_end; ++gradu_it, ++sigma_it, ++tangent_it) { \
Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
Matrix<Real> & __attribute__((unused)) sigma_tensor = *sigma_it; \
Matrix<Real> & tangent = *tangent_it
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END \
} \
/* -------------------------------------------------------------------------- */
#define INSTANSIATE_MATERIAL(mat_name) \
template class mat_name<1>; \
template class mat_name<2>; \
template class mat_name<3>
#endif /* __AKANTU_MATERIAL_HH__ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index 29f672bd4..c2449bedb 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,100 +1,126 @@
/**
* @file material_selector.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Jun 05 2014
*
* @brief class describing how to choose a material for a given element
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "mesh.hh"
#ifndef __AKANTU_MATERIAL_SELECTOR_HH__
#define __AKANTU_MATERIAL_SELECTOR_HH__
__BEGIN_AKANTU__
class SolidMechanicsModel;
/* -------------------------------------------------------------------------- */
class MaterialSelector {
public:
MaterialSelector() : fallback_value(0) {}
virtual ~MaterialSelector() {}
virtual UInt operator()(const Element & element) {
return fallback_value;
}
void setFallback(UInt f) { fallback_value = f; }
protected:
UInt fallback_value;
};
/* -------------------------------------------------------------------------- */
class DefaultMaterialSelector : public MaterialSelector {
public:
DefaultMaterialSelector(const ElementTypeMapArray<UInt> & material_index) :
material_index(material_index) { }
UInt operator()(const Element & element) {
try {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
const Array<UInt> & mat_indexes = material_index(element.type, element.ghost_type);
UInt mat = this->fallback_value;
+
if(element.element < mat_indexes.getSize())
- mat = mat_indexes(element.element);
+ mat = mat_indexes(element.element);
debug::setDebugLevel(dbl);
return mat;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
private:
const ElementTypeMapArray<UInt> & material_index;
};
/* -------------------------------------------------------------------------- */
template<typename T>
-class MeshDataMaterialSelector : public MaterialSelector {
+class ElementDataMaterialSelector : public MaterialSelector {
public:
- MeshDataMaterialSelector(const std::string & name, const SolidMechanicsModel & model) : mesh_data(name), model(model) { }
- UInt operator() (const Element & element) {
- return 0;
+ 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) {
+ return MaterialSelector::operator()(element);
}
+
private:
- std::string mesh_data;
+ const ElementTypeMapArray<T> & element_data;
const SolidMechanicsModel & model;
+ UInt first_index;
+};
+
+/* -------------------------------------------------------------------------- */
+template<typename T>
+class MeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
+public:
+ MeshDataMaterialSelector(const std::string & name, const SolidMechanicsModel & model, UInt first_index = 1);
};
__END_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 ff4394841..35dbdf388 100644
--- a/src/model/solid_mechanics/material_selector_tmpl.hh
+++ b/src/model/solid_mechanics/material_selector_tmpl.hh
@@ -1,89 +1,70 @@
/**
* @file material_selector_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
+ * @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Nov 13 2013
- * @date last modification: Thu Jun 05 2014
+ * @date last modification: Fri May 1 2015
*
* @brief Implementation of the template MaterialSelector
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_SELECTOR_TMPL_HH__
#define __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
-template<>
-class MeshDataMaterialSelector<std::string> : public MaterialSelector {
-public:
- MeshDataMaterialSelector(const std::string & name, const SolidMechanicsModel & model) :
- names(model.getMesh().getData<std::string>(name)), model(model) { }
- UInt operator() (const Element & element) {
- try {
- DebugLevel dbl = debug::getDebugLevel();
- debug::setDebugLevel(dblError);
- std::string material_name = names(element.type, element.ghost_type)(element.element);
- debug::setDebugLevel(dbl);
+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)
+{}
- return model.getMaterialIndex(material_name);
- } catch (...) {
- return MaterialSelector::operator()(element);
- }
+/* -------------------------------------------------------------------------- */
+template<>
+inline UInt ElementDataMaterialSelector<std::string>::operator() (const Element & element) {
+ try {
+ std::string material_name = this->elementData(element);
+ return model.getMaterialIndex(material_name);
+ } catch (...) {
+ return MaterialSelector::operator()(element);
}
-
-private:
- const ElementTypeMapArray<std::string> & names;
-protected:
- const SolidMechanicsModel & model;
-};
+}
/* -------------------------------------------------------------------------- */
template<>
-class MeshDataMaterialSelector<UInt> : public MaterialSelector {
-public:
- MeshDataMaterialSelector(const std::string & name, const SolidMechanicsModel & model, UInt first_index = 1) :
- indexes(model.getMesh().getData<UInt>(name)), model(model), first_index(first_index) { }
- UInt operator() (const Element & element) {
- try {
- DebugLevel dbl = debug::getDebugLevel();
- debug::setDebugLevel(dblError);
- UInt mat = indexes(element.type, element.ghost_type)(element.element) - first_index;
- debug::setDebugLevel(dbl);
- return mat;
- } catch (...) {
- return MaterialSelector::operator()(element);
- }
+inline UInt ElementDataMaterialSelector<UInt>::operator() (const Element & element) {
+ try {
+ return this->elementData(element) - first_index;
+ } catch (...) {
+ return MaterialSelector::operator()(element);
}
-protected:
- const ElementTypeMapArray<UInt> indexes;
- const SolidMechanicsModel & model;
- UInt first_index;
-};
-
+}
__END_AKANTU__
#endif /* __AKANTU_MATERIAL_SELECTOR_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
index ab360b2d9..c3bac344e 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
@@ -1,693 +1,692 @@
/**
* @file material_cohesive_linear.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Thu Aug 07 2014
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 <numeric>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
#include "dof_synchronizer.hh"
__BEGIN_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 , 0. ,
_pat_parsable | _pat_readable,
"Beta parameter" );
this->registerParam("G_c" , G_c , 0. ,
_pat_parsable | _pat_readable,
"Mode I fracture energy" );
this->registerParam("penalty", penalty, 0. ,
_pat_parsable | _pat_readable,
"Penalty coefficient" );
this->registerParam("volume_s", volume_s, 0. ,
_pat_parsable | _pat_readable,
"Reference volume for sigma_c scaling");
this->registerParam("m_s", m_s, 1. ,
_pat_parsable | _pat_readable,
"Weibull exponent for sigma_c scaling");
this->registerParam("kappa" , kappa , 1. ,
_pat_parsable | _pat_readable,
"Kappa parameter");
// if (!model->isExplicit())
use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
/// 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;
sigma_c_eff.initialize(1);
delta_c_eff.initialize(1);
insertion_stress.initialize(spatial_dimension);
if (!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>::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 FEEngine & fe_engine = model->getFEEngine();
const FEEngine & fe_engine_facet = model->getFEEngine("FacetsFEEngine");
// loop over facet type
Mesh::type_iterator first = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
Real base_sigma_c = sigma_c;
for(;first != last; ++first) {
ElementType type_facet = *first;
const Array< std::vector<Element> > & facet_to_element
= mesh_facets.getElementToSubelement(type_facet);
UInt nb_facet = facet_to_element.getSize();
UInt nb_quad_per_facet = fe_engine_facet.getNbQuadraturePoints(type_facet);
// iterator to modify sigma_c for all the quadrature points of a facet
Array<Real>::vector_iterator 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;
std::vector<Element>::const_iterator elem = element_list.begin();
std::vector<Element>::const_iterator 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.getNbQuadraturePoints(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() {
AKANTU_DEBUG_IN();
const Mesh & mesh_facets = model->getMeshFacets();
CohesiveElementInserter & inserter = model->getElementInserter();
Real tolerance = Math::getTolerance();
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
for (; it != last; ++it) {
ElementType type_facet = *it;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const Array<bool> & facets_check = inserter.getCheckFacets(type_facet);
Array<bool> & f_insertion = inserter.getInsertionFacets(type_facet);
Array<UInt> & f_filter = facet_filter(type_facet);
Array<Real> & sig_c_eff = sigma_c_eff(type_cohesive);
Array<Real> & del_c = delta_c_eff(type_cohesive);
Array<Real> & ins_stress = insertion_stress(type_cohesive);
Array<Real> & trac_old = tractions_old(type_cohesive);
const Array<Real> & f_stress = model->getStressOnFacets(type_facet);
const Array<Real> & sigma_lim = sigma_c(type_facet);
Real max_ratio = 0.;
UInt index_f = 0;
UInt index_filter = 0;
UInt nn = 0;
UInt nb_quad_facet = model->getFEEngine("FacetsFEEngine").getNbQuadraturePoints(type_facet);
UInt nb_facet = f_filter.getSize();
if (nb_facet == 0) continue;
Array<Real>::const_iterator<Real> 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 Array<Real> & tangents = model->getTangents(type_facet);
const Array<Real> & normals
= model->getFEEngine("FacetsFEEngine").getNormalsOnQuadPoints(type_facet);
Array<Real>::const_vector_iterator normal_begin = normals.begin(spatial_dimension);
Array<Real>::const_vector_iterator tangent_begin = tangents.begin(tangents.getNbComponent());
Array<Real>::const_matrix_iterator 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
if (stress_check.mean() > (*sigma_lim_it - tolerance)) {
if (model->isExplicit()){
f_insertion(facet) = true;
// 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);
}
}else{
Real ratio = stress_check.mean()/(*sigma_lim_it);
if (ratio > max_ratio){
++nn;
max_ratio = ratio;
index_f = f;
index_filter = f_filter(f);
}
}
}
}
/// insertion of only 1 cohesive element in case of implicit approach. The one subjected to the highest stress.
if (!model->isExplicit()){
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Array<Real> abs_max(comm.getNbProc());
abs_max(comm.whoAmI()) = max_ratio;
comm.allGather(abs_max.storage(), 1);
Array<Real>::scalar_iterator it = std::max_element(abs_max.begin(), abs_max.end());
Int pos = it - abs_max.begin();
if (pos != comm.whoAmI()) {
AKANTU_DEBUG_OUT();
return;
}
if (nn) {
f_insertion(index_filter) = true;
// Array<Real>::iterator<Matrix<Real> > normal_traction_it =
// normal_traction.begin_reinterpret(nb_quad_facet, spatial_dimension, nb_facet);
Array<Real>::const_iterator<Real> sigma_lim_it = sigma_lim.begin();
for (UInt q = 0; q < nb_quad_facet; ++q) {
// Vector<Real> ins_s(normal_traction_it[index_f].storage() + q * spatial_dimension,
// spatial_dimension);
Real new_sigma = (sigma_lim_it[index_f]);
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(0.0);
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 = delta_c;
else
new_delta = 2 * G_c / (new_sigma);
new_delta_c.push_back(new_delta);
}
}
}
// update material data for the new elements
UInt old_nb_quad_points = sig_c_eff.getSize();
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 dim>
-inline Real MaterialCohesiveLinear<dim>::computeEffectiveNorm(const Matrix<Real> & stress,
- const Vector<Real> & normal,
- const Vector<Real> & tangent,
- Vector<Real> & normal_traction) {
- 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(0., normal_contrib);
-
- return std::sqrt(normal_contrib * normal_contrib + tangent_contrib * tangent_contrib * beta2_inv);
-}
-
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::iterator< Vector<Real> > traction_it =
tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator< Vector<Real> > opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator< Vector<Real> > contact_traction_it =
contact_tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator< Vector<Real> > contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_iterator< Vector<Real> > normal_it =
normal.begin(spatial_dimension);
Array<Real>::iterator< Vector<Real> >traction_end =
tractions(el_type, ghost_type).end(spatial_dimension);
Array<Real>::iterator<Real>sigma_c_it =
sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_it =
delta_max(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_prev_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>damage_it =
damage(el_type, ghost_type).begin();
Array<Real>::iterator<Vector<Real> > insertion_stress_it =
insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Real * 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);
/// 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) {
if (!model->isExplicit())
*delta_max_it = *delta_max_prev_it;
/// 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 * beta2_kappa2;
bool penetration = normal_opening_norm < -Math::getTolerance();
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
normal_opening.clear();
}
else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction_it->clear();
contact_opening_it->clear();
}
delta = std::sqrt(delta);
/// update maximum displacement and damage
*delta_max_it = std::max(*delta_max_it, delta);
*damage_it = std::min(*delta_max_it / *delta_c_it, 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_it, 1.))
traction_it->clear();
else if (Math::are_float_equal(*damage_it, 0.)) {
if (penetration)
traction_it->clear();
else
*traction_it = *insertion_stress_it;
}
else {
*traction_it = tangential_opening;
*traction_it *= beta2_kappa;
*traction_it += normal_opening;
AKANTU_DEBUG_ASSERT(*delta_max_it != 0.,
"Division by zero, tolerance might be too low");
*traction_it *= *sigma_c_it / *delta_max_it * (1. - *damage_it);
}
}
delete [] memory_space;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkDeltaMax(GhostType ghost_type) {
AKANTU_DEBUG_IN();
+ /// This function set a predefined value to the parameter delta_max_prev of the
+ /// elements that have been inserted in the last loading step for which convergence
+ /// has not been reached. This is done before reducing the loading and re-doing the step.
+ /// Otherwise, the updating of delta_max_prev would be done with reference to the
+ /// non-convergent solution.
+
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension,
ghost_type, _ek_cohesive);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension,
ghost_type, _ek_cohesive);
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0) continue;
ElementType el_type = *it;
/// define iterators
Array<Real>::iterator<Real>delta_max_it =
delta_max(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_end =
delta_max(el_type, ghost_type).end();
Array<Real>::iterator<Real>delta_max_prev_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
/// loop on each quadrature point
for (; delta_max_it != delta_max_end;
++delta_max_it, ++delta_max_prev_it, ++delta_c_it) {
if (*delta_max_prev_it == 0)
+ /// elements inserted in the last step, that has not converged
*delta_max_it = *delta_c_it / 1000;
else
+ /// elements introduced in previous steps, for which a correct
+ /// value of delta_max_prev already exists
*delta_max_it = *delta_max_prev_it;
}
}
-
- // delete [] memory_space;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::matrix_iterator tangent_it =
tangent_matrix.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator tangent_end =
tangent_matrix.end(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
normal.begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator<Real>delta_max_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::iterator<Real>sigma_c_it =
sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>damage_it =
damage(el_type, ghost_type).begin();
Array<Real>::iterator< Vector<Real> > contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
+ Array<Real> tang_output(spatial_dimension,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) {
/// compute normal and tangential opening vectors
*opening_it += *contact_opening_it;
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();
-
bool penetration = normal_opening_norm < -Math::getTolerance();
-
Real derivative = 0;
Real t = 0;
Real delta = tangential_opening_norm * tangential_opening_norm * beta2_kappa2;
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_it)/1000.; //0.0000001;
+ delta = (*delta_c_it)/1000.;
if (normal_opening_norm >= 0.0){
if (delta >= *delta_max_it){
derivative = -*sigma_c_it/(delta * delta);
t = *sigma_c_it * (1 - delta / *delta_c_it);
} else if (delta < *delta_max_it){
Real tmax = *sigma_c_it * (1 - *delta_max_it / *delta_c_it);
t = tmax / *delta_max_it * delta;
}
}
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
if (penetration){
- ///don't consider penetration contribution for delta
+ /// don't consider penetration contribution for delta
*opening_it = tangential_opening;
+ /// stiffness in compression given by the penalty parameter
*tangent_it += n_outer_n;
*tangent_it *= penalty;
}
+ /// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(beta2_kappa);
Matrix<Real> nn(n_outer_n);
nn *= (1 - beta2_kappa);
nn += I;
nn *= t/delta;
Vector<Real> t_tilde(normal_opening);
t_tilde *= (1 - beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= beta2_kappa2;
t_tilde += mm;
Vector<Real> t_hat(normal_opening);
t_hat += beta2_kappa * tangential_opening;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(t_hat, t_tilde);
prov *= derivative/delta;
prov += nn;
*tangent_it += prov;
+ /// 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-13){
+ std::cout << "non symmetric cohesive matrix" << std::endl;
+ std::cout << "error " << error << std::endl;
+ }
+ }
+ }
+ }
+ }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANSIATE_MATERIAL(MaterialCohesiveLinear);
__END_AKANTU__
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
index fd50f5928..8f0425161 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
@@ -1,168 +1,168 @@
/**
* @file material_cohesive_linear.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Tue Jul 29 2014
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic type
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
/* -------------------------------------------------------------------------- */
__BEGIN_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
virtual void initMaterial();
/// check stress for cohesive elements' insertion
virtual void checkInsertion();
+ /// compute effective stress norm for insertion check
+ inline Real computeEffectiveNorm(const Matrix<Real> & stress,
+ const Vector<Real> & normal,
+ const Vector<Real> & tangent,
+ Vector<Real> & normal_stress) const;
+
protected:
/// constitutive law
virtual void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// check delta_max for cohesive elements in case of no convergence
/// in the solveStep (only for extrinsic-implicit)
void checkDeltaMax(GhostType ghost_type = _not_ghost);
- /// compute effective stress norm for insertion check
- inline Real computeEffectiveNorm(const Matrix<Real> & stress,
- const Vector<Real> & normal,
- const Vector<Real> & tangent,
- Vector<Real> & normal_stress);
-
/// compute tangent stiffness matrix
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type);
/**
* 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();
/* ------------------------------------------------------------------------ */
/* 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;
/// 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;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
-//#include "material_cohesive_linear_inline_impl.cc"
+#include "material_cohesive_linear_inline_impl.cc"
__END_AKANTU__
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
new file mode 100644
index 000000000..273427731
--- /dev/null
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
@@ -0,0 +1,58 @@
+/**
+ * @file material_cohesive_linear_inline_impl.cc
+ * @author Marco Vocialta <marco.vocialta@epfl.ch>
+ * @date Tue Apr 21 14:49:56 2015
+ *
+ * @brief Inline functions of the MaterialCohesiveLinear
+ *
+ * @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/>.
+ *
+ */
+
+/* -------------------------------------------------------------------------- */
+
+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(0., normal_contrib);
+
+ return std::sqrt(normal_contrib * normal_contrib + tangent_contrib * tangent_contrib * beta2_inv);
+}
diff --git a/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh b/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
index 2692bcc3a..37bb6dae3 100644
--- a/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
@@ -1,81 +1,85 @@
/**
* @file embedded_internal_field.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Mar 19 2015
* @date last modification: Thu Mar 19 2015
*
* @brief Embedded Material internal properties
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
#define __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
__BEGIN_AKANTU__
class Material;
class FEEngine;
+/// This class is used for MaterialReinforcement internal fields
template<typename T>
class EmbeddedInternalField : public InternalField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
+ /// Constructor
EmbeddedInternalField(const ID & id, Material & material):
InternalField<T>(id,
material,
material.getModel().getFEEngine("EmbeddedInterfaceFEEngine"),
material.getElementFilter())
{
this->spatial_dimension = 1;
}
+ /// Copy constructor
EmbeddedInternalField(const ID & id, const EmbeddedInternalField & other):
InternalField<T>(id, other)
{
this->spatial_dimension = 1;
}
void operator=(const EmbeddedInternalField & other) {
InternalField<T>::operator=(other);
this->spatial_dimension = 1;
}
};
+/// Method used to initialise the embedded internal fields from material file
template<>
inline void ParsableParamTyped< EmbeddedInternalField<Real> >::parseParam(const ParserParameter & in_param) {
ParsableParam::parseParam(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
__END_AKANTU__
#endif // __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
index 87d2e9b4b..b447fec14 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
@@ -1,703 +1,767 @@
/**
* @file material_reinforcement.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Mar 12 2015
* @date last modification: Thu Mar 12 2015
*
* @brief Reinforcement material
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_reinforcement.hh"
__BEGIN_AKANTU__
template<UInt dim>
MaterialReinforcement<dim>::MaterialReinforcement(SolidMechanicsModel & model, const ID & id):
Material(model, id),
model(NULL),
gradu("gradu_embedded", *this),
stress("stress_embedded", *this),
directing_cosines("directing_cosines", *this),
pre_stress("pre_stress", *this),
area(1.0),
shape_derivatives()
{
this->model = dynamic_cast<EmbeddedInterfaceModel *>(&model);
AKANTU_DEBUG_ASSERT(this->model != NULL, "MaterialReinforcement needs an EmbeddedInterfaceModel");
this->model->getInterfaceMesh().initElementTypeMapArray(element_filter, 1, 1,
false, _ek_regular);
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");
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
MaterialReinforcement<dim>::~MaterialReinforcement() {
AKANTU_DEBUG_IN();
ElementTypeMap<ElementTypeMapArray<Real> *>::type_iterator it = shape_derivatives.firstType();
ElementTypeMap<ElementTypeMapArray<Real> *>::type_iterator end = shape_derivatives.lastType();
for (; it != end ; ++it) {
delete shape_derivatives(*it, _not_ghost);
delete shape_derivatives(*it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::initMaterial() {
Material::initMaterial();
gradu.initialize(dim * dim);
stress.initialize(dim * dim);
pre_stress.initialize(1);
/// We initialise the stuff that is not going to change during the simulation
this->allocBackgroundShapeDerivatives();
this->initBackgroundShapeDerivatives();
this->initDirectingCosines();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::allocBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh & mesh = model->getMesh();
ghost_type_t::iterator int_ghost_it = ghost_type_t::begin();
// Loop over interface ghosts
for (; int_ghost_it != ghost_type_t::end() ; ++int_ghost_it) {
Mesh::type_iterator interface_type_it = interface_mesh.firstType();
Mesh::type_iterator interface_type_end = interface_mesh.lastType();
for (; interface_type_it != interface_type_end ; ++interface_type_it) {
Mesh::type_iterator background_type_it = mesh.firstType(dim, *int_ghost_it);
Mesh::type_iterator background_type_end = mesh.lastType(dim, *int_ghost_it);
for (; background_type_it != background_type_end ; ++background_type_it) {
const ElementType & int_type = *interface_type_it;
const ElementType & back_type = *background_type_it;
const GhostType & int_ghost = *int_ghost_it;
std::string shaped_id = "embedded_shape_derivatives";
if (int_ghost == _ghost) shaped_id += ":ghost";
ElementTypeMapArray<Real> * shaped_etma = new ElementTypeMapArray<Real>(shaped_id, this->name);
UInt nb_points = Mesh::getNbNodesPerElement(back_type);
UInt nb_quad_points = model->getFEEngine("EmbeddedInterfaceFEEngine").getNbQuadraturePoints(int_type);
UInt nb_elements = element_filter(int_type, int_ghost).getSize();
shaped_etma->alloc(nb_elements * nb_quad_points,
dim * nb_points,
back_type);
shape_derivatives(shaped_etma, int_type, int_ghost);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::initBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, _not_ghost);
Mesh::type_iterator type_end = mesh.lastType(dim, _not_ghost);
for (; type_it != type_end ; ++type_it) {
computeBackgroundShapeDerivatives(*type_it, _not_ghost);
//computeBackgroundShapeDerivatives(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::initDirectingCosines() {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = mesh.lastType(1, _not_ghost);
const UInt voigt_size = getTangentStiffnessVoigtSize(dim);
directing_cosines.initialize(voigt_size * voigt_size);
for (; type_it != type_end ; ++type_it) {
computeDirectingCosines(*type_it, _not_ghost);
computeDirectingCosines(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType();
Mesh::type_iterator type_end = interface_mesh.lastType();
for (; type_it != type_end ; ++type_it) {
assembleStiffnessMatrix(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::updateResidual(GhostType ghost_type) {
AKANTU_DEBUG_IN();
computeAllStresses(ghost_type);
assembleResidual(ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::assembleResidual(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType();
Mesh::type_iterator type_end = interface_mesh.lastType();
for (; type_it != type_end ; ++type_it) {
assembleResidual(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::computeGradU(const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nb_quad_points = model->getFEEngine("EmbeddedInterfaceFEEngine").getNbQuadraturePoints(type);
Array<Real> & gradu_vec = gradu(type, ghost_type);
Mesh::type_iterator back_it = model->getMesh().firstType(dim, ghost_type);
Mesh::type_iterator back_end = model->getMesh().lastType(dim, ghost_type);
for (; back_it != back_end ; ++back_it) {
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(*back_it);
Array<Real> * shapesd_filtered = new Array<Real>(nb_element, dim * nodes_per_background_e, "shapesd_filtered");
FEEngine::filterElementalData(model->getInterfaceMesh(),
shape_derivatives(type, ghost_type)->operator()(*back_it, ghost_type),
*shapesd_filtered,
type, ghost_type, elem_filter);
Array<UInt> * background_filter = new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter, *back_it, type, ghost_type, ghost_type);
Array<Real> * disp_per_element = new Array<Real>(0, dim * nodes_per_background_e, "disp_elem");
FEEngine::extractNodalToElementField(model->getMesh(),
model->getDisplacement(),
*disp_per_element,
*back_it, ghost_type, *background_filter);
Array<Real>::matrix_iterator disp_it = disp_per_element->begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator disp_end = disp_per_element->end(dim, nodes_per_background_e);
Array<Real>::matrix_iterator shapes_it = shapesd_filtered->begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator grad_u_it = gradu_vec.begin(dim, dim);
for (; disp_it != disp_end ; ++disp_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++shapes_it, ++grad_u_it) {
Matrix<Real> & B = *shapes_it;
Matrix<Real> & du = *grad_u_it;
Matrix<Real> & u = *disp_it;
du.mul<false, true>(u, B);
}
}
delete shapesd_filtered;
delete background_filter;
delete disp_per_element;
}
AKANTU_DEBUG_OUT();
}
template<UInt dim>
void MaterialReinforcement<dim>::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = model->getInterfaceMesh().firstType();
Mesh::type_iterator last_type = model->getInterfaceMesh().lastType();
for(; it != last_type; ++it) {
computeGradU(*it, ghost_type);
computeStress(*it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::assembleResidual(const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator type_end = mesh.lastType(dim, ghost_type);
for (; type_it != type_end ; ++type_it) {
assembleResidual(type, *type_it, ghost_type, _not_ghost);
//assembleResidual(type, *type_it, ghost_type, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::assembleResidual(const ElementType & interface_type,
const ElementType & background_type,
GhostType interface_ghost,
GhostType background_ghost) {
AKANTU_DEBUG_IN();
UInt voigt_size = getTangentStiffnessVoigtSize(dim);
Array<Real> & residual = const_cast<Array<Real> &>(model->getResidual());
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
FEEngine & background_engine = model->getFEEngine();
Array<UInt> & elem_filter = element_filter(interface_type, interface_ghost);
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points = interface_engine.getNbQuadraturePoints(interface_type, interface_ghost);
UInt nb_element = elem_filter.getSize();
UInt back_dof = dim * nodes_per_background_e;
Array<Real> & shapesd = shape_derivatives(interface_type, interface_ghost)->operator()(background_type, background_ghost);
Array<Real> * shapesd_filtered = new Array<Real>(nb_element * nb_quadrature_points,
back_dof,
"background_shapesd");
FEEngine::filterElementalData(model->getInterfaceMesh(), shapesd, *shapesd_filtered,
interface_type, interface_ghost, elem_filter);
Array<Real> * integrant = new Array<Real>(nb_quadrature_points * nb_element,
back_dof,
"integrant");
Array<Real>::vector_iterator integrant_it =
integrant->begin(back_dof);
Array<Real>::vector_iterator integrant_end =
integrant->end(back_dof);
Array<Real>::matrix_iterator B_it =
shapesd_filtered->begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, interface_ghost).begin(voigt_size, voigt_size);
Array<Real>::matrix_iterator sigma_it =
stress(interface_type, interface_ghost).begin(dim, dim);
Vector<Real> sigma(voigt_size);
Matrix<Real> Bvoigt(voigt_size, back_dof);
Vector<Real> Ct_sigma(voigt_size);
for (; integrant_it != integrant_end ; ++integrant_it,
++B_it,
++C_it,
++sigma_it) {
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*B_it, Bvoigt, nodes_per_background_e);
Matrix<Real> & C = *C_it;
Vector<Real> & BtCt_sigma = *integrant_it;
stressTensorToVoigtVector(*sigma_it, sigma);
Ct_sigma.mul<true>(C, sigma);
BtCt_sigma.mul<true>(Bvoigt, Ct_sigma);
BtCt_sigma *= area;
}
delete shapesd_filtered;
Array<Real> * residual_interface = new Array<Real>(nb_element, back_dof, "residual_interface");
interface_engine.integrate(*integrant,
*residual_interface,
back_dof,
interface_type, interface_ghost,
elem_filter);
delete integrant;
Array<UInt> * background_filter = new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter,
background_type, interface_type,
background_ghost, interface_ghost);
background_engine.assembleArray(*residual_interface, residual,
model->getDOFSynchronizer().getLocalDOFEquationNumbers(),
dim, background_type, background_ghost, *background_filter, -1.0);
delete residual_interface;
delete background_filter;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::filterInterfaceBackgroundElements(Array<UInt> & filter,
const ElementType & type,
const ElementType & interface_type,
GhostType ghost_type,
GhostType interface_ghost_type) {
AKANTU_DEBUG_IN();
filter.resize(0);
filter.clear();
Array<Element> & elements = model->getInterfaceAssociatedElements(interface_type, interface_ghost_type);
Array<UInt> & elem_filter = element_filter(interface_type, interface_ghost_type);
Array<UInt>::scalar_iterator
filter_it = elem_filter.begin(),
filter_end = elem_filter.end();
for (; filter_it != filter_end ; ++filter_it) {
Element & elem = elements(*filter_it);
if (elem.type == type) filter.push_back(elem.element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::computeDirectingCosines(const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = this->model->getInterfaceMesh();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt steel_dof = dim * nb_nodes_per_element;
const UInt voigt_size = getTangentStiffnessVoigtSize(dim);
const UInt nb_quad_points =
model->getFEEngine("EmbeddedInterfaceFEEngine").getNbQuadraturePoints(type, ghost_type);
Array<Real> node_coordinates(this->element_filter(type, ghost_type).getSize(), steel_dof);
this->model->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(voigt_size, 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);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator type_end = mesh.lastType(dim, ghost_type);
for (; type_it != type_end ; ++type_it) {
assembleStiffnessMatrix(type, *type_it, ghost_type, _not_ghost);
//assembleStiffnessMatrix(type, *type_it, ghost_type, _ghost);
}
AKANTU_DEBUG_OUT();
}
template<UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrix(const ElementType & interface_type,
const ElementType & background_type,
GhostType interface_ghost,
GhostType background_ghost) {
AKANTU_DEBUG_IN();
UInt voigt_size = getTangentStiffnessVoigtSize(dim);
SparseMatrix & K = const_cast<SparseMatrix &>(model->getStiffnessMatrix());
FEEngine & background_engine = model->getFEEngine();
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = element_filter(interface_type, interface_ghost);
Array<Real> & grad_u = gradu(interface_type, interface_ghost);
UInt nb_element = elem_filter.getSize();
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points = interface_engine.getNbQuadraturePoints(interface_type, interface_ghost);
UInt back_dof = dim * nodes_per_background_e;
UInt integrant_size = back_dof;
grad_u.resize(nb_quadrature_points * nb_element);
//need function model->getInterfaceDisplacement()
/*interface_engine.gradientOnQuadraturePoints(model->getInterfaceDisplacement(),
grad_u, dim, interface_type, interface_ghost,
elem_filter);*/
Array<Real> * tangent_moduli = new Array<Real>(nb_element * nb_quadrature_points,
1, "interface_tangent_moduli");
tangent_moduli->clear();
computeTangentModuli(interface_type, *tangent_moduli, interface_ghost);
Array<Real> & shapesd = shape_derivatives(interface_type, interface_ghost)->operator()(background_type, background_ghost);
Array<Real> * shapesd_filtered = new Array<Real>(nb_element * nb_quadrature_points,
back_dof,
"background_shapesd");
FEEngine::filterElementalData(model->getInterfaceMesh(), shapesd, *shapesd_filtered,
interface_type, interface_ghost, elem_filter);
Array<Real> * integrant = new Array<Real>(nb_element * nb_quadrature_points,
integrant_size * integrant_size,
"B^t*C^t*D*C*B");
integrant->clear();
/// Temporary matrices for integrant product
Matrix<Real> Bvoigt(voigt_size, back_dof);
Matrix<Real> DC(voigt_size, voigt_size);
Matrix<Real> DCB(voigt_size, 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, interface_ghost).begin(voigt_size, voigt_size);
Array<Real>::matrix_iterator B_it =
shapesd_filtered->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);
DC.clear();
DC(0, 0) = D * area;
DC *= C;
DCB.mul<false, false>(DC, Bvoigt);
CtDCB.mul<true, false>(C, DCB);
BtCtDCB.mul<true, false>(Bvoigt, CtDCB);
}
delete tangent_moduli;
delete shapesd_filtered;
Array<Real> * K_interface = new Array<Real>(nb_element, integrant_size * integrant_size, "K_interface");
interface_engine.integrate(*integrant, *K_interface,
integrant_size * integrant_size,
interface_type, interface_ghost,
elem_filter);
delete integrant;
Array<UInt> * background_filter = new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter,
background_type, interface_type,
background_ghost, interface_ghost);
background_engine.assembleMatrix(*K_interface, K, dim, background_type, background_ghost, *background_filter);
delete K_interface;
delete background_filter;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// In this function, type and ghost type refer to background elements
template<UInt dim>
void MaterialReinforcement<dim>::computeBackgroundShapeDerivatives(const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
FEEngine & engine = model->getFEEngine();
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
Mesh::type_iterator interface_type = interface_mesh.firstType();
Mesh::type_iterator interface_last = interface_mesh.lastType();
for (; interface_type != interface_last ; ++interface_type) {
Array<UInt> & filter = element_filter(*interface_type, ghost_type);
const UInt nb_elements = filter.getSize();
const UInt nb_nodes = Mesh::getNbNodesPerElement(type);
const UInt nb_quad_per_element = interface_engine.getNbQuadraturePoints(*interface_type);
Array<Real> quad_pos(nb_quad_per_element * nb_elements, dim, "interface_quad_points");
quad_pos.resize(nb_quad_per_element * nb_elements);
interface_engine.interpolateOnQuadraturePoints(interface_mesh.getNodes(),
quad_pos, dim, *interface_type,
ghost_type, filter);
Array<Real> & background_shapesd = shape_derivatives(*interface_type, ghost_type)->operator()(type, ghost_type);
background_shapesd.clear();
Array<UInt> * background_elements = new Array<UInt>(nb_elements, 1, "computeBackgroundShapeDerivatives:background_filter");
filterInterfaceBackgroundElements(*background_elements, type, *interface_type, ghost_type, ghost_type);
Array<UInt>::scalar_iterator
back_it = background_elements->begin(),
back_end = background_elements->end();
Array<Real>::matrix_iterator shapesd_it = background_shapesd.begin(dim, nb_nodes);
Array<Real>::vector_iterator quad_pos_it = quad_pos.begin(dim);
for (; back_it != back_end ; ++back_it) {
for (UInt i = 0 ; i < nb_quad_per_element ; i++, ++shapesd_it, ++quad_pos_it)
engine.computeShapeDerivatives(*quad_pos_it, *back_it, type, *shapesd_it, ghost_type);
}
delete background_elements;
}
AKANTU_DEBUG_OUT();
}
template<UInt dim>
Real MaterialReinforcement<dim>::getEnergy(std::string id) {
AKANTU_DEBUG_IN();
if (id == "potential") {
Real epot = 0.;
computePotentialEnergyByElements();
Mesh::type_iterator
it = element_filter.firstType(spatial_dimension),
end = element_filter.lastType(spatial_dimension);
for (; it != end ; ++it) {
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
epot += interface_engine.integrate(potential_energy(*it, _not_ghost),
*it, _not_ghost,
element_filter(*it, _not_ghost));
epot *= area;
}
return epot;
}
AKANTU_DEBUG_OUT();
return 0;
}
+// Author is Nicolas Richart, see material.cc
+template<UInt dim>
+void MaterialReinforcement<dim>::flattenInternal(const std::string & field_id,
+ ElementTypeMapArray<Real> & internal_flat,
+ const GhostType ghost_type,
+ ElementKind element_kind) {
+ AKANTU_DEBUG_IN();
+
+ typedef ElementTypeMapArray<UInt>::type_iterator iterator;
+ iterator tit = this->element_filter.firstType(1, ghost_type, element_kind);
+ iterator end = this->element_filter.lastType(1, ghost_type, element_kind);
+
+ for (; tit != end; ++tit) {
+ ElementType type = *tit;
+
+ try {
+ __attribute__((unused)) const Array<Real> & src_vect
+ = this->getArray(field_id,type,ghost_type);
+
+ } catch(debug::Exception & e) {
+ continue;
+ }
+
+ const Array<Real> & src_vect = this->getArray(field_id,type,ghost_type);
+ const Array<UInt> & filter = this->element_filter(type,ghost_type);
+
+ // total number of elements for a given type
+ UInt nb_element = this->model->getInterfaceMesh().getNbElement(type,ghost_type);
+ // number of filtered elements
+ UInt nb_element_src = filter.getSize();
+ // number of quadrature points per elem
+ UInt nb_quad_per_elem = 0;
+ // number of data per quadrature point
+ UInt nb_data_per_quad = src_vect.getNbComponent();
+
+ if (!internal_flat.exists(type,ghost_type)) {
+ internal_flat.alloc(nb_element*nb_quad_per_elem,nb_data_per_quad,type,ghost_type);
+ }
+
+ if (nb_element_src == 0) continue;
+ nb_quad_per_elem = (src_vect.getSize()/nb_element_src);
+
+ // number of data per element
+ UInt nb_data = nb_quad_per_elem * src_vect.getNbComponent();
+
+ Array<Real> & dst_vect = internal_flat(type,ghost_type);
+ dst_vect.resize(nb_element*nb_quad_per_elem);
+
+ Array<UInt>::const_scalar_iterator it = filter.begin();
+ Array<UInt>::const_scalar_iterator end = filter.end();
+ Array<Real>::const_vector_iterator it_src =
+ src_vect.begin_reinterpret(nb_data,nb_element_src);
+
+ Array<Real>::vector_iterator it_dst =
+ dst_vect.begin_reinterpret(nb_data,nb_element);
+
+ for (; it != end ; ++it,++it_src) {
+ it_dst[*it] = *it_src;
+ }
+ }
+
+ AKANTU_DEBUG_OUT();
+}
+
/* -------------------------------------------------------------------------- */
INSTANSIATE_MATERIAL(MaterialReinforcement);
/* -------------------------------------------------------------------------- */
__END_AKANTU__
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 d5022a548..fd77ec62a 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
@@ -1,171 +1,212 @@
/**
* @file material_reinforcement.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Mar 12 2015
* @date last modification: Thu Mar 12 2015
*
* @brief Reinforcement material
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_REINFORCEMENT_HH__
#define __AKANTU_MATERIAL_REINFORCEMENT_HH__
#include "aka_common.hh"
#include "material.hh"
#include "embedded_interface_model.hh"
#include "embedded_internal_field.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_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.
+ */
template<UInt dim>
class MaterialReinforcement : virtual public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcement(SolidMechanicsModel & model, const ID & id = "");
/// Destructor
virtual ~MaterialReinforcement();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Init the material
virtual void initMaterial();
/// Init the background shape derivatives
void initBackgroundShapeDerivatives();
/// Init the cosine matrices
void initDirectingCosines();
/// Assemble stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// Update the residual
virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// Assembled the residual
virtual void assembleResidual(GhostType ghost_type);
/// Compute all the stresses !
virtual void computeAllStresses(GhostType ghost_type);
/// Compute the stiffness parameter for elements of a type
virtual void computeTangentModuli(const ElementType & type,
Array<Real> & tangent,
GhostType ghost_type) = 0;
virtual Real getEnergy(std::string id);
+ /// Reimplementation of Material's function to accomodate for interface mesh
+ virtual void flattenInternal(const std::string & field_id,
+ ElementTypeMapArray<Real> & internal_flat,
+ const GhostType ghost_type = _not_ghost,
+ ElementKind element_kind = _ek_not_defined);
+
/* ------------------------------------------------------------------------ */
/* Protected methods */
/* ------------------------------------------------------------------------ */
protected:
/// Allocate the background shape derivatives
void allocBackgroundShapeDerivatives();
/// Compute the directing cosines matrix for one element type
void computeDirectingCosines(const ElementType & type, GhostType ghost_type);
- /// Compute the directing cosines matrix on quadrature points
+ /**
+ * @brief Compute the directing cosines matrix on quadrature points.
+ *
+ * The structure of the directing cosines matrix is :
+ * \f{eqnarray*}{
+ * C_{1,\cdot} & = & (l^2, m^2, n^2, lm, mn, ln) \\
+ * 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]
+ */
inline void computeDirectingCosinesOnQuad(const Matrix<Real> & nodes,
Matrix<Real> & cosines);
/// Assemble the stiffness matrix for an element type (typically _segment_2)
void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);
- /// Assemble the stiffness matrix for background & interface types
+ /**
+ * @brief Assemble the stiffness matrix for background & interface types
+ *
+ * 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]
+ */
void assembleStiffnessMatrix(const ElementType & interface_type,
const ElementType & background_type,
GhostType interface_ghost,
GhostType background_ghost);
- /// Compute the background shape derivatives for a type (typically _triangle_3 / _tetrahedron_4)
+ /// Compute the background shape derivatives for a type
void computeBackgroundShapeDerivatives(const ElementType & type, GhostType ghost_type);
/// Filter elements crossed by interface of a type
void filterInterfaceBackgroundElements(Array<UInt> & filter,
const ElementType & type,
const ElementType & interface_type,
GhostType ghost_type,
GhostType interface_ghost_type);
/// Assemble the residual of one type of element (typically _segment_2)
void assembleResidual(const ElementType & type, GhostType ghost_type);
- /// Assemble the residual for a pair of elements
+ /**
+ * @brief Assemble the residual for a pair of elements
+ *
+ * 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]
+ */
void assembleResidual(const ElementType & interface_type,
const ElementType & background_type,
GhostType interface_ghost,
GhostType background_ghost);
- /// TODO figure out why voigt size is 4 in 2D
+ // 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);
/// Compute gradu on the interface quadrature points
virtual void computeGradU(const ElementType & type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Embedded model
EmbeddedInterfaceModel * model;
/// grad_u
EmbeddedInternalField<Real> gradu;
/// stress
EmbeddedInternalField<Real> stress;
/// C matrix on quad
EmbeddedInternalField<Real> directing_cosines;
/// Prestress on quad
EmbeddedInternalField<Real> pre_stress;
/// Cross-sectional area
Real area;
/// Background mesh shape derivatives
ElementTypeMap< ElementTypeMapArray<Real> * > shape_derivatives;
};
#include "material_reinforcement_inline_impl.cc"
__END_AKANTU__
#endif // __AKANTU_MATERIAL_REINFORCEMENT_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
index 8a6c0dfd7..1514f947c 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
@@ -1,92 +1,107 @@
/**
* @file material_reinforcement_template.hh
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Mon Mar 16 2015
* @date last modification: Mon Mar 16 2015
*
* @brief Reinforcement material templated with constitutive law
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_REINFORCEMENT_TEMPLATE_HH__
#define __AKANTU_MATERIAL_REINFORCEMENT_TEMPLATE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_reinforcement.hh"
#include "material_elastic.hh"
__BEGIN_AKANTU__
+/**
+ * @brief Implementation of MaterialReinforcement with 1D constitutive law
+ * @see MaterialReinforcement, MaterialElastic
+ *
+ * This class is a reinforcement featuring a constitutive law.
+ * <strong>Be careful !</strong> Because of multiple inheritance, this class
+ * forms a diamond.
+ */
template<UInt dim, class ConstLaw = MaterialElastic<1> >
class MaterialReinforcementTemplate : public MaterialReinforcement<dim>,
public ConstLaw {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcementTemplate(SolidMechanicsModel & a_model, const ID & id = "");
/// Destructor
virtual ~MaterialReinforcementTemplate();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialises the material
void initMaterial();
/// Compute the stiffness parameter for elements of a type
virtual void computeTangentModuli(const ElementType & type,
Array<Real> & tangent,
GhostType ghost_type);
/// Computes stress used by constitutive law
virtual void computeStress(ElementType type, GhostType ghost_type);
/// Computes gradu to be used by the constitutive law
virtual void computeGradU(const ElementType & type, GhostType ghost_type);
+ /// Compute the potential energy of the reinforcement
virtual void computePotentialEnergy(ElementType type, GhostType ghost_type = _not_ghost);
+ /// Get energy in reinforcement (currently limited to potential)
virtual Real getEnergy(std::string id);
protected:
- /// Compute interface gradu from bulk gradu
+ /**
+ * @brief Compute interface gradu from bulk gradu
+ * \f[
+ * \varepsilon_s = C \varepsilon_c
+ * \f]
+ */
inline void computeInterfaceGradUOnQuad(const Matrix<Real> & full_gradu,
Real & gradu,
const Matrix<Real> & C);
};
#include "material_reinforcement_template_inline_impl.cc"
__END_AKANTU__
#endif // __AKANTU_MATERIAL_REINFORCEMENT_TEMPLATE_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template_inline_impl.cc b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template_inline_impl.cc
index a36c22dbb..7e1894f01 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template_inline_impl.cc
@@ -1,195 +1,196 @@
/**
* @file material_reinforcement_template.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Mon Mar 16 2015
* @date last modification: Mon Mar 16 2015
*
* @brief Reinforcement material templated with constitutive law
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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/>.
*
*/
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
MaterialReinforcementTemplate<dim, ConstLaw>::MaterialReinforcementTemplate(SolidMechanicsModel & model,
const ID & id):
Material(model, id),
MaterialReinforcement<dim>(model, id),
ConstLaw(model, id)
{}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
MaterialReinforcementTemplate<dim, ConstLaw>::~MaterialReinforcementTemplate()
{}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::initMaterial() {
MaterialReinforcement<dim>::initMaterial();
// Gotta change the dimension from here onwards
this->ConstLaw::spatial_dimension = 1;
ConstLaw::initMaterial();
this->ConstLaw::gradu.free();
this->ConstLaw::stress.free();
this->ConstLaw::delta_T.free();
this->ConstLaw::sigma_th.free();
this->ConstLaw::potential_energy.free();
Mesh::type_iterator type_it = this->MaterialReinforcement<dim>::model->getInterfaceMesh().firstType();
Mesh::type_iterator type_end = this->MaterialReinforcement<dim>::model->getInterfaceMesh().lastType();
// Reshape the ConstLaw internal fields
for (; type_it != type_end ; ++type_it) {
UInt nb_elements = this->MaterialReinforcement<dim>::element_filter(*type_it).getSize();
FEEngine & interface_engine =
this->MaterialReinforcement<dim>::model->getFEEngine("EmbeddedInterfaceFEEngine");
UInt nb_quad = interface_engine.getNbQuadraturePoints(*type_it);
this->ConstLaw::gradu.alloc(nb_elements * nb_quad, 1, *type_it, _not_ghost);
this->ConstLaw::stress.alloc(nb_elements * nb_quad, 1, *type_it, _not_ghost);
+ this->ConstLaw::stress.initialize(1);
this->ConstLaw::delta_T.alloc(nb_elements * nb_quad, 1, *type_it, _not_ghost);
this->ConstLaw::sigma_th.alloc(nb_elements * nb_quad, 1, *type_it, _not_ghost);
this->ConstLaw::potential_energy.alloc(nb_elements * nb_quad, 1, *type_it, _not_ghost);
//this->ConstLaw::gradu.alloc(0, dim * dim, *type_it, _ghost);
}
}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::computeGradU(const ElementType & el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialReinforcement<dim>::computeGradU(el_type, ghost_type);
const UInt voigt_size = Material::getTangentStiffnessVoigtSize(dim);
Array<Real>::matrix_iterator full_gradu_it =
this->MaterialReinforcement<dim>::gradu(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator full_gradu_end =
this->MaterialReinforcement<dim>::gradu(el_type, ghost_type).end(dim, dim);
Array<Real>::scalar_iterator gradu_it =
this->ConstLaw::gradu(el_type, ghost_type).begin();
Array<Real>::matrix_iterator cosines_it =
this->directing_cosines(el_type, ghost_type).begin(voigt_size, voigt_size);
for (; full_gradu_it != full_gradu_end ; ++full_gradu_it,
++gradu_it,
++cosines_it) {
Matrix<Real> & full_gradu = *full_gradu_it;
Real & gradu = *gradu_it;
Matrix<Real> & C = *cosines_it;
computeInterfaceGradUOnQuad(full_gradu, gradu, C);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::computeInterfaceGradUOnQuad(const Matrix<Real> & full_gradu,
Real & gradu,
const Matrix<Real> & C) {
const UInt voigt_size = Material::getTangentStiffnessVoigtSize(dim);
Matrix<Real> epsilon(dim, dim);
Vector<Real> e_voigt(voigt_size);
Vector<Real> e_interface_voigt(voigt_size);
epsilon = 0.5 * (full_gradu + full_gradu.transpose());
MaterialReinforcement<dim>::strainTensorToVoigtVector(epsilon, e_voigt);
e_interface_voigt.mul<false>(C, e_voigt);
gradu = e_interface_voigt(0);
}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(tangent.getNbComponent() == 1, "Reinforcements only work in 1D");
ConstLaw::computeTangentModuli(el_type, tangent, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::computeStress(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
ConstLaw::computeStress(type, ghost_type);
Array<Real>::matrix_iterator full_sigma_it =
this->MaterialReinforcement<dim>::stress(type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator full_sigma_end =
this->MaterialReinforcement<dim>::stress(type, ghost_type).end(dim, dim);
Array<Real>::scalar_iterator sigma_it =
this->ConstLaw::stress(type, ghost_type).begin();
Array<Real>::scalar_iterator pre_stress_it =
this->MaterialReinforcement<dim>::pre_stress(type, ghost_type).begin();
for (; full_sigma_it != full_sigma_end ; ++full_sigma_it, ++sigma_it, ++pre_stress_it) {
Matrix<Real> & sigma = *full_sigma_it;
sigma(0, 0) = *sigma_it + *pre_stress_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt dim, class ConstLaw>
Real MaterialReinforcementTemplate<dim, ConstLaw>::getEnergy(std::string id) {
return MaterialReinforcement<dim>::getEnergy(id);
}
/* -------------------------------------------------------------------------- */
template <UInt dim, class ConstLaw>
void MaterialReinforcementTemplate<dim, ConstLaw>::computePotentialEnergy(ElementType type,
GhostType ghost_type) {
ConstLaw::computePotentialEnergy(type, ghost_type);
}
diff --git a/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc b/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
index 5b4c0b21a..12bc17a34 100644
--- a/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
@@ -1,823 +1,830 @@
/**
* @file material_non_local_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Mon Jun 23 2014
*
* @brief Non-local inline implementation
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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/>.
*
*/
/* -------------------------------------------------------------------------- */
__END_AKANTU__
/* -------------------------------------------------------------------------- */
#include "aka_types.hh"
#include "grid_synchronizer.hh"
#include "synchronizer_registry.hh"
#include "integrator.hh"
+#include "dumper_paraview.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DEBUG_TOOLS)
# include "aka_debug_tools.hh"
#endif
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template<UInt DIM, template <UInt> class WeightFunction>
MaterialNonLocal<DIM, WeightFunction>::MaterialNonLocal(SolidMechanicsModel & model,
const ID & id) :
Material(model, id), weight_func(NULL), spatial_grid(NULL),
compute_stress_calls(0), is_creating_grid(false), grid_synchronizer(NULL) {
AKANTU_DEBUG_IN();
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
pair_weight[ghost_type] = NULL;
}
this->is_non_local = true;
this->weight_func = new WeightFunction<DIM>(*this);
this->registerSubSection(_st_non_local, "weight_function", *weight_func);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
MaterialNonLocal<spatial_dimension, WeightFunction>::~MaterialNonLocal() {
AKANTU_DEBUG_IN();
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
delete pair_weight[ghost_type];
}
delete spatial_grid;
delete weight_func;
delete grid_synchronizer;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::initMaterial() {
AKANTU_DEBUG_IN();
// Material::initMaterial();
Mesh & mesh = this->model->getFEEngine().getMesh();
InternalField<Real> quadrature_points_coordinates("quadrature_points_coordinates_tmp_nl", *this);
quadrature_points_coordinates.initialize(spatial_dimension);
ElementTypeMap<UInt> nb_ghost_protected;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
for(; it != last_type; ++it)
nb_ghost_protected(mesh.getNbElement(*it, _ghost), *it, _ghost);
AKANTU_DEBUG_INFO("Creating cell list");
createCellList(quadrature_points_coordinates);
AKANTU_DEBUG_INFO("Creating pairs");
updatePairList(quadrature_points_coordinates);
#if not defined(AKANTU_NDEBUG)
if(AKANTU_DEBUG_TEST(dblDump))
neighbourhoodStatistics("material_non_local.stats");
#endif
AKANTU_DEBUG_INFO("Cleaning extra ghosts");
- cleanupExtraGhostElement(nb_ghost_protected);
+ /// cleanupExtraGhostElement(nb_ghost_protected);
AKANTU_DEBUG_INFO("Computing weights");
weight_func->setRadius(weight_func->getRadius());
weight_func->init();
computeWeights(quadrature_points_coordinates);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::cleanupExtraGhostElement(const ElementTypeMap<UInt> & nb_ghost_protected) {
AKANTU_DEBUG_IN();
// Create list of element to keep
std::set<Element> relevant_ghost_element;
PairList::const_iterator first_pair = pair_list[_ghost].begin();
PairList::const_iterator last_pair = pair_list[_ghost].end();
for(;first_pair != last_pair; ++first_pair) {
const QuadraturePoint & q2 = first_pair->second;
relevant_ghost_element.insert(q2);
}
// Create list of element to remove and new numbering for element to keep
Mesh & mesh = this->model->getFEEngine().getMesh();
std::set<Element> ghost_to_erase;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
RemovedElementsEvent remove_elem(mesh);
- Element element_global; // member element corresponds to global element number
- element_global.ghost_type = _ghost;
+ Element element_local; // member element corresponds to global element number
+ element_local.ghost_type = _ghost;
for(; it != last_type; ++it) {
- element_global.type = *it;
- UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
+ element_local.type = *it;
+ UInt nb_ghost_elem_global = mesh.getNbElement(*it, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(*it, _ghost);
} catch (...) {}
if(!remove_elem.getNewNumbering().exists(*it, _ghost))
- remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, *it, _ghost);
- else remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem);
-
+ remove_elem.getNewNumbering().alloc(nb_ghost_elem_global, 1, *it, _ghost);
+ else remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem_global);
+ Array<UInt> & elem_filter = element_filter(*it, _ghost);
+ UInt nb_ghost_elem_local = elem_filter.getSize();
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
- UInt ng = 0;
- for (UInt g = 0; g < nb_ghost_elem; ++g) {
- if (element_global.element >= nb_ghost_elem_protected) {
- Element element_local = this->convertToLocalElement(element_global);
-
- if (std::find(relevant_ghost_element.begin(),
- relevant_ghost_element.end(),
- element_local) == relevant_ghost_element.end()) {
+ for (UInt g = 0; g < nb_ghost_elem_local; ++g) {
+ element_local.element = g;
+ Element element_global = this->convertToGlobalElement(element_local);
+ if (element_global.element >= nb_ghost_elem_protected &&
+ relevant_ghost_element.find(element_local) == relevant_ghost_element.end()) {
+ // (std::find(relevant_ghost_element.begin(),
+ // relevant_ghost_element.end(),
+ // element_local) == relevant_ghost_element.end())) {
+ std::cout<< "element removed" << std::endl;
remove_elem.getList().push_back(element_global);
- new_numbering(g) = UInt(-1);
+ new_numbering(element_global.element) = UInt(-1);
}
- } else {
- new_numbering(g) = ng;
+ }
+
+ UInt ng = 0;
+ for (UInt g = 0; g < nb_ghost_elem_global; ++g) {
+ if (new_numbering(g) != UInt(-1)) {
+ new_numbering(g) = ng;
++ng;
}
}
}
mesh.sendEvent(remove_elem);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::createCellList(ElementTypeMapArray<Real> & quadrature_points_coordinates) {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model->getFEEngine().getMesh();
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLocalLowerBounds();
const Vector<Real> & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension, weight_func->getRadius() * safety_factor);
spatial_grid = new SpatialGrid<QuadraturePoint>(spatial_dimension, spacing, center);
this->computeQuadraturePointsCoordinates(quadrature_points_coordinates, _not_ghost);
this->fillCellList(quadrature_points_coordinates, _not_ghost);
is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(_gst_mnl_for_average);
tags.insert(_gst_mnl_weight);
tags.insert(_gst_material_id);
SynchronizerRegistry & synch_registry = this->model->getSynchronizerRegistry();
std::stringstream sstr; sstr << getID() << ":grid_synchronizer";
grid_synchronizer = GridSynchronizer::createGridSynchronizer(mesh,
*spatial_grid,
sstr.str(),
&synch_registry,
tags);
is_creating_grid = false;
this->computeQuadraturePointsCoordinates(quadrature_points_coordinates, _ghost);
fillCellList(quadrature_points_coordinates, _ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::fillCellList(const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const GhostType & ghost_type) {
QuadraturePoint q;
q.ghost_type = ghost_type;
Mesh::type_iterator it = this->element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = this->element_filter.lastType (spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nb_quad = this->model->getFEEngine().getNbQuadraturePoints(*it, ghost_type);
const Array<Real> & quads = quadrature_points_coordinates(*it, ghost_type);
q.type = *it;
Array<Real>::const_vector_iterator quad = quads.begin(spatial_dimension);
UInt * elem = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e) {
q.element = *elem;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
//q.setPosition(*quad);
spatial_grid->insert(q, *quad);
++quad;
}
++elem;
}
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::updatePairList(const ElementTypeMapArray<Real> & quadrature_points_coordinates) {
AKANTU_DEBUG_IN();
GhostType ghost_type = _not_ghost;
QuadraturePoint q1;
q1.ghost_type = ghost_type;
// generate the pair of neighbor depending of the cell_list
Mesh::type_iterator it = this->element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = this->element_filter.lastType(spatial_dimension, ghost_type);
for(; it != last_type; ++it) {
// Preparing datas
const Array<Real> & quads = quadrature_points_coordinates(*it, ghost_type);
Array<Real>::const_vector_iterator q1_coord_it = quads.begin(spatial_dimension);
Array<Real>::const_vector_iterator last_quad = quads.end(spatial_dimension);
q1.type = *it;
q1.global_num = 0;
// loop over quad points
for(;q1_coord_it != last_quad; ++q1_coord_it, ++(q1.global_num)) {
UInt nb_quad1 =
this->model->getFEEngine().getNbQuadraturePoints(q1.type,
q1.ghost_type);
q1.element = q1.global_num / nb_quad1;
q1.num_point = q1.global_num % nb_quad1;
const Vector<Real> & q1_coord = *q1_coord_it;
SpatialGrid<QuadraturePoint>::CellID cell_id = spatial_grid->getCellID(q1_coord);
SpatialGrid<QuadraturePoint>::neighbor_cells_iterator first_neigh_cell =
spatial_grid->beginNeighborCells(cell_id);
SpatialGrid<QuadraturePoint>::neighbor_cells_iterator last_neigh_cell =
spatial_grid->endNeighborCells(cell_id);
// loop over neighbors cells of the one containing the current quadrature
// point
for (; first_neigh_cell != last_neigh_cell; ++first_neigh_cell) {
SpatialGrid<QuadraturePoint>::Cell::iterator first_neigh_quad =
spatial_grid->beginCell(*first_neigh_cell);
SpatialGrid<QuadraturePoint>::Cell::iterator last_neigh_quad =
spatial_grid->endCell(*first_neigh_cell);
// loop over the quadrature point in the current cell of the cell list
for (;first_neigh_quad != last_neigh_quad; ++first_neigh_quad){
QuadraturePoint q2 = this->convertToLocalPoint(*first_neigh_quad);
Array<Real>::const_vector_iterator q2_coord_it =
quadrature_points_coordinates(q2.type,
q2.ghost_type).begin(spatial_dimension);
const Vector<Real> & q2_coord = q2_coord_it[q2.global_num];
Real distance = q1_coord.distance(q2_coord);
if(distance <= weight_func->getRadius() &&
(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();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::computeWeights(const ElementTypeMapArray<Real> & quadrature_points_coordinates) {
AKANTU_DEBUG_IN();
InternalField<Real> quadrature_points_volumes("quadrature_points_volumes", *this);
quadrature_points_volumes.initialize(1);
const FEEngine & fem = this->model->getFEEngine();
weight_func->updateInternals(quadrature_points_volumes);
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
if(!(pair_weight[ghost_type2])) {
std::string ghost_id = "";
if (ghost_type2 == _ghost) ghost_id = ":ghost";
std::stringstream sstr; sstr << getID() << ":pair_weight:" << ghost_id;
pair_weight[ghost_type2] = new Array<Real>(0, 2, sstr.str());
}
pair_weight[ghost_type2]->resize(pair_list[ghost_type2].size());
pair_weight[ghost_type2]->clear();
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
// Compute the weights
for(;first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const QuadraturePoint & lq1 = first_pair->first;
const QuadraturePoint & lq2 = first_pair->second;
QuadraturePoint gq1 = this->convertToGlobalPoint(lq1);
QuadraturePoint gq2 = this->convertToGlobalPoint(lq2);
// const Real q2_wJ = fem.getIntegratorInterface().getJacobians(gq2.type, gq2.ghost_type)(gq2.global_num);
Array<Real>::const_vector_iterator quad_coords_1 =
quadrature_points_coordinates(lq1.type, lq1.ghost_type).begin(spatial_dimension);
Array<Real>::const_vector_iterator quad_coords_2 =
quadrature_points_coordinates(lq2.type, lq2.ghost_type).begin(spatial_dimension);
Array<Real> & quad_volumes_1 = quadrature_points_volumes(lq1.type, lq1.ghost_type);
const Array<Real> & jacobians_2 =
fem.getIntegratorInterface().getJacobians(gq2.type, gq2.ghost_type);
const Real & q2_wJ = jacobians_2(gq2.global_num);
// Real & q1_volume = quad_volumes(lq1.global_num);
const Vector<Real> & q1_coord = quad_coords_1[lq1.global_num];
// quadrature_points_coordinates(lq1.type, lq1.ghost_type).begin(spatial_dimension)[lq1.global_num];
const Vector<Real> & q2_coord = quad_coords_2[lq2.global_num];
// quadrature_points_coordinates(lq1.type, lq1.ghost_type).begin(spatial_dimension)[lq2.global_num];
this->weight_func->selectType(lq1.type, lq1.ghost_type, lq2.type, lq2.ghost_type);
// Weight function
Real r = q1_coord.distance(q2_coord);
Real w1 = this->weight_func->operator()(r, lq1, lq2);
weight(0) = q2_wJ * w1;
// q1_volume += weight(0);
quad_volumes_1(lq1.global_num) += weight(0);
if(lq2.ghost_type != _ghost && lq1.global_num != lq2.global_num) {
const Array<Real> & jacobians_1 =
fem.getIntegratorInterface().getJacobians(gq1.type, gq1.ghost_type);
Array<Real> & quad_volumes_2 =
quadrature_points_volumes(lq2.type, lq2.ghost_type);
const Real & q1_wJ = jacobians_1(gq1.global_num);
//Real & q2_volume = quad_volumes_2(lq2.global_num);
Real w2 = this->weight_func->operator()(r, lq2, lq1);
weight(1) = q1_wJ * w2;
quad_volumes_2(lq2.global_num) += weight(1);
//q2_volume += weight(1);
} else
weight(1) = 0.;
}
}
//normalize the weights
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
// Compute the weights
for(;first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const QuadraturePoint & lq1 = first_pair->first;
const QuadraturePoint & lq2 = first_pair->second;
Array<Real> & quad_volumes_1 = quadrature_points_volumes(lq1.type, lq1.ghost_type);
Array<Real> & quad_volumes_2 = quadrature_points_volumes(lq2.type, lq2.ghost_type);
Real q1_volume = quad_volumes_1(lq1.global_num);
weight(0) *= 1. / q1_volume;
if(ghost_type2 != _ghost) {
Real q2_volume = quad_volumes_2(lq2.global_num);
weight(1) *= 1. / q2_volume;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
template<typename T>
void MaterialNonLocal<spatial_dimension, WeightFunction>::weightedAvergageOnNeighbours(const InternalField<T> & to_accumulate,
InternalField<T> & accumulated,
UInt nb_degree_of_freedom,
GhostType ghost_type2) const {
AKANTU_DEBUG_IN();
if(ghost_type2 == _not_ghost) {
accumulated.reset();
}
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
// Compute the weights
for(;first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const QuadraturePoint & lq1 = first_pair->first;
const QuadraturePoint & lq2 = first_pair->second;
const Array<T> & to_acc_1 = to_accumulate(lq1.type, lq1.ghost_type);
Array<T> & acc_1 = accumulated(lq1.type, lq1.ghost_type);
const Array<T> & to_acc_2 = to_accumulate(lq2.type, lq2.ghost_type);
Array<T> & acc_2 = accumulated(lq2.type, lq2.ghost_type);
// const Vector<T> & q2_to_acc = to_acc_2[lq2.global_num];
// Vector<T> & q1_acc = acc_1[lq1.global_num];
//q1_acc += weight(0) * q2_to_acc;
for(UInt d = 0; d < nb_degree_of_freedom; ++d) {
acc_1(lq1.global_num, d) += weight(0) * to_acc_2(lq2.global_num, d);
}
if(ghost_type2 != _ghost) {
for(UInt d = 0; d < nb_degree_of_freedom; ++d) {
acc_2(lq2.global_num, d) += weight(1) * to_acc_1(lq1.global_num, d);
}
}
// if(ghost_type2 != _ghost) {
// const Vector<T> & q1_to_acc = to_acc_1[lq1.global_num];
// Vector<T> & q2_acc = acc_2[lq2.global_num];
// q2_acc += weight(1) * q1_to_acc;
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::updateResidual(GhostType ghost_type) {
AKANTU_DEBUG_IN();
// Update the weights for the non local variable averaging
if(ghost_type == _not_ghost &&
this->weight_func->getUpdateRate() &&
(this->compute_stress_calls % this->weight_func->getUpdateRate() == 0)) {
ElementTypeMapArray<Real> quadrature_points_coordinates("quadrature_points_coordinates", getID());
Mesh & mesh = this->model->getFEEngine().getMesh();
mesh.initElementTypeMapArray(quadrature_points_coordinates, spatial_dimension, spatial_dimension);
computeQuadraturePointsCoordinates(quadrature_points_coordinates, _not_ghost);
computeQuadraturePointsCoordinates(quadrature_points_coordinates, _ghost);
computeWeights(quadrature_points_coordinates);
}
if(ghost_type == _not_ghost) ++this->compute_stress_calls;
computeAllStresses(ghost_type);
computeNonLocalStresses(ghost_type);
assembleResidual(ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::computeAllNonLocalStresses(GhostType ghost_type) {
// Update the weights for the non local variable averaging
if(ghost_type == _not_ghost) {
if(this->weight_func->getUpdateRate() &&
(this->compute_stress_calls % this->weight_func->getUpdateRate() == 0)) {
this->model->getSynchronizerRegistry().asynchronousSynchronize(_gst_mnl_weight);
ElementTypeMapArray<Real> quadrature_points_coordinates("quadrature_points_coordinates", getID());
Mesh & mesh = this->model->getFEEngine().getMesh();
mesh.initElementTypeMapArray(quadrature_points_coordinates, spatial_dimension, spatial_dimension);
computeQuadraturePointsCoordinates(quadrature_points_coordinates, _not_ghost);
computeQuadraturePointsCoordinates(quadrature_points_coordinates, _ghost);
this->model->getSynchronizerRegistry().waitEndSynchronize(_gst_mnl_weight);
computeWeights(quadrature_points_coordinates);
}
typename std::map<ID, NonLocalVariable>::iterator it = non_local_variables.begin();
typename std::map<ID, NonLocalVariable>::iterator end = non_local_variables.end();
for(;it != end; ++it) {
NonLocalVariable & non_local_variable = it->second;
non_local_variable.non_local->resize();
this->weightedAvergageOnNeighbours(*non_local_variable.local, *non_local_variable.non_local,
non_local_variable.nb_component, _not_ghost);
}
++this->compute_stress_calls;
} else {
typename std::map<ID, NonLocalVariable>::iterator it = non_local_variables.begin();
typename std::map<ID, NonLocalVariable>::iterator end = non_local_variables.end();
for(;it != end; ++it) {
NonLocalVariable & non_local_variable = it->second;
this->weightedAvergageOnNeighbours(*non_local_variable.local, *non_local_variable.non_local,
non_local_variable.nb_component, _ghost);
}
computeNonLocalStresses(_not_ghost);
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::savePairs(const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
for(;first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const QuadraturePoint & lq1 = first_pair->first;
const QuadraturePoint & lq2 = first_pair->second;
pout << lq1 << " " << lq2 << " " << weight << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
void MaterialNonLocal<spatial_dimension, WeightFunction>::neighbourhoodStatistics(const std::string & filename) const {
// std::ofstream pout;
// pout.open(filename.c_str());
// const Mesh & mesh = this->model->getFEEngine().getMesh();
// GhostType ghost_type1;
// ghost_type1 = _not_ghost;
// StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// Int prank = comm.whoAmI();
// InternalField<UInt> nb_neighbors("nb_neighbours", *const_cast<MaterialNonLocal *>(this));
// nb_neighbors.initialize(1);
// for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
// GhostType ghost_type2 = (GhostType) gt;
// UInt existing_pairs_num = gt - _not_ghost;
// pair_type::const_iterator first_pair_types = existing_pairs[existing_pairs_num].begin();
// pair_type::const_iterator last_pair_types = existing_pairs[existing_pairs_num].end();
// for (; first_pair_types != last_pair_types; ++first_pair_types) {
// const Array<UInt> & pairs =
// pair_list(first_pair_types->first, ghost_type1)(first_pair_types->second, ghost_type2);
// if(prank == 0) {
// pout << ghost_type2 << " ";
// pout << "Types : " << first_pair_types->first << " " << first_pair_types->second << std::endl;
// }
// Array<UInt>::const_iterator< Vector<UInt> > first_pair = pairs.begin(2);
// Array<UInt>::const_iterator< Vector<UInt> > last_pair = pairs.end(2);
// Array<UInt> & nb_neigh_1 = nb_neighbors(first_pair_types->first, ghost_type1);
// Array<UInt> & nb_neigh_2 = nb_neighbors(first_pair_types->second, ghost_type2);
// for(;first_pair != last_pair; ++first_pair) {
// UInt q1 = (*first_pair)(0);
// UInt q2 = (*first_pair)(1);
// ++(nb_neigh_1(q1));
// if(q1 != q2) ++(nb_neigh_2(q2));
// }
// }
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type1);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, ghost_type1);
// UInt nb_quads = 0;
// Real sum_nb_neig = 0;
// UInt max_nb_neig = 0;
// UInt min_nb_neig = std::numeric_limits<UInt>::max();
// for(; it != last_type; ++it) {
// Array<UInt> & nb_neighor = nb_neighbors(*it, ghost_type1);
// Array<UInt>::iterator<UInt> nb_neigh = nb_neighor.begin();
// Array<UInt>::iterator<UInt> end_neigh = nb_neighor.end();
// for (; nb_neigh != end_neigh; ++nb_neigh, ++nb_quads) {
// UInt nb = *nb_neigh;
// sum_nb_neig += nb;
// max_nb_neig = std::max(max_nb_neig, nb);
// min_nb_neig = std::min(min_nb_neig, nb);
// }
// }
// comm.allReduce(&nb_quads, 1, _so_sum);
// comm.allReduce(&sum_nb_neig, 1, _so_sum);
// comm.allReduce(&max_nb_neig, 1, _so_max);
// comm.allReduce(&min_nb_neig, 1, _so_min);
// if(prank == 0) {
// pout << ghost_type2 << " ";
// pout << "Nb quadrature points: " << nb_quads << std::endl;
// Real mean_nb_neig = sum_nb_neig / Real(nb_quads);
// pout << ghost_type2 << " ";
// pout << "Average nb neighbors: " << mean_nb_neig << "(" << sum_nb_neig << ")" << std::endl;
// pout << ghost_type2 << " ";
// pout << "Max nb neighbors: " << max_nb_neig << std::endl;
// pout << ghost_type2 << " ";
// pout << "Min nb neighbors: " << min_nb_neig << std::endl;
// }
// }
// pout.close();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
inline UInt MaterialNonLocal<spatial_dimension, WeightFunction>::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
UInt nb_quadrature_points = this->getModel().getNbQuadraturePoints(elements);
UInt size = 0;
if(tag == _gst_mnl_for_average) {
typename std::map<ID, NonLocalVariable>::const_iterator it = non_local_variables.begin();
typename std::map<ID, NonLocalVariable>::const_iterator end = non_local_variables.end();
for(;it != end; ++it) {
const NonLocalVariable & non_local_variable = it->second;
size += non_local_variable.nb_component * sizeof(Real) * nb_quadrature_points;
}
}
size += weight_func->getNbDataForElements(elements, tag);
return size;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
inline void MaterialNonLocal<spatial_dimension, WeightFunction>::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if(tag == _gst_mnl_for_average) {
typename std::map<ID, NonLocalVariable>::const_iterator it = non_local_variables.begin();
typename std::map<ID, NonLocalVariable>::const_iterator end = non_local_variables.end();
for(;it != end; ++it) {
const NonLocalVariable & non_local_variable = it->second;
this->packElementDataHelper(*non_local_variable.local,
buffer, elements);
}
}
weight_func->packElementData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
inline void MaterialNonLocal<spatial_dimension, WeightFunction>::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if(tag == _gst_mnl_for_average) {
typename std::map<ID, NonLocalVariable>::iterator it = non_local_variables.begin();
typename std::map<ID, NonLocalVariable>::iterator end = non_local_variables.end();
for(;it != end; ++it) {
NonLocalVariable & non_local_variable = it->second;
this->unpackElementDataHelper(*non_local_variable.local,
buffer, elements);
}
}
weight_func->unpackElementData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
inline void MaterialNonLocal<spatial_dimension, WeightFunction>::onElementsAdded(const Array<Element> & element_list) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ERROR("This is a case not taken into account!!!");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template <UInt> class WeightFunction>
inline void MaterialNonLocal<spatial_dimension, WeightFunction>::onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
// Change the pairs in new global numbering
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
PairList::iterator first_pair = pair_list[ghost_type2].begin();
PairList::iterator last_pair = pair_list[ghost_type2].end();
// Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
for(;first_pair != last_pair; ++first_pair) {
QuadraturePoint & q1 = first_pair->first;
QuadraturePoint gq1 = this->convertToGlobalPoint(q1);
q1 = gq1;
if(new_numbering.exists(q1.type, q1.ghost_type)) {
UInt q1_new_el = new_numbering(q1.type, q1.ghost_type)(gq1.element);
AKANTU_DEBUG_ASSERT(q1_new_el != UInt(-1), "A local quadrature_point as been removed instead of just being renumbered");
q1.element = q1_new_el;
}
QuadraturePoint & q2 = first_pair->second;
QuadraturePoint gq2 = this->convertToGlobalPoint(q2);
q2 = gq2;
if(new_numbering.exists(q2.type, q2.ghost_type)) {
UInt q2_new_el = new_numbering(q2.type, q2.ghost_type)(gq2.element);
AKANTU_DEBUG_ASSERT(q2_new_el != UInt(-1), "A local quadrature_point as been removed instead of just being renumbered");
q2.element = q2_new_el;
}
}
}
// Change the material numbering
Material::onElementsRemoved(element_list, new_numbering, event);
// Change back the pairs to the new material numbering
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
PairList::iterator first_pair = pair_list[ghost_type2].begin();
PairList::iterator last_pair = pair_list[ghost_type2].end();
// Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
for(;first_pair != last_pair; ++first_pair) {
first_pair->first = this->convertToLocalPoint(first_pair->first );
first_pair->second = this->convertToLocalPoint(first_pair->second);
}
}
AKANTU_DEBUG_OUT();
}
diff --git a/src/model/solid_mechanics/materials/weight_function.hh b/src/model/solid_mechanics/materials/weight_function.hh
index f62661bcf..cb53123b8 100644
--- a/src/model/solid_mechanics/materials/weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_function.hh
@@ -1,373 +1,375 @@
/**
* @file weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Thu Jun 05 2014
*
* @brief Weight functions for non local materials
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_types.hh"
#include "solid_mechanics_model.hh"
#include "parsable.hh"
#include <cmath>
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#include <string>
#endif
+#include "material_list.hh"
+
/* -------------------------------------------------------------------------- */
#include <vector>
-
+#include "material_damage.hh"
#ifndef __AKANTU_WEIGHT_FUNCTION_HH__
#define __AKANTU_WEIGHT_FUNCTION_HH__
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
class BaseWeightFunction : public Parsable {
public:
BaseWeightFunction(Material & material, const std::string & type = "base") :
Parsable(_st_non_local, "weight_function:" + type), material(material), type(type) {
this->registerParam("radius" , R , 100.,
_pat_parsable | _pat_readable , "Non local radius");
this->registerParam("update_rate" , update_rate, 0U ,
_pat_parsmod, "Update frequency");
}
virtual ~BaseWeightFunction() {}
virtual void init() { R2 = R * R; };
virtual void updateInternals(__attribute__((unused)) const ElementTypeMapArray<Real> & quadrature_points_coordinates) {};
/* ------------------------------------------------------------------------ */
inline void setRadius(Real radius) { R = radius; R2 = R * R; }
/* ------------------------------------------------------------------------ */
inline void selectType(__attribute__((unused)) ElementType type1,
__attribute__((unused)) GhostType ghost_type1,
__attribute__((unused)) ElementType type2,
__attribute__((unused)) GhostType ghost_type2) {
}
/* ------------------------------------------------------------------------ */
inline Real operator()(Real r,
const __attribute__((unused)) QuadraturePoint & q1,
const __attribute__((unused)) QuadraturePoint & q2) {
Real w = 0;
if(r <= R) {
Real alpha = (1. - r*r / R2);
w = alpha * alpha;
// *weight = 1 - sqrt(r / radius);
}
return w;
}
void printself(std::ostream & stream, int indent) const {
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;
}
public:
Real getRadius() { return R; }
UInt getUpdateRate() { return update_rate; }
public:
virtual UInt getNbDataForElements(__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {
return 0;
}
virtual inline void packElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {}
virtual inline void unpackElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) {}
protected:
Material & material;
Real R;
Real R2;
UInt update_rate;
const std::string type;
};
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
class DamagedWeightFunction : public BaseWeightFunction<spatial_dimension> {
public:
DamagedWeightFunction(Material & material) : BaseWeightFunction<spatial_dimension>(material, "damaged") {
- AKANTU_DEBUG_ASSERT(dynamic_cast<MaterialDamage<spatial_dimension> *>(&material) != NULL, "This weight function works only with damage materials!");
+ //AKANTU_DEBUG_ASSERT(dynamic_cast<MaterialDamage<spatial_dimension> *>(&material) != NULL, "This weight function works only with damage materials!");
}
inline void selectType(__attribute__((unused)) ElementType type1,
__attribute__((unused)) GhostType ghost_type1,
ElementType type2,
GhostType ghost_type2) {
selected_damage = &dynamic_cast<MaterialDamage<spatial_dimension> &>(this->material).getDamage(type2, ghost_type2);
}
inline Real operator()(Real r,
const __attribute__((unused)) QuadraturePoint & q1,
const QuadraturePoint & q2) {
UInt quad = q2.global_num;
Real D = (*selected_damage)(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;
}
private:
const Array<Real> * selected_damage;
};
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
class RemoveDamagedWeightFunction : public BaseWeightFunction<spatial_dimension> {
public:
RemoveDamagedWeightFunction(Material & material) : BaseWeightFunction<spatial_dimension>(material, "remove_damaged") {
AKANTU_DEBUG_ASSERT(dynamic_cast<MaterialDamage<spatial_dimension> *>(&material) != NULL, "This weight function works only with damage materials!");
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable, "Damage Threshold");
}
inline void selectType(__attribute__((unused)) ElementType type1,
__attribute__((unused)) GhostType ghost_type1,
ElementType type2,
GhostType ghost_type2) {
MaterialDamage<spatial_dimension> & mat = dynamic_cast<MaterialDamage<spatial_dimension> &>(this->material);
selected_damage = &mat.getDamage(type2, ghost_type2);
}
inline Real operator()(Real r,
const __attribute__((unused)) QuadraturePoint & q1,
const QuadraturePoint & q2) {
UInt quad = q2.global_num;
if(q1 == q2) return 1.;
Real D = (*selected_damage)(quad);
Real w = 0.;
if(D < damage_limit) {
Real alpha = std::max(0., 1. - r*r / this->R2);
w = alpha * alpha;
}
return w;
}
virtual UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
if(tag == _gst_mnl_weight)
return this->material.getModel().getNbQuadraturePoints(elements) * sizeof(Real);
return 0;
}
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if(tag == _gst_mnl_weight) {
ElementTypeMapArray<Real> & damage = this->material.getInternal("damage");
this->material.packElementDataHelper(damage,
buffer,
elements);
}
}
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if(tag == _gst_mnl_weight) {
ElementTypeMapArray<Real> & damage = this->material.getInternal("damage");
this->material.unpackElementDataHelper(damage,
buffer,
elements);
}
}
private:
/// limit at which a point is considered as complitely broken
Real damage_limit;
/// internal pointer to the current damage vector
const Array<Real> * selected_damage;
};
/* -------------------------------------------------------------------------- */
/* Remove damaged with damage rate weight function */
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
class RemoveDamagedWithDamageRateWeightFunction : public BaseWeightFunction<spatial_dimension> {
public:
RemoveDamagedWithDamageRateWeightFunction(Material & material) : BaseWeightFunction<spatial_dimension>(material, "remove_damage_with_damage_rate") {
this->registerParam("damage_limit", this->damage_limit_with_damage_rate, 1, _pat_parsable, "Damage Threshold");
}
inline void selectType(__attribute__((unused)) ElementType type1,
__attribute__((unused)) GhostType ghost_type1,
ElementType type2,
GhostType ghost_type2) {
selected_damage_with_damage_rate = &(this->material.getArray("damage",type2, ghost_type2));
selected_damage_rate_with_damage_rate = &(this->material.getArray("damage-rate",type2, ghost_type2));
}
inline Real operator()(Real r,
const __attribute__((unused)) QuadraturePoint & q1,
const QuadraturePoint & q2) {
UInt quad = q2.global_num;
if(q1.global_num == quad) return 1.;
Real D = (*selected_damage_with_damage_rate)(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;
}
private:
/// limit at which a point is considered as complitely broken
Real damage_limit_with_damage_rate;
/// internal pointer to the current damage vector
const Array<Real> * selected_damage_with_damage_rate;
/// internal pointer to the current damage rate vector
const Array<Real> * selected_damage_rate_with_damage_rate;
};
/* -------------------------------------------------------------------------- */
/* Stress Based Weight */
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
class StressBasedWeightFunction : public BaseWeightFunction<spatial_dimension> {
public:
StressBasedWeightFunction(Material & material);
void init();
virtual void updateInternals(__attribute__((unused)) const ElementTypeMapArray<Real> & quadrature_points_coordinates) {
updatePrincipalStress(_not_ghost);
updatePrincipalStress(_ghost);
};
void updatePrincipalStress(GhostType ghost_type);
inline void updateQuadraturePointsCoordinates(ElementTypeMapArray<Real> & quadrature_points_coordinates);
inline void selectType(ElementType type1, GhostType ghost_type1,
ElementType type2, GhostType ghost_type2);
inline Real operator()(Real r,
const QuadraturePoint & q1,
const QuadraturePoint & q2);
inline Real computeRhoSquare(Real r,
Vector<Real> & eigs,
Matrix<Real> & eigenvects,
Vector<Real> & x_s);
private:
Real ft;
InternalField<Real> stress_diag;
Array<Real> * selected_stress_diag;
InternalField<Real> stress_base;
Array<Real> * selected_stress_base;
// InternalField<Real> quadrature_points_coordinates;
Array<Real> * selected_position_1;
Array<Real> * selected_position_2;
InternalField<Real> characteristic_size;
Array<Real> * selected_characteristic_size;
};
template<UInt spatial_dimension>
inline std::ostream & operator <<(std::ostream & stream,
const BaseWeightFunction<spatial_dimension> & _this)
{
_this.printself(stream);
return stream;
}
#include "weight_function_tmpl.hh"
__END_AKANTU__
#endif /* __AKANTU_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index ea0758e95..877eec3f3 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1834 +1,1834 @@
/**
* @file solid_mechanics_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.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: Tue Jul 27 2010
* @date last modification: Fri Sep 19 2014
*
* @brief Implementation of the SolidMechanicsModel class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_math.hh"
#include "aka_common.hh"
#include "solid_mechanics_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#include "integration_scheme_2nd_order.hh"
#include "element_group.hh"
#include "static_communicator.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include <cmath>
#ifdef AKANTU_USE_MUMPS
#include "solver_mumps.hh"
#endif
#ifdef AKANTU_USE_PETSC
#include "solver_petsc.hh"
#include "petsc_matrix.hh"
#endif
#ifdef AKANTU_USE_IOHELPER
# include "dumper_field.hh"
# include "dumper_paraview.hh"
# include "dumper_homogenizing_field.hh"
# include "dumper_material_internal_field.hh"
# include "dumper_elemental_field.hh"
# include "dumper_material_padders.hh"
# include "dumper_element_partition.hh"
# include "dumper_iohelper.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
const SolidMechanicsModelOptions default_solid_mechanics_model_options(_explicit_lumped_mass, false);
/* -------------------------------------------------------------------------- */
/**
* 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
*/
SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh,
UInt dim,
const ID & id,
const MemoryID & memory_id) :
Model(mesh, dim, id, memory_id),
BoundaryCondition<SolidMechanicsModel>(),
time_step(NAN), f_m2a(1.0),
mass_matrix(NULL),
velocity_damping_matrix(NULL),
stiffness_matrix(NULL),
jacobian_matrix(NULL),
material_index("material index", id),
material_local_numbering("material local numbering", id),
material_selector(new DefaultMaterialSelector(material_index)),
is_default_material_selector(true),
integrator(NULL),
increment_flag(false), solver(NULL),
synch_parallel(NULL),
are_materials_instantiated(false) {
AKANTU_DEBUG_IN();
createSynchronizerRegistry(this);
registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh, spatial_dimension);
this->displacement = NULL;
this->mass = NULL;
this->velocity = NULL;
this->acceleration = NULL;
this->force = NULL;
this->residual = NULL;
this->blocked_dofs = NULL;
this->increment = NULL;
this->increment_acceleration = NULL;
this->dof_synchronizer = NULL;
this->previous_displacement = NULL;
materials.clear();
mesh.registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() {
AKANTU_DEBUG_IN();
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
delete *mat_it;
}
materials.clear();
delete integrator;
delete solver;
delete mass_matrix;
delete velocity_damping_matrix;
if(stiffness_matrix && stiffness_matrix != jacobian_matrix)
delete stiffness_matrix;
delete jacobian_matrix;
delete synch_parallel;
if(is_default_material_selector) {
delete material_selector;
material_selector = NULL;
}
AKANTU_DEBUG_OUT();
}
void SolidMechanicsModel::setTimeStep(Real time_step) {
this->time_step = time_step;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
/**
* 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 material_file the file containing the materials to use
* @param method the analysis method wanted. See the akantu::AnalysisMethod for
* the different possibilities
*/
void SolidMechanicsModel::initFull(const ModelOptions & options) {
Model::initFull(options);
const SolidMechanicsModelOptions & smm_options =
dynamic_cast<const SolidMechanicsModelOptions &>(options);
method = smm_options.analysis_method;
// initialize the vectors
initArrays();
// set the initial condition to 0
force->clear();
velocity->clear();
acceleration->clear();
displacement->clear();
// initialize pcb
if(pbc_pair.size()!=0)
initPBC();
// initialize the time integration schemes
switch(method) {
case _explicit_lumped_mass:
initExplicit();
break;
case _explicit_consistent_mass:
initSolver();
initExplicit();
break;
case _implicit_dynamic:
initImplicit(true);
break;
case _static:
initImplicit(false);
break;
default:
AKANTU_EXCEPTION("analysis method not recognised by SolidMechanicsModel");
break;
}
// initialize the materials
if(this->parser->getLastParsedFile() != "") {
instantiateMaterials();
}
if(!smm_options.no_init_materials) {
initMaterials();
}
if(increment_flag)
initBC(*this, *displacement, *increment, *force);
else
initBC(*this, *displacement, *force);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initParallel(MeshPartition * partition,
DataAccessor * data_accessor) {
AKANTU_DEBUG_IN();
if (data_accessor == NULL) data_accessor = this;
synch_parallel = &createParallelSynch(partition,data_accessor);
synch_registry->registerSynchronizer(*synch_parallel, _gst_material_id);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_mass);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_stress);
synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_boundary);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initFEEngineBoundary() {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnControlPoints(_not_ghost);
fem_boundary.computeNormalsOnControlPoints(_ghost);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initExplicit(AnalysisMethod analysis_method) {
AKANTU_DEBUG_IN();
//in case of switch from implicit to explicit
if(!this->isExplicit())
method = analysis_method;
if (integrator) delete integrator;
integrator = new CentralDifference();
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
std::stringstream sstr; sstr << id << ":increment_acceleration";
increment_acceleration = &(alloc<Real>(sstr.str(), nb_nodes, nb_degree_of_freedom, Real()));
AKANTU_DEBUG_OUT();
}
void SolidMechanicsModel::initArraysPreviousDisplacment() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::setIncrementFlagOn();
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp_t;
sstr_disp_t << id << ":previous_displacement";
previous_displacement = &(alloc<Real > (sstr_disp_t.str(), nb_nodes, spatial_dimension, 0.));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Allocate all the needed vectors. By default their are not necessarily set to
* 0
*
*/
void SolidMechanicsModel::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp; sstr_disp << id << ":displacement";
// std::stringstream sstr_mass; sstr_mass << id << ":mass";
std::stringstream sstr_velo; sstr_velo << id << ":velocity";
std::stringstream sstr_acce; sstr_acce << id << ":acceleration";
std::stringstream sstr_forc; sstr_forc << id << ":force";
std::stringstream sstr_resi; sstr_resi << id << ":residual";
std::stringstream sstr_boun; sstr_boun << id << ":blocked_dofs";
displacement = &(alloc<Real>(sstr_disp.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
// mass = &(alloc<Real>(sstr_mass.str(), nb_nodes, spatial_dimension, 0));
velocity = &(alloc<Real>(sstr_velo.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
acceleration = &(alloc<Real>(sstr_acce.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
force = &(alloc<Real>(sstr_forc.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
residual = &(alloc<Real>(sstr_resi.str(), nb_nodes, spatial_dimension, REAL_INIT_VALUE));
blocked_dofs = &(alloc<bool>(sstr_boun.str(), nb_nodes, spatial_dimension, false));
std::stringstream sstr_curp; sstr_curp << id << ":current_position";
current_position = &(alloc<Real>(sstr_curp.str(), 0, spatial_dimension, REAL_INIT_VALUE));
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, gt);
material_index.alloc(nb_element, 1, *it, gt);
material_local_numbering.alloc(nb_element, 1, *it, gt);
}
}
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* 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::initPBC() {
Model::initPBC();
registerPBCSynchronizer();
// as long as there are ones on the diagonal of the matrix, we can put boudandary true for slaves
std::map<UInt, UInt>::iterator it = pbc_pair.begin();
std::map<UInt, UInt>::iterator end = pbc_pair.end();
UInt dim = mesh.getSpatialDimension();
while(it != end) {
for (UInt i=0; i<dim; ++i)
(*blocked_dofs)((*it).first,i) = true;
++it;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::registerPBCSynchronizer(){
PBCSynchronizer * synch = new PBCSynchronizer(pbc_pair);
synch_registry->registerSynchronizer(*synch, _gst_smm_uv);
synch_registry->registerSynchronizer(*synch, _gst_smm_mass);
synch_registry->registerSynchronizer(*synch, _gst_smm_res);
synch_registry->registerSynchronizer(*synch, _gst_for_dump);
changeLocalEquationNumberForPBC(pbc_pair, mesh.getSpatialDimension());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
current_position->resize(nb_nodes);
Real * current_position_val = current_position->storage();
Real * position_val = mesh.getNodes().storage();
Real * displacement_val = displacement->storage();
/// compute current_position = initial_position + displacement
memcpy(current_position_val, position_val, nb_nodes*spatial_dimension*sizeof(Real));
for (UInt n = 0; n < nb_nodes*spatial_dimension; ++n) {
*current_position_val++ += *displacement_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initializeUpdateResidualData() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
residual->resize(nb_nodes);
/// copy the forces in residual for boundary conditions
memcpy(residual->storage(), force->storage(), nb_nodes*spatial_dimension*sizeof(Real));
// start synchronization
synch_registry->asynchronousSynchronize(_gst_smm_uv);
synch_registry->waitEndSynchronize(_gst_smm_uv);
updateCurrentPosition();
AKANTU_DEBUG_OUT();
}
/*----------------------------------------------------------------------------*/
void SolidMechanicsModel::reInitialize()
{
}
/* -------------------------------------------------------------------------- */
/* Explicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* This function compute the second member of the motion equation. That is to
* say the sum of forces @f$ r = F_{ext} - F_{int} @f$. @f$ F_{ext} @f$ is given
* by the user in the force vector, and @f$ F_{int} @f$ is computed as @f$
* F_{int} = \int_{\Omega} N \sigma d\Omega@f$
*
*/
void SolidMechanicsModel::updateResidual(bool need_initialize) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
// f = f_ext - f_int
// f = f_ext
if(need_initialize) initializeUpdateResidualData();
AKANTU_DEBUG_INFO("Compute local stresses");
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStresses(_not_ghost);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
synch_registry->asynchronousSynchronize(_gst_mnl_for_average);
AKANTU_DEBUG_INFO("Compute non local stresses for local elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_not_ghost);
}
AKANTU_DEBUG_INFO("Wait distant non local stresses");
synch_registry->waitEndSynchronize(_gst_mnl_for_average);
AKANTU_DEBUG_INFO("Compute non local stresses for ghosts elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_ghost);
}
#endif
/* ------------------------------------------------------------------------ */
/* assembling the forces internal */
// communicate the stress
AKANTU_DEBUG_INFO("Send data for residual assembly");
synch_registry->asynchronousSynchronize(_gst_smm_stress);
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.assembleResidual(_not_ghost);
}
AKANTU_DEBUG_INFO("Wait distant stresses");
// finalize communications
synch_registry->waitEndSynchronize(_gst_smm_stress);
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.assembleResidual(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeStresses() {
if (isExplicit()) {
// start synchronization
synch_registry->asynchronousSynchronize(_gst_smm_uv);
synch_registry->waitEndSynchronize(_gst_smm_uv);
// compute stresses on all local elements for each materials
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStresses(_not_ghost);
}
/* ------------------------------------------------------------------------ */
#ifdef AKANTU_DAMAGE_NON_LOCAL
/* Computation of the non local part */
synch_registry->asynchronousSynchronize(_gst_mnl_for_average);
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_not_ghost);
}
synch_registry->waitEndSynchronize(_gst_mnl_for_average);
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllNonLocalStresses(_ghost);
}
#endif
} else {
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
mat.computeAllStressesFromTangentModuli(_not_ghost);
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateResidualInternal() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Update the residual");
// f = f_ext - f_int - Ma - Cv = r - Ma - Cv;
if(method != _static) {
// f -= Ma
if(mass_matrix) {
// if full mass_matrix
Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
*Ma *= *mass_matrix;
/// \todo check unit conversion for implicit dynamics
// *Ma /= f_m2a
*residual -= *Ma;
delete Ma;
} else if (mass) {
// else lumped mass
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
Real * mass_val = mass->storage();
Real * accel_val = acceleration->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*res_val -= *accel_val * *mass_val /f_m2a;
}
blocked_dofs_val++;
res_val++;
mass_val++;
accel_val++;
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
// f -= Cv
if(velocity_damping_matrix) {
Array<Real> * Cv = new Array<Real>(*velocity);
*Cv *= *velocity_damping_matrix;
*residual -= *Cv;
delete Cv;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateAcceleration() {
AKANTU_DEBUG_IN();
updateResidualInternal();
if(method == _explicit_lumped_mass) {
/* residual = residual_{n+1} - M * acceleration_n therefore
solution = increment acceleration not acceleration */
solveLumped(*increment_acceleration,
*mass,
*residual,
*blocked_dofs,
f_m2a);
} else if (method == _explicit_consistent_mass) {
solve<NewmarkBeta::_acceleration_corrector>(*increment_acceleration);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::solveLumped(Array<Real> & x,
const Array<Real> & A,
const Array<Real> & b,
const Array<bool> & blocked_dofs,
Real alpha) {
Real * A_val = A.storage();
Real * b_val = b.storage();
Real * x_val = x.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
UInt nb_degrees_of_freedom = x.getSize() * x.getNbComponent();
for (UInt n = 0; n < nb_degrees_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*x_val = alpha * (*b_val / *A_val);
}
x_val++;
A_val++;
b_val++;
blocked_dofs_val++;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::explicitPred() {
AKANTU_DEBUG_IN();
if(increment_flag) {
if(previous_displacement) increment->copy(*previous_displacement);
else increment->copy(*displacement);
}
AKANTU_DEBUG_ASSERT(integrator,"itegrator should have been allocated: "
<< "have called initExplicit ? "
<< "or initImplicit ?");
integrator->integrationSchemePred(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs);
if(increment_flag) {
Real * inc_val = increment->storage();
Real * dis_val = displacement->storage();
UInt nb_degree_of_freedom = displacement->getSize() * displacement->getNbComponent();
for (UInt n = 0; n < nb_degree_of_freedom; ++n) {
*inc_val = *dis_val - *inc_val;
inc_val++;
dis_val++;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::explicitCorr() {
AKANTU_DEBUG_IN();
integrator->integrationSchemeCorrAccel(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs,
*increment_acceleration);
if(previous_displacement) previous_displacement->copy(*displacement);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::solveStep() {
AKANTU_DEBUG_IN();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
this->explicitPred();
this->updateResidual();
this->updateAcceleration();
this->explicitCorr();
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Implicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Initialize the solver and create the sparse matrices needed.
*
*/
void SolidMechanicsModel::initSolver(__attribute__((unused)) SolverOptions & options) {
#if !defined(AKANTU_USE_MUMPS) && !defined(AKANTU_USE_PETSC)// or other solver in the future \todo add AKANTU_HAS_SOLVER in CMake
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#else
UInt nb_global_nodes = mesh.getNbGlobalNodes();
delete jacobian_matrix;
std::stringstream sstr; sstr << id << ":jacobian_matrix";
#ifdef AKANTU_USE_PETSC
jacobian_matrix = new PETScMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
#else
jacobian_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
#endif //AKANTU_USE PETSC
jacobian_matrix->buildProfile(mesh, *dof_synchronizer, spatial_dimension);
if (!isExplicit()) {
delete stiffness_matrix;
std::stringstream sstr_sti; sstr_sti << id << ":stiffness_matrix";
#ifdef AKANTU_USE_PETSC
stiffness_matrix = new SparseMatrix(nb_global_nodes * spatial_dimension, _symmetric, sstr.str(), memory_id);
stiffness_matrix->buildProfile(mesh, *dof_synchronizer, spatial_dimension);
#else
stiffness_matrix = new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
#endif //AKANTU_USE_PETSC
}
delete solver;
std::stringstream sstr_solv; sstr_solv << id << ":solver";
#ifdef AKANTU_USE_PETSC
solver = new SolverPETSc(*jacobian_matrix, sstr_solv.str());
#elif defined(AKANTU_USE_MUMPS)
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif //AKANTU_USE_MUMPS
if(solver)
solver->initialize(options);
#endif //AKANTU_HAS_SOLVER
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initJacobianMatrix() {
#if defined(AKANTU_USE_MUMPS) && !defined(AKANTU_USE_PETSC)
// @todo make it more flexible: this is an ugly patch to treat the case of non
// fix profile of the K matrix
delete jacobian_matrix;
std::stringstream sstr_sti; sstr_sti << id << ":jacobian_matrix";
jacobian_matrix = new SparseMatrix(*stiffness_matrix, sstr_sti.str(), memory_id);
std::stringstream sstr_solv; sstr_solv << id << ":solver";
delete solver;
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
if(solver)
solver->initialize(_solver_no_options);
#else
AKANTU_DEBUG_ERROR("You need to activate the solver mumps.");
#endif
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the implicit solver, either for dynamic or static cases,
*
* @param dynamic
*/
void SolidMechanicsModel::initImplicit(bool dynamic, SolverOptions & solver_options) {
AKANTU_DEBUG_IN();
method = dynamic ? _implicit_dynamic : _static;
if (!increment) setIncrementFlagOn();
initSolver(solver_options);
if(method == _implicit_dynamic) {
if(integrator) delete integrator;
integrator = new TrapezoidalRule2();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initialAcceleration() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Solving Ma = f");
Solver * acc_solver = NULL;
std::stringstream sstr; sstr << id << ":tmp_mass_matrix";
SparseMatrix * tmp_mass = new SparseMatrix(*mass_matrix, sstr.str(), memory_id);
#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solver; sstr << id << ":solver_mass_matrix";
acc_solver = new SolverMumps(*mass_matrix, sstr_solver.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif //AKANTU_USE_MUMPS
acc_solver->initialize();
tmp_mass->applyBoundary(*blocked_dofs);
acc_solver->setRHS(*residual);
acc_solver->solve(*acceleration);
delete acc_solver;
delete tmp_mass;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
stiffness_matrix->clear();
// call compute stiffness matrix on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->assembleStiffnessMatrix(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix & SolidMechanicsModel::initVelocityDampingMatrix() {
if(!velocity_damping_matrix)
velocity_damping_matrix =
new SparseMatrix(*jacobian_matrix, id + ":velocity_damping_matrix", memory_id);
return *velocity_damping_matrix;
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_increment>(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent();
error = 0;
Real norm[2] = {0., 0.};
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
Real * displacement_val = displacement->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val) && is_local_node) {
norm[0] += *increment_val * *increment_val;
norm[1] += *displacement_val * *displacement_val;
}
blocked_dofs_val++;
increment_val++;
displacement_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);
norm[0] = sqrt(norm[0]);
norm[1] = sqrt(norm[1]);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]), "Something goes wrong in the solve phase");
if (norm[1] < Math::getTolerance()) {
error = norm[0];
AKANTU_DEBUG_OUT();
// cout<<"Error 1: "<<error<<endl;
return error < tolerance;
}
AKANTU_DEBUG_OUT();
if(norm[1] > Math::getTolerance())
error = norm[0] / norm[1];
else
error = norm[0]; //In case the total displacement is zero!
// cout<<"Error 2: "<<error<<endl;
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_residual>(Real tolerance, Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent();
norm = 0;
Real * residual_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if(is_local_node) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val;
}
blocked_dofs_val++;
residual_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
bool SolidMechanicsModel::testConvergence<_scc_residual_mass_wgh>(Real tolerance,
Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
norm = 0;
Real * residual_val = residual->storage();
Real * mass_val = this->mass->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if(is_local_node) {
for (UInt d = 0; d < spatial_dimension; ++d) {
if(!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val/(*mass_val * *mass_val);
}
blocked_dofs_val++;
residual_val++;
mass_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
mass_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceResidual(Real tolerance){
AKANTU_DEBUG_IN();
Real error=0;
bool res = this->testConvergence<_scc_residual>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceResidual(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
bool res = this->testConvergence<_scc_residual>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance){
AKANTU_DEBUG_IN();
Real error=0;
bool res = this->testConvergence<_scc_increment>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::testConvergenceIncrement(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
bool res = this->testConvergence<_scc_increment>(tolerance, error);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::implicitPred() {
AKANTU_DEBUG_IN();
if(previous_displacement) previous_displacement->copy(*displacement);
if(method == _implicit_dynamic)
integrator->integrationSchemePred(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::implicitCorr() {
AKANTU_DEBUG_IN();
if(method == _implicit_dynamic) {
integrator->integrationSchemeCorrDispl(time_step,
*displacement,
*velocity,
*acceleration,
*blocked_dofs,
*increment);
} else {
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
Real * incr_val = increment->storage();
Real * disp_val = displacement->storage();
bool * boun_val = blocked_dofs->storage();
for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++boun_val){
*incr_val *= (1. - *boun_val);
*disp_val += *incr_val;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateIncrement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
<< " Are you working with Finite or Ineslactic deformations?");
UInt nb_nodes = displacement->getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
Real * incr_val = increment->storage();
Real * disp_val = displacement->storage();
Real * prev_disp_val = previous_displacement->storage();
for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val, ++prev_disp_val)
*incr_val = (*disp_val - *prev_disp_val);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updatePreviousDisplacement() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(previous_displacement,"The previous displacement has to be initialized."
<< " Are you working with Finite or Ineslactic deformations?");
previous_displacement->copy(*displacement);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::synchronizeBoundaries() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
<< " Did you call initParallel?");
synch_registry->synchronize(_gst_smm_boundary);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::synchronizeResidual() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(synch_registry,"Synchronizer registry was not initialized."
<< " Did you call initPBC?");
synch_registry->synchronize(_gst_smm_res);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setIncrementFlagOn() {
AKANTU_DEBUG_IN();
if(!increment) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_inc; sstr_inc << id << ":increment";
increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, spatial_dimension, 0.));
}
increment_flag = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&min_dt, 1, _so_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Material ** mat_val = &(materials.at(0));
Real min_dt = std::numeric_limits<Real>::max();
updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
elem.kind = _ek_regular;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type);
for(; it != end; ++it) {
elem.type = *it;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*it);
UInt nb_element = mesh.getNbElement(*it);
Array<UInt>::const_scalar_iterator mat_indexes = material_index(*it, ghost_type).begin();
Array<UInt>::const_scalar_iterator mat_loc_num = material_local_numbering(*it, ghost_type).begin();
Array<Real> X(0, nb_nodes_per_element*spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position,
X, *it, _not_ghost);
Array<Real>::matrix_iterator X_el =
X.begin(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, *it);
Real el_c = mat_val[*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::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real energy = 0.;
/// call update residual on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
energy += (*mat_it)->getPotentialEnergy();
}
/// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
if (!mass && !mass_matrix)
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
Real * vel_val = velocity->storage();
Real * mass_val = mass->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
Real mv2 = 0;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (count_node)
mv2 += *vel_val * *vel_val * *mass_val;
vel_val++;
mass_val++;
}
ekin += mv2;
}
StaticCommunicator::getStaticCommunicator().allReduce(&ekin, 1, _so_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy(const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnQuadraturePoints(*velocity, vel_on_quad,
spatial_dimension,
type, _not_ghost,
filter_element);
Array<Real>::vector_iterator vit = vel_on_quad.begin(spatial_dimension);
Array<Real>::vector_iterator vend = vel_on_quad.end(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();
Real * velo = velocity->storage();
Real * forc = force->storage();
Real * resi = residual->storage();
bool * boun = blocked_dofs->storage();
Real work = 0.;
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
for (UInt i = 0; i < spatial_dimension; ++i) {
if (count_node) {
if(*boun)
work -= *resi * *velo * time_step;
else
work += *forc * *velo * time_step;
}
++velo;
++forc;
++resi;
++boun;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&work, 1, _so_sum);
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
} else if (energy_id == "external work"){
return getExternalWork();
}
Real energy = 0.;
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
energy += (*mat_it)->getEnergy(energy_id);
}
/// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
const ElementType & type,
UInt index){
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
std::vector<Material *>::iterator mat_it;
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;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
this->getFEEngine().initShapeFunctions(_not_ghost);
this->getFEEngine().initShapeFunctions(_ghost);
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
Mesh::type_iterator it = this->mesh.firstType(spatial_dimension, gt, _ek_not_defined);
Mesh::type_iterator end = this->mesh.lastType(spatial_dimension, gt, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = this->mesh.getNbElement(*it, gt);
if(!material_index.exists(*it, gt)) {
this->material_index .alloc(nb_element, 1, *it, gt);
this->material_local_numbering.alloc(nb_element, 1, *it, gt);
} else {
this->material_index (*it, gt).resize(nb_element);
this->material_local_numbering(*it, gt).resize(nb_element);
}
}
}
Array<Element>::const_iterator<Element> it = element_list.begin();
Array<Element>::const_iterator<Element> end = element_list.end();
ElementTypeMapArray<UInt> filter("new_element_filter", this->getID());
for (UInt el = 0; it != end; ++it, ++el) {
const Element & elem = *it;
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->assignMaterialToElements(&filter);
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onElementsAdded(element_list, event);
}
if(method == _explicit_lumped_mass) this->assembleMassLumped();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(__attribute__((unused)) const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
this->getFEEngine().initShapeFunctions(_not_ghost);
this->getFEEngine().initShapeFunctions(_ghost);
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
__attribute__((unused)) const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if(displacement) displacement->resize(nb_nodes);
if(mass ) mass ->resize(nb_nodes);
if(velocity ) velocity ->resize(nb_nodes);
if(acceleration) acceleration->resize(nb_nodes);
if(force ) force ->resize(nb_nodes);
if(residual ) residual ->resize(nb_nodes);
if(blocked_dofs) blocked_dofs->resize(nb_nodes);
if(previous_displacement) previous_displacement->resize(nb_nodes);
if(increment_acceleration) increment_acceleration->resize(nb_nodes);
if(increment) increment->resize(nb_nodes);
if(current_position) current_position->resize(nb_nodes);
delete dof_synchronizer;
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
(*mat_it)->onNodesAdded(nodes_list, event);
}
if (method != _explicit_lumped_mass) {
this->initSolver();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(__attribute__((unused)) const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
__attribute__((unused)) const RemovedNodesEvent & event) {
if(displacement) mesh.removeNodesFromArray(*displacement, new_numbering);
if(mass ) mesh.removeNodesFromArray(*mass , new_numbering);
if(velocity ) mesh.removeNodesFromArray(*velocity , new_numbering);
if(acceleration) mesh.removeNodesFromArray(*acceleration, new_numbering);
if(force ) mesh.removeNodesFromArray(*force , new_numbering);
if(residual ) mesh.removeNodesFromArray(*residual , new_numbering);
if(blocked_dofs) mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
if(increment_acceleration) mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
if(increment) mesh.removeNodesFromArray(*increment , new_numbering);
delete dof_synchronizer;
dof_synchronizer = new DOFSynchronizer(mesh, spatial_dimension);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
if (method != _explicit_lumped_mass) {
this->initSolver();
}
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
const ElementKind & element_kind){
bool is_internal = false;
/// check if at least one material contains field_id as an internal
for (UInt m = 0; m < materials.size() && !is_internal; ++m) {
is_internal |= materials[m]->isInternal(field_name, element_kind);
}
return is_internal;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt> SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
- const ElementKind & element_kind,
- const std::string & fe_engine_id){
+ const ElementKind & element_kind){
if (!(this->isInternal(field_name,element_kind))) AKANTU_EXCEPTION("unknown internal " << field_name);
for (UInt m = 0; m < materials.size() ; ++m) {
if (materials[m]->isInternal(field_name, element_kind))
- return materials[m]->getInternalDataPerElem(field_name,element_kind,fe_engine_id);
+ return materials[m]->getInternalDataPerElem(field_name,element_kind);
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> & SolidMechanicsModel::flattenInternal(const std::string & field_name,
const ElementKind & kind, const GhostType ghost_type){
std::pair<std::string,ElementKind> key(field_name,kind);
if (this->registered_internals.count(key) == 0){
this->registered_internals[key] =
new ElementTypeMapArray<Real>(field_name,this->id);
}
ElementTypeMapArray<Real> * internal_flat = this->registered_internals[key];
for (UInt m = 0; m < materials.size(); ++m)
materials[m]->flattenInternal(field_name,*internal_flat,ghost_type,kind);
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(const ElementKind & kind){
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *> ::iterator it = this->registered_internals.begin();
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *>::iterator end = this->registered_internals.end();
while (it != end){
if (kind == it->first.second)
this->flattenInternal(it->first.first,kind);
++it;
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump(){
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * SolidMechanicsModel
::createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
- const ElementKind & kind,
- const std::string & fe_engine_id){
+ const UInt & spatial_dimension,
+ const ElementKind & kind) {
dumper::Field * field = NULL;
if(field_name == "partitions")
- field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(mesh.getConnectivities(),group_name,this->spatial_dimension,kind);
+ field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(mesh.getConnectivities(),group_name,spatial_dimension,kind);
else if(field_name == "material_index")
- field = mesh.createElementalField<UInt, Vector, dumper::ElementalField >(material_index,group_name,this->spatial_dimension,kind);
+ field = mesh.createElementalField<UInt, Vector, dumper::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) {
- ElementTypeMap<UInt> nb_data_per_elem = this->getInternalDataPerElem(field_name_copy,kind,fe_engine_id);
+ ElementTypeMap<UInt> nb_data_per_elem = this->getInternalDataPerElem(field_name_copy,kind);
ElementTypeMapArray<Real> & internal_flat = this->flattenInternal(field_name_copy,kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(internal_flat,
group_name,
- this->spatial_dimension,kind,nb_data_per_elem);
+ spatial_dimension,kind,nb_data_per_elem);
if (field_name == "strain"){
dumper::ComputeStrain<false> * foo = new dumper::ComputeStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
} else if (field_name == "Von Mises stress") {
dumper::ComputeVonMisesStress * foo = new dumper::ComputeVonMisesStress(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
} else if (field_name == "Green strain") {
dumper::ComputeStrain<true> * foo = new dumper::ComputeStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
} else if (field_name == "principal strain") {
dumper::ComputePrincipalStrain<false> * foo = new dumper::ComputePrincipalStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
} else if (field_name == "principal Green strain") {
dumper::ComputePrincipalStrain<true> * foo = new dumper::ComputePrincipalStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
//treat the paddings
if (padding_flag){
if (field_name == "stress"){
- if (this->spatial_dimension == 2) {
+ if (spatial_dimension == 2) {
dumper::StressPadder<2> * foo = new dumper::StressPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
} else if (field_name == "strain" || field_name == "Green strain"){
- if (this->spatial_dimension == 2) {
+ if (spatial_dimension == 2) {
dumper::StrainPadder<2> * foo = new dumper::StrainPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
}
}
// homogenize the field
dumper::ComputeFunctorInterface * foo =
dumper::HomogenizerProxy::createHomogenizer(*field);
field = dumper::FieldComputeProxy::createFieldCompute(field,*foo);
}
}
return field;
}
/* -------------------------------------------------------------------------- */
dumper::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" ] = displacement;
real_nodal_fields["mass" ] = mass;
real_nodal_fields["velocity" ] = velocity;
real_nodal_fields["acceleration" ] = acceleration;
real_nodal_fields["force" ] = force;
real_nodal_fields["residual" ] = residual;
real_nodal_fields["increment" ] = increment;
dumper::Field * field = NULL;
if (padding_flag)
field = mesh.createNodalField(real_nodal_fields[field_name],group_name, 3);
else
field = mesh.createNodalField(real_nodal_fields[field_name],group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string,Array<bool>* > uint_nodal_fields;
uint_nodal_fields["blocked_dofs" ] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name],group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel
::createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
- const ElementKind & kind){
+ const ElementKind & kind,
+ const std::string & fe_engine_id){
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * SolidMechanicsModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
return NULL;
}
#endif
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
mesh.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
mesh.dump(dumper_name, step);
}
/* ------------------------------------------------------------------------- */
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
synch_registry->synchronize(_gst_for_dump);
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);
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeCauchyStresses() {
AKANTU_DEBUG_IN();
// call compute stiffness matrix on each local elements
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
if(mat.isFiniteDeformation())
mat.computeAllCauchyStresses(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::saveStressAndStrainBeforeDamage() {
EventManager::sendEvent(SolidMechanicsModelEvent::BeginningOfDamageIterationEvent());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateEnergiesAfterDamage() {
EventManager::sendEvent(SolidMechanicsModelEvent::AfterDamageEvent());
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "Solid Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << 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;
displacement->printself(stream, indent + 2);
mass ->printself(stream, indent + 2);
velocity ->printself(stream, indent + 2);
acceleration->printself(stream, indent + 2);
force ->printself(stream, indent + 2);
residual ->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + material information [" << std::endl;
material_index.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + materials [" << std::endl;
std::vector<Material *>::const_iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
const Material & mat = *(*mat_it);
mat.printself(stream, indent + 1);
}
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index 3f610dc1f..1fa6a05af 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,747 +1,746 @@
/**
* @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: Tue Sep 16 2014
*
* @brief Model of Solid Mechanics
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_SOLID_MECHANICS_MODEL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
#include "model.hh"
#include "data_accessor.hh"
#include "mesh.hh"
#include "dumpable.hh"
#include "boundary_condition.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "integration_scheme_2nd_order.hh"
#include "solver.hh"
#include "material_selector.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class IntegrationScheme2ndOrder;
class SparseMatrix;
class DumperIOHelper;
}
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
struct SolidMechanicsModelOptions : public ModelOptions {
SolidMechanicsModelOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
bool no_init_materials = false) :
analysis_method(analysis_method),
no_init_materials(no_init_materials) { }
AnalysisMethod analysis_method;
bool no_init_materials;
};
extern const SolidMechanicsModelOptions default_solid_mechanics_model_options;
class SolidMechanicsModel : public Model,
public DataAccessor,
public MeshEventHandler,
public BoundaryCondition<SolidMechanicsModel>,
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;
};
typedef FEEngineTemplate <IntegratorGauss, ShapeLagrange> MyFEEngineType;
protected:
typedef EventHandlerManager <SolidMechanicsModelEventHandler> EventManager;
public:
SolidMechanicsModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize completely the model
virtual void initFull(const ModelOptions & options = default_solid_mechanics_model_options);
/// initialize the fem object needed for boundary conditions
void initFEEngineBoundary();
/// register the tags associated with the parallel synchronizer
void initParallel(MeshPartition *partition, DataAccessor *data_accessor = NULL);
/// allocate all vectors
void initArrays();
/// allocate all vectors
void initArraysPreviousDisplacment();
/// initialize all internal arrays for materials
virtual void initMaterials();
/// initialize the model
virtual void initModel();
/// init PBC synchronizer
void initPBC();
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// re-initialize model to set fields to 0
void reInitialize();
/* ------------------------------------------------------------------------ */
/* PBC */
/* ------------------------------------------------------------------------ */
public:
/// change the equation number for proper assembly when using PBC
// void changeEquationNumberforPBC(std::map <UInt, UInt> & pbc_pair);
/// synchronize Residual for output
void synchronizeResidual();
protected:
/// register PBC synchronizer
void registerPBCSynchronizer();
/* ------------------------------------------------------------------------ */
/* Explicit */
/* ------------------------------------------------------------------------ */
public:
/// initialize the stuff for the explicit scheme
void initExplicit(AnalysisMethod analysis_method = _explicit_lumped_mass);
bool isExplicit() {
return method == _explicit_lumped_mass || method == _explicit_consistent_mass;
}
/// initialize the array needed by updateResidual (residual, current_position)
void initializeUpdateResidualData();
/// update the current position vector
void updateCurrentPosition();
/// assemble the residual for the explicit scheme
virtual void updateResidual(bool need_initialize = true);
/**
* \brief compute the acceleration from the residual
* this function is the explicit equivalent to solveDynamic in implicit
* In the case of lumped mass just divide the residual by the mass
* In the case of not lumped mass call solveDynamic<_acceleration_corrector>
*/
void updateAcceleration();
void updateIncrement();
void updatePreviousDisplacement();
void saveStressAndStrainBeforeDamage();
void updateEnergiesAfterDamage();
/// Solve the system @f[ A x = \alpha b @f] with A a lumped matrix
void solveLumped(Array <Real> & x,
const Array <Real> & A,
const Array <Real> & b,
const Array <bool> & blocked_dofs,
Real alpha);
/// explicit integration predictor
void explicitPred();
/// explicit integration corrector
void explicitCorr();
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Implicit */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver and the jacobian_matrix (called by initImplicit)
void initSolver(SolverOptions & options = _solver_no_options);
/// initialize the stuff for the implicit solver
void initImplicit(bool dynamic = false,
SolverOptions & solver_options = _solver_no_options);
/// solve Ma = f to get the initial acceleration
void initialAcceleration();
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
public:
/**
* solve a step (predictor + convergence loop + corrector) using the
* the given convergence method (see akantu::SolveConvergenceMethod)
* and the given convergence criteria (see
* akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance, UInt max_iteration = 100);
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance,
Real & error,
UInt max_iteration = 100,
bool do_not_factorize = false);
public:
/**
* solve Ku = f using the the given convergence method (see
* akantu::SolveConvergenceMethod) and the given convergence
* criteria (see akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool solveStatic(Real tolerance, UInt max_iteration,
bool do_not_factorize = false);
/// test if the system is converged
template <SolveConvergenceCriteria criteria>
bool testConvergence(Real tolerance, Real & error);
/// test the convergence (norm of increment)
bool testConvergenceIncrement(Real tolerance) __attribute__((deprecated));
bool testConvergenceIncrement(Real tolerance, Real & error) __attribute__((deprecated));
/// test the convergence (norm of residual)
bool testConvergenceResidual(Real tolerance) __attribute__((deprecated));
bool testConvergenceResidual(Real tolerance, Real & error) __attribute__((deprecated));
/// create and return the velocity damping matrix
SparseMatrix & initVelocityDampingMatrix();
/// implicit time integration predictor
void implicitPred();
/// implicit time integration corrector
void implicitCorr();
/// compute the Cauchy stress on user demand.
void computeCauchyStresses();
protected:
/// finish the computation of residual to solve in increment
void updateResidualInternal();
/// compute the support reaction and store it in force
void updateSupportReaction();
public:
//protected: Daniel changed it just for a test
/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
template <NewmarkBeta::IntegrationSchemeCorrectorType type>
void solve(Array<Real> &increment, Real block_val = 1.,
bool need_factorize = true, bool has_profile_changed = false);
private:
/// re-initialize the J matrix (to use if the profile of K changed)
void initJacobianMatrix();
/* ------------------------------------------------------------------------ */
/* Explicit/Implicit */
/* ------------------------------------------------------------------------ */
public:
/// Update the stresses for the computation of the residual of the Stiffness
/// matrix in the case of finite deformation
void computeStresses();
/// synchronize the ghost element boundaries values
void synchronizeBoundaries();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// registers all the custom materials of a given type present in the input file
template <typename M>
void registerNewCustomMaterials(const ID & mat_type);
/// register an empty material of a given type
template <typename M>
Material & registerNewEmptyMaterial(const std::string & name);
// /// Use a UIntData in the mesh to specify the material to use per element
// void setMaterialIDsFromIntData(const std::string & data_name);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
protected:
/// register a material in the dynamic database
template <typename M>
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
void assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = NULL);
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
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);
/// fill a vector of rho
void computeRho(Array <Real> & rho,
ElementType type,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline virtual UInt getNbDataForElements(const Array <Element> & elements,
SynchronizationTag tag) const;
inline virtual void packElementData(CommunicationBuffer & buffer,
const Array <Element> & elements,
SynchronizationTag tag) const;
inline virtual void unpackElementData(CommunicationBuffer & buffer,
const Array <Element> & elements,
SynchronizationTag tag);
inline virtual UInt getNbDataToPack(SynchronizationTag tag) const;
inline virtual UInt getNbDataToUnpack(SynchronizationTag tag) const;
inline virtual void packData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) const;
inline virtual void unpackData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag);
protected:
inline void splitElementByMaterial(const Array <Element> & elements,
Array <Element> * elements_per_mat) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
virtual void onNodesAdded(const Array <UInt> & nodes_list,
const NewNodesEvent & event);
virtual void onNodesRemoved(const Array <UInt> & element_list,
const Array <UInt> & new_numbering,
const RemovedNodesEvent & event);
virtual void onElementsAdded(const Array <Element> & nodes_list,
const NewElementsEvent & event);
virtual void onElementsRemoved(const Array <Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* 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, const ElementKind & element_kind);
#ifndef SWIG
//! give the amount of data per element
- ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
- const ElementKind & kind,
- const std::string & fe_engine_id = "");
+ virtual ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
+ const ElementKind & kind);
//! flatten a given material internal field
ElementTypeMapArray<Real> & flattenInternal(const std::string & field_name,
const ElementKind & kind,
const GhostType ghost_type = _not_ghost);
//! flatten all the registered material internals
void flattenAllRegisteredInternals(const ElementKind & kind);
#endif
virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
- const ElementKind & kind,
- const std::string & fe_engine_id = "");
+ const UInt & spatial_dimension,
+ const ElementKind & kind);
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);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the current value of the time step
AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// set the value of the time step
void setTimeStep(Real time_step);
/// 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 vector
AKANTU_GET_MACRO(Displacement, *displacement, Array <Real> &);
/// get the SolidMechanicsModel::previous_displacement vector
AKANTU_GET_MACRO(PreviousDisplacement, *previous_displacement, Array <Real> &);
/// get the SolidMechanicsModel::current_position vector \warn only consistent
/// after a call to SolidMechanicsModel::updateCurrentPosition
AKANTU_GET_MACRO(CurrentPosition, *current_position, const Array <Real> &);
/// get the SolidMechanicsModel::increment vector \warn only consistent if
/// SolidMechanicsModel::setIncrementFlagOn has been called before
AKANTU_GET_MACRO(Increment, *increment, Array <Real> &);
/// get the lumped SolidMechanicsModel::mass vector
AKANTU_GET_MACRO(Mass, *mass, Array <Real> &);
/// get the SolidMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array <Real> &);
/// get the SolidMechanicsModel::acceleration vector, updated by
/// SolidMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array <Real> &);
/// get the SolidMechanicsModel::force vector (boundary forces)
AKANTU_GET_MACRO(Force, *force, Array <Real> &);
/// get the SolidMechanicsModel::residual vector, computed by
/// SolidMechanicsModel::updateResidual
AKANTU_GET_MACRO(Residual, *residual, Array <Real> &);
/// get the SolidMechanicsModel::blocked_dofs vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array <bool> &);
/// get the SolidMechnicsModel::incrementAcceleration vector
AKANTU_GET_MACRO(IncrementAcceleration, *increment_acceleration, Array <Real> &);
/// get the value of the SolidMechanicsModel::increment_flag
AKANTU_GET_MACRO(IncrementFlag, increment_flag, bool);
/// get a particular material (by material index)
inline Material & getMaterial(UInt mat_index);
/// get a particular material (by 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();
}
inline void setMaterialSelector(MaterialSelector & selector);
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/// compute the potential energy
Real getPotentialEnergy();
/// compute the kinetic energy
Real getKineticEnergy();
Real getKineticEnergy(const ElementType & type, UInt index);
/// compute the external work (for impose displacement, the velocity should be given too)
Real getExternalWork();
/// get the energies
Real getEnergy(const std::string & energy_id);
/// compute the energy for energy
Real getEnergy(const std::string & energy_id, const ElementType & type, UInt index);
/**
* @brief set the SolidMechanicsModel::increment_flag to on, the activate the
* update of the SolidMechanicsModel::increment vector
*/
void setIncrementFlagOn();
/// get the stiffness matrix
AKANTU_GET_MACRO(StiffnessMatrix, *stiffness_matrix, SparseMatrix &);
/// get the global jacobian matrix of the system
AKANTU_GET_MACRO(GlobalJacobianMatrix, *jacobian_matrix, const SparseMatrix &);
/// get the mass matrix
AKANTU_GET_MACRO(MassMatrix, *mass_matrix, SparseMatrix &);
/// get the velocity damping matrix
AKANTU_GET_MACRO(VelocityDampingMatrix, *velocity_damping_matrix, SparseMatrix &);
/// get the FEEngine object to integrate or interpolate on the boundary
inline FEEngine & getFEEngineBoundary(const ID & name = "");
/// get integrator
AKANTU_GET_MACRO(Integrator, *integrator, const IntegrationScheme2ndOrder &);
/// get access to the internal solver
AKANTU_GET_MACRO(Solver, *solver, Solver &);
/// get synchronizer
AKANTU_GET_MACRO(Synchronizer, *synch_parallel, const DistributedSynchronizer &);
AKANTU_GET_MACRO(MaterialByElement, material_index, 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);
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
template <int dim, class model_type>
friend struct ContactData;
template <int Dim, AnalysisMethod s, ContactResolutionMethod r>
friend class ContactResolution;
protected:
friend class Material;
protected:
/// compute the stable time step
Real getStableTimeStep(const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array <Real> *displacement;
/// displacements array at the previous time step (used in finite deformation)
Array <Real> *previous_displacement;
/// lumped mass array
Array <Real> *mass;
/// velocities array
Array <Real> *velocity;
/// accelerations array
Array <Real> *acceleration;
/// accelerations array
Array <Real> *increment_acceleration;
/// forces array
Array <Real> *force;
/// residuals array
Array <Real> *residual;
/// array specifing if a degree of freedom is blocked or not
Array <bool> *blocked_dofs;
/// array of current position used during update residual
Array <Real> *current_position;
/// mass matrix
SparseMatrix *mass_matrix;
/// velocity damping matrix
SparseMatrix *velocity_damping_matrix;
/// stiffness matrix
SparseMatrix *stiffness_matrix;
/// jacobian matrix @f[A = cM + dD + K@f] with @f[c = \frac{1}{\beta \Delta
/// t^2}, d = \frac{\gamma}{\beta \Delta t} @f]
SparseMatrix *jacobian_matrix;
/// 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 <Material *> materials;
/// mapping between material name and material internal id
std::map <std::string, UInt> materials_names_to_id;
/// class defining of to choose a material
MaterialSelector *material_selector;
/// define if it is the default selector or not
bool is_default_material_selector;
/// integration scheme of second order used
IntegrationScheme2ndOrder *integrator;
/// increment of displacement
Array <Real> *increment;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// solver for implicit
Solver *solver;
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// internal synchronizer for parallel computations
DistributedSynchronizer *synch_parallel;
/// tells if the material are instantiated
bool are_materials_instantiated;
/// map a registered internals to be flattened for dump purposes
std::map<std::pair<std::string,ElementKind>,ElementTypeMapArray<Real> *> registered_internals;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
typedef FromHigherDim FromStress;
typedef FromSameDim FromTraction;
}
}
__END_AKANTU__
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "material.hh"
__BEGIN_AKANTU__
#include "solid_mechanics_model_tmpl.hh"
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "solid_mechanics_model_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator << (std::ostream & stream, const SolidMechanicsModel &_this) {
_this.printself(stream);
return stream;
}
__END_AKANTU__
#include "material_selector_tmpl.hh"
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive.cc
index e418083d0..cdf29f034 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive.cc
@@ -1,709 +1,705 @@
/**
* @file solid_mechanics_model_cohesive.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Fri Sep 05 2014
*
* @brief Solid mechanics model for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 <algorithm>
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "dumpable_inline_impl.hh"
#include "material_cohesive.hh"
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
const SolidMechanicsModelCohesiveOptions default_solid_mechanics_model_cohesive_options(_explicit_lumped_mass,
false,
false);
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(Mesh & mesh,
UInt dim,
const ID & id,
const MemoryID & memory_id) :
SolidMechanicsModel(mesh, dim, id, memory_id),
tangents("tangents", id),
facet_stress("facet_stress", id),
facet_material("facet_material", id) {
AKANTU_DEBUG_IN();
inserter = NULL;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
facet_synchronizer = NULL;
facet_stress_synchronizer = NULL;
cohesive_distributed_synchronizer = NULL;
global_connectivity = NULL;
#endif
delete material_selector;
material_selector = new DefaultMaterialCohesiveSelector(*this);
this->registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
this->mesh.addDumpMeshToDumper("cohesive elements",
mesh, spatial_dimension, _not_ghost, _ek_cohesive);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() {
AKANTU_DEBUG_IN();
delete inserter;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
delete cohesive_distributed_synchronizer;
delete facet_synchronizer;
delete facet_stress_synchronizer;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::setTimeStep(Real time_step) {
SolidMechanicsModel::setTimeStep(time_step);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("cohesive elements").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initFull(const ModelOptions & options) {
AKANTU_DEBUG_IN();
const SolidMechanicsModelCohesiveOptions & smmc_options =
dynamic_cast<const SolidMechanicsModelCohesiveOptions &>(options);
this->is_extrinsic = smmc_options.extrinsic;
if (!inserter)
inserter = new CohesiveElementInserter(mesh, is_extrinsic, synch_parallel,
id+":cohesive_element_inserter");
SolidMechanicsModel::initFull(options);
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != NULL)
inserter->initParallel(facet_synchronizer);
#endif
if (is_extrinsic)
initAutomaticInsertion();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if(!are_materials_instantiated) instantiateMaterials();
/// find the first cohesive material
UInt cohesive_index = 0;
while ((dynamic_cast<MaterialCohesive *>(materials[cohesive_index]) == NULL)
&& cohesive_index <= materials.size())
++cohesive_index;
AKANTU_DEBUG_ASSERT(cohesive_index != materials.size(),
"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
if (is_extrinsic) {
const Mesh & mesh_facets = inserter->getMeshFacets();
mesh_facets.initElementTypeMapArray(facet_material, 1, spatial_dimension - 1);
Element element;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
element.ghost_type = *gt;
Mesh::type_iterator first = mesh_facets.firstType(spatial_dimension - 1, *gt);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1, *gt);
for(;first != last; ++first) {
element.type = *first;
Array<UInt> & f_material = facet_material(*first, *gt);
UInt nb_element = mesh_facets.getNbElement(*first, *gt);
f_material.resize(nb_element);
f_material.set(cohesive_index);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt mat_index = (*material_selector)(element);
f_material(el) = mat_index;
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[mat_index]);
mat.addFacet(element);
}
}
}
} else {
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(spatial_dimension, *gt, _ek_cohesive);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, *gt, _ek_cohesive);
for(;first != last; ++first) {
Array<UInt> & mat_indexes = this->material_index(*first, *gt);
Array<UInt> & mat_loc_num = this->material_local_numbering(*first, *gt);
mat_indexes.set(cohesive_index);
mat_loc_num.clear();
}
}
}
SolidMechanicsModel::initMaterials();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*
*/
void SolidMechanicsModelCohesive::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh, spatial_dimension);
/// add cohesive type connectivity
ElementType type = _not_defined;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType type_ghost = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, type_ghost);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, type_ghost);
for (; it != last; ++it) {
const Array<UInt> & connectivity = mesh.getConnectivity(*it, type_ghost);
if (connectivity.getSize() != 0) {
type = *it;
ElementType type_facet = Mesh::getFacetType(type);
ElementType 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);
registerFEEngineObject<MyFEEngineType>("FacetsFEEngine",
mesh.getMeshFacets(),
spatial_dimension - 1);
if (is_extrinsic) {
getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::limitInsertion(BC::Axis axis,
Real first_limit,
Real second_limit) {
AKANTU_DEBUG_IN();
inserter->setLimit(axis, first_limit, second_limit);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
inserter->insertIntrinsicElements();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initAutomaticInsertion() {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_stress_synchronizer != NULL) {
DataAccessor * data_accessor = this;
const ElementTypeMapArray<UInt> & rank_to_element = synch_parallel->getPrankToElement();
facet_stress_synchronizer->updateFacetStressSynchronizer(*inserter,
rank_to_element,
*data_accessor);
}
#endif
inserter->getMeshFacets().initElementTypeMapArray(facet_stress,
2 * spatial_dimension * spatial_dimension,
spatial_dimension - 1);
resizeFacetStress();
/// compute normals on facets
computeNormals();
initStressInterpolation();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
AKANTU_DEBUG_IN();
inserter->limitCheckFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_stress_synchronizer != NULL) {
DataAccessor * data_accessor = this;
const ElementTypeMapArray<UInt> & rank_to_element = synch_parallel->getPrankToElement();
facet_stress_synchronizer->updateFacetStressSynchronizer(*inserter,
rank_to_element,
*data_accessor);
}
#endif
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);
mesh_facets.initElementTypeMapArray(quad_facets,
spatial_dimension, spatial_dimension - 1);
getFEEngine("FacetsFEEngine").interpolateOnQuadraturePoints(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);
mesh.initElementTypeMapArray(elements_quad_facets,
spatial_dimension,
spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType elem_gt = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, elem_gt);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, elem_gt);
for (; it != last; ++it) {
ElementType type = *it;
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
Array<Element> & facet_to_element = mesh_facets.getSubelementToElement(type,
elem_gt);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
Array<Real> & el_q_facet = elements_quad_facets(type, elem_gt);
ElementType facet_type = Mesh::getFacetType(type);
UInt nb_quad_per_facet =
getFEEngine("FacetsFEEngine").getNbQuadraturePoints(facet_type);
el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element global_facet_elem = facet_to_element(el, f);
UInt global_facet = global_facet_elem.element;
GhostType facet_gt = global_facet_elem.ghost_type;
const Array<Real> & quad_f = quad_facets(facet_type, facet_gt);
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_f(global_facet * nb_quad_per_facet + q, s);
}
}
}
}
}
}
/// loop over non cohesive materials
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat __attribute__((unused)) =
dynamic_cast<MaterialCohesive &>(*materials[m]);
} catch(std::bad_cast&) {
/// initialize the interpolation function
materials[m]->initElementalFieldInterpolation(elements_quad_facets);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateResidual(bool need_initialize) {
AKANTU_DEBUG_IN();
if (need_initialize) initializeUpdateResidualData();
// f -= fint
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
mat.computeTraction(_not_ghost);
} catch (std::bad_cast & bce) { }
}
SolidMechanicsModel::updateResidual(false);
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
mat.computeEnergies();
} catch (std::bad_cast & bce) { }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::computeNormals() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = inserter->getMeshFacets();
getFEEngine("FacetsFEEngine").computeNormalsOnControlPoints(_not_ghost);
/**
* @todo store tangents while computing normals instead of
* recomputing them as follows:
*/
/* ------------------------------------------------------------------------ */
UInt tangent_components = spatial_dimension * (spatial_dimension - 1);
mesh_facets.initElementTypeMapArray(tangents,
tangent_components,
spatial_dimension - 1);
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
for (; it != last; ++it) {
ElementType facet_type = *it;
const Array<Real> & normals =
getFEEngine("FacetsFEEngine").getNormalsOnQuadPoints(facet_type);
UInt nb_quad = normals.getSize();
Array<Real> & tang = tangents(facet_type);
tang.resize(nb_quad);
Real * normal_it = normals.storage();
Real * tangent_it = tang.storage();
/// compute first tangent
for (UInt q = 0; q < nb_quad; ++q) {
/// if normal is orthogonal to xy plane, arbitrarly define tangent
if ( Math::are_float_equal(Math::norm2(normal_it), 0) )
tangent_it[0] = 1;
else
Math::normal2(normal_it, tangent_it);
normal_it += spatial_dimension;
tangent_it += tangent_components;
}
/// compute second tangent (3D case)
if (spatial_dimension == 3) {
normal_it = normals.storage();
tangent_it = tang.storage();
for (UInt q = 0; q < nb_quad; ++q) {
Math::normal3(normal_it, tangent_it, tangent_it + spatial_dimension);
normal_it += spatial_dimension;
tangent_it += tangent_components;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::interpolateStress() {
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat __attribute__((unused)) =
dynamic_cast<MaterialCohesive &>(*materials[m]);
} catch(std::bad_cast&) {
/// interpolate stress on facet quadrature points positions
materials[m]->interpolateStressOnFacets(facet_stress);
}
}
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_model_cohesive,
"Interpolated stresses before",
facet_stress);
#endif
synch_registry->synchronize(_gst_smmc_facets_stress);
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_model_cohesive,
"Interpolated stresses",
facet_stress);
#endif
}
/* -------------------------------------------------------------------------- */
-void SolidMechanicsModelCohesive::checkCohesiveStress() {
- AKANTU_DEBUG_IN();
-
+UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
interpolateStress();
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat_cohesive = dynamic_cast<MaterialCohesive &>(*materials[m]);
/// check which not ghost cohesive elements are to be created
mat_cohesive.checkInsertion();
} catch(std::bad_cast&) { }
}
/* if(static and extrinsic) {
check max mean stresses
and change inserter.getInsertionFacets(type_facet);
}
*/
/// communicate data among processors
synch_registry->synchronize(_gst_smmc_facets);
/// insert cohesive elements
- inserter->insertElements();
-
- AKANTU_DEBUG_OUT();
+ return inserter->insertElements();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
updateCohesiveSynchronizers();
#endif
SolidMechanicsModel::onElementsAdded(element_list, event);
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (cohesive_distributed_synchronizer != NULL)
cohesive_distributed_synchronizer->computeAllBufferSizes(*this);
#endif
/// update shape functions
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
if (is_extrinsic) resizeFacetStress();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onNodesAdded(const Array<UInt> & doubled_nodes,
__attribute__((unused)) const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_new_nodes = doubled_nodes.getSize();
Array<UInt> nodes_list(nb_new_nodes);
for (UInt n = 0; n < nb_new_nodes; ++n)
nodes_list(n) = doubled_nodes(n, 1);
SolidMechanicsModel::onNodesAdded(nodes_list, event);
for (UInt n = 0; n < nb_new_nodes; ++n) {
UInt old_node = doubled_nodes(n, 0);
UInt new_node = doubled_nodes(n, 1);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
(*displacement)(new_node, dim) = (*displacement)(old_node, dim);
(*velocity) (new_node, dim) = (*velocity) (old_node, dim);
(*acceleration)(new_node, dim) = (*acceleration)(old_node, dim);
(*blocked_dofs)(new_node, dim) = (*blocked_dofs)(old_node, dim);
if (current_position)
(*current_position)(new_node, dim) = (*current_position)(old_node, dim);
if (increment_acceleration)
(*increment_acceleration)(new_node, dim)
= (*increment_acceleration)(old_node, dim);
if (increment)
(*increment)(new_node, dim) = (*increment)(old_node, dim);
if (previous_displacement)
(*previous_displacement)(new_node, dim)
= (*previous_displacement)(old_node, dim);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onEndSolveStep(const AnalysisMethod & method) {
AKANTU_DEBUG_IN();
/******************************************************************************
This is required because the Cauchy stress is the stress measure that is used
to check the insertion of cohesive elements
******************************************************************************/
std::vector<Material *>::iterator mat_it;
for(mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
if(mat.isFiniteDeformation())
mat.computeAllCauchyStresses(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "SolidMechanicsModelCohesive [" << std::endl;
SolidMechanicsModel::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::resizeFacetStress() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = inserter->getMeshFacets();
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;
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
UInt nb_quadrature_points =
getFEEngine("FacetsFEEngine").getNbQuadraturePoints(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,
const ElementKind & element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
ElementKind _element_kind = element_kind;
if (dumper_name == "cohesive elements") {
_element_kind = _ek_cohesive;
}
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name,
field_id,
group_name,
_element_kind,
padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onDump(){
this->flattenAllRegisteredInternals(_ek_cohesive);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive.hh
index e853fe01a..daba20874 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive.hh
@@ -1,293 +1,290 @@
/**
* @file solid_mechanics_model_cohesive.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Tue Sep 02 2014
*
* @brief Solid mechanics model for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_SOLID_MECHANICS_MODEL_COHESIVE_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
#include "solid_mechanics_model.hh"
#include "solid_mechanics_model_event_handler.hh"
#include "cohesive_element_inserter.hh"
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "facet_synchronizer.hh"
# include "facet_stress_synchronizer.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelCohesiveOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelCohesiveOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false,
bool no_init_materials = false) :
SolidMechanicsModelOptions(analysis_method, no_init_materials),
extrinsic(extrinsic) {}
bool extrinsic;
};
extern const SolidMechanicsModelCohesiveOptions default_solid_mechanics_model_cohesive_options;
/* -------------------------------------------------------------------------- */
/* 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;
};
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive> MyFEEngineCohesiveType;
SolidMechanicsModelCohesive(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model_cohesive",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModelCohesive();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step);
/// assemble the residual for the explicit scheme
virtual void updateResidual(bool need_initialize = true);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// function to perform a stress check on each facet and insert
- /// cohesive elements if needed
- void checkCohesiveStress();
+ /// cohesive elements if needed (returns the number of new cohesive
+ /// elements)
+ UInt checkCohesiveStress();
/// interpolate stress on facets
void interpolateStress();
/// initialize the cohesive model
void initFull(const ModelOptions & options = default_solid_mechanics_model_cohesive_options);
/// initialize the model
void initModel();
/// initialize cohesive material
void initMaterials();
/// init facet filters for cohesive materials
void initFacetFilter();
/// limit the cohesive element insertion to a given area
void limitInsertion(BC::Axis axis, Real first_limit, Real second_limit);
/// update automatic insertion after a change in the element inserter
void updateAutomaticInsertion();
/// insert intrinsic cohesive elements
void insertIntrinsicElements();
-
- // template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
- // bool solveStepCohesive(Real tolerance, UInt max_iteration = 100);
-
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool solveStepCohesive(Real tolerance,
Real & error,
UInt max_iteration = 100,
+ UInt cont = 1,
bool do_not_factorize = false);
+ /// initialize stress interpolation
+ void initStressInterpolation();
private:
/// initialize completely the model for extrinsic elements
void initAutomaticInsertion();
- /// initialize stress interpolation
- void initStressInterpolation();
-
/// compute facets' normals
void computeNormals();
/// resize facet stress
void resizeFacetStress();
/// init facets_check array
void initFacetsCheck();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
virtual void onNodesAdded (const Array<UInt> & nodes_list,
const NewNodesEvent & event);
virtual void onElementsAdded (const Array<Element> & nodes_list,
const NewElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void onEndSolveStep(const AnalysisMethod & method);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag);
/* ------------------------------------------------------------------------ */
/* 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);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// @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;
/// cohesive element inserter
CohesiveElementInserter * inserter;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive_parallel.hh"
#endif
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class DefaultMaterialCohesiveSelector : public DefaultMaterialSelector {
public:
DefaultMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model) :
DefaultMaterialSelector(model.getMaterialByElement()),
facet_material(model.getFacetMaterial()),
mesh(model.getMesh()) { }
inline virtual UInt 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, third_dimension);
if(facet_material.exists(facet.type, facet.ghost_type)) {
return facet_material(facet.type, facet.ghost_type)(facet.element);
} else {
return MaterialSelector::operator()(element);
}
} catch (...) {
return MaterialSelector::operator()(element);
}
} else if (Mesh::getSpatialDimension(element.type) == mesh.getSpatialDimension() - 1) {
return facet_material(element.type, element.ghost_type)(element.element);
} else {
return DefaultMaterialSelector::operator()(element);
}
}
private:
const ElementTypeMapArray<UInt> & facet_material;
const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const SolidMechanicsModelCohesive & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "solid_mechanics_model_cohesive_inline_impl.cc"
#endif
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive_inline_impl.cc
index 6d56d64e1..50a9dc1ec 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive_inline_impl.cc
@@ -1,261 +1,257 @@
/**
* @file solid_mechanics_model_cohesive_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date Thu Feb 26 14:23:45 2015
*
* @brief Implementation of inline functions for the Cohesive element model
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
-#include "dumpable_inline_impl.hh"
#include "material_cohesive.hh"
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModelCohesive::solveStepCohesive(Real tolerance,
Real & error,
UInt max_iteration,
+ UInt cont,
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();
while (insertion_new_element) { //loop for insertion of new cohesive elements
if (is_extrinsic) {
// If in extrinsic saves the current displacements, velocities and accelerations
Array<Real> * tmp_swap;
if(!displacement_tmp) {
displacement_tmp = new Array<Real>(*(this->displacement));
} else {
(*displacement_tmp).resize(this->displacement->getSize());
- // displacement_tmp->resize(this->displacement->getSize());
+ //displacement_tmp->resize(this->displacement->getSize());
(*displacement_tmp).copy(*(this->displacement));
//displacement_tmp->copy(*(this->displacement));
}
tmp_swap = displacement_tmp;
displacement_tmp = this->displacement;
this->displacement = tmp_swap;
if(!velocity_tmp) {
velocity_tmp = new Array<Real>(*(this->velocity));
} else {
velocity_tmp->resize(this->velocity->getSize());
velocity_tmp->copy(*(this->velocity));
}
tmp_swap = velocity_tmp;
velocity_tmp = this->velocity;
this->velocity = tmp_swap;
if(!acceleration_tmp) {
acceleration_tmp = new Array<Real>(*(this->acceleration));
} else {
acceleration_tmp->resize(this->acceleration->getSize());
acceleration_tmp->copy(*(this->acceleration));
}
tmp_swap = acceleration_tmp;
acceleration_tmp = this->acceleration;
this->acceleration = tmp_swap;
}
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_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
UInt iter = 0;
converged = false;
error = 0.;
if(criteria == _scc_residual) {
converged = this->testConvergence<criteria> (tolerance, error);
if(converged) return converged;
}
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);
- // dump();
- // dump("cohesive elements");
- //std::cout << "Error after loop: " << error << std::endl;
-
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_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
} while (!converged && iter < max_iteration);
if (converged) {
//// EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
// !!! add sendEvent to call computeCauchyStress !!!!
if (prank==0){
std::cout << "Error after convergence: " << error << std::endl;
std::cout << "no. of iterations: " << iter << std::endl;
}
} 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);
std::cout << "Error after NON convergence: " << error << std::endl;
}
}
if (is_extrinsic) {
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 (converged){
+ if (converged || cont == 2){
UInt nb_cohesive_elements = this->mesh.getNbElement(this->spatial_dimension, _not_ghost, _ek_cohesive);
this->checkCohesiveStress();
UInt new_nb_cohesive_elements = this->mesh.getNbElement(this->spatial_dimension, _not_ghost, _ek_cohesive);
UInt nb_cohe[2];
nb_cohe[0] = nb_cohesive_elements;
nb_cohe[1] = new_nb_cohesive_elements;
StaticCommunicator::getStaticCommunicator().allReduce(nb_cohe, 2, _so_sum);
if(nb_cohe[0] == nb_cohe[1]) {
insertion_new_element = false;
} else {
insertion_new_element = true;
if (prank==0)
std::cout << "1 cohesive element has been inserted" << std::endl;
}
}
}
- if (!converged){
+ if (!converged && cont != 2){
insertion_new_element = false;
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[m]);
mat.checkDeltaMax(_not_ghost);
} catch(std::bad_cast&) { }
}
}
} //end while insertion_new_element
- if(is_extrinsic && converged) {
+ if ((is_extrinsic && converged) || (is_extrinsic && cont == 2)) {
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
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;
}
__END_AKANTU__
#if defined (AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "solid_mechanics_model_cohesive_parallel_inline_impl.cc"
#endif
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
index ac9d5db47..004c1744b 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_inline_impl.cc
@@ -1,613 +1,613 @@
/**
* @file solid_mechanics_model_inline_impl.cc
*
* @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: Mon Sep 15 2014
*
* @brief Implementation of the inline functions of the SolidMechanicsModel class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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/>.
*
*/
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(UInt mat_index) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "<< mat_index);
AKANTU_DEBUG_OUT();
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(UInt mat_index) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The model " << id << " has no material no "<< mat_index);
AKANTU_DEBUG_OUT();
return *materials[mat_index];
}
/* -------------------------------------------------------------------------- */
inline Material & SolidMechanicsModel::getMaterial(const std::string & name) {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getMaterialIndex(const std::string & name) const {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return it->second;
}
/* -------------------------------------------------------------------------- */
inline const Material & SolidMechanicsModel::getMaterial(const std::string & name) const {
AKANTU_DEBUG_IN();
std::map<std::string, UInt>::const_iterator it = materials_names_to_id.find(name);
AKANTU_DEBUG_ASSERT(it != materials_names_to_id.end(),
"The model " << id << " has no material named "<< name);
AKANTU_DEBUG_OUT();
return *materials[it->second];
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::setMaterialSelector(MaterialSelector & selector) {
if(is_default_material_selector) delete material_selector;
material_selector = &selector;
is_default_material_selector = false;
}
/* -------------------------------------------------------------------------- */
inline FEEngine & SolidMechanicsModel::getFEEngineBoundary(const ID & name) {
return dynamic_cast<FEEngine &>(getFEEngineClassBoundary<MyFEEngineType>(name));
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::splitElementByMaterial(const Array<Element> & elements,
Array<Element> * elements_per_mat) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
const Array<UInt> * mat_indexes = NULL;
const Array<UInt> * mat_loc_num = NULL;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
Element el = *it;
if(el.type != current_element_type || el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
mat_indexes = &(this->material_index(el.type, el.ghost_type));
mat_loc_num = &(this->material_local_numbering(el.type, el.ghost_type));
}
UInt old_id = el.element;
el.element = (*mat_loc_num)(old_id);
elements_per_mat[(*mat_indexes)(old_id)].push_back(el);
}
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataForElements(const Array<Element> & elements,
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 _gst_material_id: {
size += elements.getSize() * sizeof(UInt);
break;
}
case _gst_smm_mass: {
size += nb_nodes_per_element * sizeof(Real) * spatial_dimension; // mass vector
break;
}
case _gst_smm_for_gradu: {
size += nb_nodes_per_element * spatial_dimension * sizeof(Real); // displacement
break;
}
case _gst_smm_boundary: {
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension * (2 * sizeof(Real) + sizeof(bool));
break;
}
default: { }
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
this->splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
size += materials[i]->getNbDataForElements(elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_material_id: {
packElementalDataHelper(material_index, buffer, elements, false, getFEEngine());
break;
}
case _gst_smm_mass: {
packNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case _gst_smm_for_gradu: {
packNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
packNodalDataHelper(*force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
materials[i]->packElementData(buffer, elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_material_id: {
unpackElementalDataHelper(material_index, buffer, elements,
false, getFEEngine());
break;
}
case _gst_smm_mass: {
unpackNodalDataHelper(*mass, buffer, elements, mesh);
break;
}
case _gst_smm_for_gradu: {
unpackNodalDataHelper(*displacement, buffer, elements, mesh);
break;
}
case _gst_smm_boundary: {
unpackNodalDataHelper(*force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {
}
}
if(tag != _gst_material_id) {
Array<Element> * elements_per_mat = new Array<Element>[materials.size()];
splitElementByMaterial(elements, elements_per_mat);
for (UInt i = 0; i < materials.size(); ++i) {
materials[i]->unpackElementData(buffer, elements_per_mat[i], tag);
}
delete [] elements_per_mat;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataToPack(SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch(tag) {
case _gst_smm_uv: {
size += sizeof(Real) * spatial_dimension * 2;
break;
}
case _gst_smm_res: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_smm_mass: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_for_dump: {
size += sizeof(Real) * spatial_dimension * 5;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline UInt SolidMechanicsModel::getNbDataToUnpack(SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
// UInt nb_nodes = mesh.getNbNodes();
switch(tag) {
case _gst_smm_uv: {
size += sizeof(Real) * spatial_dimension * 2;
break;
}
case _gst_smm_res: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_smm_mass: {
size += sizeof(Real) * spatial_dimension;
break;
}
case _gst_for_dump: {
size += sizeof(Real) * spatial_dimension * 5;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::packData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) const {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_smm_uv: {
Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
- buffer << it_disp[index];
- buffer << it_velo[index];
+ Vector<Real> disp(it_disp[index]); buffer << disp;
+ Vector<Real> velo(it_velo[index]); buffer << velo;
break;
}
case _gst_smm_res: {
Array<Real>::const_vector_iterator it_res = residual->begin(spatial_dimension);
- buffer << it_res[index];
+ Vector<Real> resi(it_res[index]); buffer << resi;
break;
}
case _gst_smm_mass: {
AKANTU_DEBUG_INFO("pack mass of node " << index << " which is " << (*mass)(index,0));
Array<Real>::const_vector_iterator it_mass = mass->begin(spatial_dimension);
- buffer << it_mass[index];
+ Vector<Real> mass(it_mass[index]); buffer << mass;
break;
}
case _gst_for_dump: {
Array<Real>::const_vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_velo = velocity->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_acce = acceleration->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_resi = residual->begin(spatial_dimension);
Array<Real>::const_vector_iterator it_forc = force->begin(spatial_dimension);
- buffer << it_disp[index];
- buffer << it_velo[index];
- buffer << it_acce[index];
- buffer << it_resi[index];
- buffer << it_forc[index];
+ Vector<Real> disp(it_disp[index]); buffer << disp;
+ Vector<Real> velo(it_velo[index]); buffer << velo;
+ Vector<Real> acce(it_acce[index]); buffer << acce;
+ Vector<Real> resi(it_resi[index]); buffer << resi;
+ Vector<Real> forc(it_forc[index]); buffer << forc;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void SolidMechanicsModel::unpackData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
switch(tag) {
case _gst_smm_uv: {
Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
Vector<Real> disp(it_disp[index]); buffer >> disp;
Vector<Real> velo(it_velo[index]); buffer >> velo;
break;
}
case _gst_smm_res: {
Array<Real>::vector_iterator it_res = residual->begin(spatial_dimension);
Vector<Real> res(it_res[index]); buffer >> res;
break;
}
case _gst_smm_mass: {
AKANTU_DEBUG_INFO("mass of node " << index << " was " << (*mass)(index,0));
Array<Real>::vector_iterator it_mass = mass->begin(spatial_dimension);
Vector<Real> mass_v(it_mass[index]); buffer >> mass_v;
AKANTU_DEBUG_INFO("mass of node " << index << " is now " << (*mass)(index,0));
break;
}
case _gst_for_dump: {
Array<Real>::vector_iterator it_disp = displacement->begin(spatial_dimension);
Array<Real>::vector_iterator it_velo = velocity->begin(spatial_dimension);
Array<Real>::vector_iterator it_acce = acceleration->begin(spatial_dimension);
Array<Real>::vector_iterator it_resi = residual->begin(spatial_dimension);
Array<Real>::vector_iterator it_forc = force->begin(spatial_dimension);
Vector<Real> disp(it_disp[index]); buffer >> disp;
Vector<Real> velo(it_velo[index]); buffer >> velo;
Vector<Real> acce(it_acce[index]); buffer >> acce;
Vector<Real> resi(it_resi[index]); buffer >> resi;
Vector<Real> forc(it_forc[index]); buffer >> forc;
break;
}
default: {
AKANTU_DEBUG_ERROR("Unknown ghost synchronization tag : " << tag);
}
}
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
#include "sparse_matrix.hh"
#include "solver.hh"
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
template <NewmarkBeta::IntegrationSchemeCorrectorType type>
void SolidMechanicsModel::solve(Array<Real> &increment, Real block_val,
bool need_factorize, bool has_profile_changed) {
if(has_profile_changed) {
this->initJacobianMatrix();
need_factorize = true;
}
updateResidualInternal(); //doesn't do anything for static
if(need_factorize) {
Real c = 0.,d = 0.,e = 0.;
if(method == _static) {
AKANTU_DEBUG_INFO("Solving K inc = r");
e = 1.;
} else {
AKANTU_DEBUG_INFO("Solving (c M + d C + e K) inc = r");
NewmarkBeta * nmb_int = dynamic_cast<NewmarkBeta *>(integrator);
c = nmb_int->getAccelerationCoefficient<type>(time_step);
d = nmb_int->getVelocityCoefficient<type>(time_step);
e = nmb_int->getDisplacementCoefficient<type>(time_step);
}
jacobian_matrix->clear();
// J = c M + d C + e K
if(stiffness_matrix)
jacobian_matrix->add(*stiffness_matrix, e);
if(mass_matrix)
jacobian_matrix->add(*mass_matrix, c);
#if !defined(AKANTU_NDEBUG)
if(mass_matrix && AKANTU_DEBUG_TEST(dblDump))
mass_matrix->saveMatrix("M.mtx");
#endif
if(velocity_damping_matrix)
jacobian_matrix->add(*velocity_damping_matrix, d);
jacobian_matrix->applyBoundary(*blocked_dofs, block_val);
#if !defined(AKANTU_NDEBUG)
if(AKANTU_DEBUG_TEST(dblDump))
jacobian_matrix->saveMatrix("J.mtx");
#endif
solver->factorize();
}
// if (rhs.getSize() != 0)
// solver->setRHS(rhs);
// else
solver->setOperators();
solver->setRHS(*residual);
// solve @f[ J \delta w = r @f]
solver->solve(increment);
UInt nb_nodes = displacement-> getSize();
UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
bool * blocked_dofs_val = blocked_dofs->storage();
Real * increment_val = increment.storage();
for (UInt j = 0; j < nb_degree_of_freedom;
++j,++increment_val, ++blocked_dofs_val) {
if ((*blocked_dofs_val))
*increment_val = 0.0;
}
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStatic(Real tolerance, UInt max_iteration,
bool do_not_factorize) {
AKANTU_DEBUG_INFO("Solving Ku = f");
AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
"You should first initialize the implicit solver and assemble the stiffness matrix by calling initImplicit");
AnalysisMethod analysis_method=method;
Real error = 0.;
method=_static;
bool converged = this->template solveStep<cmethod, criteria>(tolerance, error, max_iteration, do_not_factorize);
method=analysis_method;
return converged;
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStep(Real tolerance,
UInt max_iteration) {
Real error = 0.;
return this->template solveStep<cmethod,criteria>(tolerance,
error,
max_iteration);
}
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModel::solveStep(Real tolerance, Real & error, UInt max_iteration,
bool do_not_factorize) {
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
this->implicitPred();
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_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
UInt iter = 0;
bool converged = false;
error = 0.;
if(criteria == _scc_residual) {
converged = this->testConvergence<criteria> (tolerance, error);
if(converged) return converged;
}
do {
if (cmethod == _scm_newton_raphson_tangent)
this->assembleStiffnessMatrix();
solve<NewmarkBeta::_displacement_corrector> (*increment, 1., need_factorize);
this->implicitCorr();
if(criteria == _scc_residual) this->updateResidual();
converged = this->testConvergence<criteria> (tolerance, error);
if(criteria == _scc_increment && !converged) this->updateResidual();
//this->dump();
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_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
} while (!converged && iter < max_iteration);
// this makes sure that you have correct strains and stresses after the solveStep function (e.g., for dumping)
if(criteria == _scc_increment) this->updateResidual();
if (converged) {
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
} else if(iter == max_iteration) {
AKANTU_DEBUG_WARNING("[" << criteria << "] Convergence not reached after "
<< std::setw(std::log10(max_iteration)) << iter <<
" iteration" << (iter == 1 ? "" : "s") << "!" << std::endl);
}
return converged;
}
diff --git a/src/model/structural_mechanics/structural_mechanics_model.cc b/src/model/structural_mechanics/structural_mechanics_model.cc
index 2c41ab2ac..69555bd2f 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model.cc
@@ -1,1147 +1,1148 @@
/**
* @file structural_mechanics_model.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Mon Sep 15 2014
*
* @brief Model implementation for StucturalMechanics elements
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "structural_mechanics_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#include "aka_math.hh"
#include "integration_scheme_2nd_order.hh"
#include "static_communicator.hh"
#include "sparse_matrix.hh"
#include "solver.hh"
#ifdef AKANTU_USE_MUMPS
#include "solver_mumps.hh"
#endif
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
# include "dumper_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
const StructuralMechanicsModelOptions default_structural_mechanics_model_options(_static);
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::StructuralMechanicsModel(Mesh & mesh,
UInt dim,
const ID & id,
const MemoryID & memory_id) :
Model(mesh, dim, id, memory_id),
time_step(NAN), f_m2a(1.0),
stress("stress", id, memory_id),
element_material("element_material", id, memory_id),
set_ID("beam sets", id, memory_id),
stiffness_matrix(NULL),
mass_matrix(NULL),
velocity_damping_matrix(NULL),
jacobian_matrix(NULL),
solver(NULL),
rotation_matrix("rotation_matices", id, memory_id),
increment_flag(false),
integrator(NULL) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineType>("StructuralMechanicsFEEngine", mesh, spatial_dimension);
this->displacement_rotation = NULL;
this->mass = NULL;
this->velocity = NULL;
this->acceleration = NULL;
this->force_momentum = NULL;
this->residual = NULL;
this->blocked_dofs = NULL;
this->increment = NULL;
this->previous_displacement = NULL;
if(spatial_dimension == 2)
nb_degree_of_freedom = 3;
else if (spatial_dimension == 3)
nb_degree_of_freedom = 6;
else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_structural);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::~StructuralMechanicsModel() {
AKANTU_DEBUG_IN();
delete integrator;
delete solver;
delete stiffness_matrix;
delete jacobian_matrix;
delete mass_matrix;
delete velocity_damping_matrix;
AKANTU_DEBUG_OUT();
}
void StructuralMechanicsModel::setTimeStep(Real time_step) {
this->time_step = time_step;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFull(const ModelOptions & options) {
const StructuralMechanicsModelOptions & stmm_options =
dynamic_cast<const StructuralMechanicsModelOptions &>(options);
method = stmm_options.analysis_method;
initModel();
initArrays();
displacement_rotation->clear();
velocity ->clear();
acceleration ->clear();
force_momentum ->clear();
residual ->clear();
blocked_dofs ->clear();
increment ->clear();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
computeRotationMatrix(*it);
}
switch(method) {
case _implicit_dynamic:
initImplicit();
break;
case _static:
initSolver();
break;
default:
AKANTU_EXCEPTION("analysis method not recognised by StructuralMechanicsModel");
break;
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = getFEEngine().getMesh().getNbNodes();
std::stringstream sstr_disp; sstr_disp << id << ":displacement";
std::stringstream sstr_velo; sstr_velo << id << ":velocity";
std::stringstream sstr_acce; sstr_acce << id << ":acceleration";
std::stringstream sstr_forc; sstr_forc << id << ":force";
std::stringstream sstr_resi; sstr_resi << id << ":residual";
std::stringstream sstr_boun; sstr_boun << id << ":blocked_dofs";
std::stringstream sstr_incr; sstr_incr << id << ":increment";
displacement_rotation = &(alloc<Real>(sstr_disp.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
velocity = &(alloc<Real>(sstr_velo.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
acceleration = &(alloc<Real>(sstr_acce.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
force_momentum = &(alloc<Real>(sstr_forc.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
residual = &(alloc<Real>(sstr_resi.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
blocked_dofs = &(alloc<bool>(sstr_boun.str(), nb_nodes, nb_degree_of_freedom, false));
increment = &(alloc<Real>(sstr_incr.str(), nb_nodes, nb_degree_of_freedom, REAL_INIT_VALUE));
Mesh::type_iterator it = getFEEngine().getMesh().firstType(spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
UInt nb_element = getFEEngine().getMesh().getNbElement(*it);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(*it);
element_material.alloc(nb_element, 1, *it, _not_ghost);
set_ID.alloc(nb_element, 1, *it, _not_ghost);
UInt size = getTangentStiffnessVoigtSize(*it);
stress.alloc(nb_element * nb_quadrature_points, size , *it, _not_ghost);
}
dof_synchronizer = new DOFSynchronizer(getFEEngine().getMesh(), nb_degree_of_freedom);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initModel() {
getFEEngine().initShapeFunctions(_not_ghost);
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initSolver(__attribute__((unused)) SolverOptions & options) {
AKANTU_DEBUG_IN();
const Mesh & mesh = getFEEngine().getMesh();
#if !defined(AKANTU_USE_MUMPS) // or other solver in the future \todo add AKANTU_HAS_SOLVER in CMake
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#else
UInt nb_global_node = mesh.getNbGlobalNodes();
std::stringstream sstr; sstr << id << ":jacobian_matrix";
jacobian_matrix = new SparseMatrix(nb_global_node * nb_degree_of_freedom, _symmetric, sstr.str(), memory_id);
jacobian_matrix->buildProfile(mesh, *dof_synchronizer, nb_degree_of_freedom);
std::stringstream sstr_sti; sstr_sti << id << ":stiffness_matrix";
stiffness_matrix = new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solv; sstr_solv << id << ":solver";
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif //AKANTU_USE_MUMPS
solver->initialize(options);
#endif //AKANTU_HAS_SOLVER
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initImplicit(bool dynamic, SolverOptions & solver_options) {
AKANTU_DEBUG_IN();
if (!increment) setIncrementFlagOn();
initSolver(solver_options);
if(integrator) delete integrator;
integrator = new TrapezoidalRule2();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt StructuralMechanicsModel::getTangentStiffnessVoigtSize(const ElementType & type) {
UInt size;
#define GET_TANGENT_STIFFNESS_VOIGT_SIZE(type) \
size = getTangentStiffnessVoigtSize<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_TANGENT_STIFFNESS_VOIGT_SIZE);
#undef GET_TANGENT_STIFFNESS_VOIGT_SIZE
return size;
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
stiffness_matrix->clear();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
ElementType type = *it;
#define ASSEMBLE_STIFFNESS_MATRIX(type) \
assembleStiffnessMatrix<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_STIFFNESS_MATRIX);
#undef ASSEMBLE_STIFFNESS_MATRIX
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_2>(Array<Real> & rotations){
ElementType type = _bernoulli_beam_2;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<UInt>::iterator< Vector<UInt> > connec_it = mesh.getConnectivity(type).begin(2);
Array<Real>::vector_iterator nodes_it = mesh.getNodes().begin(spatial_dimension);
Array<Real>::matrix_iterator R_it = rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++R_it, ++connec_it) {
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x2;
x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1;
x1 = nodes_it[connec(0)]; // X1
Real le = x1.distance(x2);
Real c = (x2(0) - x1(0)) / le;
Real s = (x2(1) - x1(1)) / le;
/// Definition of the rotation matrix
R(0,0) = c; R(0,1) = s; R(0,2) = 0.;
R(1,0) = -s; R(1,1) = c; R(1,2) = 0.;
R(2,0) = 0.; R(2,1) = 0.; R(2,2) = 1.;
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_3>(Array<Real> & rotations){
ElementType type = _bernoulli_beam_3;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<Real>::vector_iterator n_it = mesh.getNormals(type).begin(spatial_dimension);
Array<UInt>::iterator< Vector<UInt> > connec_it = mesh.getConnectivity(type).begin(2);
Array<Real>::vector_iterator nodes_it = mesh.getNodes().begin(spatial_dimension);
Matrix<Real> Pe (spatial_dimension, spatial_dimension);
Matrix<Real> Pg (spatial_dimension, spatial_dimension);
Matrix<Real> inv_Pg(spatial_dimension, spatial_dimension);
Vector<Real> x_n(spatial_dimension); // x vect n
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e=0 ; e < nb_element; ++e, ++n_it, ++connec_it, ++R_it) {
Vector<Real> & n = *n_it;
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x;
x = nodes_it[connec(1)]; // X2
Vector<Real> y;
y = nodes_it[connec(0)]; // X1
Real l = x.distance(y);
x -= y; // X2 - X1
x_n.crossProduct(x, n);
Pe.eye();
Pe(0, 0) *= l;
Pe(1, 1) *= -l;
Pg(0,0) = x(0); Pg(0,1) = x_n(0); Pg(0,2) = n(0);
Pg(1,0) = x(1); Pg(1,1) = x_n(1); Pg(1,2) = n(1);
Pg(2,0) = x(2); Pg(2,1) = x_n(2); Pg(2,2) = n(2);
inv_Pg.inverse(Pg);
Pe *= inv_Pg;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
R(i, j) = Pe(i, j);
R(i + spatial_dimension,j + spatial_dimension) = Pe(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::computeRotationMatrix<_kirchhoff_shell>(Array<Real> & rotations){
ElementType type = _kirchhoff_shell;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<UInt>::iterator< Vector<UInt> > connec_it = mesh.getConnectivity(type).begin(3);
Array<Real>::vector_iterator nodes_it = mesh.getNodes().begin(spatial_dimension);
Matrix<Real> Pe (spatial_dimension, spatial_dimension);
Matrix<Real> Pg (spatial_dimension, spatial_dimension);
Matrix<Real> inv_Pg(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e=0 ; e < nb_element; ++e, ++connec_it, ++R_it) {
Pe.eye();
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x2;
x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1;
x1 = nodes_it[connec(0)]; // X1
Vector<Real> x3;
x3 = nodes_it[connec(2)]; // X3
Vector<Real> Pg_col_1=x2-x1;
Vector<Real> Pg_col_2 = x3-x1;
Vector<Real> Pg_col_3(spatial_dimension);
Pg_col_3.crossProduct(Pg_col_1, Pg_col_2);
for (UInt i = 0; i <spatial_dimension; ++i) {
Pg(i,0) = Pg_col_1(i);
Pg(i,1) = Pg_col_2(i);
Pg(i,2) = Pg_col_3(i);
}
inv_Pg.inverse(Pg);
// Pe *= inv_Pg;
Pe.eye();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
R(i, j) = Pe(i, j);
R(i + spatial_dimension,j + spatial_dimension) = Pe(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeRotationMatrix(const ElementType & type) {
Mesh & mesh = getFEEngine().getMesh();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
if(!rotation_matrix.exists(type)) {
rotation_matrix.alloc(nb_element,
nb_degree_of_freedom*nb_nodes_per_element * nb_degree_of_freedom*nb_nodes_per_element,
type);
} else {
rotation_matrix(type).resize(nb_element);
}
rotation_matrix(type).clear();
Array<Real>rotations(nb_element, nb_degree_of_freedom * nb_degree_of_freedom);
rotations.clear();
#define COMPUTE_ROTATION_MATRIX(type) \
computeRotationMatrix<type>(rotations);
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_ROTATION_MATRIX);
#undef COMPUTE_ROTATION_MATRIX
Array<Real>::matrix_iterator R_it = rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
Array<Real>::matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom*nb_nodes_per_element,
nb_degree_of_freedom*nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++R_it, ++T_it) {
Matrix<Real> & T = *T_it;
Matrix<Real> & R = *R_it;
T.clear();
for (UInt k = 0; k < nb_nodes_per_element; ++k){
for (UInt i = 0; i < nb_degree_of_freedom; ++i)
for (UInt j = 0; j < nb_degree_of_freedom; ++j)
T(k*nb_degree_of_freedom + i, k*nb_degree_of_freedom + j) = R(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeStresses() {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
ElementType type = *it;
#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();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::updateResidual() {
AKANTU_DEBUG_IN();
residual->copy(*force_momentum);
Array<Real> ku(*displacement_rotation, true);
ku *= *stiffness_matrix;
*residual -= ku;
this->updateResidualInternal();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::implicitPred() {
AKANTU_DEBUG_IN();
if(previous_displacement) previous_displacement->copy(*displacement_rotation);
if(method == _implicit_dynamic)
integrator->integrationSchemePred(time_step,
*displacement_rotation,
*velocity,
*acceleration,
*blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::implicitCorr() {
AKANTU_DEBUG_IN();
Real * incr_val = increment->storage();
bool * boun_val = blocked_dofs->storage();
UInt nb_nodes = displacement_rotation->getSize();
for (UInt j = 0; j < nb_nodes * nb_degree_of_freedom; ++j, ++incr_val, ++boun_val){
*incr_val *= (1. - *boun_val);
}
if(method == _implicit_dynamic) {
integrator->integrationSchemeCorrDispl(time_step,
*displacement_rotation,
*velocity,
*acceleration,
*blocked_dofs,
*increment);
} else {
Real * disp_val = displacement_rotation->storage();
incr_val = increment->storage();
for (UInt j = 0; j < nb_nodes *nb_degree_of_freedom; ++j, ++disp_val, ++incr_val){
*disp_val += *incr_val;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::updateResidualInternal() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Update the residual");
// f = f_ext - f_int - Ma - Cv = r - Ma - Cv;
if(method != _static) {
// f -= Ma
if(mass_matrix) {
// if full mass_matrix
Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
*Ma *= *mass_matrix;
/// \todo check unit conversion for implicit dynamics
// *Ma /= f_m2a
*residual -= *Ma;
delete Ma;
} else if (mass) {
// else lumped mass
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
Real * mass_val = mass->storage();
Real * accel_val = acceleration->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*res_val -= *accel_val * *mass_val /f_m2a;
}
blocked_dofs_val++;
res_val++;
mass_val++;
accel_val++;
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
// f -= Cv
if(velocity_damping_matrix) {
Array<Real> * Cv = new Array<Real>(*velocity);
*Cv *= *velocity_damping_matrix;
*residual -= *Cv;
delete Cv;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::setIncrementFlagOn() {
AKANTU_DEBUG_IN();
if(!increment) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_inc; sstr_inc << id << ":increment";
increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, spatial_dimension, 0.));
}
increment_flag = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::solve() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Solving an implicit step.");
UInt nb_nodes = displacement_rotation->getSize();
/// todo residual = force - Kxr * d_bloq
jacobian_matrix->copyContent(*stiffness_matrix);
jacobian_matrix->applyBoundary(*blocked_dofs);
jacobian_matrix->saveMatrix("Kbound.mtx");
increment->clear();
solver->setRHS(*residual);
solver->factorize();
solver->solve(*increment);
Real * increment_val = increment->storage();
Real * displacement_val = displacement_rotation->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if(!(*blocked_dofs_val)) {
*displacement_val += *increment_val;
}
else {
*increment_val = 0.0;
}
displacement_val++;
blocked_dofs_val++;
increment_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<>
bool StructuralMechanicsModel::testConvergence<_scc_increment>(Real tolerance, Real & error){
AKANTU_DEBUG_IN();
UInt nb_nodes = displacement_rotation->getSize();
UInt nb_degree_of_freedom = displacement_rotation->getNbComponent();
error = 0;
Real norm[2] = {0., 0.};
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
Real * displacement_val = displacement_rotation->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val)) {
norm[0] += *increment_val * *increment_val;
norm[1] += *displacement_val * *displacement_val;
}
blocked_dofs_val++;
increment_val++;
displacement_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);
norm[0] = sqrt(norm[0]);
norm[1] = sqrt(norm[1]);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]), "Something went wrong in the solve phase");
AKANTU_DEBUG_OUT();
if(norm[1] > Math::getTolerance())
error = norm[0] / norm[1];
else
error = norm[0]; //In case the total displacement is zero!
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
bool StructuralMechanicsModel::testConvergence<_scc_residual>(Real tolerance, Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
norm = 0;
Real * residual_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if(is_local_node) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val;
}
blocked_dofs_val++;
residual_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
bool StructuralMechanicsModel::testConvergenceIncrement(Real tolerance) {
Real error;
bool tmp = testConvergenceIncrement(tolerance, error);
AKANTU_DEBUG_INFO("Norm of increment : " << error);
return tmp;
}
/* -------------------------------------------------------------------------- */
bool StructuralMechanicsModel::testConvergenceIncrement(Real tolerance, Real & error) {
AKANTU_DEBUG_IN();
Mesh & mesh= getFEEngine().getMesh();
UInt nb_nodes = displacement_rotation->getSize();
UInt nb_degree_of_freedom = displacement_rotation->getNbComponent();
Real norm = 0;
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if(!(*blocked_dofs_val) && is_local_node) {
norm += *increment_val * *increment_val;
}
blocked_dofs_val++;
increment_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
error = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm), "Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_2>(Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(_bernoulli_beam_2);
UInt tangent_size = 2;
Array<Real>::matrix_iterator D_it = tangent_moduli.begin(tangent_size, tangent_size);
Array<UInt> & el_mat = element_material(_bernoulli_beam_2, _not_ghost);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = el_mat(e);
Real E = materials[mat].E;
Real A = materials[mat].A;
Real I = materials[mat].I;
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 * I;
}
}
}
/* -------------------------------------------------------------------------- */
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().getNbQuadraturePoints(_bernoulli_beam_3);
UInt tangent_size = 4;
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;
}
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::computeTangentModuli<_kirchhoff_shell>(Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_kirchhoff_shell);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(_kirchhoff_shell);
UInt tangent_size = 6;
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(_kirchhoff_shell, _not_ghost)(e);
Real E = materials[mat].E;
Real nu = materials[mat].nu;
Real t = materials[mat].t;
Real HH=E*t/(1-nu*nu);
Real DD=E*t*t*t/(12*(1-nu*nu));
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0,0) = HH;
D(0,1) = HH*nu;
D(1,0) = HH*nu;
D(1,1) = HH;
D(2,2) = HH*(1-nu)/2;
D(3,3) = DD;
D(3,4) = DD*nu;
D(4,3) = DD*nu;
D(4,4) = DD;
D(5,5) = DD*(1-nu)/2;
}
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<_bernoulli_beam_2>(Array<Real> & b, bool local) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_bernoulli_beam_2);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(_bernoulli_beam_2);
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
Array<Real>::const_vector_iterator shape_Np = fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 0).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mpp = fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 1).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lpp = fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 2).begin(nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_bernoulli_beam_2>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Vector<Real> & Np = *shape_Np;
const Vector<Real> & Lpp = *shape_Lpp;
const Vector<Real> & Mpp = *shape_Mpp;
B(0,0) = Np(0);
B(0,3) = Np(1);
B(1,1) = Mpp(0);
B(1,2) = Lpp(0);
B(1,4) = Mpp(1);
B(1,5) = Lpp(1);
++B_it;
++shape_Np;
++shape_Mpp;
++shape_Lpp;
}
// ++R_it;
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<_bernoulli_beam_3>(Array<Real> & b, bool local) {
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_bernoulli_beam_3);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(_bernoulli_beam_3);
Array<Real>::const_vector_iterator shape_Np = fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 0).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mpp = fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 1).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lpp = fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 2).begin(nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_bernoulli_beam_3>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Vector<Real> & Np = *shape_Np;
const Vector<Real> & Lpp = *shape_Lpp;
const Vector<Real> & Mpp = *shape_Mpp;
B(0,0) = Np(0);
B(0,6) = Np(1);
B(1,1) = Mpp(0);
B(1,5) = Lpp(0);
B(1,7) = Mpp(1);
B(1,11) = Lpp(1);
B(2,2) = Mpp(0);
B(2,4) = -Lpp(0);
B(2,8) = Mpp(1);
B(2,10) = -Lpp(1);
B(3,3) = Np(0);
B(3,9) = Np(1);
++B_it;
++shape_Np;
++shape_Mpp;
++shape_Lpp;
}
}
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<_kirchhoff_shell>(Array<Real> & b, bool local) {
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(_kirchhoff_shell);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_kirchhoff_shell);
UInt nb_quadrature_points = getFEEngine().getNbQuadraturePoints(_kirchhoff_shell);
Array<Real>::const_matrix_iterator shape_Np = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 0).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx1p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 1).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx2p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 2).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx3p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 3).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny1p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 4).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny2p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 5).begin(2,nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny3p = fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 6).begin(2,nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_kirchhoff_shell>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Matrix<Real> & Np = *shape_Np;
const Matrix<Real> & Nx1p = *shape_Nx1p;
const Matrix<Real> & Nx2p = *shape_Nx2p;
const Matrix<Real> & Nx3p = *shape_Nx3p;
const Matrix<Real> & Ny1p = *shape_Ny1p;
const Matrix<Real> & Ny2p = *shape_Ny2p;
const Matrix<Real> & Ny3p = *shape_Ny3p;
B(0,0) = Np(0,0);
B(0,6) = Np(0,1);
B(0,12) = Np(0,2);
B(1,1) = Np(1,0);
B(1,7) = Np(1,1);
B(1,13) = Np(1,2);
B(2,0) = Np(1,0);
B(2,1) = Np(0,0);
B(2,6) = Np(1,1);
B(2,7) = Np(0,1);
B(2,12) = Np(1,2);
B(2,13) = Np(0,2);
B(3,2) = Nx1p(0,0);
B(3,3) = Nx2p(0,0);
B(3,4) = Nx3p(0,0);
B(3,8) = Nx1p(0,1);
B(3,9) = Nx2p(0,1);
B(3,10) = Nx3p(0,1);
B(3,14) = Nx1p(0,2);
B(3,15) = Nx2p(0,2);
B(3,16) = Nx3p(0,2);
B(4,2) = Ny1p(1,0);
B(4,3) = Ny2p(1,0);
B(4,4) = Ny3p(1,0);
B(4,8) = Ny1p(1,1);
B(4,9) = Ny2p(1,1);
B(4,10) = Ny3p(1,1);
B(4,14) = Ny1p(1,2);
B(4,15) = Ny2p(1,2);
B(4,16) = Ny3p(1,2);
B(5,2) = Nx1p(1,0) + Ny1p(0,0);
B(5,3) = Nx2p(1,0) + Ny2p(0,0);
B(5,4) = Nx3p(1,0) + Ny3p(0,0);
B(5,8) = Nx1p(1,1) + Ny1p(0,1);
B(5,9) = Nx2p(1,1) + Ny2p(0,1);
B(5,10) = Nx3p(1,1) + Ny3p(0,1);
B(5,14) = Nx1p(1,2) + Ny1p(0,2);
B(5,15) = Nx2p(1,2) + Ny2p(0,2);
B(5,16) = Nx3p(1,2) + Ny3p(0,2);
++B_it;
++shape_Np;
++shape_Nx1p;
++shape_Nx2p;
++shape_Nx3p;
++shape_Ny1p;
++shape_Ny2p;
++shape_Ny3p;
}
}
}
/* -------------------------------------------------------------------------- */
dumper::Field * StructuralMechanicsModel
::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string,Array<bool>* > uint_nodal_fields;
uint_nodal_fields["blocked_dofs" ] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name],group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::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;
dumper::Field * field = NULL;
if (field_name == "displacement"){
field = mesh.createStridedNodalField(displacement_rotation,group_name,n,0,padding_flag);
}
if (field_name == "rotation"){
field = mesh.createStridedNodalField(displacement_rotation,group_name,
nb_degree_of_freedom-n,n,padding_flag);
}
if (field_name == "force"){
field = mesh.createStridedNodalField(force_momentum,group_name,n,0,padding_flag);
}
if (field_name == "momentum"){
field = mesh.createStridedNodalField(force_momentum,group_name,
nb_degree_of_freedom-n,n,padding_flag);
}
if (field_name == "residual"){
field = mesh.createNodalField(residual,group_name,padding_flag);
}
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * StructuralMechanicsModel
::createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
- const ElementKind & kind){
+ const ElementKind & kind,
+ const std::string & fe_engine_id){
dumper::Field * field = NULL;
if(field_name == "element_index_by_material")
field = mesh.createElementalField<UInt, Vector, dumper::ElementalField >(field_name,group_name,this->spatial_dimension,kind);
return field;
}
/* -------------------------------------------------------------------------- */
__END_AKANTU__
diff --git a/src/model/structural_mechanics/structural_mechanics_model.hh b/src/model/structural_mechanics/structural_mechanics_model.hh
index 741652314..9a214db8e 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model.hh
@@ -1,400 +1,401 @@
/**
* @file structural_mechanics_model.hh
*
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Tue Sep 02 2014
*
* @brief Particular implementation of the structural elements in the StructuralMechanicsModel
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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_STRUCTURAL_MECHANICS_MODEL_HH__
#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "model.hh"
#include "integrator_gauss.hh"
#include "shape_linked.hh"
#include "aka_types.hh"
#include "dumpable.hh"
#include "solver.hh"
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class SparseMatrix;
}
__BEGIN_AKANTU__
struct StructuralMaterial {
Real E;
Real A;
Real I;
Real Iz;
Real Iy;
Real GJ;
Real rho;
Real t;
Real nu;
};
struct StructuralMechanicsModelOptions : public ModelOptions {
StructuralMechanicsModelOptions(AnalysisMethod analysis_method = _static) :
analysis_method(analysis_method) {}
AnalysisMethod analysis_method;
};
extern const StructuralMechanicsModelOptions default_structural_mechanics_model_options;
class StructuralMechanicsModel : public Model {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss, ShapeLinked, _ek_structural> MyFEEngineType;
StructuralMechanicsModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "structural_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~StructuralMechanicsModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize fully the model
void initFull(const ModelOptions & options = default_structural_mechanics_model_options);
/// initialize the internal vectors
void initArrays();
/// initialize the model
void initModel();
/// initialize the solver
void initSolver(SolverOptions & options = _solver_no_options);
/// initialize the stuff for the implicit solver
void initImplicit(bool dynamic = false,
SolverOptions & solver_options = _solver_no_options);
/// compute the stresses per elements
void computeStresses();
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
/// implicit time integration predictor
void implicitPred();
/// implicit time integration corrector
void implicitCorr();
/// update the residual vector
void updateResidual();
/// solve the system
void solve();
bool testConvergenceIncrement(Real tolerance);
bool testConvergenceIncrement(Real tolerance, Real & error);
virtual void printself(std::ostream & stream, int indent = 0) const {};
void computeRotationMatrix(const ElementType & type);
protected:
UInt getTangentStiffnessVoigtSize(const ElementType & type);
/// compute Rotation Matrices
template<const ElementType type>
void computeRotationMatrix(Array<Real> & rotations) {};
/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
template<NewmarkBeta::IntegrationSchemeCorrectorType type>
void solve(Array<Real> & increment, Real block_val = 1.);
/* ------------------------------------------------------------------------ */
/* Mass (structural_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(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>
inline UInt getTangentStiffnessVoigtSize();
template <ElementType type>
void assembleStiffnessMatrix();
template <ElementType type>
void assembleMass();
template<ElementType type>
void computeStressOnQuad();
template <ElementType type>
void computeTangentModuli(Array<Real> & tangent_moduli);
template <ElementType type>
void transferBMatrixToSymVoigtBMatrix(Array<Real> & B, bool local = false);
template <ElementType type>
void transferNMatrixToSymVoigtNMatrix(Array<Real> & N_matrix);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
- const ElementKind & kind);
+ const ElementKind & kind,
+ const std::string & fe_engine_id = "");
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step);
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// 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::force vector (boundary forces)
AKANTU_GET_MACRO(Force, *force_momentum, Array<Real> &);
/// get the StructuralMechanicsModel::residual vector, computed by StructuralMechanicsModel::updateResidual
AKANTU_GET_MACRO(Residual, *residual, const 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(StiffnessMatrix, *stiffness_matrix, const SparseMatrix &);
AKANTU_GET_MACRO(MassMatrix, *mass_matrix, const SparseMatrix &);
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);
void addMaterial(StructuralMaterial & material) { materials.push_back(material); }
/**
* @brief set the StructuralMechanicsModel::increment_flag to on, the activate the
* update of the StructuralMechanicsModel::increment vector
*/
void setIncrementFlagOn();
/* ------------------------------------------------------------------------ */
/* Boundaries (structural_mechanics_model_boundary.cc) */
/* ------------------------------------------------------------------------ */
public:
/// Compute Linear load function set in global axis
template <ElementType type>
void computeForcesByGlobalTractionArray(const Array<Real> & tractions);
/// Compute Linear load function set in local axis
template <ElementType type>
void computeForcesByLocalTractionArray(const Array<Real> & tractions);
/// compute force vector from a function(x,y,momentum) that describe stresses
template <ElementType type>
void computeForcesFromFunction(BoundaryFunction in_function,
BoundaryFunctionType function_type);
/**
* solve a step (predictor + convergence loop + corrector) using the
* the given convergence method (see akantu::SolveConvergenceMethod)
* and the given convergence criteria (see
* akantu::SolveConvergenceCriteria)
**/
template<SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance,
UInt max_iteration = 100);
template<SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance,
Real & error,
UInt max_iteration = 100);
/// test if the system is converged
template<SolveConvergenceCriteria criteria>
bool testConvergence(Real tolerance, Real & error);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement_rotation;
/// displacements array at the previous time step (used in finite deformation)
Array<Real> * previous_displacement;
/// velocities array
Array<Real> * velocity;
/// accelerations array
Array<Real> * acceleration;
/// forces array
Array<Real> * force_momentum;
/// lumped mass array
Array<Real> * mass;
/// stress arraz
ElementTypeMapArray<Real> stress;
/// residuals array
Array<Real> * residual;
/// boundaries array
Array<bool> * blocked_dofs;
/// position of a dof in the K matrix
Array<Int> * equation_number;
ElementTypeMapArray<UInt> element_material;
// Define sets of beams
ElementTypeMapArray<UInt> set_ID;
/// local equation_number to global
unordered_map<UInt, UInt>::type local_eq_num_to_global;
/// stiffness matrix
SparseMatrix * stiffness_matrix;
/// mass matrix
SparseMatrix * mass_matrix;
/// velocity damping matrix
SparseMatrix * velocity_damping_matrix;
/// jacobian matrix
SparseMatrix * jacobian_matrix;
/// increment of displacement
Array<Real> * increment;
/// solver for implicit
Solver * solver;
/// 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;
/// integration scheme of second order used
IntegrationScheme2ndOrder * integrator;
/* -------------------------------------------------------------------------- */
std::vector<StructuralMaterial> materials;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const StructuralMechanicsModel & _this)
{
_this.printself(stream);
return stream;
}
__END_AKANTU__
#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__ */
diff --git a/src/solver/petsc_matrix.cc b/src/solver/petsc_matrix.cc
index 35b40980f..45698bf58 100644
--- a/src/solver/petsc_matrix.cc
+++ b/src/solver/petsc_matrix.cc
@@ -1,630 +1,636 @@
/**
* @file petsc_matrix.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 17:40:41 2014
*
* @brief Implementation of PETSc matrix class
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "petsc_matrix.hh"
#include "static_communicator.hh"
#include "static_communicator_mpi.hh"
#include "mpi_type_wrapper.hh"
#include "dof_synchronizer.hh"
#include "petsc_wrapper.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <petscsys.h>
__BEGIN_AKANTU__
// struct PETScWrapper {
// Mat mat;
// AO ao;
// ISLocalToGlobalMapping mapping;
// /// pointer to the MPI communicator for PETSc commands
// MPI_Comm communicator;
// };
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(UInt size,
const SparseMatrixType & sparse_matrix_type,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(size, sparse_matrix_type, id, memory_id),
petsc_matrix_wrapper(new PETScMatrixWrapper),
d_nnz(0,1,"dnnz"),
o_nnz(0,1,"onnz"),
first_global_index(0),
is_petsc_matrix_initialized(false) {
AKANTU_DEBUG_IN();
StaticSolver::getStaticSolver().registerEventHandler(*this);
this->offset = 0;
this->init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::PETScMatrix(const SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
SparseMatrix(matrix, id, memory_id),
petsc_matrix_wrapper(new PETScMatrixWrapper),
d_nnz(0,1,"dnnz"),
o_nnz(0,1,"onnz"),
first_global_index(0),
is_petsc_matrix_initialized(false) {
// AKANTU_DEBUG_IN();
// StaticSolver::getStaticSolver().registerEventHandler(*this);
// this->offset = 0;
// this->init();
// AKANTU_DEBUG_OUT();
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
PETScMatrix::~PETScMatrix() {
AKANTU_DEBUG_IN();
/// destroy all the PETSc data structures used for this matrix
this->destroyInternalData();
+ StaticSolver::getStaticSolver().unregisterEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void PETScMatrix::init() {
AKANTU_DEBUG_IN();
/// set the communicator that should be used by PETSc
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
this->petsc_matrix_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->petsc_matrix_wrapper->communicator = PETSC_COMM_SELF;
#endif
PetscErrorCode ierr;
/// create the PETSc matrix object
ierr = MatCreate(this->petsc_matrix_wrapper->communicator, &(this->petsc_matrix_wrapper->mat)); CHKERRXX(ierr);
/**
* Set the matrix type
* @todo PETSc does currently not support a straightforward way to
* apply Dirichlet boundary conditions for MPISBAIJ
* matrices. Therefore always the entire matrix is allocated. It
* would be possible to use MATSBAIJ for sequential matrices in case
* memory becomes critical. Also, block matrices would give a much
* better performance. Modify this in the future!
*/
ierr = MatSetType(this->petsc_matrix_wrapper->mat, MATAIJ); CHKERRXX(ierr);
this->is_petsc_matrix_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* With this method each processor computes the dimensions of the
* local matrix, i.e. the part of the global matrix it is storing.
* @param dof_synchronizer dof synchronizer that maps the local
* dofs to the global dofs and the equation numbers, i.e., the
* position at which the dof is assembled in the matrix
*/
void PETScMatrix::setSize() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// find the number of dofs corresponding to master or local nodes
UInt nb_dofs = this->dof_synchronizer->getNbDOFs();
UInt nb_local_master_dofs = 0;
/// create array to store the global equation number of all local and master dofs
Array<Int> local_master_eq_nbs(nb_dofs);
Array<Int>::scalar_iterator it_eq_nb = local_master_eq_nbs.begin();
/// get the pointer to the global equation number array
Int * eq_nb_val = this->dof_synchronizer->getGlobalDOFEquationNumbers().storage();
for (UInt i = 0; i <nb_dofs; ++i) {
if (this->dof_synchronizer->isLocalOrMasterDOF(i) ) {
*it_eq_nb = eq_nb_val[i];
++it_eq_nb;
++nb_local_master_dofs;
}
}
local_master_eq_nbs.resize(nb_local_master_dofs);
/// set the local size
this->local_size = nb_local_master_dofs;
/// resize PETSc matrix
#if defined(AKANTU_USE_MPI)
ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size, this->local_size, this->size, this->size); CHKERRXX(ierr);
#else
ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size, this->local_size); CHKERRXX(ierr);
#endif
/// create mapping from akantu global numbering to petsc global numbering
this->createGlobalAkantuToPETScMap(local_master_eq_nbs.storage());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* This method generates a mapping from the global Akantu equation
* numbering to the global PETSc dof ordering
* @param local_master_eq_nbs_ptr Int pointer to the array of equation
* numbers of all local or master dofs, i.e. the row indices of the
* local matrix
*/
void PETScMatrix::createGlobalAkantuToPETScMap(Int* local_master_eq_nbs_ptr) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
//initialize vector to store the number of local and master nodes that are assigned to each processor
Vector<UInt> master_local_ndofs_per_proc(nb_proc);
/// store the nb of master and local dofs on each processor
master_local_ndofs_per_proc(rank) = this->local_size;
/// exchange the information among all processors
comm.allGather(master_local_ndofs_per_proc.storage(), 1);
/// each processor creates a map for his akantu global dofs to the corresponding petsc global dofs
/// determine the PETSc-index for the first dof on each processor
for (UInt i = 0; i < rank; ++i) {
this->first_global_index += master_local_ndofs_per_proc(i);
}
/// create array for petsc ordering
Array<Int> petsc_dofs(this->local_size);
Array<Int>::scalar_iterator it_petsc_dofs = petsc_dofs.begin();
for (Int i = this->first_global_index; i < this->first_global_index + this->local_size; ++i, ++it_petsc_dofs) {
*it_petsc_dofs = i;
}
ierr = AOCreateBasic(this->petsc_matrix_wrapper->communicator, this->local_size, local_master_eq_nbs_ptr, petsc_dofs.storage(), &(this->petsc_matrix_wrapper->ao)); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void PETScMatrix::createLocalAkantuToPETScMap(const DOFSynchronizer & dof_synchronizer) {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT(this->petsc_matrix_wrapper->ao != NULL,
// "You should first create a mapping from the global"
// << " Akantu numbering to the global PETSc numbering");
// PetscErrorCode ierr;
// this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// /// get the number of dofs
// Int nb_dofs = dof_synchronizer.getNbDOFs();
// /// get the global equation numbers for each node
// Array<Int> global_dof_equation_numbers = dof_synchronizer.getGlobalDOFEquationNumbers();
// /// map the global dof equation numbers to the corresponding PETSc ordering
// ierr = AOApplicationToPETSc(this->petsc_matrix_wrapper->ao, nb_dofs,
// global_dof_equation_numbers.storage()); CHKERRXX(ierr);
// /// create the mapping from the local Akantu ordering to the global PETSc ordering
// ierr = ISLocalToGlobalMappingCreate(this->petsc_matrix_wrapper->communicator,
// 1, nb_dofs, global_dof_equation_numbers.storage(),
// PETSC_COPY_VALUES, &(this->petsc_matrix_wrapper-mapping)); CHKERRXX(ierr);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
/**
* This function creates the non-zero pattern of the PETSc matrix. In
* PETSc the parallel matrix is partitioned across processors such
* that the first m0 rows belong to process 0, the next m1 rows belong
* to process 1, the next m2 rows belong to process 2 etc.. where
* m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores
* values corresponding to [m x N] submatrix
* (http://www.mcs.anl.gov/petsc/).
* @param mesh mesh discretizing the domain we want to analyze
* @param dof_synchronizer dof synchronizer that maps the local
* dofs to the global dofs and the equation numbers, i.e., the
* position at which the dof is assembled in the matrix
*/
void PETScMatrix::buildProfile(const Mesh & mesh, const DOFSynchronizer & dof_synchronizer, UInt nb_degree_of_freedom) {
AKANTU_DEBUG_IN();
//clearProfile();
this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
this->setSize();
PetscErrorCode ierr;
/// resize arrays to store the number of nonzeros in each row
this->d_nnz.resize(this->local_size);
this->o_nnz.resize(this->local_size);
/// set arrays to zero everywhere
this->d_nnz.set(0);
this->o_nnz.set(0);
// if(irn_jcn_to_k) delete irn_jcn_to_k;
// irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
coordinate_list_map::iterator irn_jcn_k_it;
Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
UInt nb_global_dofs = dof_synchronizer.getNbGlobalDOFs();
+ Array<Int> index_pair(2);
/// Loop over all the ghost types
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
const GhostType & ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType (mesh.getSpatialDimension(), ghost_type, _ek_not_defined);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
UInt * conn_val = mesh.getConnectivity(*it, ghost_type).storage();
Int * local_eq_nb_val = new Int[nb_degree_of_freedom * nb_nodes_per_element];
for (UInt e = 0; e < nb_element; ++e) {
Int * tmp_local_eq_nb_val = local_eq_nb_val;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
UInt n = conn_val[i];
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
/**
* !!!!!!Careful!!!!!! This is a ugly fix. @todo this is a
* very ugly fix, because the offset for the global
* equation number, where the dof will be assembled, is
* hardcoded. In the future a class dof manager has to be
* added to Akantu to handle the mapping between the dofs
* and the equation numbers
*
*/
*tmp_local_eq_nb_val++ = eq_nb_val[n * nb_degree_of_freedom + d] - (dof_synchronizer.isPureGhostDOF(n * nb_degree_of_freedom + d) ? nb_global_dofs : 0);
}
}
for (UInt i = 0; i < size_mat; ++i) {
Int c_irn = local_eq_nb_val[i];
UInt j_start = 0;
for (UInt j = j_start; j < size_mat; ++j) {
Int c_jcn = local_eq_nb_val[j];
- Array<Int> index_pair(2,1);
index_pair(0) = c_irn;
index_pair(1) = c_jcn;
AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index_pair.storage());
if (index_pair(0) >= first_global_index && index_pair(0) < first_global_index + this->local_size) {
KeyCOO irn_jcn = keyPETSc(c_irn, c_jcn);
irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
if (irn_jcn_k_it == irn_jcn_k.end()) {
irn_jcn_k[irn_jcn] = nb_non_zero;
// check if node is slave node
if (index_pair(1) >= first_global_index && index_pair(1) < first_global_index + this->local_size)
this->d_nnz(index_pair(0) - first_global_index) += 1;
else
this->o_nnz(index_pair(0) - first_global_index) += 1;
nb_non_zero++;
}
}
}
}
conn_val += nb_nodes_per_element;
}
delete [] local_eq_nb_val;
}
}
// /// for pbc @todo correct it for parallel
// if(StaticCommunicator::getStaticCommunicator().getNbProc() == 1) {
// for (UInt i = 0; i < size; ++i) {
// KeyCOO irn_jcn = key(i, i);
// irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
// if(irn_jcn_k_it == irn_jcn_k.end()) {
// irn_jcn_k[irn_jcn] = nb_non_zero;
// irn.push_back(i + 1);
// jcn.push_back(i + 1);
// nb_non_zero++;
// }
// }
// }
// std::string mat_type;
// mat_type.resize(20, 'a');
// std::cout << "MatType: " << mat_type << std::endl;
// const char * mat_type_ptr = mat_type.c_str();
MatType type;
MatGetType(this->petsc_matrix_wrapper->mat, &type);
- std::cout << "the matrix type is: " << type << std::endl;
+ /// std::cout << "the matrix type is: " << type << std::endl;
/**
* PETSc will use only one of the following preallocation commands
* depending on the matrix type and ignore the rest. Note that for
* the block matrix format a block size of 1 is used. This might
* result in bad performance. @todo For better results implement
* buildProfile() with larger block size.
*
*/
/// build profile:
if (strcmp(type, MATSEQAIJ) == 0) {
ierr = MatSeqAIJSetPreallocation(this->petsc_matrix_wrapper->mat,
0, d_nnz.storage()); CHKERRXX(ierr);
} else if ((strcmp(type, MATMPIAIJ) == 0)) {
ierr = MatMPIAIJSetPreallocation(this->petsc_matrix_wrapper->mat,
0, d_nnz.storage(), 0,
o_nnz.storage()); CHKERRXX(ierr);
} else {
AKANTU_DEBUG_ERROR("The type " << type << " of PETSc matrix is not handled by"
<< " akantu in the preallocation step");
}
//ierr = MatSeqSBAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 1,
// 0, d_nnz.storage()); CHKERRXX(ierr);
if (this->sparse_matrix_type==_symmetric) {
/// set flag for symmetry to enable ICC/Cholesky preconditioner
ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SYMMETRIC, PETSC_TRUE); CHKERRXX(ierr);
/// set flag for symmetric positive definite
ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SPD, PETSC_TRUE); CHKERRXX(ierr);
}
/// once the profile has been build ignore any new nonzero locations
ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* 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 PETScMatrix::saveMatrix(const std::string & filename) const{
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// create Petsc viewer
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(this->petsc_matrix_wrapper->communicator, filename.c_str(), &viewer); CHKERRXX(ierr);
/// set the format
PetscViewerSetFormat(viewer, PETSC_VIEWER_DEFAULT); CHKERRXX(ierr);
/// save the matrix
+ /// @todo Write should be done in serial -> might cause problems
ierr = MatView(this->petsc_matrix_wrapper->mat, viewer); CHKERRXX(ierr);
/// destroy the viewer
ierr = PetscViewerDestroy(&viewer); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Method to add an Akantu sparse matrix to the PETSc matrix
* @param matrix Akantu sparse matrix to be added
* @param alpha the factor specifying how many times the matrix should be added
*/
void PETScMatrix::add(const SparseMatrix & matrix, Real alpha) {
PetscErrorCode ierr;
// AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
// "The two matrix don't have the same profiles");
+ Real val_to_add = 0;
+ Array<Int> index(2);
for (UInt n = 0; n < matrix.getNbNonZero(); ++n) {
- Array<Int> index(2,1);
- index(0) = matrix.getIRN()(n)-matrix.getOffset();
- index(1) = matrix.getJCN()(n)-matrix.getOffset();
+ UInt mat_to_add_offset = matrix.getOffset();
+ index(0) = matrix.getIRN()(n)-mat_to_add_offset;
+ index(1) = matrix.getJCN()(n)-mat_to_add_offset;
AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
if (this->sparse_matrix_type == _symmetric && index(0) > index(1))
std::swap(index(0), index(1));
+
+ val_to_add = matrix.getA()(n) * alpha;
/// MatSetValue might be very slow for MATBAIJ, might need to use MatSetValuesBlocked
- ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(0), index(1), matrix.getA()(n) * alpha, ADD_VALUES); CHKERRXX(ierr);
+ ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(0), index(1), val_to_add, ADD_VALUES); CHKERRXX(ierr);
/// chek if sparse matrix to be added is symmetric. In this case
/// the value also needs to be added at the transposed location in
/// the matrix because PETSc is using the full profile, also for symmetric matrices
if (matrix.getSparseMatrixType() == _symmetric && index(0) != index(1))
- ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(1), index(0), matrix.getA()(n) * alpha, ADD_VALUES); CHKERRXX(ierr);
+ ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(1), index(0), val_to_add, ADD_VALUES); CHKERRXX(ierr);
}
this->performAssembly();
}
/* -------------------------------------------------------------------------- */
/**
* Method to add another PETSc matrix to this PETSc matrix
* @param matrix PETSc matrix to be added
* @param alpha the factor specifying how many times the matrix should be added
*/
void PETScMatrix::add(const PETScMatrix & matrix, Real alpha) {
PetscErrorCode ierr;
ierr = MatAXPY(this->petsc_matrix_wrapper->mat, alpha, matrix.petsc_matrix_wrapper->mat, SAME_NONZERO_PATTERN); CHKERRXX(ierr);
this->performAssembly();
}
/* -------------------------------------------------------------------------- */
/**
* 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 PETScMatrix::performAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyBegin(this->petsc_matrix_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
ierr = MatAssemblyEnd(this->petsc_matrix_wrapper->mat, MAT_FINAL_ASSEMBLY); CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/**
* Method is called when the static solver is destroyed, just before
* PETSc is finalized. So all PETSc objects need to be destroyed at
* this point.
*/
void PETScMatrix::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try{
this->destroyInternalData();
} catch(...) {}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// destroy all the PETSc data structures used for this matrix
void PETScMatrix::destroyInternalData() {
AKANTU_DEBUG_IN();
if(this->is_petsc_matrix_initialized) {
PetscErrorCode ierr;
ierr = MatDestroy(&(this->petsc_matrix_wrapper->mat)); CHKERRXX(ierr);
delete petsc_matrix_wrapper;
this->is_petsc_matrix_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// access K(i, j). Works only for dofs on this processor!!!!
Real PETScMatrix::operator()(UInt i, UInt j) const{
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->dof_synchronizer->isLocalOrMasterDOF(i) && this->dof_synchronizer->isLocalOrMasterDOF(j), "Operator works only for dofs on this processor");
Array<Int> index(2,1);
index(0) = this->dof_synchronizer->getDOFGlobalID(i);
index(1) = this->dof_synchronizer->getDOFGlobalID(j);
AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
Real value = 0;
PetscErrorCode ierr;
/// @todo MatGetValue might be very slow for MATBAIJ, might need to use MatGetValuesBlocked
ierr = MatGetValues(this->petsc_matrix_wrapper->mat, 1, &index(0), 1, &index(1), &value); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
return value;
}
/* -------------------------------------------------------------------------- */
/**
* Apply Dirichlet boundary conditions by zeroing the rows and columns which correspond to blocked dofs
* @param boundary array of booleans which are true if the dof at this position is blocked
* @param block_val the value in the diagonal entry of blocked rows
*/
void PETScMatrix::applyBoundary(const Array<bool> & boundary, Real block_val) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// get the global equation numbers to find the rows that need to be zeroed for the blocked dofs
Int * eq_nb_val = dof_synchronizer->getGlobalDOFEquationNumbers().storage();
/// every processor calls the MatSetZero() only for his local or master dofs. This assures that not two processors or more try to zero the same row
- Int nb_blocked_local_master_eq_nb = 0;
- Array<Int> blocked_local_master_eq_nb(this->local_size / boundary.getNbComponent(), boundary.getNbComponent());
- Int * blocked_lm_eq_nb_ptr = blocked_local_master_eq_nb.storage();
UInt nb_component = boundary.getNbComponent();
UInt size = boundary.getSize();
+ Int nb_blocked_local_master_eq_nb = 0;
+ Array<Int> blocked_local_master_eq_nb(this->local_size);
+ Int * blocked_lm_eq_nb_ptr = blocked_local_master_eq_nb.storage();
for (UInt i = 0; i < size; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
UInt local_dof = i * nb_component + j;
if (boundary(i, j) == true && this->dof_synchronizer->isLocalOrMasterDOF(local_dof)) {
Int global_eq_nb = *eq_nb_val;
*blocked_lm_eq_nb_ptr = global_eq_nb;
++nb_blocked_local_master_eq_nb;
++blocked_lm_eq_nb_ptr;
}
++eq_nb_val;
}
}
- blocked_local_master_eq_nb.resize(nb_blocked_local_master_eq_nb/boundary.getNbComponent());
+ blocked_local_master_eq_nb.resize(nb_blocked_local_master_eq_nb);
ierr = AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, nb_blocked_local_master_eq_nb, blocked_local_master_eq_nb.storage() ); CHKERRXX(ierr);
ierr = MatZeroRowsColumns(this->petsc_matrix_wrapper->mat, nb_blocked_local_master_eq_nb, blocked_local_master_eq_nb.storage(), block_val, 0, 0); CHKERRXX(ierr);
this->performAssembly();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// set all entries to zero while keeping the same nonzero pattern
void PETScMatrix::clear() {
MatZeroEntries(this->petsc_matrix_wrapper->mat);
}
__END_AKANTU__
diff --git a/src/solver/solver.cc b/src/solver/solver.cc
index 7d9d4746e..2cb5865f9 100644
--- a/src/solver/solver.cc
+++ b/src/solver/solver.cc
@@ -1,87 +1,88 @@
/**
* @file solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Wed Nov 13 2013
*
* @brief Solver interface class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
SolverOptions _solver_no_options(true);
/* -------------------------------------------------------------------------- */
Solver::Solver(SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Memory(id, memory_id), StaticSolverEventHandler(),
matrix(&matrix),
is_matrix_allocated(false),
mesh(NULL),
communicator(StaticCommunicator::getStaticCommunicator()),
solution(NULL),
synch_registry(NULL) {
AKANTU_DEBUG_IN();
StaticSolver::getStaticSolver().registerEventHandler(*this);
//createSynchronizerRegistry();
this->synch_registry = new SynchronizerRegistry(*this);
synch_registry->registerSynchronizer(this->matrix->getDOFSynchronizer(), _gst_solver_solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Solver::~Solver() {
AKANTU_DEBUG_IN();
this->destroyInternalData();
delete synch_registry;
+ StaticSolver::getStaticSolver().unregisterEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Solver::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try{
this->destroyInternalData();
} catch(...) {}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Solver::createSynchronizerRegistry() {
//this->synch_registry = new SynchronizerRegistry(this);
}
__END_AKANTU__
diff --git a/src/solver/solver_mumps.cc b/src/solver/solver_mumps.cc
index 727cfcc15..970001120 100644
--- a/src/solver/solver_mumps.cc
+++ b/src/solver/solver_mumps.cc
@@ -1,383 +1,383 @@
/**
* @file solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Sep 15 2014
*
* @brief implem of SolverMumps class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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
*
* @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"
#if defined(AKANTU_USE_MPI)
# include "static_communicator_mpi.hh"
# include "mpi_type_wrapper.hh"
#endif
#include "solver_mumps.hh"
#include "dof_synchronizer.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;
// }
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
SolverMumps::SolverMumps(SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Solver(matrix, id, memory_id), is_mumps_data_initialized(false), rhs_is_local(true) {
AKANTU_DEBUG_IN();
#ifdef AKANTU_USE_MPI
parallel_method = SolverMumpsOptions::_fully_distributed;
#else //AKANTU_USE_MPI
parallel_method = SolverMumpsOptions::_not_parallel;
#endif //AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolverMumps::~SolverMumps() { }
/* -------------------------------------------------------------------------- */
void SolverMumps::destroyInternalData() {
AKANTU_DEBUG_IN();
if(this->is_mumps_data_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_mumps_data_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::initMumpsData() {
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
icntl(28) = 0; //automatic choice for analysis analysis
switch(this->parallel_method) {
case SolverMumpsOptions::_fully_distributed:
icntl(18) = 3; //fully distributed
this->mumps_data.nz_loc = matrix->getNbNonZero();
this->mumps_data.irn_loc = matrix->getIRN().storage();
this->mumps_data.jcn_loc = matrix->getJCN().storage();
break;
case SolverMumpsOptions::_not_parallel:
case SolverMumpsOptions::_master_slave_distributed:
icntl(18) = 0; //centralized
if(prank == 0) {
this->mumps_data.nz = matrix->getNbNonZero();
this->mumps_data.irn = matrix->getIRN().storage();
this->mumps_data.jcn = matrix->getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = NULL;
this->mumps_data.jcn = NULL;
}
break;
default:
AKANTU_DEBUG_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SolverMumps::initialize(SolverOptions & options) {
AKANTU_DEBUG_IN();
if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options)) {
this->parallel_method = opt->parallel_method;
}
this->mumps_data.par = 1; // The host is part of computations
switch(this->parallel_method) {
case SolverMumpsOptions::_not_parallel: break;
case SolverMumpsOptions::_master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
case SolverMumpsOptions::_fully_distributed:
#ifdef AKANTU_USE_MPI
const StaticCommunicatorMPI & mpi_st_comm = dynamic_cast<const StaticCommunicatorMPI &>(communicator.getRealStaticCommunicator());
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_st_comm.getMPITypeWrapper().getMPICommunicator());
#endif
break;
}
this->mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->mumps_data.job = _smj_initialize; //initialize
dmumps_c(&this->mumps_data);
this->is_mumps_data_initialized = true;
/* ------------------------------------------------------------------------ */
UInt size = matrix->getSize();
if(prank == 0) {
std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
this->rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, 0.));
} else {
this->rhs = NULL;
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
/* ------------------------------------------------------------------------ */
// Output setup
if(AKANTU_DEBUG_TEST(dblTrace)) {
icntl(1) = 6;
icntl(2) = 2;
icntl(3) = 2;
icntl(4) = 4;
} else {
/// No outputs
icntl(1) = 6; // error output
icntl(2) = 0; // dignostics output
icntl(3) = 0; // informations
icntl(4) = 0; // no outputs
}
if(AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
this->analysis();
// icntl(14) = 80;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::setRHS(Array<Real> & rhs) {
if(prank == 0) {
//std::copy(rhs.storage(), rhs.storage() + this->rhs->getSize(), this->rhs->storage());
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
debug::setDebugLevel(dbl);
} else {
this->matrix->getDOFSynchronizer().gather(rhs, 0);
}
}
/* -------------------------------------------------------------------------- */
void SolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; //analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::factorize() {
AKANTU_DEBUG_IN();
if(parallel_method == SolverMumpsOptions::_fully_distributed)
this->mumps_data.a_loc = this->matrix->getA().storage();
else {
if(prank == 0)
this->mumps_data.a = this->matrix->getA().storage();
}
if(prank == 0) {
this->mumps_data.rhs = this->rhs->storage();
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::solve() {
AKANTU_DEBUG_IN();
if(prank == 0) {
this->mumps_data.rhs = this->rhs->storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::solve(Array<Real> & solution) {
AKANTU_DEBUG_IN();
this->solve();
if(prank == 0) {
matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
// std::copy(this->rhs->storage(), this->rhs->storage() + this->rhs->getSize(), solution.storage());
} else {
this->matrix->getDOFSynchronizer().scatter(solution, 0);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverMumps::printError() {
- UInt _info_v[2];
+ Int _info_v[2];
_info_v[0] = info(1); // to get errors
_info_v[1] = -info(1); // to get warnings
communicator.allReduce(_info_v, 2, _so_min);
_info_v[1] = -_info_v[1];
if(_info_v[0] < 0) { // < 0 is an error
switch(_info_v[0]) {
case -10: AKANTU_DEBUG_ERROR("The matrix is singular"); 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 of 10%");
this->analysis();
this->factorize();
this->solve();
} else {
AKANTU_DEBUG_ERROR("The MUMPS workarray is too small INFO(2)=" << info(2) << "No further increase possible"); break;
}
}
default:
AKANTU_DEBUG_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]);
}
}
__END_AKANTU__
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index dc9f44e7b..635c10ae6 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,1106 +1,1109 @@
/**
* @file solver_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
# @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date Mon Dec 13 10:48:06 2010
*
* @brief Solver class implementation for the petsc solver
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
#include "solver_petsc.hh"
#include "petsc_wrapper.hh"
#include "petsc_matrix.hh"
#include "static_communicator.hh"
#include "static_communicator_mpi.hh"
#include "mpi_type_wrapper.hh"
#include "dof_synchronizer.hh"
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
SolverPETSc::SolverPETSc(SparseMatrix & matrix,
const ID & id,
const MemoryID & memory_id) :
Solver(matrix, id, memory_id), is_petsc_data_initialized(false),
petsc_solver_wrapper(new PETScSolverWrapper) {
}
/* -------------------------------------------------------------------------- */
SolverPETSc::~SolverPETSc() {
AKANTU_DEBUG_IN();
this->destroyInternalData();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::destroyInternalData() {
AKANTU_DEBUG_IN();
if(this->is_petsc_data_initialized) {
PetscErrorCode ierr;
ierr = KSPDestroy(&(this->petsc_solver_wrapper->ksp)); CHKERRXX(ierr);
ierr = VecDestroy(&(this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
ierr = VecDestroy(&(this->petsc_solver_wrapper->solution)); CHKERRXX(ierr);
delete petsc_solver_wrapper;
this->is_petsc_data_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::initialize(SolverOptions & options) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
this->petsc_solver_wrapper->communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->petsc_solver_wrapper->communicator = PETSC_COMM_SELF;
#endif
PetscErrorCode ierr;
PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
/// create a solver context
ierr = KSPCreate(this->petsc_solver_wrapper->communicator, &(this->petsc_solver_wrapper->ksp)); CHKERRXX(ierr);
+ /// create the PETSc vector for the right-hand side
ierr = VecCreate(this->petsc_solver_wrapper->communicator, &(this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
ierr = VecSetSizes((this->petsc_solver_wrapper->rhs),
petsc_matrix->getLocalSize(),
petsc_matrix->getSize()); CHKERRXX(ierr);
ierr = VecSetFromOptions((this->petsc_solver_wrapper->rhs)); CHKERRXX(ierr);
+ /// create the PETSc vector for the solution
ierr = VecDuplicate((this->petsc_solver_wrapper->rhs), &(this->petsc_solver_wrapper->solution)); CHKERRXX(ierr);
+ /// set the solution to zero
ierr = VecZeroEntries(this->petsc_solver_wrapper->solution);
this->is_petsc_data_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::setRHS(Array<Real> & rhs) {
PetscErrorCode ierr;
PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
UInt nb_component = rhs.getNbComponent();
UInt size = rhs.getSize();
for (UInt i = 0; i < size; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
UInt i_local = i * nb_component + j;
if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i_local)) {
Int i_global = this->matrix->getDOFSynchronizer().getDOFGlobalID(i_local);
AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao, 1, &(i_global) );
ierr = VecSetValue((this->petsc_solver_wrapper->rhs), i_global, rhs(i,j), INSERT_VALUES); CHKERRXX(ierr);
}
}
}
ierr = VecAssemblyBegin(this->petsc_solver_wrapper->rhs); CHKERRXX(ierr);
ierr = VecAssemblyEnd(this->petsc_solver_wrapper->rhs); CHKERRXX(ierr);
/// ierr = VecCopy((this->petsc_solver_wrapper->rhs), (this->petsc_solver_wrapper->solution)); CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
ierr = KSPSolve(this->petsc_solver_wrapper->ksp, this->petsc_solver_wrapper->rhs, this->petsc_solver_wrapper->solution); CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve(Array<Real> & solution) {
AKANTU_DEBUG_IN();
this->solution = &solution;
this->solve();
PetscErrorCode ierr;
PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
// ierr = VecGetOwnershipRange(this->petsc_solver_wrapper->solution, solution_begin, solution_end); CHKERRXX(ierr);
// ierr = VecGetArray(this->petsc_solver_wrapper->solution, PetscScalar **array); CHKERRXX(ierr);
UInt nb_component = solution.getNbComponent();
UInt size = solution.getSize();
for (UInt i = 0; i < size; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
UInt i_local = i * nb_component + j;
if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i_local)) {
Int i_global = this->matrix->getDOFSynchronizer().getDOFGlobalID(i_local);
ierr = AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao, 1, &(i_global) ); CHKERRXX(ierr);
ierr = VecGetValues(this->petsc_solver_wrapper->solution, 1, &i_global, &solution(i,j)); CHKERRXX(ierr);
}
}
}
synch_registry->synchronize(_gst_solver_solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::setOperators() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// set the matrix that defines the linear system and the matrix for preconditioning (here they are the same)
PETScMatrix * petsc_matrix = static_cast<PETScMatrix*>(this->matrix);
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ierr = KSPSetOperators(this->petsc_solver_wrapper->ksp, petsc_matrix->getPETScMatrixWrapper()->mat, petsc_matrix->getPETScMatrixWrapper()->mat); CHKERRXX(ierr);
#else
ierr = KSPSetOperators(this->petsc_solver_wrapper->ksp, petsc_matrix->getPETScMatrixWrapper()->mat, petsc_matrix->getPETScMatrixWrapper()->mat, SAME_NONZERO_PATTERN); CHKERRXX(ierr);
#endif
/// If this is not called the solution vector is zeroed in the call to KSPSolve().
ierr = KSPSetInitialGuessNonzero(this->petsc_solver_wrapper->ksp, PETSC_TRUE);
KSPSetFromOptions(this->petsc_solver_wrapper->ksp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void finalize_petsc() {
// static bool finalized = false;
// if (!finalized) {
// cout<<"*** INFO *** PETSc is finalizing..."<<endl;
// // finalize PETSc
// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
// finalized = true;
// }
// }
// SolverPETSc::sparse_vector_type
// SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& AA,
// const SolverPETSc::sparse_vector_type& bb) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside PETSc solver: "<<timer<<endl;
// #endif
// #ifdef CPPUTILS_VERBOSE
// out<<" Inside operator()(const sparse_matrix_type&, const sparse_vector_type&)... "<<timer<<endl;
// #endif
// assert(AA.rows() == bb.size());
// // KSP ksp; //!< linear solver context
// Vec b; /* RHS */
// PC pc; /* preconditioner context */
// PetscErrorCode ierr;
// PetscInt nlocal;
// PetscInt n = bb.size();
// VecScatter ctx;
// /*
// Create vectors. Note that we form 1 vector from scratch and
// then duplicate as needed. For this simple case let PETSc decide how
// many elements of the vector are stored on each processor. The second
// argument to VecSetSizes() below causes PETSc to decide.
// */
// ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(b);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// ierr = VecDuplicate(b,&x_);CHKERRCONTINUE(ierr);
// } else
// VecZeroEntries(x_);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(b, 1, &row, &it->second, ADD_VALUES);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Right hand side set... "<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(b);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(b);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Right-hand-side vector assembled... "<<timer<<endl;
// ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// Vec b_all;
// ierr = VecScatterCreateToAll(b, &ctx, &b_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(b_all,NORM_2,&nrm);
// out<<" Norm of right hand side... "<<nrm<<endl;
// #endif
// /* Identify the starting and ending mesh points on each
// processor for the interior part of the mesh. We let PETSc decide
// above. */
// // PetscInt rstart,rend;
// // ierr = VecGetOwnershipRange(x_,&rstart,&rend);CHKERRCONTINUE(ierr);
// ierr = VecGetLocalSize(x_,&nlocal);CHKERRCONTINUE(ierr);
// /*
// Create matrix. When using MatCreate(), the matrix format can
// be specified at runtime.
// Performance tuning note: For problems of substantial size,
// preallocation of matrix memory is crucial for attaining good
// performance. See the matrix chapter of the users manual for details.
// We pass in nlocal as the "local" size of the matrix to force it
// to have the same parallel layout as the vector created above.
// */
// if (!allocated_) {
// ierr = MatCreate(PETSC_COMM_WORLD,&A_);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(A_,nlocal,nlocal,n,n);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(A_);CHKERRCONTINUE(ierr);
// ierr = MatSetUp(A_);CHKERRCONTINUE(ierr);
// } else {
// // zero-out matrix
// MatZeroEntries(A_);
// }
// /*
// Assemble matrix.
// The linear system is distributed across the processors by
// chunks of contiguous rows, which correspond to contiguous
// sections of the mesh on which the problem is discretized.
// For matrix assembly, each processor contributes entries for
// the part that it owns locally.
// */
// #ifdef CPPUTILS_VERBOSE
// out<<" Zeroed-out sparse matrix entries... "<<timer<<endl;
// #endif
// for (sparse_matrix_type::const_hash_iterator it = AA.map_.begin(); it != AA.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = AA.unhash(it->first);
// PetscInt row = subs.first;
// PetscInt col = subs.second;
// ierr = MatSetValues(A_, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrix... "<<timer<<endl;
// #endif
// /* Assemble the matrix */
// ierr = MatAssemblyBegin(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// // set after the first MatAssemblyEnd
// // ierr = MatSetOption(A_, MAT_NEW_NONZERO_LOCATIONS, PETSC_FALSE);CHKERRCONTINUE(ierr);
// ierr = MatSetOption(A_, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrix assembled... "<<timer<<endl;
// // view matrix
// MatView(A_, PETSC_VIEWER_STDOUT_WORLD);
// MatNorm(A_,NORM_FROBENIUS,&nrm);
// out<<" Norm of stiffness matrix... "<<nrm<<endl;
// #endif
// /*
// Set operators. Here the matrix that defines the linear system
// also serves as the preconditioning matrix.
// */
// // ierr = KSPSetOperators(ksp,A_,A_,DIFFERENT_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// ierr = KSPSetOperators(ksp_,A_,A_,SAME_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// //
// // /*
// // Set runtime options, e.g.,
// // -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
// // These options will override those specified above as long as
// // KSPSetFromOptions() is called _after_ any other customization
// // routines.
// // */
// // ierr = KSPSetFromOptions(ksp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solving system... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Solve the linear system
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// /*
// Solve linear system
// */
// ierr = KSPSolve(ksp_,b,x_);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// /*
// View solver info; we could instead use the option -ksp_view to
// print this info to the screen at the conclusion of KSPSolve().
// */
// ierr = KSPView(ksp_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// int iter;
// KSPGetIterationNumber(ksp_, &iter);
// out<<" System solved in "<<iter<<" iterations... "<<timer<<endl;
// KSPConvergedReason reason;
// ierr = KSPGetConvergedReason(ksp_,&reason);CHKERRCONTINUE(ierr);
// if (reason < 0)
// out<<"*** WARNING *** PETSc solver diverged with flag ";
// else
// out<<"*** INFO *** PETSc solver converged with flag ";
// if (reason == KSP_CONVERGED_RTOL)
// out<<"KSP_CONVERGED_RTOL"<<endl;
// else if (reason == KSP_CONVERGED_ATOL)
// out<<"KSP_CONVERGED_ATOL"<<endl;
// else if (reason == KSP_CONVERGED_ITS)
// out<<"KSP_CONVERGED_ITS"<<endl;
// else if (reason == KSP_CONVERGED_CG_NEG_CURVE)
// out<<"KSP_CONVERGED_CG_NEG_CURVE"<<endl;
// else if (reason == KSP_CONVERGED_CG_CONSTRAINED)
// out<<"KSP_CONVERGED_CG_CONSTRAINED"<<endl;
// else if (reason == KSP_CONVERGED_STEP_LENGTH)
// out<<"KSP_CONVERGED_STEP_LENGTH"<<endl;
// else if (reason == KSP_CONVERGED_HAPPY_BREAKDOWN)
// out<<"KSP_CONVERGED_HAPPY_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_NULL)
// out<<"KSP_DIVERGED_NULL"<<endl;
// else if (reason == KSP_DIVERGED_ITS)
// out<<"KSP_DIVERGED_ITS"<<endl;
// else if (reason == KSP_DIVERGED_DTOL)
// out<<"KSP_DIVERGED_DTOL"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN)
// out<<"KSP_DIVERGED_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
// out<<"KSP_DIVERGED_BREAKDOWN_BICG"<<endl;
// else if (reason == KSP_DIVERGED_NONSYMMETRIC)
// out<<"KSP_DIVERGED_NONSYMMETRIC"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_PC)
// out<<"KSP_DIVERGED_INDEFINITE_PC"<<endl;
// else if (reason == KSP_DIVERGED_NAN)
// out<<"KSP_DIVERGED_NAN"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_MAT)
// out<<"KSP_DIVERGED_INDEFINITE_MAT"<<endl;
// else if (reason == KSP_CONVERGED_ITERATING)
// out<<"KSP_CONVERGED_ITERATING"<<endl;
// PetscReal rnorm;
// ierr = KSPGetResidualNorm(ksp_,&rnorm);CHKERRCONTINUE(ierr);
// out<<"PETSc last residual norm computed: "<<rnorm<<endl;
// ierr = VecView(x_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// VecNorm(x_,NORM_2,&nrm);
// out<<" Norm of solution vector... "<<nrm<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Check solution and clean up
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// Vec x_all;
// ierr = VecScatterCreateToAll(x_, &ctx, &x_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector scattered... "<<timer<<endl;
// VecNorm(x_all,NORM_2,&nrm);
// out<<" Norm of scattered vector... "<<nrm<<endl;
// // ierr = VecView(x_all,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type xx(bb.size());
// /* Set solution vector */
// double zero = 0.;
// double val;
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(x_all, 1, &row, &val);
// if (val != zero)
// xx[row] = val;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector copied... "<<timer<<endl;
// // out<<" Norm of copied solution vector... "<<norm(xx, Insert_t)<<endl;
// #endif
// /*
// Free work space. All PETSc objects should be destroyed when they
// are no longer needed.
// */
// ierr = VecDestroy(&b);CHKERRCONTINUE(ierr);
// // ierr = KSPDestroy(&ksp);CHKERRCONTINUE(ierr);
// // set allocated flag
// if (!allocated_) {
// allocated_ = true;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return xx;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& KKpf, const SolverPETSc::sparse_matrix_type& KKpp, const SolverPETSc::sparse_vector_type& UUp) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_matrix&, const sparse_matrix&, const sparse_vector&). "<<timer<<endl;
// #endif
// Mat Kpf, Kpp;
// Vec Up, Pf, Pp;
// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatCreate(PETSC_COMM_WORLD,&Kpp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Allocating memory... "<<timer<<endl;
// #endif
// ierr = MatSetFromOptions(Kpf);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(Kpp);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpf,PETSC_DECIDE,PETSC_DECIDE, KKpf.rows(), KKpf.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpp,PETSC_DECIDE,PETSC_DECIDE, KKpp.rows(), KKpp.columns());CHKERRCONTINUE(ierr);
// // get number of non-zeros in both diagonal and non-diagonal portions of the matrix
// std::pair<size_t,size_t> Kpf_nz = KKpf.non_zero_off_diagonal();
// std::pair<size_t,size_t> Kpp_nz = KKpp.non_zero_off_diagonal();
// ierr = MatMPIAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL, Kpf_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatMPIAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL, Kpp_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL); CHKERRCONTINUE(ierr);
// for (sparse_matrix_type::const_hash_iterator it = KKpf.map_.begin(); it != KKpf.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpf.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// for (sparse_matrix_type::const_hash_iterator it = KKpp.map_.begin(); it != KKpp.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpp.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second, ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrices... "<<timer<<endl;
// #endif
// /*
// Assemble matrix, using the 2-step process:
// MatAssemblyBegin(), MatAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyBegin(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrices assembled... "<<timer<<endl;
// #endif
// ierr = VecCreate(PETSC_COMM_WORLD,&Up);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Up,PETSC_DECIDE, UUp.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Up);CHKERRCONTINUE(ierr);
// ierr = VecCreate(PETSC_COMM_WORLD,&Pf);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Pf,PETSC_DECIDE, KKpf.rows());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Pf);CHKERRCONTINUE(ierr);
// ierr = VecDuplicate(Pf,&Pp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = UUp.map_.begin(); it != UUp.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(Up, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(Up);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(Up);CHKERRCONTINUE(ierr);
// // add Kpf*Uf
// ierr = MatMult(Kpf, x_, Pf);
// // add Kpp*Up
// ierr = MatMultAdd(Kpp, Up, Pf, Pp);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrices multiplied... "<<timer<<endl;
// #endif
// VecScatter ctx;
// Vec Pp_all;
// ierr = VecScatterCreateToAll(Pp, &ctx, &Pp_all);CHKERRCONTINUE(ierr);
// ierr = VecScatterBegin(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr = VecScatterEnd(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector scattered... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type pp(KKpf.rows());
// // get reaction vector
// for (int i=0; i<KKpf.rows(); ++i) {
// PetscScalar v;
// ierr = VecGetValues(Pp_all, 1, &i, &v);
// if (v != PetscScalar())
// pp[i] = v;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatDestroy(&Kpp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Up);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pf);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp_all);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return pp;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const SolverPETSc::sparse_vector_type& aa, const SolverPETSc::sparse_vector_type& bb) {
// assert(aa.size() == bb.size());
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_vector&, const sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// sparse_vector_type rr(aa.size());
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it != bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return rr;
// }
// SolverPETSc::value_type SolverPETSc::norm(const SolverPETSc::sparse_matrix_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_matrix&). "<<timer<<endl;
// #endif
// Mat r;
// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(r,PETSC_DECIDE,PETSC_DECIDE, aa.rows(), aa.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = aa.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// if (flag == Add_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// value_type nrm;
// MatNorm(r,NORM_FROBENIUS,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// SolverPETSc::value_type SolverPETSc::norm(const SolverPETSc::sparse_vector_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it != aa.map_.end(); ++it) {
// int row = it->first;
// if (flag == Add_t)
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = VecSetValues(r, 1, &row, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(r,NORM_2,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// //
// ///* -------------------------------------------------------------------------- */
// //SolverMumps::SolverMumps(SparseMatrix & matrix,
// // const ID & id,
// // const MemoryID & memory_id) :
// //Solver(matrix, id, memory_id), is_mumps_data_initialized(false), rhs_is_local(true) {
// // AKANTU_DEBUG_IN();
// //
// //#ifdef AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_fully_distributed;
// //#else //AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_master_slave_distributed;
// //#endif //AKANTU_USE_MPI
// //
// // CommunicatorEventHandler & comm_event_handler = *this;
// //
// // communicator.registerEventHandler(comm_event_handler);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //SolverMumps::~SolverMumps() {
// // AKANTU_DEBUG_IN();
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::destroyMumpsData() {
// // AKANTU_DEBUG_IN();
// //
// // if(is_mumps_data_initialized) {
// // mumps_data.job = _smj_destroy; // destroy
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = false;
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::onCommunicatorFinalize(const StaticCommunicator & comm) {
// // AKANTU_DEBUG_IN();
// //
// // try{
// // const StaticCommunicatorMPI & comm_mpi =
// // dynamic_cast<const StaticCommunicatorMPI &>(comm.getRealStaticCommunicator());
// // if(mumps_data.comm_fortran == MPI_Comm_c2f(comm_mpi.getMPICommunicator()))
// // destroyMumpsData();
// // } catch(...) {}
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::initMumpsData(SolverMumpsOptions::ParallelMethod parallel_method) {
// // switch(parallel_method) {
// // case SolverMumpsOptions::_fully_distributed:
// // icntl(18) = 3; //fully distributed
// // icntl(28) = 0; //automatic choice
// //
// // mumps_data.nz_loc = matrix->getNbNonZero();
// // mumps_data.irn_loc = matrix->getIRN().values;
// // mumps_data.jcn_loc = matrix->getJCN().values;
// // break;
// // case SolverMumpsOptions::_master_slave_distributed:
// // if(prank == 0) {
// // mumps_data.nz = matrix->getNbNonZero();
// // mumps_data.irn = matrix->getIRN().values;
// // mumps_data.jcn = matrix->getJCN().values;
// // } else {
// // mumps_data.nz = 0;
// // mumps_data.irn = NULL;
// // mumps_data.jcn = NULL;
// //
// // icntl(18) = 0; //centralized
// // icntl(28) = 0; //sequential analysis
// // }
// // break;
// // }
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::initialize(SolverOptions & options) {
// // AKANTU_DEBUG_IN();
// //
// // mumps_data.par = 1;
// //
// // if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options)) {
// // if(opt->parallel_method == SolverMumpsOptions::_master_slave_distributed) {
// // mumps_data.par = 0;
// // }
// // }
// //
// // mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
// // prank = communicator.whoAmI();
// //#ifdef AKANTU_USE_MPI
// // mumps_data.comm_fortran = MPI_Comm_c2f(dynamic_cast<const StaticCommunicatorMPI &>(communicator.getRealStaticCommunicator()).getMPICommunicator());
// //#endif
// //
// // if(AKANTU_DEBUG_TEST(dblTrace)) {
// // icntl(1) = 2;
// // icntl(2) = 2;
// // icntl(3) = 2;
// // icntl(4) = 4;
// // }
// //
// // mumps_data.job = _smj_initialize; //initialize
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = true;
// //
// // /* ------------------------------------------------------------------------ */
// // UInt size = matrix->getSize();
// //
// // if(prank == 0) {
// // std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
// // rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, REAL_INIT_VALUE));
// // } else {
// // rhs = NULL;
// // }
// //
// // /// No outputs
// // icntl(1) = 0;
// // icntl(2) = 0;
// // icntl(3) = 0;
// // icntl(4) = 0;
// // mumps_data.nz_alloc = 0;
// //
// // if (AKANTU_DEBUG_TEST(dblDump)) icntl(4) = 4;
// //
// // mumps_data.n = size;
// //
// // if(AKANTU_DEBUG_TEST(dblDump)) {
// // strcpy(mumps_data.write_problem, "mumps_matrix.mtx");
// // }
// //
// // /* ------------------------------------------------------------------------ */
// // // Default Scaling
// // icntl(8) = 77;
// //
// // icntl(5) = 0; // Assembled matrix
// //
// // SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options);
// // if(opt)
// // parallel_method = opt->parallel_method;
// //
// // initMumpsData(parallel_method);
// //
// // mumps_data.job = _smj_analyze; //analyze
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::setRHS(Array<Real> & rhs) {
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().gather(rhs, 0);
// // }
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::solve() {
// // AKANTU_DEBUG_IN();
// //
// // if(parallel_method == SolverMumpsOptions::_fully_distributed)
// // mumps_data.a_loc = matrix->getA().values;
// // else
// // if(prank == 0) {
// // mumps_data.a = matrix->getA().values;
// // }
// //
// // if(prank == 0) {
// // mumps_data.rhs = rhs->values;
// // }
// //
// // /// Default centralized dense second member
// // icntl(20) = 0;
// // icntl(21) = 0;
// //
// // mumps_data.job = _smj_factorize_solve; //solve
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_ASSERT(info(1) != -10, "Singular matrix");
// // AKANTU_DEBUG_ASSERT(info(1) == 0,
// // "Error in mumps during solve process, check mumps user guide INFO(1) ="
// // << info(1));
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///* -------------------------------------------------------------------------- */
// //void SolverMumps::solve(Array<Real> & solution) {
// // AKANTU_DEBUG_IN();
// //
// // solve();
// //
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().scatter(solution, 0);
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
__END_AKANTU__
diff --git a/src/solver/static_solver.cc b/src/solver/static_solver.cc
index 006df3123..b95ae0fa3 100644
--- a/src/solver/static_solver.cc
+++ b/src/solver/static_solver.cc
@@ -1,109 +1,111 @@
/**
* @file static_solver.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jul 30 15:35:01 2014
*
* @brief implementation of the static solver
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "static_solver.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_PETSC
#include <petscsys.h>
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
StaticSolver::StaticSolver() : CommunicatorEventHandler(), is_initialized(false) {
StaticCommunicator::getStaticCommunicator().registerEventHandler(*this);
}
/* -------------------------------------------------------------------------- */
StaticSolver::~StaticSolver() {
--this->nb_references;
- if(this->nb_references == 0)
+ if(this->nb_references == 0) {
+ StaticCommunicator::getStaticCommunicator().unregisterEventHandler(*this);
delete this->static_solver;
+ }
}
/* -------------------------------------------------------------------------- */
StaticSolver & StaticSolver::getStaticSolver() {
if(nb_references == 0)
static_solver = new StaticSolver();
++nb_references;
return *static_solver;
}
#ifdef AKANTU_USE_PETSC
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
static PetscErrorCode PETScErrorHandler(MPI_Comm,
int line, const char * dir, const char *file,
PetscErrorCode number,
PetscErrorType type,
const char *message,
void *) {
AKANTU_DEBUG_ERROR("An error occured in PETSc in file \"" << file << ":" << line << "\" - PetscErrorCode "<< number << " - \""<< message << "\"");
}
#else
static PetscErrorCode PETScErrorHandler(MPI_Comm,
int line, const char * func, const char * dir, const char *file,
PetscErrorCode number,
PetscErrorType type,
const char *message,
void *) {
AKANTU_DEBUG_ERROR("An error occured in PETSc in file \"" << file << ":" << line << "\" - PetscErrorCode "<< number << " - \""<< message << "\"");
}
#endif
#endif
/* -------------------------------------------------------------------------- */
void StaticSolver::initialize(int & argc, char ** & argv) {
AKANTU_DEBUG_ASSERT(this->is_initialized != true, "The static solver has already been initialized");
#ifdef AKANTU_USE_PETSC
PetscErrorCode petsc_error = PetscInitialize(&argc, &argv, NULL, NULL);
if(petsc_error != 0) {
AKANTU_DEBUG_ERROR("An error occured while initializing Petsc (PetscErrorCode "<< petsc_error << ")");
}
PetscPushErrorHandler(PETScErrorHandler, NULL);
#endif
this->is_initialized = true;
}
/* -------------------------------------------------------------------------- */
void StaticSolver::finalize() {
ParentEventHandler::sendEvent(StaticSolverEvent::BeforeStaticSolverDestroyEvent());
AKANTU_DEBUG_ASSERT(this->is_initialized == true, "The static solver has not been initialized");
#ifdef AKANTU_USE_PETSC
PetscFinalize();
#endif
this->is_initialized = false;
}
__END_AKANTU__
diff --git a/src/synchronizer/distributed_synchronizer.cc b/src/synchronizer/distributed_synchronizer.cc
index ab9b4e10f..a32dd53dc 100644
--- a/src/synchronizer/distributed_synchronizer.cc
+++ b/src/synchronizer/distributed_synchronizer.cc
@@ -1,1663 +1,1663 @@
/**
* @file distributed_synchronizer.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Fri Sep 05 2014
*
* @brief implementation of a communicator using a static_communicator for real
* send/receive
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 "distributed_synchronizer.hh"
#include "static_communicator.hh"
#include "mesh_utils.hh"
#include "mesh_data.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <iostream>
#include <algorithm>
#if defined(AKANTU_DEBUG_TOOLS)
# include "aka_debug_tools.hh"
#endif
/* -------------------------------------------------------------------------- */
__BEGIN_AKANTU__
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::DistributedSynchronizer(Mesh & mesh,
SynchronizerID id,
MemoryID memory_id) :
Synchronizer(id, memory_id),
mesh(mesh),
prank_to_element("prank_to_element", id)
{
AKANTU_DEBUG_IN();
nb_proc = static_communicator->getNbProc();
rank = static_communicator->whoAmI();
send_element = new Array<Element>[nb_proc];
recv_element = new Array<Element>[nb_proc];
mesh.registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer::~DistributedSynchronizer() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].clear();
recv_element[p].clear();
}
delete [] send_element;
delete [] recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DistributedSynchronizer * DistributedSynchronizer::
createDistributedSynchronizerMesh(Mesh & mesh,
const MeshPartition * partition,
UInt root,
SynchronizerID id,
MemoryID memory_id) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DistributedSynchronizer & communicator = *(new DistributedSynchronizer(mesh, id, memory_id));
if(nb_proc == 1) return &communicator;
UInt * local_connectivity = NULL;
UInt * local_partitions = NULL;
Array<UInt> * old_nodes = mesh.getNodesGlobalIdsPointer();
old_nodes->resize(0);
Array<Real> * nodes = mesh.getNodesPointer();
UInt spatial_dimension = nodes->getNbComponent();
mesh.synchronizeGroupNames();
/* ------------------------------------------------------------------------ */
/* Local (rank == root) */
/* ------------------------------------------------------------------------ */
if(my_rank == root) {
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
*/
Mesh::type_iterator it = mesh.firstType(_all_dimensions,
_not_ghost,
_ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions,
_not_ghost,
_ek_not_defined);
UInt count = 0;
/* --- MAIN LOOP ON TYPES --- */
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(*it);
UInt nb_local_element[nb_proc];
UInt nb_ghost_element[nb_proc];
UInt nb_element_to_send[nb_proc];
memset(nb_local_element, 0, nb_proc*sizeof(UInt));
memset(nb_ghost_element, 0, nb_proc*sizeof(UInt));
memset(nb_element_to_send, 0, nb_proc*sizeof(UInt));
/// \todo change this ugly way to avoid a problem if an element
/// type is present in the mesh but not in the partitions
const Array<UInt> * tmp_partition_num = NULL;
try {
tmp_partition_num = &partition->getPartition(type, _not_ghost);
} catch(...) {
continue;
}
const Array<UInt> & partition_num = *tmp_partition_num;
const CSR<UInt> & ghost_partition = partition->getGhostPartitionCSR()(type, _not_ghost);
/* -------------------------------------------------------------------- */
/// constructing the reordering structures
for (UInt el = 0; el < nb_element; ++el) {
nb_local_element[partition_num(el)]++;
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
nb_ghost_element[*part]++;
}
nb_element_to_send[partition_num(el)] += ghost_partition.getNbCols(el) + 1;
}
/// allocating buffers
UInt * buffers[nb_proc];
UInt * buffers_tmp[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
UInt size = nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]);
buffers[p] = new UInt[size];
buffers_tmp[p] = buffers[p];
}
/// copying the local connectivity
UInt * conn_val = mesh.getConnectivity(type, _not_ghost).storage();
for (UInt el = 0; el < nb_element; ++el) {
memcpy(buffers_tmp[partition_num(el)],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[partition_num(el)] += nb_nodes_per_element;
}
/// copying the connectivity of ghost element
for (UInt el = 0; el < nb_element; ++el) {
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part) {
UInt proc = *part;
memcpy(buffers_tmp[proc],
conn_val + el * nb_nodes_per_element,
nb_nodes_per_element * sizeof(UInt));
buffers_tmp[proc] += nb_nodes_per_element;
}
}
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().getTagNames(tag_names, type);
UInt nb_tags = tag_names.size();
/* -------->>>>-SIZE + CONNECTIVITY------------------------------------ */
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[5];
size[0] = (UInt) type;
size[1] = nb_local_element[p];
size[2] = nb_ghost_element[p];
size[3] = nb_element_to_send[p];
size[4] = nb_tags;
AKANTU_DEBUG_INFO("Sending connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, p, Tag::genTag(my_rank, count, TAG_SIZES));
AKANTU_DEBUG_INFO("Sending connectivities to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_CONNECTIVITY) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_nodes_per_element * (nb_local_element[p] +
nb_ghost_element[p]),
p, Tag::genTag(my_rank, count, TAG_CONNECTIVITY)));
} else {
local_connectivity = buffers[p];
}
}
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element[root],
nb_ghost_element[root],
type,
*old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
buffers[p] = new UInt[nb_ghost_element[p] + nb_element_to_send[p]];
buffers_tmp[p] = buffers[p];
}
/// splitting the partition information to send them to processors
UInt count_by_proc[nb_proc];
memset(count_by_proc, 0, nb_proc*sizeof(UInt));
for (UInt el = 0; el < nb_element; ++el) {
*(buffers_tmp[partition_num(el)]++) = ghost_partition.getNbCols(el);
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part, ++i) {
*(buffers_tmp[partition_num(el)]++) = *part;
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el);
++part, ++i) {
*(buffers_tmp[*part]++) = partition_num(el);
}
}
/* -------->>>>-PARTITIONS--------------------------------------------- */
/// last data to compute the communication scheme
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending partition informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_PARTITIONS) <<")");
requests.push_back(comm.asyncSend(buffers[p],
nb_element_to_send[p] + nb_ghost_element[p],
p, Tag::genTag(my_rank, count, TAG_PARTITIONS)));
} else {
local_partitions = buffers[p];
}
}
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element[root],
nb_ghost_element[root],
type);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
delete [] buffers[p];
}
/* -------------------------------------------------------------------- */
/// send data assossiated to the mesh
/* -------->>>>-TAGS--------------------------------------------------- */
synchronizeTagsSend(communicator, root, mesh, nb_tags, type,
partition_num,
ghost_partition,
nb_local_element[root],
nb_ghost_element[root]);
/* -------------------------------------------------------------------- */
/// send data assossiated to groups
/* -------->>>>-GROUPS------------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type,
partition_num,
ghost_partition,
nb_element);
++count;
}
/* -------->>>>-SIZE----------------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
UInt size[5];
size[0] = (UInt) _not_defined;
size[1] = 0;
size[2] = 0;
size[3] = 0;
size[4] = 0;
AKANTU_DEBUG_INFO("Sending empty connectivities informations to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_SIZES) <<")");
comm.send(size, 5, p, Tag::genTag(my_rank, count, TAG_SIZES));
}
}
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/**
* Nodes coordinate construction and synchronization
*/
std::multimap< UInt, std::pair<UInt, UInt> > nodes_to_proc;
/// get the list of nodes to send and send them
Real * local_nodes = NULL;
UInt nb_nodes_per_proc[nb_proc];
UInt * nodes_per_proc[nb_proc];
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* --------<<<<-NB_NODES + NODES----------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
if(p != root) {
AKANTU_DEBUG_INFO("Receiving number of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NB_NODES) <<")");
comm.receive(&nb_nodes, 1, p, Tag::genTag(p, 0, TAG_NB_NODES));
nodes_per_proc[p] = new UInt[nb_nodes];
nb_nodes_per_proc[p] = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc " << p << " TAG("<< Tag::genTag(p, 0, TAG_NODES) <<")");
comm.receive(nodes_per_proc[p], nb_nodes, p, Tag::genTag(p, 0, TAG_NODES));
} else {
nb_nodes = old_nodes->getSize();
nb_nodes_per_proc[p] = nb_nodes;
nodes_per_proc[p] = old_nodes->storage();
}
/// get the coordinates for the selected nodes
Real * nodes_to_send = new Real[nb_nodes * spatial_dimension];
Real * nodes_to_send_tmp = nodes_to_send;
for (UInt n = 0; n < nb_nodes; ++n) {
memcpy(nodes_to_send_tmp,
nodes->storage() + spatial_dimension * nodes_per_proc[p][n],
spatial_dimension * sizeof(Real));
// nodes_to_proc.insert(std::make_pair(buffer[n], std::make_pair(p, n)));
nodes_to_send_tmp += spatial_dimension;
}
/* -------->>>>-COORDINATES-------------------------------------------- */
if(p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_COORDINATES) <<")");
comm.send(nodes_to_send, nb_nodes * spatial_dimension, p, Tag::genTag(my_rank, 0, TAG_COORDINATES));
delete [] nodes_to_send;
} else { /// save them for local processor
local_nodes = nodes_to_send;
}
}
/// construct the local nodes coordinates
UInt nb_nodes = old_nodes->getSize();
nodes->resize(nb_nodes);
memcpy(nodes->storage(), local_nodes, nb_nodes * spatial_dimension * sizeof(Real));
delete [] local_nodes;
Array<Int> * nodes_type_per_proc[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p] = new Array<Int>(nb_nodes_per_proc[p]);
}
communicator.fillNodesType(mesh);
/* --------<<<<-NODES_TYPE-1--------------------------------------------- */
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Receiving first nodes types from proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_NODES_TYPE) <<")");
comm.receive(nodes_type_per_proc[p]->storage(),
nb_nodes_per_proc[p], p, Tag::genTag(p, 0, TAG_NODES_TYPE));
} else {
nodes_type_per_proc[p]->copy(mesh.getNodesType());
}
for (UInt n = 0; n < nb_nodes_per_proc[p]; ++n) {
if((*nodes_type_per_proc[p])(n) == -2)
nodes_to_proc.insert(std::make_pair(nodes_per_proc[p][n], std::make_pair(p, n)));
}
}
std::multimap< UInt, std::pair<UInt, UInt> >::iterator it_node;
std::pair< std::multimap< UInt, std::pair<UInt, UInt> >::iterator,
std::multimap< UInt, std::pair<UInt, UInt> >::iterator > it_range;
for (UInt i = 0; i < mesh.nb_global_nodes; ++i) {
it_range = nodes_to_proc.equal_range(i);
if(it_range.first == nodes_to_proc.end() || it_range.first->first != i) continue;
UInt node_type = (it_range.first)->second.first;
for (it_node = it_range.first; it_node != it_range.second; ++it_node) {
UInt proc = it_node->second.first;
UInt node = it_node->second.second;
if(proc != node_type)
nodes_type_per_proc[proc]->storage()[node] = node_type;
}
}
/* -------->>>>-NODES_TYPE-2--------------------------------------------- */
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc " << p << " TAG("<< Tag::genTag(my_rank, 0, TAG_NODES_TYPE) <<")");
requests.push_back(comm.asyncSend(nodes_type_per_proc[p]->storage(),
nb_nodes_per_proc[p], p, Tag::genTag(my_rank, 0, TAG_NODES_TYPE)));
} else {
mesh.getNodesTypePointer()->copy(*nodes_type_per_proc[p]);
}
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) delete [] nodes_per_proc[p];
delete nodes_type_per_proc[p];
}
/* -------->>>>-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsMaster(communicator, root, mesh);
/* ---------------------------------------------------------------------- */
/* Distant (rank != root) */
/* ---------------------------------------------------------------------- */
} else {
/**
* connectivity and communications scheme construction on distant processors
*/
ElementType type = _not_defined;
UInt count = 0;
do {
/* --------<<<<-SIZE--------------------------------------------------- */
UInt size[5] = { 0 };
comm.receive(size, 5, root, Tag::genTag(root, count, TAG_SIZES));
type = (ElementType) size[0];
UInt nb_local_element = size[1];
UInt nb_ghost_element = size[2];
UInt nb_element_to_send = size[3];
UInt nb_tags = size[4];
if(type != _not_defined) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
/* --------<<<<-CONNECTIVITY----------------------------------------- */
local_connectivity = new UInt[(nb_local_element + nb_ghost_element) *
nb_nodes_per_element];
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(local_connectivity, nb_nodes_per_element * (nb_local_element +
nb_ghost_element),
root, Tag::genTag(root, count, TAG_CONNECTIVITY));
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh,
local_connectivity,
nb_local_element,
nb_ghost_element,
type,
*old_nodes);
delete [] local_connectivity;
/* --------<<<<-PARTITIONS--------------------------------------------- */
local_partitions = new UInt[nb_element_to_send + nb_ghost_element * 2];
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
comm.receive(local_partitions,
nb_element_to_send + nb_ghost_element * 2,
root, Tag::genTag(root, count, TAG_PARTITIONS));
if(Mesh::getSpatialDimension(type) == mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
communicator.fillCommunicationScheme(local_partitions,
nb_local_element,
nb_ghost_element,
type);
}
delete [] local_partitions;
/* --------<<<<-TAGS------------------------------------------------- */
synchronizeTagsRecv(communicator, root, mesh, nb_tags, type,
nb_local_element,
nb_ghost_element);
/* --------<<<<-GROUPS----------------------------------------------- */
synchronizeElementGroups(communicator, root, mesh, type);
}
++count;
} while(type != _not_defined);
/**
* Nodes coordinate construction and synchronization on distant processors
*/
comm.broadcast(&(mesh.nb_global_nodes), 1, root);
/* -------->>>>-NB_NODES + NODES----------------------------------------- */
AKANTU_DEBUG_INFO("Sending list of nodes to proc " << root);
UInt nb_nodes = old_nodes->getSize();
comm.send(&nb_nodes, 1, root, Tag::genTag(my_rank, 0, TAG_NB_NODES));
comm.send(old_nodes->storage(), nb_nodes, root, Tag::genTag(my_rank, 0, TAG_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes->resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc " << root);
comm.receive(nodes->storage(), nb_nodes * spatial_dimension, root, Tag::genTag(root, 0, TAG_COORDINATES));
communicator.fillNodesType(mesh);
/* -------->>>>-NODES_TYPE-1--------------------------------------------- */
Int * nodes_types = mesh.getNodesTypePointer()->storage();
AKANTU_DEBUG_INFO("Sending first nodes types to proc " << root);
comm.send(nodes_types, nb_nodes,
root, Tag::genTag(my_rank, 0, TAG_NODES_TYPE));
/* --------<<<<-NODES_TYPE-2--------------------------------------------- */
AKANTU_DEBUG_INFO("Receiving nodes types from proc " << root);
comm.receive(nodes_types, nb_nodes,
root, Tag::genTag(root, 0, TAG_NODES_TYPE));
/* --------<<<<-NODE GROUPS --------------------------------------------- */
synchronizeNodeGroupsSlaves(communicator, root, mesh);
}
MeshUtils::fillElementToSubElementsData(mesh);
mesh.is_distributed = true;
AKANTU_DEBUG_OUT();
return &communicator;
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { \
fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(mesh_data, buffers, tag_name, el_type, partition_num, ghost_partition); \
break; \
} \
MeshDataTypeCode data_type_code = mesh_data.getTypeCode(tag_name);
switch(data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, , AKANTU_MESH_DATA_TYPES)
default : AKANTU_DEBUG_ERROR("Could not obtain the type of tag" << tag_name << "!"); break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillNodesType(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
Int * nodes_type = mesh.getNodesTypePointer()->storage();
UInt * nodes_set = new UInt[nb_nodes];
std::fill_n(nodes_set, nb_nodes, 0);
const UInt NORMAL_SET = 1;
const UInt GHOST_SET = 2;
bool * already_seen = new bool[nb_nodes];
for(UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType) g;
UInt set = NORMAL_SET;
if (gt == _ghost) set = GHOST_SET;
std::fill_n(already_seen, nb_nodes, false);
Mesh::type_iterator it = mesh.firstType(_all_dimensions, gt, _ek_not_defined);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, gt, _ek_not_defined);
for(; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type, gt);
Array<UInt>::iterator< Vector<UInt> > conn_it = mesh.getConnectivity(type, gt).begin(nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++conn_it) {
Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < nb_nodes_per_element; ++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;
}
}
}
}
}
delete [] already_seen;
for (UInt i = 0; i < nb_nodes; ++i) {
if(nodes_set[i] == NORMAL_SET) nodes_type[i] = -1;
else if(nodes_set[i] == GHOST_SET) nodes_type[i] = -3;
else if(nodes_set[i] == (GHOST_SET + NORMAL_SET)) nodes_type[i] = -2;
}
delete [] nodes_set;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::fillCommunicationScheme(const UInt * partition,
UInt nb_local_element,
UInt nb_ghost_element,
ElementType type) {
AKANTU_DEBUG_IN();
Element element;
element.type = type;
element.kind = Mesh::getKind(type);
const UInt * part = partition;
part = partition;
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) {
UInt proc = *part; part++;
AKANTU_DEBUG(dblAccessory, "Must send : " << element << " to proc " << proc);
(send_element[proc]).push_back(element);
}
}
for (UInt gel = 0; gel < nb_ghost_element; ++gel) {
UInt proc = *part; part++;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory, "Must recv : " << element << " from proc " << proc);
recv_element[proc].push_back(element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::asynchronousSynchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
if (communications.find(tag) == communications.end())
computeBufferSize(data_accessor, tag);
Communication & communication = communications[tag];
AKANTU_DEBUG_ASSERT(communication.send_requests.size() == 0,
"There must be some pending sending communications. Tag is " << tag);
std::map<SynchronizationTag, UInt>::iterator t_it = tag_counter.find(tag);
UInt counter = 0;
if(t_it == tag_counter.end()) {
tag_counter[tag] = 0;
} else {
counter = ++(t_it->second);
}
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssize = communication.size_to_send[p];
if(p == rank || ssize == 0) continue;
CommunicationBuffer & buffer = communication.send_buffer[p];
buffer.resize(ssize);
#ifndef AKANTU_NDEBUG
UInt nb_elements = send_element[p].getSize();
AKANTU_DEBUG_INFO("Packing data for proc " << p
<< " (" << ssize << "/" << nb_elements
<<" data to send/elements)");
/// pack barycenters in debug mode
Array<Element>::const_iterator<Element> bit = send_element[p].begin();
Array<Element>::const_iterator<Element> bend = send_element[p].end();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter(mesh.getSpatialDimension());
mesh.getBarycenter(element.element, element.type, barycenter.storage(), element.ghost_type);
buffer << barycenter;
}
#endif
data_accessor.packElementData(buffer, send_element[p], tag);
AKANTU_DEBUG_ASSERT(buffer.getPackedSize() == ssize,
"a problem have been introduced with "
<< "false sent sizes declaration "
<< buffer.getPackedSize() << " != " << ssize);
AKANTU_DEBUG_INFO("Posting send to proc " << p
<< " (tag: " << tag << " - " << ssize << " data to send)"
<< " [" << Tag::genTag(rank, counter, tag) << "]");
communication.send_requests.push_back(static_communicator->asyncSend(buffer.storage(),
ssize,
p,
Tag::genTag(rank, counter, tag)));
}
AKANTU_DEBUG_ASSERT(communication.recv_requests.size() == 0,
"There must be some pending receive communications");
for (UInt p = 0; p < nb_proc; ++p) {
UInt rsize = communication.size_to_receive[p];
if(p == rank || rsize == 0) continue;
CommunicationBuffer & buffer = communication.recv_buffer[p];
buffer.resize(rsize);
AKANTU_DEBUG_INFO("Posting receive from proc " << p
<< " (tag: " << tag << " - " << rsize << " data to receive) "
<< " [" << Tag::genTag(p, counter, tag) << "]");
communication.recv_requests.push_back(static_communicator->asyncReceive(buffer.storage(),
rsize,
p,
Tag::genTag(p, counter, tag)));
}
#if defined(AKANTU_DEBUG_TOOLS) && defined(AKANTU_CORE_CXX11)
static std::set<SynchronizationTag> tags;
if(tags.find(tag) == tags.end()) {
debug::element_manager.print(debug::_dm_synch,
[&send_element, rank, nb_proc, tag, id](const Element & el)->std::string {
std::stringstream out;
UInt elp = 0;
for (UInt p = 0; p < nb_proc; ++p) {
UInt pos = send_element[p].find(el);
if(pos != UInt(-1)) {
if(elp > 0) out << std::endl;
out << id << " send (" << pos << "/" << send_element[p].getSize() << ") to proc " << p << " tag:" << tag;
++elp;
}
}
return out.str();
});
debug::element_manager.print(debug::_dm_synch,
[&recv_element, rank, nb_proc, tag, id](const Element & el)->std::string {
std::stringstream out;
UInt elp = 0;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == rank) continue;
UInt pos = recv_element[p].find(el);
if(pos != UInt(-1)) {
if(elp > 0) out << std::endl;
out << id << " recv (" << pos << "/" << recv_element[p].getSize() << ") from proc " << p << " tag:" << tag;
++elp;
}
}
return out.str();
});
tags.insert(tag);
}
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::waitEndSynchronize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(communications.find(tag) != communications.end(), "No communication with the tag \""
<< tag <<"\" started");
Communication & communication = communications[tag];
std::vector<CommunicationRequest *> req_not_finished;
std::vector<CommunicationRequest *> * req_not_finished_tmp = &req_not_finished;
std::vector<CommunicationRequest *> * recv_requests_tmp = &(communication.recv_requests);
// static_communicator->waitAll(recv_requests);
while(!recv_requests_tmp->empty()) {
for (std::vector<CommunicationRequest *>::iterator req_it = recv_requests_tmp->begin();
req_it != recv_requests_tmp->end() ; ++req_it) {
CommunicationRequest * req = *req_it;
if(static_communicator->testRequest(req)) {
UInt proc = req->getSource();
AKANTU_DEBUG_INFO("Unpacking data coming from proc " << proc);
CommunicationBuffer & buffer = communication.recv_buffer[proc];
#ifndef AKANTU_NDEBUG
Array<Element>::const_iterator<Element> bit = recv_element[proc].begin();
Array<Element>::const_iterator<Element> bend = recv_element[proc].end();
UInt spatial_dimension = mesh.getSpatialDimension();
for (; bit != bend; ++bit) {
const Element & element = *bit;
Vector<Real> barycenter_loc(spatial_dimension);
mesh.getBarycenter(element.element,
element.type,
barycenter_loc.storage(),
element.ghost_type);
Vector<Real> barycenter(spatial_dimension);
buffer >> barycenter;
Real tolerance = Math::getTolerance();
Real bary_norm = barycenter.norm();
for (UInt i = 0; i < spatial_dimension; ++i) {
- if((std::abs((barycenter(i) - barycenter_loc(i))/bary_norm) <= tolerance) ||
- (std::abs(barycenter_loc(i)) <= tolerance && std::abs(barycenter(i)) <= tolerance)) continue;
+ if((std::abs(barycenter_loc(i)) <= tolerance && std::abs(barycenter(i)) <= tolerance) ||
+ (std::abs((barycenter(i) - barycenter_loc(i))/bary_norm) <= tolerance)) continue;
AKANTU_DEBUG_ERROR("Unpacking an unknown value for the element: "
<< element
<< "(barycenter[" << i << "] = " << barycenter_loc(i)
<< " and buffer[" << i << "] = " << barycenter(i) << ") ["
- << std::abs((barycenter(i) - barycenter_loc(i))/barycenter_loc(i))
+ << std::abs((barycenter(i) - barycenter_loc(i))/bary_norm)
<< "] - tag: " << tag);
}
}
#endif
data_accessor.unpackElementData(buffer, recv_element[proc], tag);
buffer.resize(0);
AKANTU_DEBUG_ASSERT(buffer.getLeftToUnpack() == 0,
"all data have not been unpacked: "
<< buffer.getLeftToUnpack() << " bytes left");
static_communicator->freeCommunicationRequest(req);
} else {
req_not_finished_tmp->push_back(req);
}
}
std::vector<CommunicationRequest *> * swap = req_not_finished_tmp;
req_not_finished_tmp = recv_requests_tmp;
recv_requests_tmp = swap;
req_not_finished_tmp->clear();
}
AKANTU_DEBUG_INFO("Waiting that every send requests are received");
static_communicator->waitAll(communication.send_requests);
for (std::vector<CommunicationRequest *>::iterator req_it = communication.send_requests.begin();
req_it != communication.send_requests.end() ; ++req_it) {
CommunicationRequest & req = *(*req_it);
if(static_communicator->testRequest(&req)) {
UInt proc = req.getDestination();
CommunicationBuffer & buffer = communication.send_buffer[proc];
buffer.resize(0);
static_communicator->freeCommunicationRequest(&req);
}
}
communication.send_requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::computeBufferSize(DataAccessor & data_accessor,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
communications[tag].resize(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
UInt ssend = 0;
UInt sreceive = 0;
if(p != rank) {
if(send_element[p].getSize() != 0) {
#ifndef AKANTU_NDEBUG
ssend += send_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
ssend += data_accessor.getNbDataForElements(send_element[p], tag);
AKANTU_DEBUG_INFO("I have " << ssend << "(" << ssend / 1024.
<< "kB - "<< send_element[p].getSize() <<" element(s)) data to send to " << p << " for tag "
<< tag);
}
if(recv_element[p].getSize() != 0) {
#ifndef AKANTU_NDEBUG
sreceive += recv_element[p].getSize() * mesh.getSpatialDimension() * sizeof(Real);
#endif
sreceive += data_accessor.getNbDataForElements(recv_element[p], tag);
AKANTU_DEBUG_INFO("I have " << sreceive << "(" << sreceive / 1024.
<< "kB - "<< recv_element[p].getSize() <<" element(s)) data to receive for tag "
<< tag);
}
}
communications[tag].size_to_send [p] = ssend;
communications[tag].size_to_receive[p] = sreceive;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::computeAllBufferSizes(DataAccessor & data_accessor) {
std::map<SynchronizationTag, Communication>::iterator it = this->communications.begin();
std::map<SynchronizationTag, Communication>::iterator end = this->communications.end();
for (; it != end; ++it) {
SynchronizationTag tag = it->first;
this->computeBufferSize(data_accessor, tag);
}
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
Int prank = StaticCommunicator::getStaticCommunicator().whoAmI();
Int psize = StaticCommunicator::getStaticCommunicator().getNbProc();
stream << "[" << prank << "/" << psize << "]" << space << "DistributedSynchronizer [" << std::endl;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(prank)) continue;
stream << "[" << prank << "/" << psize << "]" << space
<< " + Communication to proc " << p << " [" << std::endl;
if(AKANTU_DEBUG_TEST(dblDump)) {
stream << "[" << prank << "/" << psize << "]" << space
<< " - Element to send to proc " << p << " [" << std::endl;
Array<Element>::iterator<Element> it_el = send_element[p].begin();
Array<Element>::iterator<Element> end_el = send_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]" << space << " " << *it_el << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
stream << "[" << prank << "/" << psize << "]" << space
<< " - Element to recv from proc " << p << " [" << std::endl;
it_el = recv_element[p].begin();
end_el = recv_element[p].end();
for(;it_el != end_el; ++it_el)
stream << "[" << prank << "/" << psize << "]"
<< space << " " << *it_el << std::endl;
stream << "[" << prank << "/" << psize << "]" << space << " ]" << std::endl;
}
std::map< SynchronizationTag, Communication>::const_iterator it = communications.begin();
std::map< SynchronizationTag, Communication>::const_iterator end = communications.end();
for (; it != end; ++it) {
const SynchronizationTag & tag = it->first;
const Communication & communication = it->second;
UInt ssend = communication.size_to_send[p];
UInt sreceive = communication.size_to_receive[p];
stream << "[" << prank << "/" << psize << "]" << space << " - Tag " << tag << " -> " << ssend << "byte(s) -- <- " << sreceive << "byte(s)" << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::onElementsRemoved(const Array<Element> & element_to_remove,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt psize = comm.getNbProc();
UInt prank = comm.whoAmI();
std::vector<CommunicationRequest *> isend_requests;
Array<UInt> * list_of_el = new Array<UInt>[nb_proc];
// Handling ghost elements
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Array<Element> & recv = recv_element[p];
if(recv.getSize() == 0) continue;
Array<Element>::iterator<Element> recv_begin = recv.begin();
Array<Element>::iterator<Element> recv_end = recv.end();
Array<Element>::const_iterator<Element> er_it = element_to_remove.begin();
Array<Element>::const_iterator<Element> er_end = element_to_remove.end();
Array<UInt> & list = list_of_el[p];
for (UInt i = 0; recv_begin != recv_end; ++i, ++recv_begin) {
const Element & el = *recv_begin;
Array<Element>::const_iterator<Element> pos = std::find(er_it, er_end, el);
if(pos == er_end) {
list.push_back(i);
}
}
if(list.getSize() == recv.getSize())
list.push_back(UInt(0));
else list.push_back(UInt(-1));
AKANTU_DEBUG_INFO("Sending a message of size " << list.getSize() << " to proc " << p << " TAG(" << Tag::genTag(prank, 0, 0) << ")");
isend_requests.push_back(comm.asyncSend(list.storage(), list.getSize(),
p, Tag::genTag(prank, 0, 0)));
list.erase(list.getSize() - 1);
if(list.getSize() == recv.getSize()) continue;
Array<Element> new_recv;
for (UInt nr = 0; nr < list.getSize(); ++nr) {
Element & el = recv(list(nr));
el.element = new_numbering(el.type, el.ghost_type)(el.element);
new_recv.push_back(el);
}
AKANTU_DEBUG_INFO("I had " << recv.getSize() << " elements to recv from proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_recv.getSize() << " elements left.");
recv.copy(new_recv);
}
for (UInt p = 0; p < psize; ++p) {
if (p == prank) continue;
Array<Element> & send = send_element[p];
if(send.getSize() == 0) continue;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Getting number of elements of proc " << p << " not needed anymore TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.probe<UInt>(p, Tag::genTag(p, 0, 0), status);
Array<UInt> list(status.getSize());
AKANTU_DEBUG_INFO("Receiving list of elements (" << status.getSize() - 1
<< " elements) no longer needed by proc " << p
<< " TAG("<< Tag::genTag(p, 0, 0) <<")");
comm.receive(list.storage(), list.getSize(),
p, Tag::genTag(p, 0, 0));
if(list.getSize() == 1 && list(0) == 0) continue;
list.erase(list.getSize() - 1);
Array<Element> new_send;
for (UInt ns = 0; ns < list.getSize(); ++ns) {
new_send.push_back(send(list(ns)));
}
AKANTU_DEBUG_INFO("I had " << send.getSize() << " elements to send to proc " << p << " and "
<< list.getSize() << " elements to keep. I have "
<< new_send.getSize() << " elements left.");
send.copy(new_send);
}
comm.waitAll(isend_requests);
comm.freeCommunicationRequest(isend_requests);
delete [] list_of_el;
AKANTU_DEBUG_OUT();
}
// void DistributedSynchronizer::checkCommunicationScheme() {
// for (UInt p = 0; p < psize; ++p) {
// if (p == prank) continue;
// for(UInt e(0), e < recv_element.getSize())
// }
// }
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::buildPrankToElement() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(prank_to_element,
1,
spatial_dimension,
false,
_ek_not_defined,
true);
Mesh::type_iterator it = mesh.firstType(spatial_dimension,
_not_ghost,
_ek_not_defined);
Mesh::type_iterator end = mesh.lastType(spatial_dimension,
_not_ghost,
_ek_not_defined);
/// assign prank to all not ghost elements
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
Array<UInt> & prank_to_el = prank_to_element(*it);
for (UInt el = 0; el < nb_element; ++el) {
prank_to_el(el) = rank;
}
}
/// assign prank to all ghost elements
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_ghost_element = recv_element[p].getSize();
for (UInt el = 0; el < nb_ghost_element; ++el) {
UInt element = recv_element[p](el).element;
ElementType type = recv_element[p](el).type;
GhostType ghost_type = recv_element[p](el).ghost_type;
Array<UInt> & prank_to_el = prank_to_element(type, ghost_type);
prank_to_el(element) = p;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::filterElementsByKind(DistributedSynchronizer * new_synchronizer,
ElementKind kind) {
AKANTU_DEBUG_IN();
Array<Element> * newsy_send_element = new_synchronizer->send_element;
Array<Element> * newsy_recv_element = new_synchronizer->recv_element;
Array<Element> * new_send_element = new Array<Element>[nb_proc];
Array<Element> * new_recv_element = new Array<Element>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
/// send element copying part
new_send_element[p].resize(0);
for (UInt el = 0; el < send_element[p].getSize(); ++el) {
Element & element = send_element[p](el);
if (element.kind == kind)
newsy_send_element[p].push_back(element);
else
new_send_element[p].push_back(element);
}
/// recv element copying part
new_recv_element[p].resize(0);
for (UInt el = 0; el < recv_element[p].getSize(); ++el) {
Element & element = recv_element[p](el);
if (element.kind == kind)
newsy_recv_element[p].push_back(element);
else
new_recv_element[p].push_back(element);
}
}
/// deleting and reassigning old pointers
delete [] send_element;
delete [] recv_element;
send_element = new_send_element;
recv_element = new_recv_element;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::reset() {
AKANTU_DEBUG_IN();
for (UInt p = 0; p < nb_proc; ++p) {
send_element[p].resize(0);
recv_element[p].resize(0);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsSend(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
MeshData & mesh_data = mesh.getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh.getMeshData().getTagNames(tag_names, 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;
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
for(;names_it != names_end; ++names_it) {
mesh_data_sizes_buffer << *names_it;
mesh_data_sizes_buffer << mesh_data.getTypeCode(*names_it);
mesh_data_sizes_buffer << mesh_data.getNbComponent(*names_it, type);
}
mesh_data_sizes_buffer_length = mesh_data_sizes_buffer.getSize();
AKANTU_DEBUG_INFO("Broadcasting the size of the information about the mesh data tags: (" << mesh_data_sizes_buffer_length << ")." );
comm.broadcast(&mesh_data_sizes_buffer_length, 1, root);
AKANTU_DEBUG_INFO("Broadcasting the information about the mesh data tags, addr " << (void*)mesh_data_sizes_buffer.storage());
if(mesh_data_sizes_buffer_length !=0)
comm.broadcast(mesh_data_sizes_buffer.storage(), mesh_data_sizes_buffer.getSize(), root);
if(mesh_data_sizes_buffer_length !=0) {
//Sending the actual data to each processor
DynamicCommunicationBuffer buffers[nb_proc];
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
// Loop over each tag for the current type
for(;names_it != names_end; ++names_it) {
// Type code of the current tag (i.e. the tag named *names_it)
communicator.fillTagBuffer(mesh_data,
buffers,
*names_it,
type,
partition_num,
ghost_partition);
}
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p != root) {
AKANTU_DEBUG_INFO("Sending " << buffers[p].getSize() << " bytes of mesh data to proc " << p << " TAG("<< Tag::genTag(my_rank, count, TAG_MESH_DATA) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(), p, Tag::genTag(my_rank, count, TAG_MESH_DATA)));
}
}
names_it = tag_names.begin();
// Loop over each tag for the current type
for(;names_it != names_end; ++names_it) {
// Reinitializing the mesh data on the master
communicator.populateMeshData(mesh_data,
buffers[root],
*names_it,
type,
mesh_data.getTypeCode(*names_it),
mesh_data.getNbComponent(*names_it, type),
nb_local_element,
nb_ghost_element);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeTagsRecv(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
UInt nb_tags,
const ElementType & type,
UInt nb_local_element,
UInt nb_ghost_element) {
AKANTU_DEBUG_IN();
static UInt count = 0;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
if(nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
UInt mesh_data_sizes_buffer_length = 0;
CommunicationBuffer mesh_data_sizes_buffer;
MeshData & mesh_data = mesh.getMeshData();
AKANTU_DEBUG_INFO("Receiving the size of the information about the mesh data tags.");
comm.broadcast(&mesh_data_sizes_buffer_length, 1, root);
if(mesh_data_sizes_buffer_length != 0) {
mesh_data_sizes_buffer.resize(mesh_data_sizes_buffer_length);
AKANTU_DEBUG_INFO("Receiving the information about the mesh data tags, addr " << (void*)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer.storage(), mesh_data_sizes_buffer_length, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: " << mesh_data_sizes_buffer_length);
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, count, TAG_MESH_DATA) << ")");
comm.probe<char>(root, Tag::genTag(root, count, TAG_MESH_DATA), mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.getSize());
AKANTU_DEBUG_INFO("Receiving " << mesh_data_buffer_size
<< " bytes of mesh data TAG("
<< Tag::genTag(root, count, TAG_MESH_DATA) << ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer.storage(),
mesh_data_buffer_size,
root,
Tag::genTag(root, count, TAG_MESH_DATA));
// Loop over each tag for the current type
UInt k(0);
for(; names_it != names_end; ++names_it, ++k) {
communicator.populateMeshData(mesh_data, mesh_data_buffer,
*names_it, type,
tag_type_codes[k],
tag_nb_component[k],
nb_local_element, nb_ghost_element);
}
}
++count;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillElementGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
const ElementType & type,
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
UInt nb_element = mesh.getNbElement(type, *gt);
el.ghost_type = *gt;
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, *gt), "The mesh does not have the element " << e);
std::vector<std::string>::iterator it = element_to_group.begin();
std::vector<std::string>::iterator end = element_to_group.end();
for (; it != end; ++it) {
mesh.getElementGroup(*it).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
DynamicCommunicationBuffer buffers[nb_proc];
typedef std::vector< std::vector<std::string> > ElementToGroup;
ElementToGroup element_to_group;
element_to_group.resize(nb_element);
GroupManager::const_element_group_iterator egi = mesh.element_group_begin();
GroupManager::const_element_group_iterator ege = mesh.element_group_end();
for (; egi != ege; ++egi) {
ElementGroup & eg = *(egi->second);
std::string name = egi->first;
ElementGroup::const_element_iterator eit = eg.element_begin(type, _not_ghost);
ElementGroup::const_element_iterator eend = eg.element_end(type, _not_ghost);
for (; eit != eend; ++eit) {
element_to_group[*eit].push_back(name);
}
eit = eg.element_begin(type, _not_ghost);
if(eit != eend)
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
/// preparing the buffers
const UInt * part = partition_num.storage();
/// copying the data, element by element
ElementToGroup::const_iterator data_it = element_to_group.begin();
ElementToGroup::const_iterator data_end = element_to_group.end();
for (; data_it != data_end; ++part, ++data_it) {
buffers[*part] << *data_it;
}
data_it = element_to_group.begin();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end; ++data_it, ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (;it != end; ++it) {
UInt proc = *it;
buffers[proc] << *data_it;
}
}
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == my_rank) continue;
AKANTU_DEBUG_INFO("Sending element groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP) <<")");
requests.push_back(comm.asyncSend(buffers[p].storage(),
buffers[p].getSize(),
p,
Tag::genTag(my_rank, p, TAG_ELEMENT_GROUP)));
}
fillElementGroupsFromBuffer(communicator, mesh, type, buffers[my_rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeElementGroups(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh,
const ElementType & type) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
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.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_ELEMENT_GROUP));
fillElementGroupsFromBuffer(communicator, mesh, type, buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class CommunicationBuffer>
void DistributedSynchronizer::fillNodeGroupsFromBuffer(DistributedSynchronizer & communicator,
Mesh & mesh,
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 Array<UInt> & global_nodes = mesh.getGlobalNodesIds();
Array<UInt>::const_scalar_iterator nbegin = global_nodes.begin();
Array<UInt>::const_scalar_iterator nit = global_nodes.begin();
Array<UInt>::const_scalar_iterator nend = global_nodes.end();
for (; nit != nend; ++nit) {
std::vector<std::string>::iterator it = node_to_group[*nit].begin();
std::vector<std::string>::iterator end = node_to_group[*nit].end();
for (; it != end; ++it) {
mesh.getNodeGroup(*it).add(nit - nbegin, false);
}
}
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
ng.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeNodeGroupsMaster(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
typedef std::vector< std::vector<std::string> > NodeToGroup;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
std::string name = ngi->first;
NodeGroup::const_node_iterator nit = ng.begin();
NodeGroup::const_node_iterator nend = ng.end();
for (; nit != nend; ++nit) {
node_to_group[*nit].push_back(name);
}
nit = ng.begin();
if(nit != nend)
ng.empty();
}
buffer << node_to_group;
std::vector<CommunicationRequest *> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if(p == my_rank) continue;
AKANTU_DEBUG_INFO("Sending node groups to proc " << p
<< " TAG("<< Tag::genTag(my_rank, p, TAG_NODE_GROUP) <<")");
requests.push_back(comm.asyncSend(buffer.storage(),
buffer.getSize(),
p,
Tag::genTag(my_rank, p, TAG_NODE_GROUP)));
}
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DistributedSynchronizer::synchronizeNodeGroupsSlaves(DistributedSynchronizer & communicator,
UInt root,
Mesh & mesh) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving node groups from proc " << root
<< " TAG("<< Tag::genTag(root, my_rank, TAG_NODE_GROUP) <<")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, TAG_NODE_GROUP), status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer.storage(), buffer.getSize(), root, Tag::genTag(root, my_rank, TAG_NODE_GROUP));
fillNodeGroupsFromBuffer(communicator, mesh, buffer);
AKANTU_DEBUG_OUT();
}
__END_AKANTU__
diff --git a/test/test_geometry/CMakeLists.txt b/test/test_geometry/CMakeLists.txt
index 307793fab..082d96d22 100644
--- a/test/test_geometry/CMakeLists.txt
+++ b/test/test_geometry/CMakeLists.txt
@@ -1,57 +1,57 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Lucas Frerot <lucas.frerot@epfl.ch>
#
# @date creation: Fri Feb 27 2015
# @date last modification: Fri Feb 27 2015
#
# @brief configuration for solver tests
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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_geometry_intersection_triangle_3_mesh triangle_3.geo 2 1)
add_mesh(test_geometry_intersection_tetrahedron_4_mesh tetrahedron_4.geo 3 1)
register_test(test_geometry_predicates
SOURCES test_geometry_predicates.cc
PACKAGE CGAL
)
register_test(test_geometry_intersection
SOURCES test_geometry_intersection.cc
- DEPENDENCIES test_geometry_intersection_triangle_3_mesh
+ FILES_TO_COPY test_geometry_triangle.msh
PACKAGE CGAL
)
register_test(test_geometry_intersection_triangle_3
SOURCES test_geometry_intersection_triangle_3.cc
- DEPENDENCIES test_geometry_intersection_triangle_3_mesh
+ FILES_TO_COPY test_geometry_triangle.msh
PACKAGE CGAL
)
register_test(test_geometry_intersection_tetrahedron_4
SOURCES test_geometry_intersection_tetrahedron_4.cc
- DEPENDENCIES test_geometry_intersection_tetrahedron_4_mesh
+ 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 6112dbd68..7f17c37c1 100644
--- a/test/test_geometry/test_geometry_intersection.cc
+++ b/test/test_geometry/test_geometry_intersection.cc
@@ -1,102 +1,96 @@
/**
* @file test_geometry_intersection.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Thu Mar 5 2015
*
* @brief Tests the intersection module
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
-#include "mesh_geom_container.hh"
#include "mesh_geom_factory.hh"
#include "tree_type_helper.hh"
#include "geom_helper_functions.hh"
#include <CGAL/Cartesian.h>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef CGAL::Cartesian<Real> K;
-typedef TreeTypeHelper<2, _triangle_3>::linear_intersection Line_intersection;
-typedef TreeTypeHelper<2, _triangle_3>::tree::Primitive_id Primitive_id;
+typedef IntersectionTypeHelper<TreeTypeHelper<Triangle<K>, K>, K::Segment_3>::intersection_type result_type;
/* -------------------------------------------------------------------------- */
int main (int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("", argc, argv);
Math::setTolerance(1e-10);
Mesh mesh(2);
- mesh.read("triangle_3.msh");
+ mesh.read("test_geometry_triangle.msh");
- MeshGeomContainer container(mesh);
- container.constructData();
+ MeshGeomFactory<2, _triangle_3, Triangle<K>, K> factory(mesh);
+ factory.constructData();
- const MeshGeomFactory<2, _triangle_3> * factory = dynamic_cast<const MeshGeomFactory<2, _triangle_3> *>(container.getFactoryForElementType(_triangle_3));
- const TreeTypeHelper<2, _triangle_3>::tree & tree = factory->getTree();
+ 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);
- if (container.numberOfIntersectionsWithInterface(line) != 2)
- return EXIT_FAILURE;
-
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<Line_intersection> list_of_intersections;
+ std::list<result_type> list_of_intersections;
tree.all_intersections(line, std::back_inserter(list_of_intersections));
- const Line_intersection & intersection_0 = list_of_intersections.front();
- const Line_intersection & intersection_1 = list_of_intersections.back();
+ const result_type & intersection_0 = list_of_intersections.front();
+ const result_type & intersection_1 = list_of_intersections.back();
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;
}
}
if (const K::Segment_3 * segment = boost::get<K::Segment_3>(&(intersection_1->first))) {
if (!compareSegments(*segment, result_1)) {
return EXIT_FAILURE;
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_geometry_intersection_tetrahedron_4.cc b/test/test_geometry/test_geometry_intersection_tetrahedron_4.cc
index 5487390dd..876e21db0 100644
--- a/test/test_geometry/test_geometry_intersection_tetrahedron_4.cc
+++ b/test/test_geometry/test_geometry_intersection_tetrahedron_4.cc
@@ -1,75 +1,69 @@
/**
* @file test_geometry_intersection_tetrahedron_4.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Thu Mar 26 2015
* @date last modification: Thu Mar 26 2015
*
* @brief Tests the intersection module with _tetrahedron_4 elements
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
-#include "mesh_geom_container.hh"
-#include "mesh_geom_factory.hh"
-#include "tree_type_helper.hh"
-#include "geom_helper_functions.hh"
+#include "mesh_segment_intersector.hh"
#include <CGAL/Cartesian.h>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef CGAL::Cartesian<Real> K;
typedef K::Point_3 Point;
typedef K::Segment_3 Segment;
/* -------------------------------------------------------------------------- */
int main (int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("", argc, argv);
- Mesh mesh(3);
- mesh.read("tetrahedron_4.msh");
+ Mesh mesh(3), interface_mesh(3, "interface_mesh");
+ mesh.read("test_geometry_tetrahedron.msh");
- MeshGeomContainer container(mesh);
- container.constructData();
+ MeshSegmentIntersector<3, _tetrahedron_4> intersector(mesh, interface_mesh);
+ intersector.constructData();
Point point(1., 1., 1.);
Segment segment(CGAL::ORIGIN, point);
- std::list<std::pair<Segment, std::string> > interfaces;
- interfaces.push_back(std::make_pair(segment, "mat"));
-
- Mesh & interface_mesh = container.meshOfLinearInterfaces(interfaces);
+ intersector.computeIntersectionQuery(segment);
if (interface_mesh.getNbElement(_segment_2) != 4)
return EXIT_FAILURE;
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_geometry_intersection_triangle_3.cc b/test/test_geometry/test_geometry_intersection_triangle_3.cc
index 8c437e2e8..c40306c9e 100644
--- a/test/test_geometry/test_geometry_intersection_triangle_3.cc
+++ b/test/test_geometry/test_geometry_intersection_triangle_3.cc
@@ -1,93 +1,93 @@
/**
* @file test_geometry_mesh.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Fri Mar 13 2015
*
* @brief Tests the interface mesh generation
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
-#include "mesh_geom_container.hh"
+#include "mesh_segment_intersector.hh"
#include "geom_helper_functions.hh"
#include <CGAL/Cartesian.h>
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef CGAL::Cartesian<Real> K;
/* -------------------------------------------------------------------------- */
int main (int argc, char * argv[]) {
- debug::setDebugLevel(dblWarning);
+ debug::setDebugLevel(dblError);
initialize("", argc, argv);
Math::setTolerance(1e-10);
- Mesh mesh(2);
- mesh.read("triangle_3.msh");
+ Mesh mesh(2), interface_mesh(2, "interface_mesh");
+ mesh.read("test_geometry_triangle.msh");
- MeshGeomContainer container(mesh);
- container.constructData();
+ MeshSegmentIntersector<2, _triangle_3> intersector(mesh, interface_mesh);
+ intersector.constructData();
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<std::pair<K::Segment_3, std::string> > interface_list;
- interface_list.push_back(std::make_pair(h_interface, "mat"));
- interface_list.push_back(std::make_pair(v_interface, "mat"));
+ std::list<K::Segment_3> interface_list;
+ interface_list.push_back(h_interface);
+ interface_list.push_back(v_interface);
- Mesh & interface_mesh = container.meshOfLinearInterfaces(interface_list);
+ intersector.computeIntersectionQueryList(interface_list);
if (interface_mesh.getNbElement(_segment_2) != 4)
return EXIT_FAILURE;
Vector<Real> bary(2);
Element test;
test.element = 1;
test.type = _segment_2;
interface_mesh.getBarycenter(test, bary);
if (!Math::are_float_equal(bary(0), 0.5) || !Math::are_float_equal(bary(1), 0.25))
return EXIT_FAILURE;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_geometry/test_geometry_tetrahedron.msh b/test/test_geometry/test_geometry_tetrahedron.msh
new file mode 100644
index 000000000..26ed3254a
--- /dev/null
+++ b/test/test_geometry/test_geometry_tetrahedron.msh
@@ -0,0 +1,91 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+14
+1 0 0 0
+2 1 0 0
+3 1 1 0
+4 0 1 0
+5 0 1 1
+6 0 0 1
+7 1 0 1
+8 1 1 1
+9 0.5 0.5 0
+10 0 0.5 0.5
+11 0.5 0 0.5
+12 1 0.5 0.5
+13 0.5 1 0.5
+14 0.5 0.5 1
+$EndNodes
+$Elements
+68
+1 15 2 0 1 1
+2 15 2 0 2 2
+3 15 2 0 3 3
+4 15 2 0 4 4
+5 15 2 0 5 5
+6 15 2 0 6 6
+7 15 2 0 10 7
+8 15 2 0 14 8
+9 1 2 0 1 4 3
+10 1 2 0 2 3 2
+11 1 2 0 3 1 2
+12 1 2 0 4 4 1
+13 1 2 0 8 5 6
+14 1 2 0 9 6 7
+15 1 2 0 10 7 8
+16 1 2 0 11 8 5
+17 1 2 0 13 4 5
+18 1 2 0 14 1 6
+19 1 2 0 18 2 7
+20 1 2 0 22 3 8
+21 2 2 0 6 1 2 9
+22 2 2 0 6 3 9 2
+23 2 2 0 6 4 1 9
+24 2 2 0 6 3 4 9
+25 2 2 0 15 10 6 5
+26 2 2 0 15 10 4 1
+27 2 2 0 15 4 10 5
+28 2 2 0 15 6 10 1
+29 2 2 0 19 11 6 1
+30 2 2 0 19 11 2 7
+31 2 2 0 19 2 11 1
+32 2 2 0 19 6 11 7
+33 2 2 0 23 12 3 8
+34 2 2 0 23 12 7 2
+35 2 2 0 23 7 12 8
+36 2 2 0 23 3 12 2
+37 2 2 0 27 13 8 3
+38 2 2 0 27 13 4 5
+39 2 2 0 27 4 13 3
+40 2 2 0 27 8 13 5
+41 2 2 0 28 6 7 14
+42 2 2 0 28 7 8 14
+43 2 2 0 28 6 14 5
+44 2 2 0 28 8 5 14
+45 4 2 0 1 13 12 9 3
+46 4 2 0 1 12 2 9 3
+47 4 2 0 1 12 2 11 9
+48 4 2 0 1 8 12 14 13
+49 4 2 0 1 11 12 9 14
+50 4 2 0 1 4 13 9 3
+51 4 2 0 1 11 14 9 10
+52 4 2 0 1 13 8 5 14
+53 4 2 0 1 13 4 10 5
+54 4 2 0 1 8 12 13 3
+55 4 2 0 1 8 12 7 14
+56 4 2 0 1 11 1 10 9
+57 4 2 0 1 11 2 1 9
+58 4 2 0 1 12 13 9 14
+59 4 2 0 1 14 13 10 5
+60 4 2 0 1 12 2 7 11
+61 4 2 0 1 12 11 7 14
+62 4 2 0 1 11 6 10 1
+63 4 2 0 1 6 14 10 5
+64 4 2 0 1 11 6 7 14
+65 4 2 0 1 14 13 9 10
+66 4 2 0 1 1 4 10 9
+67 4 2 0 1 4 13 10 9
+68 4 2 0 1 6 11 10 14
+$EndElements
diff --git a/test/test_geometry/test_geometry_triangle.msh b/test/test_geometry/test_geometry_triangle.msh
new file mode 100644
index 000000000..27322b855
--- /dev/null
+++ b/test/test_geometry/test_geometry_triangle.msh
@@ -0,0 +1,22 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+3 0 1 0
+4 0.5000000000016841 0.4999999999983159 0
+$EndNodes
+$Elements
+9
+1 15 2 0 1 1
+2 15 2 0 2 2
+3 15 2 0 3 3
+4 1 2 0 1 1 2
+5 1 2 0 2 2 4
+6 1 2 0 2 4 3
+7 1 2 0 3 3 1
+8 2 2 0 5 1 4 3
+9 2 2 0 5 2 4 1
+$EndElements
diff --git a/test/test_geometry/tetrahedron_4.geo b/test/test_geometry/tetrahedron_4.geo
deleted file mode 100644
index dce326158..000000000
--- a/test/test_geometry/tetrahedron_4.geo
+++ /dev/null
@@ -1,14 +0,0 @@
-f = 1.0;
-Point(1) = {0, 0, 0, f};
-Point(2) = {1, 0, 0, f};
-Point(3) = {1, 1, 0, f};
-Point(4) = {0, 1, 0, f};
-Line(1) = {4, 3};
-Line(2) = {3, 2};
-Line(3) = {1, 2};
-Line(4) = {4, 1};
-Line Loop(5) = {4, 3, -2, -1};
-Plane Surface(6) = {5};
-Extrude {0, 0, 1} {
- Surface{6};
-}
diff --git a/test/test_geometry/triangle_3.geo b/test/test_geometry/triangle_3.geo
deleted file mode 100644
index bd7d096ca..000000000
--- a/test/test_geometry/triangle_3.geo
+++ /dev/null
@@ -1,9 +0,0 @@
-cl__1 = 1;
-Point(1) = {0, 0, 0, 1};
-Point(2) = {1, 0, 0, 1};
-Point(3) = {0, 1, 0, 1};
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 1};
-Line Loop(5) = {2, 3, 1};
-Plane Surface(5) = {5};
diff --git a/test/test_model/test_solid_mechanics_model/CMakeLists.txt b/test/test_model/test_solid_mechanics_model/CMakeLists.txt
index 327aaafd3..fc14d4a6e 100644
--- a/test/test_model/test_solid_mechanics_model/CMakeLists.txt
+++ b/test/test_model/test_solid_mechanics_model/CMakeLists.txt
@@ -1,224 +1,231 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
#
# @date creation: Fri Sep 03 2010
# @date last modification: Thu Mar 27 2014
#
# @brief configuratio for SolidMechanicsModel tests
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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(patch_tests "patch_tests")
add_akantu_test(test_cohesive "cohesive_test")
add_akantu_test(test_embedded_interface "test_embedded_interface")
#===============================================================================
add_mesh(test_solid_mechanics_model_square_mesh square.geo 2 1)
add_mesh(test_solid_mechanics_model_circle_mesh1 circle.geo 2 1 OUTPUT circle1.msh)
add_mesh(test_solid_mechanics_model_circle_mesh2 circle.geo 2 2 OUTPUT circle2.msh)
register_test(test_solid_mechanics_model_square
SOURCES test_solid_mechanics_model_square.cc
DEPENDENCIES test_solid_mechanics_model_square_mesh
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
register_test(test_solid_mechanics_model_circle_2
SOURCES test_solid_mechanics_model_circle_2.cc
DEPENDENCIES test_solid_mechanics_model_circle_mesh2
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
#===============================================================================
add_mesh(test_bar_traction_2d_mesh1 bar.geo 2 1 OUTPUT bar1.msh)
add_mesh(test_bar_traction_2d_mesh2 bar.geo 2 2 OUTPUT bar2.msh)
add_mesh(test_bar_traction_2d_mesh_structured1 bar_structured.geo 2 1 OUTPUT bar_structured1.msh)
register_test(test_solid_mechanics_model_bar_traction2d
SOURCES test_solid_mechanics_model_bar_traction2d.cc
DEPENDENCIES test_bar_traction_2d_mesh1 test_bar_traction_2d_mesh2
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
register_test(test_solid_mechanics_model_bar_traction2d_structured
SOURCES test_solid_mechanics_model_bar_traction2d_structured.cc
DEPENDENCIES test_bar_traction_2d_mesh_structured1
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
#===============================================================================
add_mesh(test_solid_mechanics_model_segment_mesh segment.geo 1 2)
register_test(test_solid_mechanics_model_bar_traction2d_parallel
SOURCES test_solid_mechanics_model_bar_traction2d_parallel.cc
DEPENDENCIES test_bar_traction_2d_mesh2
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE parallel
)
register_test(test_solid_mechanics_model_segment_parallel
SOURCES test_solid_mechanics_model_segment_parallel.cc
DEPENDENCIES test_solid_mechanics_model_segment_mesh
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE parallel
)
#===============================================================================
#register_test(test_solid_mechanics_model_bar_traction2d_mass_not_lumped
# SOURCES test_solid_mechanics_model_bar_traction2d_mass_not_lumped.cc
# DEPENDENCIES test_bar_traction_2d_mesh1 test_bar_traction_2d_mesh2
# FILES_TO_COPY material.dat
# DIRECTORIES_TO_CREATE paraview
# PACKAGE implicit
# )
#===============================================================================
add_mesh(test_solid_mechanics_model_segment_mesh1 segment.geo 1 1 OUTPUT segment1.msh)
add_mesh(test_implicit_mesh1 square_implicit.geo 2 1 OUTPUT square_implicit1.msh)
add_mesh(test_implicit_mesh2 square_implicit.geo 2 2 OUTPUT square_implicit2.msh)
register_test(test_solid_mechanics_model_implicit_1d
SOURCES test_solid_mechanics_model_implicit_1d.cc
DEPENDENCIES test_solid_mechanics_model_segment_mesh1
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE implicit
)
register_test(test_solid_mechanics_model_implicit_2d
SOURCES test_solid_mechanics_model_implicit_2d.cc
DEPENDENCIES test_implicit_mesh1 test_implicit_mesh2
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE implicit
)
#===============================================================================
add_mesh(test_implicit_beam_2d_1 beam_2d.geo 2 1 OUTPUT beam_2d_lin.msh)
add_mesh(test_implicit_beam_2d_2 beam_2d.geo 2 2 OUTPUT beam_2d_quad.msh)
add_mesh(test_implicit_beam_3d_2 beam_3d.geo 3 2 OUTPUT beam_3d_quad.msh)
add_mesh(test_implicit_beam_3d_1 beam_3d.geo 3 1 OUTPUT beam_3d_lin.msh)
register_test(test_solid_mechanics_model_implicit_dynamic_2d
SOURCES test_solid_mechanics_model_implicit_dynamic_2d.cc
DEPENDENCIES test_implicit_beam_2d_1 test_implicit_beam_2d_2 test_implicit_beam_3d_2 test_implicit_beam_3d_1
FILES_TO_COPY material_implicit_dynamic.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE implicit
)
#===============================================================================
add_mesh(test_pbc_parallel_mesh square_structured.geo 2 1 OUTPUT square_structured.msh)
register_test(test_solid_mechanics_model_bar_traction2d_structured_pbc
SOURCES test_solid_mechanics_model_bar_traction2d_structured_pbc.cc
DEPENDENCIES test_bar_traction_2d_mesh_structured1
FILES_TO_COPY material.dat test_cst_energy.pl
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
#register_test(test_solid_mechanics_model_pbc_parallel
# SOURCES test_solid_mechanics_model_pbc_parallel.cc
# DEPENDENCIES test_pbc_parallel_mesh
# FILES_TO_COPY material.dat
# DIRECTORIES_TO_CREATE paraview
# PACKAGE parallel
# )
#===============================================================================
add_mesh(test_cube3d_mesh1 cube.geo 3 1 OUTPUT cube1.msh)
add_mesh(test_cube3d_mesh2 cube.geo 3 2 OUTPUT cube2.msh)
add_mesh(test_cube3d_mesh_structured cube_structured.geo 3 1 OUTPUT cube_structured.msh)
register_test(test_solid_mechanics_model_cube3d
SOURCES test_solid_mechanics_model_cube3d.cc
DEPENDENCIES test_cube3d_mesh1
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
register_test(test_solid_mechanics_model_cube3d_tetra10
SOURCES test_solid_mechanics_model_cube3d_tetra10.cc
DEPENDENCIES test_cube3d_mesh2
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
register_test(test_solid_mechanics_model_cube3d_pbc
SOURCES test_solid_mechanics_model_cube3d_pbc.cc
DEPENDENCIES test_cube3d_mesh_structured
FILES_TO_COPY material.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
#add_mesh(test_solid_mechanics_model_boundary_condition_mesh cube_physical_names.geo 3 1)
register_test(test_solid_mechanics_model_boundary_condition
SOURCES test_solid_mechanics_model_boundary_condition.cc
FILES_TO_COPY material.dat cube_physical_names.msh
PACKAGE core
)
#===============================================================================
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
DEPENDENCIES test_cube3d_two_mat_mesh
FILES_TO_COPY two_materials.dat
PACKAGE implicit
)
#===============================================================================
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 core
)
#===============================================================================
register_test(test_solid_mechanics_model_orthotropic
SOURCES test_solid_mechanics_model_orthotropic.cc
DEPENDENCIES test_solid_mechanics_model_square_mesh
FILES_TO_COPY orthotropic.dat
DIRECTORIES_TO_CREATE paraview
PACKAGE core
)
+
+#===============================================================================
+register_test(test_material_selector
+ SOURCES test_material_selector.cc
+ FILES_TO_COPY material_selector.dat material_selector.msh
+ PACKAGE core
+ )
diff --git a/test/test_model/test_solid_mechanics_model/material_selector.dat b/test/test_model/test_solid_mechanics_model/material_selector.dat
new file mode 100644
index 000000000..b7ecb2831
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/material_selector.dat
@@ -0,0 +1,14 @@
+material elastic [
+ name = chocolate
+ E = 2
+]
+
+material elastic [
+ name = chewing-gum
+ E = 1
+]
+
+material elastic [
+ name = candy
+ E = 3
+]
diff --git a/test/test_model/test_solid_mechanics_model/material_selector.geo b/test/test_model/test_solid_mechanics_model/material_selector.geo
new file mode 100644
index 000000000..f09b4d68d
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/material_selector.geo
@@ -0,0 +1,10 @@
+Point(1) = {0, 0, 0, 1};
+Point(2) = {1, 0, 0, 1};
+Point(3) = {2, 0, 0, 1};
+Point(4) = {3, 0, 0, 1};
+Line(5) = {1, 2};
+Line(6) = {2, 3};
+Line(7) = {3, 4};
+Physical Line("chocolate") = {5};
+Physical Line("chewing-gum") = {6};
+Physical Line("candy") = {7};
diff --git a/test/test_model/test_solid_mechanics_model/material_selector.msh b/test/test_model/test_solid_mechanics_model/material_selector.msh
new file mode 100644
index 000000000..afb5cdac7
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/material_selector.msh
@@ -0,0 +1,22 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$PhysicalNames
+3
+1 1 "chocolate"
+1 2 "chewing-gum"
+1 3 "candy"
+$EndPhysicalNames
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+3 2 0 0
+4 3 0 0
+$EndNodes
+$Elements
+3
+1 1 2 1 5 1 2
+2 1 2 2 6 2 3
+3 1 2 3 7 3 4
+$EndElements
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 a6a688623..84a2ddabf 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
@@ -1,43 +1,49 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Lucas Frérot <lucas.frerot@epfl.ch>
#
# @date creation: Wed Mar 25 2015
# @date last modification: Wed Mar 25 2015
#
# @brief configuration for embedded interface tests
#
# @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
#
#===============================================================================
register_test(test_embedded_element_matrix
SOURCES test_embedded_element_matrix.cc
FILES_TO_COPY triangle.msh embedded_element.dat
PACKAGE embedded
)
register_test(test_embedded_interface_model
SOURCES test_embedded_interface_model.cc
FILES_TO_COPY embedded_mesh.msh material.dat matrix
PACKAGE embedded
)
+
+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
+ )
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_element.dat b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_element.dat
index 286250d80..d68d274d9 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_element.dat
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_element.dat
@@ -1,22 +1,12 @@
-embedded_interface truc [
- name = reinforcement
- material = elastic_r
- points = [[0, 0.5], [1, 0.5]]
-]
-
material reinforcement elastic [
- name = elastic_r
+ name = reinforcement
E = 1
area = 1
]
material elastic [
- name = truc
+ name = null
rho = 0
E = 0
nu = 0
]
-
-user parameters [
- height = 0.5
-]
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh.msh b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh.msh
index a01ac11c7..f7a1dfc04 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh.msh
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh.msh
@@ -1,26 +1,30 @@
$MeshFormat
2.2 0 8
$EndMeshFormat
+$PhysicalNames
+1
+2 1 "concrete"
+$EndPhysicalNames
$Nodes
9
1 0 0 0
2 0.5 0 0
3 1 0 0
4 0 0.5 0
5 0.5 0.5 0
6 1 0.5 0
7 0 1 0
8 0.5 1 0
9 1 1 0
$EndNodes
$Elements
8
-1 2 2 99 99 1 2 5
-2 2 2 99 99 2 3 6
-3 2 2 99 99 1 5 4
-4 2 2 99 99 2 6 5
-5 2 2 99 99 4 5 8
-6 2 2 99 99 5 6 9
-7 2 2 99 99 4 8 7
-8 2 2 99 99 5 9 8
+1 2 2 1 99 1 2 5
+2 2 2 1 99 2 3 6
+3 2 2 1 99 1 5 4
+4 2 2 1 99 2 6 5
+5 2 2 1 99 4 5 8
+6 2 2 1 99 5 6 9
+7 2 2 1 99 4 8 7
+8 2 2 1 99 5 9 8
$EndElements
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress.msh b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress.msh
new file mode 100644
index 000000000..a799996b4
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress.msh
@@ -0,0 +1,15856 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$PhysicalNames
+4
+0 2 "YBlocked"
+0 3 "EndNode"
+1 1 "XBlocked"
+2 4 "concrete"
+$EndPhysicalNames
+$Nodes
+5420
+1 0 0 0
+2 10 0 0
+3 10 0.25 0
+4 10 1 0
+5 0 1 0
+6 0.04999999999996232 0 0
+7 0.09999999999992584 0 0
+8 0.1499999999998909 0 0
+9 0.199999999999856 0 0
+10 0.249999999999819 0 0
+11 0.2999999999997771 0 0
+12 0.3499999999997248 0 0
+13 0.3999999999996677 0 0
+14 0.4499999999996051 0 0
+15 0.4999999999995511 0 0
+16 0.5499999999995031 0 0
+17 0.5999999999994683 0 0
+18 0.6499999999994334 0 0
+19 0.6999999999993983 0 0
+20 0.7499999999993634 0 0
+21 0.7999999999993286 0 0
+22 0.8499999999992935 0 0
+23 0.8999999999992587 0 0
+24 0.9499999999992237 0 0
+25 0.9999999999991888 0 0
+26 1.049999999999154 0 0
+27 1.099999999999119 0 0
+28 1.149999999999084 0 0
+29 1.199999999999033 0 0
+30 1.24999999999897 0 0
+31 1.299999999998852 0 0
+32 1.349999999998722 0 0
+33 1.399999999998576 0 0
+34 1.44999999999843 0 0
+35 1.499999999998284 0 0
+36 1.549999999998138 0 0
+37 1.599999999997992 0 0
+38 1.649999999997846 0 0
+39 1.6999999999977 0 0
+40 1.749999999997554 0 0
+41 1.799999999997408 0 0
+42 1.849999999997263 0 0
+43 1.899999999997116 0 0
+44 1.949999999996971 0 0
+45 1.999999999996825 0 0
+46 2.049999999996679 0 0
+47 2.099999999996533 0 0
+48 2.149999999996387 0 0
+49 2.199999999996241 0 0
+50 2.249999999996095 0 0
+51 2.299999999995949 0 0
+52 2.349999999995803 0 0
+53 2.399999999995657 0 0
+54 2.449999999995511 0 0
+55 2.499999999995365 0 0
+56 2.54999999999522 0 0
+57 2.599999999995073 0 0
+58 2.649999999994928 0 0
+59 2.699999999994782 0 0
+60 2.749999999994635 0 0
+61 2.79999999999449 0 0
+62 2.849999999994344 0 0
+63 2.899999999994198 0 0
+64 2.949999999994052 0 0
+65 2.999999999993906 0 0
+66 3.04999999999376 0 0
+67 3.099999999993614 0 0
+68 3.149999999993468 0 0
+69 3.199999999993322 0 0
+70 3.249999999993176 0 0
+71 3.299999999993029 0 0
+72 3.349999999992884 0 0
+73 3.399999999992738 0 0
+74 3.449999999992592 0 0
+75 3.499999999992446 0 0
+76 3.5499999999923 0 0
+77 3.599999999992154 0 0
+78 3.649999999992009 0 0
+79 3.699999999991863 0 0
+80 3.749999999991717 0 0
+81 3.799999999991571 0 0
+82 3.849999999991425 0 0
+83 3.899999999991278 0 0
+84 3.949999999991132 0 0
+85 3.999999999991022 0 0
+86 4.049999999990987 0 0
+87 4.099999999991035 0 0
+88 4.149999999991111 0 0
+89 4.199999999991187 0 0
+90 4.249999999991263 0 0
+91 4.299999999991338 0 0
+92 4.349999999991415 0 0
+93 4.399999999991491 0 0
+94 4.449999999991566 0 0
+95 4.499999999991642 0 0
+96 4.549999999991719 0 0
+97 4.599999999991795 0 0
+98 4.649999999991871 0 0
+99 4.699999999991947 0 0
+100 4.749999999992022 0 0
+101 4.799999999992099 0 0
+102 4.849999999992175 0 0
+103 4.89999999999225 0 0
+104 4.949999999992326 0 0
+105 4.999999999992403 0 0
+106 5.049999999992478 0 0
+107 5.099999999992555 0 0
+108 5.14999999999263 0 0
+109 5.199999999992706 0 0
+110 5.249999999992783 0 0
+111 5.299999999992858 0 0
+112 5.349999999992933 0 0
+113 5.39999999999301 0 0
+114 5.449999999993086 0 0
+115 5.499999999993161 0 0
+116 5.549999999993238 0 0
+117 5.599999999993313 0 0
+118 5.649999999993391 0 0
+119 5.699999999993466 0 0
+120 5.749999999993543 0 0
+121 5.799999999993618 0 0
+122 5.849999999993694 0 0
+123 5.899999999993771 0 0
+124 5.949999999993846 0 0
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diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress_reinforcement.msh b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress_reinforcement.msh
new file mode 100644
index 000000000..5dd1487ce
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/embedded_mesh_prestress_reinforcement.msh
@@ -0,0 +1,414 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$PhysicalNames
+1
+1 1 "reinforcement"
+$EndPhysicalNames
+$Nodes
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diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat b/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat
index 3baedcc01..23e677b42 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat
@@ -1,19 +1,13 @@
-embedded_interface truc [
- name = reinforcement
- material = elastic_r
- points = [[0, 0.5], [1, 0.5]]
-]
-
material reinforcement elastic [
- name = elastic_r
+ name = reinforcement
E = 210e9
area = 0.1
]
material elastic [
name = concrete
rho = 2500 # density
E = 30e9 # young's modulus
nu = 0.0 # poisson's ratio
Plane_Stress = true
]
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat b/test/test_model/test_solid_mechanics_model/test_embedded_interface/prestress.dat
similarity index 65%
copy from test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat
copy to test/test_model/test_solid_mechanics_model/test_embedded_interface/prestress.dat
index 3baedcc01..55f8b64d2 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/material.dat
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/prestress.dat
@@ -1,19 +1,14 @@
-embedded_interface truc [
- name = reinforcement
- material = elastic_r
- points = [[0, 0.5], [1, 0.5]]
-]
-
material reinforcement elastic [
- name = elastic_r
+ name = reinforcement
E = 210e9
- area = 0.1
+ area = 1e-2
+ pre_stress = 1e6
]
material elastic [
name = concrete
rho = 2500 # density
E = 30e9 # young's modulus
nu = 0.0 # poisson's ratio
Plane_Stress = true
]
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 efb93663b..a597947f5 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
@@ -1,74 +1,89 @@
/**
* @file test_embedded_interface_model.cc
*
* @author Lucas Frérot <lucas.frerot@epfl.ch>
*
* @date Thu 19 Mar 2015
*
* @brief test of the class EmbeddedInterfaceModel
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "embedded_interface_model.hh"
using namespace akantu;
int main(int argc, char * argv[]) {
debug::setDebugLevel(dblWarning);
initialize("embedded_element.dat", argc, argv);
const UInt dim = 2;
+ const Real height = 0.5;
Mesh mesh(dim);
mesh.read("triangle.msh");
- EmbeddedInterfaceModel model(mesh, dim);
+ Array<Real> nodes_vec(2, dim, "reinforcement_nodes");
+ nodes_vec.storage()[0] = 0; nodes_vec.storage()[1] = height;
+ nodes_vec.storage()[2] = 1; nodes_vec.storage()[3] = height;
- const Real height = 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.registerData<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(SolidMechanicsModelOptions(_static));
if (model.getInterfaceMesh().getNbElement(_segment_2) != 1)
return EXIT_FAILURE;
if (model.getInterfaceMesh().getSpatialDimension() != 2)
return EXIT_FAILURE;
model.assembleStiffnessMatrix();
SparseMatrix & K = model.getStiffnessMatrix();
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;
model.updateResidual();
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 0a5beef3b..7ed6dde50 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
@@ -1,82 +1,98 @@
/**
- * @file reinforced_concrete
+ * @file test_embedded_interface_model.cc
*
- * @author Lucas Frerot
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date lun. 09 29 16:03:10 2014
*
- * @brief Reinforced concrete simulation
+ * @brief Embedded model test based on potential energy
*
* @section LICENSE
*
* Copyright (©) 2010-2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 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 <iostream>
#include "aka_common.hh"
#include "embedded_interface_model.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");
- EmbeddedInterfaceModel model(mesh, dim);
+ 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.registerData<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(SolidMechanicsModelOptions(_static));
Array<Real> & nodes = mesh.getNodes();
Array<Real> & forces = model.getForce();
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;
}
// Assemble the global stiffness matrix
model.assembleStiffnessMatrix();
model.updateResidual();
model.getStiffnessMatrix().saveMatrix("matrix_test");
model.solveStatic<_scm_newton_raphson_tangent_not_computed, _scc_residual>(1e-7, 1);
model.updateResidual();
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
new file mode 100644
index 000000000..57f9b33ff
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/test_embedded_interface_model_prestress.cc
@@ -0,0 +1,225 @@
+/**
+ * @file test_embedded_interface_model_prestress.cc
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: mar. avril 28 2015
+ * @date last modification: mar. avril 28 2015
+ *
+ * @brief Embedded model test for prestressing (bases on stress norm)
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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 "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 QuadraturePoint & quad_point,
+ Vector<Real> & dual,
+ const Vector<Real> & coord,
+ const Vector<Real> & normals) const {
+ UInt dim = coord.size();
+
+ if (dim < 2) AKANTU_DEBUG_ERROR("Solution not valid for 1D");
+
+ Matrix<Real> stress(dim, dim); stress.clear();
+ 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(SolidMechanicsModelOptions(_static));
+
+/* -------------------------------------------------------------------------- */
+/* Computation of analytical residual */
+/* -------------------------------------------------------------------------- */
+
+ /*
+ * q = 1000 N/m
+ * L = 20 m
+ * a = 1 m
+ */
+
+ Real steel_area = model.getMaterial("reinforcement").getParam<Real>("area");
+ Real pre_stress = 1e6;
+ Real stress_norm = 0.;
+
+ StressSolution * concrete_stress = NULL, * steel_stress = NULL;
+
+ 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");
+ ElementGroup & end_node = mesh.getElementGroup("EndNode");
+ NodeGroup & end_node_group = end_node.getNodeGroup();
+ NodeGroup::const_node_iterator end_node_it = end_node_group.begin();
+
+ Vector<Real> end_node_force = model.getForce().begin(dim)[*end_node_it];
+ end_node_force(0) += steel_stress->stress(0.25) * steel_area;
+
+ Array<Real> analytical_residual(mesh.getNbNodes(), dim, "analytical_residual");
+ analytical_residual.copy(model.getForce());
+ model.getForce().clear();
+
+ delete concrete_stress;
+ delete steel_stress;
+
+/* -------------------------------------------------------------------------- */
+
+ model.applyBC(BC::Dirichlet::FixedValue(0.0, _x), "XBlocked");
+ model.applyBC(BC::Dirichlet::FixedValue(0.0, _y), "YBlocked");
+
+ // Assemble the global stiffness matrix
+ model.assembleStiffnessMatrix();
+
+ model.updateResidual();
+
+ if (!model.solveStatic<_scm_newton_raphson_tangent_not_computed, _scc_residual>(1e-6, 1))
+ return EXIT_FAILURE;
+
+ model.updateResidual();
+
+/* -------------------------------------------------------------------------- */
+/* 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();
+ Array<Real>::vector_iterator com_res = model.getResidual().begin(dim);
+ Array<Real>::vector_iterator ana_res = analytical_residual.begin(dim);
+ Array<Real>::vector_iterator 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> ana = ana_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_it];
+ 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)
+ return EXIT_FAILURE;
+
+ finalize();
+ return 0;
+}
diff --git a/test/test_model/test_solid_mechanics_model/test_embedded_interface/triangle.msh b/test/test_model/test_solid_mechanics_model/test_embedded_interface/triangle.msh
index 924ed76e5..94ac34b28 100644
--- a/test/test_model/test_solid_mechanics_model/test_embedded_interface/triangle.msh
+++ b/test/test_model/test_solid_mechanics_model/test_embedded_interface/triangle.msh
@@ -1,13 +1,17 @@
$MeshFormat
2.2 0 8
$EndMeshFormat
+$PhysicalNames
+1
+2 1 "null"
+$EndPhysicalNames
$Nodes
3
1 0 0 0
2 1 0 0
3 0 1 0
$EndNodes
$Elements
1
-1 2 2 0 5 1 2 3
+2 2 2 1 6 1 2 3
$EndElements
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
new file mode 100644
index 000000000..c082e2ef7
--- /dev/null
+++ b/test/test_model/test_solid_mechanics_model/test_material_selector.cc
@@ -0,0 +1,64 @@
+/**
+ * @file test_material_selector.cc
+ *
+ * @author Lucas Frerot <lucas.frerot@epfl.ch>
+ *
+ * @date creation: Fri May 01 2015
+ * @date last modification: Fri May 01 2015
+ *
+ * @brief Test for material selector
+ *
+ * @section LICENSE
+ *
+ * Copyright (©) 2010-2015 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 "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);
+ MeshDataMaterialSelector<std::string> selector("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_structural_mechanics_model/CMakeLists.txt b/test/test_model/test_structural_mechanics_model/CMakeLists.txt
index 7ba2bce7e..61e318ca2 100644
--- a/test/test_model/test_structural_mechanics_model/CMakeLists.txt
+++ b/test/test_model/test_structural_mechanics_model/CMakeLists.txt
@@ -1,72 +1,72 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Fabian Barras <fabian.barras@epfl.ch>
#
# @date creation: Fri Jul 15 2011
# @date last modification: Mon Jul 07 2014
#
# @brief Structural Mechanics Model Tests
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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_structural_mechanics_model_bernoulli_beam_2_exemple_1_1
test_structural_mechanics_model_bernoulli_beam_2_exemple_1_1.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_bernoulli_beam_2_exemple_1_1_y
test_structural_mechanics_model_bernoulli_beam_2_exemple_1_1_y.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_bernoulli_beam_3_exemple_1_1_xy
test_structural_mechanics_model_bernoulli_beam_3_exemple_1_1_xy.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_bernoulli_beam_3_exemple_1_1_zy
test_structural_mechanics_model_bernoulli_beam_3_exemple_1_1_zy.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_bernoulli_beam_3_exercice_12_10_13
test_structural_mechanics_model_bernoulli_beam_3_exercice_12_10_13.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_bernoulli_beam_dynamics
test_structural_mechanics_model_bernoulli_beam_dynamics.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
register_test(test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5
test_structural_mechanics_model_kirchhoff_shell_patch_test_4_5_5.cc
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
add_mesh(complicated_mesh complicated.geo 1 1)
register_test(test_structural_mechanics_model_bernoulli_beam_2_complicated
test_structural_mechanics_model_bernoulli_beam_2_complicated.cc
DEPENDENCIES complicated_mesh
- PACKAGE structural_mechanics_model
+ PACKAGE structural_mechanics
)
diff --git a/test/test_solver/1D_bar.geo b/test/test_solver/1D_bar.geo
new file mode 100644
index 000000000..235f16da2
--- /dev/null
+++ b/test/test_solver/1D_bar.geo
@@ -0,0 +1,4 @@
+Point(1) = {0, 0, 0, 1};
+Point(2) = {10, 0, 0, 1};
+Line(1) = {1, 2};
+Physical Line(2) = {1};
diff --git a/test/test_solver/CMakeLists.txt b/test/test_solver/CMakeLists.txt
index fd1de042c..61ee1e556 100644
--- a/test/test_solver/CMakeLists.txt
+++ b/test/test_solver/CMakeLists.txt
@@ -1,70 +1,84 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Mon Dec 13 2010
# @date last modification: Tue Nov 06 2012
#
# @brief configuration for solver tests
#
# @section LICENSE
#
# Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 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
DEPENDENCIES test_solver_mesh
PACKAGE implicit
)
register_test(test_sparse_matrix_assemble
SOURCES test_sparse_matrix_assemble.cc
DEPENDENCIES 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_petsc_matrix_profile
SOURCES test_petsc_matrix_profile.cc
+ DEPENDENCIES test_matrix_mesh
+ PACKAGE petsc
+ )
+
+register_test(test_petsc_matrix_profile_parallel
+ SOURCES test_petsc_matrix_profile_parallel.cc
+ DEPENDENCIES test_matrix_mesh
+ PACKAGE petsc
+ )
+
+register_test(test_petsc_matrix_diagonal
+ SOURCES test_petsc_matrix_diagonal.cc
DEPENDENCIES test_solver_mesh
PACKAGE petsc
)
register_test(test_petsc_matrix_apply_boundary
SOURCES test_petsc_matrix_apply_boundary.cc
DEPENDENCIES test_solver_mesh
PACKAGE petsc
)
register_test(test_solver_petsc
SOURCES test_solver_petsc.cc
- DEPENDENCIES profile.mtx
+ DEPENDENCIES test_solver_petsc_mesh
PACKAGE petsc
)
\ No newline at end of file
diff --git a/test/test_solver/square.geo b/test/test_solver/square.geo
new file mode 100644
index 000000000..67df205f8
--- /dev/null
+++ b/test/test_solver/square.geo
@@ -0,0 +1,28 @@
+// Mesh size
+h = 1.0; // Top cube
+
+// Dimensions of top cube
+Lx = 1;
+Ly = 1;
+
+// ------------------------------------------
+// Geometry
+// ------------------------------------------
+
+// Base Cube
+Point(101) = { 0.0, 0.0, 0.0, h}; // Bottom Face
+Point(102) = { Lx, 0.0, 0.0, h}; // Bottom Face
+Point(103) = { Lx, Ly, 0.0, h}; // Bottom Face
+Point(104) = { 0.0, Ly, 0.0, h}; // Bottom Face
+
+// Base Cube
+Line(101) = {101,102}; // Bottom Face
+Line(102) = {102,103}; // Bottom Face
+Line(103) = {103,104}; // Bottom Face
+Line(104) = {104,101}; // Bottom Face
+
+// Base Cube
+Line Loop(101) = {101:104};
+
+// Base Cube
+Plane Surface(101) = {101};
diff --git a/test/test_solver/test_petsc_matrix_apply_boundary.cc b/test/test_solver/test_petsc_matrix_apply_boundary.cc
index 068750a25..92e598bab 100644
--- a/test/test_solver/test_petsc_matrix_apply_boundary.cc
+++ b/test/test_solver/test_petsc_matrix_apply_boundary.cc
@@ -1,151 +1,140 @@
/**
* @file test_petsc_matrix_profile.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jul 30 12:34:08 2014
*
* @brief test the applyBoundary method of the PETScMatrix class
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.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;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::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);
- //boundary(2,1) = true;
-
-
- std::cout << dof_synchronizer.getDOFGlobalID(2*2+1) <<std::endl;
-
-
-
// 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;
- UInt global_i = dof_synchronizer.getDOFGlobalID(i);
- UInt global_j = dof_synchronizer.getDOFGlobalID(j);
- std::cout << "K(" << global_i << "," << global_j << ")=" << petsc_matrix(i, j) << std::endl;
}
}
}
}
- petsc_matrix.saveMatrix("profile_after_boundary.mtx");
+
+ if (std::abs(test_passed) > Math::getTolerance())
+ return EXIT_FAILURE;
+
delete communicator;
finalize();
- // if (std::abs(test_passed) > Math::getTolerance())
- // return EXIT_FAILURE;
-
- std::cout << " Test passed!!!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_apply_boundary.sh b/test/test_solver/test_petsc_matrix_apply_boundary.sh
new file mode 100755
index 000000000..f053c4da0
--- /dev/null
+++ b/test/test_solver/test_petsc_matrix_apply_boundary.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpirun -np 4 ./test_petsc_matrix_apply_boundary
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_diagonal.cc
similarity index 61%
copy from test/test_solver/test_petsc_matrix_profile.cc
copy to test/test_solver/test_petsc_matrix_diagonal.cc
index 1a8f2f4e7..eef514153 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_diagonal.cc
@@ -1,137 +1,146 @@
/**
- * @file test_petsc_matrix_profile.cc
- * @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
- * @date Wed Jul 30 12:34:08 2014
+ * @file test_petsc_matrix_diagonal.cc
+ * @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
+ * @date Wed Apr 22 09:41:14 2015
*
- * @brief test the profile generation of the PETScMatrix class
+ * @brief test the connectivity is correctly represented in the PETScMatrix
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.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;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::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();
- // fill the matrix with
+ // 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(nb_global_nodes * spatial_dimension, _unsymmetric);
- K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
- Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
+ 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, spatial_dimension, element_type, ghost_type);
-
+ 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);
- for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- std::cout << node_to_elem.getNbCols(i) << std::endl;
+ /// 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));
+ }
+ }
}
- PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _unsymmetric);
-
- petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
-
-
- petsc_matrix.add(K, 1);
-
- // for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- // for (UInt j = 0; j < spatial_dimension; ++j) {
- // UInt dof = i * spatial_dimension + j;
- // if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
- // UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
- // std::cout << "K(" << global_dof << "," << global_dof << ")=" << petsc_matrix(dof,dof) << std::endl;
- // std::cout << node_to_elem.getNbCols(i) << std::endl;
- // }
- // }
- // }
-
-
-
-
- petsc_matrix.saveMatrix("profile.dat");
+ if(error > Math::getTolerance() ) {
+ std::cout << "error in the stiffness matrix!!!" << std::cout;
+ return EXIT_FAILURE;
+ }
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_diagonal.sh b/test/test_solver/test_petsc_matrix_diagonal.sh
new file mode 100755
index 000000000..5f592e4b2
--- /dev/null
+++ b/test/test_solver/test_petsc_matrix_diagonal.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpirun -np 4 ./test_petsc_matrix_diagonal
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_profile.cc
index 1a8f2f4e7..bff41dcfd 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_profile.cc
@@ -1,137 +1,131 @@
/**
* @file test_petsc_matrix_profile.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jul 30 12:34:08 2014
*
* @brief test the profile generation of the PETScMatrix class
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
+#include <fstream>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.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;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
- mesh.read("triangle.msh");
+ mesh.read("square.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::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();
- // fill the matrix with
+ // 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(nb_global_nodes * spatial_dimension, _unsymmetric);
- K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
- Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
+ 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, spatial_dimension, element_type, ghost_type);
-
- CSR<Element> node_to_elem;
-
- MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
-
- for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- std::cout << node_to_elem.getNbCols(i) << std::endl;
- }
-
- PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _unsymmetric);
-
- petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
-
-
- petsc_matrix.add(K, 1);
+ fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type, ghost_type);
- // for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- // for (UInt j = 0; j < spatial_dimension; ++j) {
- // UInt dof = i * spatial_dimension + j;
- // if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
- // UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
- // std::cout << "K(" << global_dof << "," << global_dof << ")=" << petsc_matrix(dof,dof) << std::endl;
- // std::cout << node_to_elem.getNbCols(i) << std::endl;
- // }
- // }
- // }
-
-
-
-
- petsc_matrix.saveMatrix("profile.dat");
+ /// 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.verified b/test/test_solver/test_petsc_matrix_profile.verified
new file mode 100644
index 000000000..4213dba00
--- /dev/null
+++ b/test/test_solver/test_petsc_matrix_profile.verified
@@ -0,0 +1,12 @@
+Matrix Object: 1 MPI processes
+ type: seqaij
+row 0: (0, 2) (1, 2) (2, 1) (3, 1) (6, 1) (7, 1) (8, 2) (9, 2)
+row 1: (0, 2) (1, 2) (2, 1) (3, 1) (6, 1) (7, 1) (8, 2) (9, 2)
+row 2: (0, 1) (1, 1) (2, 2) (3, 2) (4, 1) (5, 1) (8, 2) (9, 2)
+row 3: (0, 1) (1, 1) (2, 2) (3, 2) (4, 1) (5, 1) (8, 2) (9, 2)
+row 4: (2, 1) (3, 1) (4, 2) (5, 2) (6, 1) (7, 1) (8, 2) (9, 2)
+row 5: (2, 1) (3, 1) (4, 2) (5, 2) (6, 1) (7, 1) (8, 2) (9, 2)
+row 6: (0, 1) (1, 1) (4, 1) (5, 1) (6, 2) (7, 2) (8, 2) (9, 2)
+row 7: (0, 1) (1, 1) (4, 1) (5, 1) (6, 2) (7, 2) (8, 2) (9, 2)
+row 8: (0, 2) (1, 2) (2, 2) (3, 2) (4, 2) (5, 2) (6, 2) (7, 2) (8, 4) (9, 4)
+row 9: (0, 2) (1, 2) (2, 2) (3, 2) (4, 2) (5, 2) (6, 2) (7, 2) (8, 4) (9, 4)
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_profile_parallel.cc
similarity index 71%
copy from test/test_solver/test_petsc_matrix_profile.cc
copy to test/test_solver/test_petsc_matrix_profile_parallel.cc
index 1a8f2f4e7..2ec40523c 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_profile_parallel.cc
@@ -1,137 +1,130 @@
/**
* @file test_petsc_matrix_profile.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Wed Jul 30 12:34:08 2014
*
- * @brief test the profile generation of the PETScMatrix class
+ * @brief test the profile generation of the PETScMatrix class in parallel
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <cstdlib>
+#include <fstream>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.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;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
- mesh.read("triangle.msh");
+ mesh.read("square.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::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();
- // fill the matrix with
+ // 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(nb_global_nodes * spatial_dimension, _unsymmetric);
- K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
- Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
+ 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, spatial_dimension, element_type, ghost_type);
-
- CSR<Element> node_to_elem;
-
- MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
-
- for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- std::cout << node_to_elem.getNbCols(i) << std::endl;
- }
-
- PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _unsymmetric);
-
- petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
-
-
- petsc_matrix.add(K, 1);
+ fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type, ghost_type);
- // for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
- // for (UInt j = 0; j < spatial_dimension; ++j) {
- // UInt dof = i * spatial_dimension + j;
- // if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
- // UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
- // std::cout << "K(" << global_dof << "," << global_dof << ")=" << petsc_matrix(dof,dof) << std::endl;
- // std::cout << node_to_elem.getNbCols(i) << std::endl;
- // }
- // }
- // }
-
-
-
-
- petsc_matrix.saveMatrix("profile.dat");
+ /// 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
+ 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_petsc_matrix_profile_parallel.sh b/test/test_solver/test_petsc_matrix_profile_parallel.sh
new file mode 100755
index 000000000..2dd775687
--- /dev/null
+++ b/test/test_solver/test_petsc_matrix_profile_parallel.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpirun -np 2 ./test_petsc_matrix_profile_parallel
diff --git a/test/test_solver/test_petsc_matrix_profile_parallel.verified b/test/test_solver/test_petsc_matrix_profile_parallel.verified
new file mode 100644
index 000000000..662687ada
--- /dev/null
+++ b/test/test_solver/test_petsc_matrix_profile_parallel.verified
@@ -0,0 +1,12 @@
+Matrix Object: 1 MPI processes
+ type: mpiaij
+row 0: (0, 2) (1, 2) (2, 1) (3, 1) (4, 1) (5, 1) (6, 2) (7, 2)
+row 1: (0, 2) (1, 2) (2, 1) (3, 1) (4, 1) (5, 1) (6, 2) (7, 2)
+row 2: (0, 1) (1, 1) (2, 2) (3, 2) (6, 2) (7, 2) (8, 1) (9, 1)
+row 3: (0, 1) (1, 1) (2, 2) (3, 2) (6, 2) (7, 2) (8, 1) (9, 1)
+row 4: (0, 1) (1, 1) (4, 2) (5, 2) (6, 2) (7, 2) (8, 1) (9, 1)
+row 5: (0, 1) (1, 1) (4, 2) (5, 2) (6, 2) (7, 2) (8, 1) (9, 1)
+row 6: (0, 2) (1, 2) (2, 2) (3, 2) (4, 2) (5, 2) (6, 4) (7, 4) (8, 2) (9, 2)
+row 7: (0, 2) (1, 2) (2, 2) (3, 2) (4, 2) (5, 2) (6, 4) (7, 4) (8, 2) (9, 2)
+row 8: (2, 1) (3, 1) (4, 1) (5, 1) (6, 2) (7, 2) (8, 2) (9, 2)
+row 9: (2, 1) (3, 1) (4, 1) (5, 1) (6, 2) (7, 2) (8, 2) (9, 2)
diff --git a/test/test_solver/test_solver_petsc.cc b/test/test_solver/test_solver_petsc.cc
index 41aaea640..2eb172f50 100644
--- a/test/test_solver/test_solver_petsc.cc
+++ b/test/test_solver/test_solver_petsc.cc
@@ -1,154 +1,161 @@
/**
* @file test_solver_petsc.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Tue Dec 2 17:17:34 2014
*
* @brief test the PETSc solver interface
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <cstdlib>
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "distributed_synchronizer.hh"
#include "petsc_matrix.hh"
#include "solver_petsc.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.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;
StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
DistributedSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("1D_bar.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = DistributedSynchronizer::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);
- std::cout << mesh.getNbElement(element_type, _ghost) <<std::endl;
-
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.);
- residual -= internal_forces;
+
for (UInt i = 0; i < nb_nodes; ++i) {
if (std::abs(position(i, 0) - 10) < Math::getTolerance() )
residual(i, 0) += 2;
}
- /// solve the matrix before the solve step
- petsc_matrix.saveMatrix("1D_bar.mtx");
+ 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;
+ return EXIT_FAILURE;
+ }
+ }
+
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_solver_petsc.sh b/test/test_solver/test_solver_petsc.sh
new file mode 100755
index 000000000..edcc7916c
--- /dev/null
+++ b/test/test_solver/test_solver_petsc.sh
@@ -0,0 +1,5 @@
+#! /bin/bash
+
+# choose solver Mumps through the PETSc interface
+./test_solver_petsc -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package mumps -mat_mumps_icntl_7 2
+mpirun -np 4 ./test_solver_petsc -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package mumps -mat_mumps_icntl_7 2